Peru herbarium data for accurate IUCN threat assessments
Data downloaded from Solanaceae Source and the Begonia Resource Centre for use in analyses in the following paper: Delves, J., J. Albán-Castillo, A. Cano, E. Gagnon, C. Fernández Aviles, P. Gonzáles, S. Knapp, B. León, C. Reynel R., E.F. Rodriguez Rodríguez, R.P. Rojas Gonzáles, T. Särkinen, R. Vásquez Martínez & P.W. Moonlight. 2023 (2024). Small and in-country herbaria are vital for accurate plant threat assessments: a case study from Perú. Plants, People, Planet 6(1): 174-185, published online 4 September 2023, https://doi.org/10.1002/ppp3.10425
Sandra Knapp; Peter Moonlight; Tiina Särkinen
Lycianthes (Solanaceae) in Asia (excluding New Guinea)
Collection event and specimen datasets used for the publication: Knapp S (2024) A revision of _Lycianthes_ (Solanaceae) in tropical Asia. PhytoKeys 245:1-1-6, https://doi.org/10.3897/phytokeys.245.121988 . Abstract. The genus _Lycianthes_ (Dunal) Hassl. (Solanaceae) has in the past been treated as a section of the large genus _Solanum_ L. but is more closely related to _Capsicum_ L. Outside of the Americas, where the highest species diversity occurs, the genus is found in tropical and subtropical habitats from India to Japan and the Philippines, including the islands of Indonesia, New Guinea and the Solomons. The 19 species from Australia, New Guinea and the Pacific were treated in ‘PhytoKeys 209’. Here I treat the remaining 10 species occurring across Asia; including two native species, _L. biflora_ (Lour.) Bitter and _L. oliveriana_ (Lauterb. & K.Schum) Bitter, and one cultivated species, _L. rantonnetii_ (Carrière) Bitter that were also included in the earlier work. The Asian species treated here occupy a wide range of forested and disturbed habitats and are diverse in habit, ranging from epiphytic vines to small or medium sized trees, shrubs or creeping herbs. Many of the species are weedy plants of highly disturbed habitats and are best characterised as “ochlospecies”, with complex polymorphic variation. _Lycianthes rantonnetii_, a species native to southern South America, is recorded as cultivated in India and Pakistan, but may be more widespread than collections indicate. The history of taxonomic treatments of _Lycianthes_ in Asia is discussed, along with details of morphology found in all species. All species are treated in full, with complete morphological descriptions, including synonymy, lecto- or neotypifications, discussions of ecology and vernacular names, distribution maps and preliminary conservation assessments (for all except the cultivated _L. rantonnetii_). Searchable lists of all specimens examined are presented as Supplementary Material.
Clade III STRUCTURE file (Species delimitation)
Link to the Coccoidea slide collection specimen records from the NHM catalogue, published as part of the wider NHM collection dataset.
This Index to the collections is arranged as per family alphabetically. One can locate the collections taxa wise and looking at the cabinet/shelf/tray number on the right hand side of the table. Taxa names as recorded originally have been checked for current taxonomy and where names have changed, they are reflected in new determination. Country, locality details, habitat notes, plant description, name of the collector (s) followed by collection number, collection date and registration numbers (barcode numbers) of the specimens databased have also been given. Several specimens have corresponding herbarium sheets in the General Herbarium. Type specimens are highlighted in red.
Index to the seed plants fluid collection.xlsx
The Biodiversity Intactness Index developed by The Natural History Museum, London, v2.1.1 (Open Access, Limited Release)
A temporally limited release of The Biodiversity Intactness Index developed by the Natural History Museum, London, v2.1.1 is made available here for non-commercial use under a CC-BY-NC-SA license (https://creativecommons.org/licenses/by-nc-sa/4.0/). By downloading this data, you agree to be bound by these terms. For the most recent, complete dataset (annual, from 2000 to 2020 with regular updates, and improved spatial resolution), or to use the data for commercial use, please contact biodiversityfuturesexplorer@nhm.ac.uk. © The Trustees of the Natural History Museum, London 2024. Some Rights Reserved.
Adriana De Palma; Sara Contu; Gareth E Thomas; Connor Duffin; Sabine Nix; Andy Purvis
Trait data extracted from Flora of Pakistan descriptions
Extant phylogeny for taxa used in biogeography analyses in paper 2.
Raw data from GBIF. Please cite GBIF if you use this data: > GBIF, GBIF Occurrence Download https://doi.org/10.15468/dl.vnu6bk. Accessed 21st April 2021 (2021). (amphibians)
Browse collection titles or search by donor, collector, taxonomy, stratigraphic location or country of origin.
The former British Petroleum microfossil collection
The database represents the microfossil well-run collection resulting from British Petroleum's exploration activities since the 1950s. It holds details of material from over 3,500 individual well runs. The main purpose of the database is to allow researchers to identify material of interest, based on its geographical location. Please note that if you're using Excel to work with this dataset, you will need to import the .csv file as text and specifically set the 'Well_Name' and 'Well_Number' column data types to 'text' to avoid corruption of the data.
Andrew S Henderson; Giles Miller; Geoff Eaton
Ipomoea tiliacea (Wild.) Choisy (Convolvulaceae) seeds stranded on the south-west coast of Ireland (H1)
Alignment of 399bp fragment of the nuclear ribosomal Internal Transcribed Spacer region comprising 132 samples of the Ipomoea batatas group, used by Minchin, Griffin and Carine to investigate the identity of three Ipomoea specimens grown from seeds stranded on the south-west coast of Ireland. See: Minchin, Griffin and Carine (submitted) Ipomoea tiliacea (Wild.) Choisy (Convolvulaceae) seeds stranded on the south-west coast of Ireland (H1). British and Irish Botany
Dan Minchin; Claire Griffin; Mark Carine
Sceloporus climate data (population comparisons)
List of accepted reptile names and synonyms. Downloaded from: > Uetz, P., Freed, P., Aguilar, R. & Hosˇek, J., The Reptile Database, http://www.reptile-database.org. Accessed April 2022. (2022).
Fossil phylogeny used in diversification analyses in paper 2.
Link to the Chrysopidae Collection specimen records from the NHM catalogue, published as part of the wider NHM collection dataset.
Reference list for entries in the references column of the *Fossil-proxy-measurement-data.csv* dataset.
Cleaned and anonymised data from the Earthworm Watch citizen science project run by the Natural History Museum, London and Earthwatch Institute (Europe) April 2016 to August 2018. Includes imputed and reshaped data used for the submitted manuscript paper Earthworm Watch: modelling the functional distribution of UK earthworms using a matched pair citizen science survey.
Victoria Burton; Alan G. Jones; Lucy Robinson; Paul Eggleton; Andy Purvis
All accepted genera and their number of component species in the December 2023 update of the World Flora Online (www.wfo.org). These data are licensed CC0.
WFO accepted genera and sizes December 2023 update
Phylogeny for Cetacea, containing only the species included in the analyses. This tree contains 285 taxa, excluding those with zero length branches (ZBL).
The Linnaean Plant Name Typification Project
## Project Summary Carl Linnaeus (1707-1778) introduced the consistent use of binomial names for both plants and animals, validly publishing over 9,000 plant names. Since 1981 the Linnaean Plant Name Typification Project, based at The Natural History Museum, has been collating and cataloguing information on published type designations for Linnaean plant names and, where none exists, has been collaborating with specialists in designating appropriate types. A type specimen is one which is permanently associated with a given scientific name, and acts as a permanent reference collection to confirm the identity of the species to which the name must apply. The Project's main aim is to promote nomenclatural stability in Linnaean plant names by establishing clear typifications for each of the names involved. The Project is necessarily international in scope, receiving enquiries and requests for information on Linnaean names from all over the world. We are always keen to develop further collaboration with taxonomic or regional specialists in the evaluation of Linnaean names and their types. Based at The Natural History Museum, the Project is also indebted to the Linnean Society of London for generous grant support. For more information, see the 'Supplementary Information' resource.
Folder ‘Raman files’ contains individual folders for raw and processed Raman spectra for specimen Harriota raleighana. Raw data is recorded in TXT format, processed data in CSV format. Processed data was treated by the following: 1) cosmic ray removal, 2) background subtraction, 3) normalisation, 4) automatic peak detection. For maps & line scans that consist of more than 1 measurement, positional (x,y) data is recorded in raw data files.
This is a dataset to accompany a paper to Nature Ecology and Evolution: Carter, Hugh. F; Bribiesca-Contreras, G; Williams, Suzanne T. 2025. Deep seafloor diversity in Asteroidea is shaped by competing processes across different latitudes and oceans. The dataset consists of a manually curated set of occurrence records for 1751 species of Asteroidea (Echinodermata). Fields presented are: Order, Family, Genus, Species, Subspecies, Latitude, Longitude, Minimum Depth, Maximum Depth and Reference (for Manually added specimens only). The full geographic validation and cleaning process is laid out in the methods of the paper attached to this dataset. These data were used to generate spatial patterns of Asteroidea species richness across the global oceans. Most data were compiled from the Global Biodiversity Information Facility (GBIF ) or the Ocean Biodiversity Information System (OBIS). An additional set of occurrence records were compiled from literature sources and collection specimens at the Natural History Museum (London) and a reference is provided for these records.
Hugh F Carter; Guadalupe Bribiesca-Contreras; Suzanne T Williams
### The Linnaean Database This page contains a searchable database containing typification details for all Linnaean plant names. For each binomial, we provide the place of publication, stated provenance, the type specimen (or illustration) and a reference to where the type choice was published, and an indication of the current name of the taxon within which Linnaeus' original binomial now falls (binomial and family names). Where relevant, detailed notes are provided (initially for the generitypes and the families Asteraceae and part of the Fabaceae). In particular, these notes aim to account for published observations that may fall short of formal typification. Detailed notes are being prepared and will be added to the database records as they are completed. Consequently, their absence from a given record does not necessarily mean that additional relevant literature has been overlooked. While these online records reflect our current knowledge, the typifications listed here are subject to continuous revision, not least because priority of choice (Art. 9.17) governs any decision. Consequently, the discovery of an earlier choice of type will lead to the displacement of the typification currently accepted here. While the Project has conducted (and continues to conduct) an extensive literature review, it is inevitable that significant contributions have either been overlooked or not yet taken into consideration. We would therefore be most grateful to learn of literature containing typifications of which we appear to have been unaware in reaching our current conclusions. Where available, we provide an image of the type material, in the form of a small thumbnail linked to a full-size image. Approximately 50% of the types are accompanied by images, principally from the Clayton, Clifford and Hermann herbaria at BM. However, we are most grateful to the Linnean Society of London for their permission to display images of those types that are housed in LINN. We also hope to be able add images of type collections from other herbaria, as well as illustrations, in due course. Please note: The 'Images' field in the full view of the dataset is a utility field to facilitate display of images on the NHM Data Portal: it just contains a semicolon delimited list of all the direct image URLs found elsewhere in the record.
Phylogeny for Cetacea excluding Archaeocetes, containing only the species included in the analyses. This tree contains 267 taxa, excluding those with zero length branches (ZBL)
csv files of country, subregion, region and global-level averages of annual BII (2001-2012)
As for "all-specimen-data" but includes unsexed records. * **sex** = Female, Male or NA
Mitochondrial alignment (Mega formatted)
Link to the iCollections: British and Irish Pyraloidea (Moths) Collection specimen records from the NHM catalogue, published as part of the wider NHM collection dataset.
"iCollections: British and Irish Pyraloidea (Moths) Collection" specimens
The Biodiversity Intactness Index - country, region and global-level summaries for the year 1970 to 2050 under various scenarios
Using the PREDICTS database of local biodiversity measures at thousands of sites around the world, we statistically modelled how total abundance of organisms and compositional similarity responded to land use and related pressures. We combined these models with spatio-temporal projections of explanatory variables (at 0.25 degrees spatial resolution) from the year 1970 to 2050 under five Shared Socioeconomic Pathways (SSPs) to project the Biodiversity Intactness Index (BII). Mean BII (weighted by cell area) was calculated at the country, subregion, interregion and global level. We used cross-validation (leaving one biome out in turn) to produce decadal upper and lower uncertainty margins for 1970-2050. These summary data were uploaded to the Natural History Museum's Biodiversity Trends Explorer on 2021-10-27. We have also provided mean values of some of the pressures, as changes in these contribute to changes in BII. Please note that this data product is deprecated. Please see here for the latest public release of the Biodiversity Intactness Index: https://data.nhm.ac.uk/dataset/bii-developed-by-nhm-v2-1-1-limited-release
Helen Phillips; Adriana De Palma; Ricardo E Gonzalez; Sara Contu; Samantha L L Hill; Andrés Baselga; Luca Borger; Andy Purvis
Link to the “Malvales Digitisation” specimen records from the NHM catalogue, published as part of the wider NHM collection dataset.
Metadata about 6753 Bombus hortorum, B.hypnorum, B.lapidarius, B.muscorum, B.pascuorum, B.ruderatus and B.sylvarum specimens for the Bee Land-use Change Project.
Link to the Data mobilisation for IUCN conservation assessments of global freshwater bioindicators specimen records from the NHM catalogue, published as part of the wider NHM collection dataset.
Data mobilisation for IUCN conservation assessments of global freshwater bioindicators specimens
Drawer-level images of specimens in the Wallace and Banks collections held by the Natural History Museum, London.
Plants from Fort St. George India collected by Samuel Browne in 1697
Samuel Browne (d. 1698) was a surgeon employed by the English East India Company (EIC) at Fort St. George, Madras (now Chennai) in India. In 1697, Browne sent a herbarium of 316 specimens collected in and around Chennai to the EIC. Many of those specimens were accompanied with vernacular names, descriptions and notes on their properties and uses. Browne’s specimens were studied by James Petiver who published descriptions with Browne as co-author. Those descriptions made reference to polynomial names in many other published works. This dataset comprises the specimens included in the Browne herbarium with identifications for all specimens. A paper describing this dataset by Prakash, R. O. et al (2024) can be found here: https://www.tandfonline.com/eprint/CZGKSJUBDFA687KPPI9H/full?target=10.1080/23818107.2023.2296095. Further to Prakash et al. (2024), the determinations have been further revised and are reflected in the portal.
Link to the European Brassicales specimen records from the NHM catalogue, published as part of the wider NHM collection dataset.
The project entailed to stub-record, image and transcribe all of the Triticeae tribe from General Herbarium, British & Irish Herbarium and Percival Collection at the Natural History Museum, London, at the time of project completion (April 2023). This included wheat and wild crop relatives. Digitising this collection will help identify specimens that represent times and locations of wheat & relatives that have not yet been genome sequenced. The output of this project is part of a much larger dataset with the same name, to which two other European institutions also contribute. This collection was digitised as part of the Museum's Digital Collections Programme and was funded by Synthesys+ Virtual Access.
Larissa Welton; Krisztina Lohonya; Peter Wing; Hillery Warner; Mark Carine; Chris Dixon; Norbert Holstein; John Hunnex
Georeferenced NHM Botanical TYPE Data for Australia
A list of publications by Dr John E. Whittaker
This list is based mainly on data provided by the late Dr John E. Whittaker from his CV when he kept it up to date during his career at the British Museum (Natural History)/Natural History Museum. Publications post retirement and also since his death have been added to this list and serve to enhance the published and unpublished research collections that he made that are deposited at the Natural History Museum. An almost complete set of these publications is deposited in the Micropalaeontology Library at the Natural History Museum. This list was compiled for a presentation by Giles Miller at a meeting on 22nd April 2025 to celebrate the life and works of Dr John E. Whittaker.
Annotations in Hans Sloane's copy of John Ray's Historia Plantarum (1686-1704)
John Ray’s Historia Plantarum is a three-volume work in Latin comprising three volumes. Volumes I and II were published in 1686 and 1688, and contain approximately 1,000 pages each. Volume III is a supplementary volume published in 1704 consisting of three parts (the Supplementum, Dendrologia and the Appendix) that are separately numbered. Like other botanical publications of the early modern period, it is a work that aimed to create a world-wide encyclopaedia of the flora then known to European Natural Historians, listing and describing the known species at the time. Increasing numbers of new species were reaching taxonomists in Britain and Europe every year, and Ray classified in the Historia Plantarum, approximately 18,000 plant species with details about their structures, anatomy, and botanical differences. Common names are often provided and the descriptions typically also included details related to habitats, times of flowering, whether annual or perennial as well as medicinal properties. Historia Plantarum pre-dates the Linnean binomial system of nomenclature and so the names it enumerates are typically polynomial names. Hans Sloane (1660-1753) and his assistants used Sloane’s personal copy of Ray’s Historia Plantarum to classify and catalogue the plant specimens found throughout the 337 Horti Sicci in his herbarium. This copy, which is housed within the NHM’s Historical Botanical Collection, alongside the Sloane Herbarium, contains a plethora of handwritten annotations and markings. In the side margins of the folios are handwritten notations that are next to, or, in very close proximity to a plant name. These annotations take the form of ‘H.S. [Hortus siccus number] [folio number] and act as an indexing reference to the physical location of a specimen within the herbarium. In some cases, an additional numbers specifies a precise specimen on a folio or page. At the top and bottom margins of the pages (headers and footers), are additional handwritten annotations containing plant names and indexing references to the herbarium following the same volume and folio format found within the side margins. Here, the plant species names are those not already included within Ray’s list. Together, the marginal annotations, along with the headers and footers provide the most comprehensive (albeit still partial) index to the Sloane Herbarium. As a result of the AHRC-funded project Sloane Lab: looking back to build future shared collections, which forms part of the Towards a National Collection (TaNC) programme, the data in this copy of Ray’s Historia Plantarum, most relevant for digitally searching the Sloane Herbarium (and therefore the founding botanical collection of the NHM), has been mobilised and is presented here in an excel format. A total of 39.903 specimens are referred to across the three volumes of Ray's Historia Plantarum. The majority (29604) are referred to names enumerated by Ray; while the remainder are referred to additional names listed in the headers and footers. The Data description provides details of the data contained in this dataset: https://data.nhm.ac.uk/dataset/sloane-historia-plantarum/resource/a4a8f309-f496-40d9-af76-730adade9cb8 This work was supported by a grant from the Arts and Humanities Research Council Towards a National Collection Programme (Grant AH/W003457/1).
Victoria Pickering; Jawad Sadek; Foteini Valeonti; Shirley Chang; Jiawei Liu; Yuyan Yang; Binkai Ma; Siyi Zhang; Jiayi Du; Julianne Nyhan; Andreas Vlachidis; Mark Carine
Data downloaded from the International Plant Names Index representing species described since the year 2000. These data are licensed by IPNI as CC BY (see https://ipni.org/terms-and-conditions).
This contains the large BSBI flowering plants update
area codes, along with hierarchy information and names, using the UN M49 area codes for countries, interregions, subregions and regions.
Raw data for proxy measurements to estimate total length from fossil taxa, along with references for where the data came from. The reference list is available in XXX * Specimen number - registered accession number of specimen in holding institution * (Super)Family - Superfamily (ends 'oidea') or family (ends 'idae') the species belongs to * Genus - genus name * Species - species name * TL (mm) - total length (in millimetres) * CBL (mm) - condylobasal length (in millimetres) * BIZYG (mm) - bizygomatic width (in millimetres) * EXOC (mm) - exoccipital width (in millimetre * OCB (mm) - occipital condyle breadth (in millimetres) * AON (mm) - distance between antorbital notches (in millimetres) * NFW (mm) - narial fossa width (in millimetres) * BNW (mm) - binasal width (width across the two nasal bones) (in millimetres) * AAFW (mm) - width of the articular facets of the atlas vertebra (in millimetres) * HL (mm) - humerus length (in millimetres) * Notes - additional information about species where necessary *NA - Not applicable/No data* *LEA2010 - Lambert et al 2010 Livyatan paper in Nature* ### INSTITUTIONAL ABBREVIATIONS AMP - Ashoro Museum of Paleontology; APA - Private collection of Dr. Alejandro Pezzia Assereto; CAS - California Academy of Sciences; CASG - California Academy of Sciences Department of Geology; CCNHM - College of Charleston Museum of Natural History; ChM PV - Charleston Museum Vertebrate Palaeontology; CMM V - Calvert Marine Museum Vertebrate; CMUO - Condon Museum University of Oregon; CMT - Central Museum of Taurida (Crimean Regional Museum, KKM); CPC - Commonwealth Paleontological Collections (Australian Geological Survey Organisation); CZA - Universidade Agostinho Neto, Luanda, Angola; FCCP - Fukagawa City Cultural Properties; FCMM - Coleccion de Referencia del Estado de Baja California; GMNH-PV - Gunma Museum of Natural History; GNHM - Gamagori Natural History Museum; GSP_UM - University of Michigan, Geological Survey of Pakistan; H-GSP - Howard University, Geological Survey of Pakistan; HMG - Hobetsu Museum; HMH - Historical Museum of Hokkaido; HMN - Hiwa Museum for Natural History; HMNH - Haboro Museum of Natural History; IRSNB - Institut Royal des Sciences Naturelles de Belgique; JGU - Johannes Gutenberg University Palaeontological Institute; KMNH - Kitakyushu Museum of Natural and Human History; LACM - Department of Vertebrate Paleontology, Natural History Museum of Los Angeles County; MAUL - Museo dell'Ambiente, Universite di Lecce; MB - Museum fur Naturkunde Berlin; MBGPT - Museo Geopaleontologico, Universita di Torino; MCZ - Museum of Comparative Zoology, Harvard University; MDLP - Museo de La Plata, La Plata; MGB - Geological and Paleontological Museum ëGiovanni Capellini, University of Bologna; MGNS - Museum of Gruppo Naturalisti Salentini; MGUH - Geological Museum, University of Copenhagen; MHNL - Museum d'Histoire naturelle de Lyon; MFM - Mizunami Fossil Museum; ML - Museu da Lourinhe; MLP - Museo de La Plata, La Plata; MMGUL - Museu Mineralogico da Universidade de Lisboa; MMNS - Mississippi Museum of Natural Science; MNHN - Museum National d'Histoire Naturelle; MO - Montaoita/Olon collection, at Universidad Estatal Peninsula de Santa Elena (UPSE); MPEF_PV - Museo Paleontologico Egidio Feruglio, Trelew; MPTAM - Museo Paleontologico Territoriale dell'Astigiano e del Monferrato, Asti; MSM - Museum Sunderjylland, Department Natural History and Palaeontology MSNTUP - Museo di Storia Naturale e del Territorio, Universita di Pisa; MTM - Magyar Termeszettudomanyi Muzeum (Hungarian Natural History Museum); MUEcSj - Museum of Natural History, Autonomous University of Baja California Sur; MUSM - Museo de Historia Natural, Universidad Nacional Mayor de San Marco; MZ - Museum of the Earth, Polish Academy of Sciences; NFL - Numata Fossil Laboratory, Hokkaido; NMB - Natuurmuseum Brabant, Tilburg; NMC VP - National Museum of Canada, Vertebrate Palaeontolgoy Collection; NMNH P - Academician V. A. Topachevsky Paleontological Museum of the National Museum of Natural History of the National Academy of Sciences of Ukraine; NMR - Natuurhistorisch Museum Rotterdam; NMRA - National Museum of the Republic of Adygea, Maykop; NMV - Nakagawa Museum of Natural History; NMV P - Museums Victoria Palaeontology; OU - University of Otago Geology Museum; PEM - Port Elizabeth Museum; PIN - Paleontological Institute, Russian Academy of Sciences; PU - Museo Regionale di Storia Naturale di Torino; RBINS M - Institut Royal des Sciences Naturelles de Belgique, Mammals; SAMP - South Australian Museum Palaeontology Collection; SAM PQ - Iziko South African Museum; SAS - Museum National d'Histoire Naturelle, Sud Sacaco collection; SBAER - Soprintendenza per i Beni Archeologici dell'Emilia Romagna; SBCM - San Bernardino County Museum, Division ofGeological Sciences; SC - South Carolina State Museum; SDSNH - San Diego Natural History Museum; SGHN - Museo da Natureza da Sociedade Galega de Historia Natural; SGHNMF - Museo da Natureza da Sociedade Galega de Historia Natural; SMAC - Sapporo Museum Activity Center; SMNH - Saitama Museum of Natural History; SMNK - Staatliches Museum fur Naturkunde; SMNS - Staatlischte Museum fur Naturkunde, Stuttgart; TNU - Zoological Museum, Taurida National University; UABCS/ISJ/ - Museo de Historia Natural, Universidad Autunoma de Baja California Sur; UCMP - University of California Museum of Paleontology; UCR - University of California at Riverside; UF - Florida Museum of Natural History; UM - University of Michigan; UMMP - University of Michigan Museum of Paleontology; USNM - National Museum of Natural History, Smithsonian Institution; UWBM - Burke Museum, University of Washington; VMNH - Virginia Museum of Natural History; YPM - Yale Peabody Museum; 2016_MT-GIU - Museo Archeologico Nazionale Domenico Ridola, Matera.
Details for the collection of American type specimens (Diptera: Psychodidae, Phlebotominae) held at The Natural History Museum, London.
Paloma Helena Fernandes Shimabukuro; Zoe J. O. Adams
The Herbarium of William Bartram (1739 – 1823)
The renowned artist & naturalist William Bartram was born in in Kingsessing, near Philadelphia in 1739, the son of acclaimed horticulturalist John Bartram. His love of nature & skills of observation & artistry were honed on many botanical collecting trips with his father (Magee, 2019). With the financial support of the English Quaker, botanist and collector John Fothergill, Bartram undertook an extended expedition to the southeastern United States between 1773 and 1776 “for the discovery of rare & useful productions of nature, chiefly in the vegetable kingdom”.. Exploring Georgia in 1773, he then travelled to Florida the following year before a journey that took him through North Carolina, west Florida, southern Alabama and Mississippi over the following two years. In 1791, Bartram published his Travels through North and South Carolina, Georgia and Florida, an account of those explorations between 1773 and 1776. The specimens collected by Bartram during his 1773-1776 expedition are preserved at the NHM. They were originally sent to Fothergill, his patron, between 1774 and 1776. An additional set of specimens were sent by Bartram to Robert Barclay (1751-1830), one of the founders of the Linnean Society of London, in 1786. Some of the latter were duplicates that he had retained but others represented species that were not represented in the earlier sets of specimens sent to Fothergill. The specimens are arranged in seven books as follows: Book I. East Florida Plants. For Doct. Fothergill London Doct[o]r L. Chalmers. [50 specimens] Book II. East Florida Plants. [30 specimens] Book A. For Doctor Fothergill. Specimens. Plants of Province of Georgia. [30 specimens] Book B. On way to Cherokee Country. [52 specimens] Book C. For Doctr Fothergill. Remarks on the Specimens of Plants natives of So. Carolina. [26 specimens] Book [D]. [Presumably West Florida]. [19 specimens] Book [E]. Mr Barclay’s Book. [38 specimens] Many of the specimens have detailed notes accompanying them. For the most part, the original folios have been remounted onto larger herbarium sheets and are housed in the botany historical collections room, in their original book order. Within each book, specimens are numbered. Twelve specimens, nearly all recognised as types, were removed from that collection and are now housed in the General Herbarium although the notes that accompanied the specimen remain with the other specimens. Among those housed in the General Herbarium are the types of species described by Bartram, including Franklinia alatamaha Bartram and Hydrangea quercifolia W.Bartram. The binomial names used here largely follow those of Joseph Ewan, who published a detailed account of the collection in Ewan (1968) that included transcriptions of the notes that accompanied the specimens. Specimens in the William Bartram Herbarium. To access, click on the ‘Go to resource’ button below. You can access the collection in three ways. The table view displays the collection in table format; the list view shows the data accompanying each specimen, together with a thumbnail of the image of the specimen sheet; gallery view allows you to browse the images and access the dataset in that way. Images carry a CC-BY licence and can be downloaded at full resolution. For details regarding terms and conditions of resuse, please see: https://data.nhm.ac.uk/terms-conditions References Ewan, J., 1968. William Bartram: Botanical and Zoological Drawings, 1756-1788. American Philosophical Society. Magee, J., 2019. William Bartram – The first ecologist. In: Anon. Nature’s Explorers – Adventurers who recorded the wonder of the natural world. The Natural History Museum, London. Pp 36-45.
Technical overview of the UK Species Inventory
Cleaned and anonymised data from the Earthworm Watch citizen science project run by the Natural History Museum, London and Earthwatch Institute (Europe) April 2016 to August 2018.
Imperial College of London Royal School of Mines Micropalaeontological Collection
This dataset provides a drawer level listing of the Imperial College Royal School of Mines microfossil collection of mainly Foraminifera collected by Dr David Carter. It was compiled by Jonathan Whittaker and includes information about collections from 89 different countries worldwide. Significant collections include material from the Channel Tunnel investigations in the English Channel and for the Thames Barrier in the Thames Estuary. Column headers provide details of David Carter's own numbering system as well as location of collection details. Most slides are assemblage material but some are thin sections. Stratigraphic information is available via an associated card index.
A manual authored by Scott Wilson to aid creation and scoring of individual Collections Units as part of the Join the Dots collections assessment exercise.
Join the Dots Collections Assessment Exercise Manual
This document outlines the data and processes used for The Biodiversity Intactness Index developed by the Natural History Museum, London, v2.1.1. This document is available for non-commercial uses under a CC-BY-NC-SA 4.0 license (https://creativecommons.org/licenses/by-nc-sa/4.0/). By downloading this document, you agree to be bound by these terms. © The Trustees of the Natural History Museum, London 2024. Some Rights Reserved.
The Biodiversity Intactness Index (BII) developed by the Natural History Museum: Methodology, v2.1.1
Clade I STRUCTURE file (Species delimitation)
The Aphidoidea collection comprises the records of all the slide-mounted Aphidoidea material at the Natural History Museum, London at the time of the project completion (December 2023). This includes the main collection and discrete collection of Frederick Vincent Theobald. Each specimen record has been published with an image capturing both the specimen and its associated labels and creating an inventory record with a unique identifier (Data Matrix barcode), taxon information, type status, country level collection locality. Additional images were taken to capture any information on the reverse of the slides and/or the paper envelopes that house the slides. The data resource generated by the project is available using the link. Please search for the relevant taxa as this dataset if part of a larger project covering a range of Orders and Superfamilies. This collection was digitised as part of the Museum's Digital Collections Programme.
Peter Wing; Louise Berridge; Emma Bonzo; Joseph Deane; Noelia Gahan; Ying Luo; Skye Neal; Megan Squire; Glory Turnbull; Larissa Welton; Chrissy Williams; Janice Wu; Louise Allan; Krisztina Lohonya; Chiho Ikebe; Marla Spencer; Hillery Warner; Paul Andrew Brown
Phylogeny for Cetacea excluding living taxa, containing only the species included in the analyses. This tree contains 207 taxa, excluding those with zero length branches (ZBL)
All node probabilities from the DEC+J model for all taxa. *node* = node number on tree (see `node-labels-tree.png`) *ML* = Maximum Likelihood state for the node under the DEC+J model All other columns represent a single state and the marginal probability of that state being at that node. A = area A, AB is either area A or B and so on...
The Ocean Bottom Deposits Collection contains over 28,000 items derived from sea floor sediment collections. These include sediment residues in tubes/bottles/jars, hand specimens and slides. This dataset is a Darwin Core export of specimen records available individually on the Data Portal with some additional information.
Link to the World Brassicales specimen records from the NHM catalogue, published as part of the wider NHM collection dataset.
**Specimen number**: NHMUK C.1934.5.25.1 **Specimen Link**: http://data.nhm.ac.uk/object/106cdf7b-7545-4e4e-aa8d-6ec2300e48fc **Decription**: _Balaenoptera borealis_ -- Balaenopteridae; Cetacea; Mammalia
Specimens in the William Bartram Herbarium. To access, click on the ‘Go to resource’ button below. You can access the collection in three ways. The table view displays the collection in table format; the list view shows the data accompanying each specimen, together with a thumbnail of the image of the specimen sheet; gallery view allows you to browse the images and access the dataset in that way. Images carry a CC-BY licence and can be downloaded at full resolution. For details regarding terms and conditions of reuse, please see: https://data.nhm.ac.uk/terms-conditions
SNAPPER trees file ingroup (Fig. 2, Fig. S1A)
Summary Statistics derived from a full shelf audit compared to CMS/GBIF data
A searchable csv file of all _Lycianthes_ specimens examined from the specific area treated (Australia, New Guinea and the Pacific) in the monograph. Column headings are: Herbarium = herbarium acronym acc. to Index Herbariorum; Category = specimen or photograph of specimen; SpecID = brahms specimen ID; Brahms = Brahms collection event ID; Accession = accession number of specimen; Barcode = barcode of specimen; Collector = principal collector; Prefix = collection number prefix (if applicable); Number = collection number; Suffix = collection number suffix (if applicable); AddColl = additional collectors; Type = type of type; Type of = type of what species; Day -= day of collection; Month = month of collection; Year = year of collection; DateRes = date resolution (if applicable); Family = plant family; Genus = genus name; Species = species epithet; Author = species author name(s); Country = country of collection; Majorarea = first political division; Minorarea = second political division; Gazetteer = nearby town or place; Locnotes = locality; Habitattxt = vegetation characteristics; Lat = latitude; NS = north or south; Longitude = longitude; EW = east or west; LLunit = coordinate units (DD = decimal degrees; DM = decimal minutes; DMS = degrees, minutes, seconds); LLres = coordinate resolution (4 = nearest minute; 7 = area centroid); LLorigin = origin of coordinates; LatLong = coordinates in DMS; LatDec = decimal latitude; LongDec = decimal longitude; Alt = elevation minimum; AltMax = elevation maximum; AltRes = elevation resolution; AltUnit = elevation units (all metres); AltRange = elevational range.
Specimen data for Australia, New Guinea and the Pacific (SM 2)
The Cooper collection comprises the records of all material from the Martin Cooper acquisition (BMNH-ENT-2018-128) at the Natural History Museum, London at the time of project completion (March 2019). The Cooper collection primarily consists of Hymenoptera specimens and nests but also includs specimens from 16 other Orders (Coleoptera, Diptera, Hemiptera, Blattodea, Dermaptera, Embioptera, Mantodea, Mecoptera, Megaloptera, Neuroptera, Odonata, Orthoptera, Phasmatodea, Plecoptera, Psocoptera and Trichoptera). The Cooper collection was digitised to refine our pinned insect workflow, where the labels do not need to be removed (ALICE - Angled Label Image Capture and Extraction), and to develop protocols for entry point digitisation for acquisition material. Each specimen record has been published with six images capturing dorsal, lateral and multiple angled views of the specimen and its associated labels and creating an inventory record with a unique identifier (Data Matrix barcode), taxon information and type status. The data resource generated by the project is available using the link. Please search for the relevant taxa. This collection was digitised as part of the Museum's Digital Collections Programme.
Phaedra Kokkini; Nicola Lowndes; Louise Allan; Charlotte Barclay; Gavin Broad; Natalie Dale-Skey; David G. Notton
This is a tidied version of specimen records data downloaded from GBIF. If using this data please cite the sources listed below. The raw data input files come from: * GBIF, GBIF Occurrence Download https://doi.org/10.15468/dl.vnu6bk. Accessed 21st April 2021 (2021). (amphibians) * GBIF, GBIF Occurrence Download https://doi.org/10.15468/dl.ub7yfv. Accessed 21st April 2021. (2021). (reptiles) Columns contain the following. * **institutionCode** = museum the specimen came from. See GBIF for. * **specID** = Specimen ID (made up of institutionCode_specimen ID). * **sex** = Female or Male. * **class** = Amphibians or Reptiles. * **order** = Order. * **continent** = Continent specimen was collected from. * **countryCode** = Code for country * **year** = Year of collection. * **decade** = Decade of collection. * **typeStatus** = NA if not a type, if a type the kind of type (e.g. Holotype, Syntype etc.) is listed. * **type** = Type or NonType. * **iucnRedListCategory** = IUCN Red List category * **family** = Family. * **binomial** = Species binomial name * **genus** = Genus. * **higher1** = Higher taxonomic grouping 1 * **higher2** = Higher taxonomic grouping 2
Data tables for living foraminifera studies by John Murray and colleagues
All the images featured in the mentioned work are inside the folder “Images”. All the images display the name of the species and the museum number. Images are recorded in lossless TIFF format and include a 10 mm scale bar for the whole specimens and a 5 cm scale bar for the polished blocks.
Folder “XRD files” contains individual folders for each specimen studied with the raw X-ray diffractograms, recorded in ASCII format using the Highscore program (Malvern Panalytical). The PDF generated with the spectra, the peak list and the reference material for each specimen is included in each folder.
Part-processed Indonesian Fossil Specimens
Collections of marine invertebrates from the Miocene and Pliocene of East Kalimantan Indonesia that have not been identified to specific taxa so cannot be added to the NHMUK catalogue. These collections are intended primarily for taxonomists and other researchers looking at the origins of marine biodiversity hotspots in Southeast Asia. Palaeontology and molecular studies have suggested that the formation of the ancestral centre of diversity could be related to the constriction of the Indonesian Throughflow Current during the Cenozoic resulting in increasing speciation and/or immigration from other regions. The Throughflow Project was Marie Curie Innovative Training Network that included members of Seven European Institutions with Eleven Early Stage Researchers completing PhD degrees within the framework. At the NHM the coral and bryozoan components were studied and collections remain here. These specimens resulted from collecting trips to East Kalimantan Indoneisa in in 2010 and 2011 by project team members. The deposits were Early Miocene – Pliocene in age. Most samples collected during the field work were fully processed and have been registered in the NHM collections management system. Other samples were part processed and not catalogued and they are currently stored in clear covered trays with labels of sample numbers, stratigraphy & full locality details of sites. Tray samples are stored numerically in numbered Really Useful Boxes. Funding for the Throughflow Project was provided by European Union as part of the Marie Curie Actions Plan Framework 7 Programme (Grant No 237922)
Function and ecology of Solanum underground organs
Datasets used for analyses in the publication: Gagnon E, Baldaszti L, Moonlight P, Knapp S, Lehmann C, Särkinen T (2023) Functional and ecological diversification of underground organs in _Solanum_. Frontiers in Genetics 14: 1231413, https://doi.org/10.3389/fgene.2023.1231413.
Edeline Gagnon; Tiina Särkinen; Sandra Knapp
Description of the fields found in [JtD collection-level records](https://data.nhm.ac.uk/dataset/join-the-dots-collection-level-descriptions/resource/660de433-447b-40ad-9aaf-77c98f8c2ba9)
Link to the Psylloidea slide collection specimen records from the NHM catalogue, published as part of the wider NHM collection dataset.
This repository contains all the training data used to train the Sediment Analysis Neural-network Data-engine (SAND-e). SAND-e was created as part of the PhD thesis of G. William M. Harrison under the supervision of Ken Johnson and Willem Renema and the master’s thesis of Teigan Collins under the supervision of Ken Johnson and Nadia Santodomingo with major contributions made by Allia Rosedy. This study is part of the Reef Refugia project (NE/R011044/1) funded by NERC. William Harrison’s PhD is being conducted with 4D-REEF project funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 813360. The images and .json files corresponding to the relevant masks for each image used to train the segmenter can be found in the “segmenter_training_data.zip". The classifier was trained with the images in the “classifier_training_data.zip” images for classifier training are sorted into separate folders by type. The "AI vs Human testing.zip” file contains the raw images input into SAND-e (“raw images”) and the labelled version of those images given to human testers (“labelled images”), the outputs produced by SAND-e (“Segmenter_Classifier_Outputs.csv”), the answers given by the humans (“Human_annotations_anonymized.csv”), and a form of them in which SAND-e’s outputs have been aligned grain-to-grain with the human answers (“Human_AI_Grain_IDS.csv”). Finally, the “Deployment” folder contains the raw images fed into SAND-e for the analysis part of this study in the “raw images” folder and SAND-e’s outputs in the “AI_ouputs.zip” file.
George William Harrison; Teigan Georgia Collins; Nadiezhda Santodomingo; Kenneth Johnson; Willem Renema
This is a .xlsx version of Table S4 of the Supplementary Material supporting Griffiths et al. (2025). It contains data collected from 213 Hoplopteryx spp. specimens. Notes: Abbreviations in the table are as follows: SL = Standard Length, TL = Trunk Length, HL = Head Length, HH = Head Height, JL = Jaw Length, OD = Orbit Diameter, VW = Vertebrae Width. BGS = British Geological Survey (Keyworth, UK), CSM = Sedgwick Museum of Earth Sciences (Cambridge, UK), GMZ = Grant Museum of Zoology (London, UK) NHMUK = Natural History Museum (London, UK). Estimated SL are in bold. Italicised SL are the mean of two measurements.
Greg Phillpotts Paul Weedon Joan Mason Keith Poynton Joe Botting Lucy Muir Michael Rosenbaum Kate Andrew Giles Miller
Ludlow Museum Fossils in Shropshire Project data
The Fossils in Shropshire project dataset includes collections data and images of geological specimens from Shropshire Museums collections. The collection is principally comprised of paleontological specimens from Shropshire and the Welsh Marches and illustrates Shropshire’s diverse geology. It also has representative material from the rest of Britain and further afield. The most important or illustrative examples from this diverse collection are being digitised and key information captured by a small team of staff and volunteers. The project aims to increase awareness and access to this collection and is managed by the Friends of Ludlow Museum. The project is based at Ludlow Museum Resource Centre where the bulk of the 35,000 specimens are stored. Further information can be obtained at the following project website. http://fishproject2020.wixsite.com/news
Friends of the Ludlow Museum, Ludlow Museum Resource Centre
An up to date export of the UK Species Inventory database in its simplified form. This dataset contains all names and all taxonomic concepts in 2 tables, which can be used to derive NBN TAXON_VERSION_KEYs (TVKs) for names on observations held in non-NBN compatible systems.
This is a family-level pruned tree matched to the seabird list from Clements 2025 taxonomy. Pruned tree from Claramunt et al 2025: BBtree3 at family-level Available from: https://raw.githubusercontent.com/evolucionario/BigBirdTree
The Diatoms Herbarium is an ancillary collection in the Diatoms Collections at the Natural History Museum. It comprises processed and unprocessed samples preserved dried directly onto paper, glass or mica sheets and stored in paper packets mounted on standard herbarium sheets. Each herbarium sheet may contain one to several of these packets. This collection is rich in samples containing type material, including many by F. T. Kützing and W. Smith, as well as historical exsiccate sets such as G.L. Rabenhorst's _Algarum europaearum Exsiccatarum_ and Ardissone's _Erbario Critogammico Italiano_ and represent a valuable resource for diatoms taxonomy investigations using modern techniques such as Scanning Electron Microscopy. This dataset provides a complete catalogue of the Diatom Herbarium. Each specimen has been databased to capture, minimally, its registration number (barcode) and the 'filed as' name, which may or may not be the currently accepted name. Most of these specimens have images associated with them, such as a photograph of the herbarium sheet.
Index Lot records from the Natural History Museum's collection
Link to the John Chainey Lepidoptera Collection specimen records from the NHM catalogue, published as part of the wider NHM collection dataset.
John Chainey Lepidoptera Collection Specimens
Full list of 383 seabird species found in the Clements et al 2025 taxonomy and the Claramnut et al 2025 phylogeny, along with information on the number of birds sampled, number of plastic ingestion studies, number of birds ingesting plastic, mean weighted frequency of occurrence of plastic ingestion, and whether or not plastic was recorded. For species not found in our plastic ingestion dataset, all entries are NA aside from FO which is zero. Column contents are as follows. * **tips**. Species name from Clements et al 2025 taxonomy. * **total_plastic**. Total number of birds recorded to ingest plastic. * **total_n**. Total number of birds studied. **species_FO**. Mean weighted frequency of occurrence of plastic ingestion (i.e. total_plastic / total_n weighted by total_n. * **n_studies**. Number of plastic ingestion studies. * **plastic**. Does the species ingest plastic? Yes/No/NA for species that do not appear in our plastic ingestion dataset.
The Convolvulaceae collection comprises the records of all the sheet-mounted material at the Natural History Museum, London at the time of project completion (September 2023). Each specimen record has been published with an image capturing both the specimen and its associated labels and creating an inventory record with a unique identifier (barcode), taxon information and geographical locality. The data resource generated by the project is available using the link. This collection was digitised as part of the Museum's Digital Collections Programme.
Ranee Om Prakash; Krisztina Lohonya; Hillery Warner; Larissa Welton; Chiho Ikebe; Louise Berridge; Ashleigh Whittaker; Skye Neal; Emma Bonzo; Glory Turnbull; John Wood; Jovita C. Yesilyurt; Mark Carine; Rinku Desai; Peter Wing; Louise Allan
First report of the biomineral whitlockite from the fossil record of holocephalans
Data from paper: First report of the biomineral whitlockite from the fosssil record of holocpehalans submitted to Royal Society Open Science All the images featured in the mentioned work are inside the folder “Images”. All the images display the name of the species and the museum number. Images are recorded in lossless TIFF format and include a 10 mm scale bar for the whole specimens and a 5 cm scale bar for the polished blocks. Folder “XRD files” contains individual folders for each specimen studied with the raw X-ray diffractograms, recorded in ASCII format using the Highscore program (Malvern Panalytical). The PDF generated with the spectra, the peak list and the reference material for each specimen is included in each folder. Folder ‘Raman files’ contains individual folders for raw and processed Raman spectra for specimen Harriota raleighana. Raw data is recorded in TXT format, processed data in CSV format. Processed data was treated by the following: 1) cosmic ray removal, 2) background subtraction, 3) normalisation, 4) automatic peak detection. For maps & line scans that consist of more than 1 measurement, positional (x,y) data is recorded in raw data files.
Esther Manzanares Ubeda; Zerina Johanson; Jens Najorka; Joseph Razzell Hollis; Charlie Underwood; Richard John Twitchett
Former Aberystwyth microfossil collection
A catalogue of information about discrete collections within the Former Aberystwyth University Micropalaeontology Collection, now housed the Natural History Museum. The catalogue is designed for **university academics** and **industrial micropalaeontologists** interested in post-Palaeozoic ostracods and foraminifera. Collection records generally include: * the title of the study that produced the collection * information about the collector * any associated documentation (e.g. thesis, record file or publications) held at the Museum. * brief geological ages based on the Gradstein et al. (1996) geological timescale * locality information. The database is searchable by surname, year, fossil type, collector, country/sea/ocean, or by stratigraphical unit.
A csv file of all occurrence records from Solanaceae Source used in the analyses of ecological role of underground storage organs in Solanum (Supplementary Material 3 file)
Occurrence data for USO in Solanum (SM3)
An initial listing of UK Silurian assemblage slides from the collection of Prof. Richard J. Aldridge formerly of the University of Leicester. The file synthesises data from the slides themselves and several unpublished documents relating to details of the collection site, a listing of the samples taken, lithological descriptions along with details of sample weights and yields. The collection underpins type and figured specimens already donated to the Natural History Museum and is a major resource for anyone wishing to study British Silurian conodonts.
The Birdwing Butterfly collection comprises the records of all the pinned material of Ornithoptera, Trogonoptera and Troides at the Natural History Museum, London at the time of project completion (March 2019). Each specimen record has been published with an image capturing both the specimen and its associated labels and creating an inventory record with a unique identifier (Data Matrix barcode), taxon information, type status and country level collection locality. All specimens will have an additional image capturing the ventral (adult specimens) or lateral (immature stages) view as well as the reverse side of labels. The data resource generated by the project is available using the link. Please search for the relevant taxa. This collection was digitised as part of the Museum's Digital Collections Programme through the funding of an anonymous donor.
Peter Wing; Louise Allan; James Ayre; Blanca Huertas; Charlotte Barclay; Laurence Livermore; Geoff Martin
Link to the Cooper collection specimen records from the NHM catalogue, published as part of the wider NHM collection dataset.
Documentation produced for NHM staff in 2018: a thorough overview of the Join the Dots data, processes and rationale. Some elements of the JtD framework have been amended slightly since this document was assembled, but it remains a useful reference for navigating the collection-level dataset presented in this package.
The Castniidae Collection comprises the records of all the pinned and spirit material of family Castniidae housed in the Lepidoptera Collection at the Natural History Museum, London at the time of project completion (April 2025). The Castniidae Collection was digitised to improve access and support research into the family. Each specimen record has been published with two images capturing a dorsal and ventral view of the specimen and its associated labels, creating an inventory record with a unique identifier (Data Matrix barcode) taxon information, country of origin, and type status. The data resource generated by the project is available using the Data and Resources link.
Glory Turnbull; Glory Turnbull; Louise Berridge; Emma Bonzo; Elizabeth Church; Xinzhu He; Leo Le Good; Roisin Mackie; Skye Neal; Sara Pomposelli; Zhonghui Qu; Kathryn Royce Schronk; Larissa Welton; Peter Wing; Chiho Ikebe; Hillery Warner; Geoff Martin; Alberto Zilli; Robert Worthy
**Specimen number**: NHMUK C.1920.12.31.1 **Specimen Link**: http://data.nhm.ac.uk/object/69947b29-5d22-47ae-8703-245d1b7642a0 **Decription**: _Balaenoptera edeni_ -- Balaenopteridae; Cetacea; Mammalia, female
Large RDS file containing the imputed body size data used in all analyses.
Georeferenced NHM Australian Botanical Data
We calculated the mean values for each year of the Biodiversity Intactness Index (BII) (weighted by cell area) as well as a number of pressure variables (as change in pressures drive change in BII). We used cross-validation (leaving one biome out in turn) to provide decadal upper and lower uncertainty margins for BII. The variables include: bii: mean Biodiversity Intactness Index crops: mean grid cell fraction assigned to annual, perennial and nitrogen-fixing crops pastureland: mean grid cell fraction assigned to pasture and rangeland urban extent: mean grid cell fraction assigned to urban highintensityag: mean grid cell fraction assigned to high-intensity agriculture (annual, perennial and nitrogen fixing crops and pasture) qualitynatural: primary and mature secondary vegetation that is either under minimal or light use hpd: mean human population density Area codes correspond to the UN M49 area codes for countries, interregions, subregions and regions. See associated json file. The summary data are provided for all variables in long format (i.e., one row for each scenario, year, variable and area code combination). Previous version included only data for 2000-2050, and did not include uncertainty limits.
FineRAD structure input (prelim filtered)
The state of the world’s seaweeds is an up-to-date review, prompted by an urgent need to conserve and protect the world’s seaweeds in the face of devastating impacts due to human activities and the triple planetary crisis of climate change, pollution and biodiversity loss. Bringing together multiple sources of evidence on global seaweed distribution, habitats and ecosystem services, with how seaweeds are threatened, protected and restored, this document provides the evidence for a Seaweed Breakthrough conservation initiative.
List of accepted amphibian names and synonyms. Downloaded from: > Frost DR, Amphibian Species of the World: an online reference. Version 6.1 (Accessed 21st April 2022). Electronic Database accessible at https://amphibiansoftheworld.amnh.org/index.php. American Museum of Natural History, New York, USA. doi.org/10.5531/db.vz.0001 (2022). 502 28
Phylogeny for extant Cetacea, containing only the species included in the analyses. This tree contains 89 taxa. Note that as this tree only contains extant species there are no taxa with zero length branches, so there is no equivalent wZBL tree with these included.
JW Murray publications with associated samples now housed at the NHM
Sceloporus morphology data (population comparisons)
This data is made available under a CC-BY-NC-SA license (https://creativecommons.org/licenses/by-nc-sa/4.0/). By downloading this data, you agree to be bound by these terms. This directory contains BII v2.1.1 data. The data download is a .zip file of global rasters (.tif) at approximately 10km resolution at the equator, for the years 2000, 2005, 2010, 2015, and 2020. BII rasters are values between zero and 100%, indicating the intactness of the ecosystem: zero meaning completely degraded and 100% being completely intact. The .zip file also includes a README with metadata for the spatial rasters, and a LICENSE file. This dataset was developed using methodology described here: De Palma, A., Contu, S., Thomas, G. E., Duffin, C., Nix, S., & Purvis, A. (2024). The Biodiversity Intactness Index (BII) developed by the Natural History Museum: Methodology (v2.1.1). https://data.nhm.ac.uk/dataset/bii-developed-by-nhm-v2-1-1-methodology © The Trustees of the Natural History Museum, London 2024. Some Rights Reserved.
**Specimen number**: NHMUK 1965.11.2.1 **Specimen Link**: http://data.nhm.ac.uk/object/9461141d-2261-419c-a0e3-9b1784711b05 **Decription**: _Balaenoptera acutrostrata_ -- Balaenopteridae;
A word file of all numbered specimens examined for this revision ordered by primary collector. Suppl. Mat. 1 in Knapp et al. (2023). Here we only cite numbered collections examined for this monograph from plants collected in South America (incl. the Juan Fernández islands). First collectors in collections made by two or more collectors are listed here rather than complete collector strings. Collections by anonymous collectors without date or other identifying features are not included. Morelloids are prone to being found in mixed collections, so where we have identified these, or have identified the same number used for a different taxon, we have added [a] or [b] in square brackets. Any suffixes not in square brackets are part of the original collection. All collections seen and full collector strings can be found in searchable csv files (SM 2 for South American collections; SM 3 for all collections of morelloids examined worldwide).
Index to numbered collections South American morelloid Solanum
Link to the Atlas of Living Malaysia specimen records from the NHM catalogue, published as part of the wider NHM collection dataset.
Data used in Figure 1 (a & b) of Sanchez-Ortiz et al. (2019) (bioRxiv).
Global maps of Biodiversity Intactness from Sanchez-Ortiz et al. (2019) (bioRxiv)
This data contains the georeferenced locations of the Botanical TYPES held at the Natural History Museum that have been collected in Australia. Each location Lat and Long has been carefully georeferenced, using label information from the specimen, and collector research. All sources of information have been noted in the notes. The data can be downloaded and imported to ArcGIS Pro or Google Earth and shows the spatial location of NHM Botanical TYPES specimens held at the Natural History Museum, London.
NHM Botanical Type Georeferenced for China
Micropalaeontology citations and visitors
Herbarium specimens of Solanum occurring in Peru, downloaded from Solanaceae Source xx/xx/2021
This zip file contains (1) the final dataset of valid extant marine gastropod species occurrences, (2) a subset final dataset of dated observations, (3) a subset final dataset of georeferenced records with lat/lon z-score < 3 per species, (4) metadata of COI barcodes from BOLD, (5) metadata of full mitogenomes from GenBank, and (6) the R script used for analysis and visualisation.
All node probabilities from the DEC model for all taxa. *node* = node number on tree (see `node-labels-tree.png`) *ML* = Maximum Likelihood state for the node under the DEC model All other columns represent a single state and the marginal probability of that state being at that node. A = area A, AB is either area A or B and so on...
Time periods for stratified time biogeography analyses in paper 2.
Summary table of annual averages of BII for each country, subregion and region.
Total number of species in each amphibian and reptile order as of April 2022. Taken from: > Frost DR, Amphibian Species of the World: an online reference. Version 6.1 (Accessed 21st April 2022). Electronic Database accessible at https://amphibiansoftheworld.amnh.org/index.php. American Museum of Natural History, New York, USA. doi.org/10.5531/db.vz.0001 (2022). 502 28 > Uetz, P., Freed, P., Aguilar, R. & Hosˇek, J., The Reptile Database, http://www.reptile-database.org. Accessed April 2022. (2022). * **order** = order * **species** = number of species
Clade IV PCA file (Species delimitation)
A dataset listing items in Sir John Murray's HMS Challenger Ocean Sediment Collection to accompany a paper Miller, C. Giles and Jouet-Sarkany, Monique M. H. 2025. Sir John Murray’s H.M.S. Challenger Sedimentary Deposits Collection at the Natural History Museum, London. Preprint available: https://www.biorxiv.org/content/10.1101/2025.03.21.644325v1 and contains descriptions of column headers.
Sir John Murray's Challenger Sediment Collection
An illustrated listing of some common cabinet types in the Natural History Museum collection, with suggested scores as part of the Condition - Storage Equipment question for the "Join the Dots" collections assessment exercise at the Natural History Museum.
The Ceratopogonidae Slide Collection comprises the records of all the slide-mounted Ceratopogonidae (Diptera) material at the Natural History Museum, London at the time of project completion (August 2022). This collection comprises substantial amounts of material from John Boorman. Each specimen record has been published with an image capturing both the specimen and its associated labels and creating an inventory record with a unique identifier (Data Matrix barcode), taxon information, type status, country level collection locality. Additional images were taken to capture any information on the reverse of the slides and/or the paper envelopes that house the slides. This collection was digitised as part of the Museum's Digital Collections Programme.
Daniel Hall; Louise Berridge; Joseph Deane; Phaedra Kokkini; Leo Le Good; Krisztina Lohonya; Zoe J. O. Adams; Duncan Sivell; Peter Wing; Marla Spencer
csv files of country, subregion, region and global-level averages of annual land use amounts (primary vegetation, secondary vegetation, cropland, pasture and urban) (2001-2012)
Catalogue records of specimens from the Herbarium of Samuel Dale M.D. (1659-1739), presented by the Society of Apothecaries, 1862.
Link to the “British and Irish Agromyzidae (Diptera)” specimen records from the NHM catalogue, published as part of the wider NHM collection dataset.
“British and Irish Agromyzidae (Diptera)” specimens
Hans Sloane's Collection of Vegetables and Vegetable Substances
Hans Sloane’s Collection of Vegetables and Vegetable Substances originally consisted of 12,752 botanical specimens, most housed in small glass and wooden boxes. Sealed inside these boxes were parts of plants such as seeds, beans, leaves, bark and gum, that were collected between the 1680s and 1750s. All sorts of people from around the world were involved in the transportation and exchange of these specimens. In London, Sloane had these items put into boxes, where they were numbered and a corresponding description of the item was entered into his manuscript catalogue. Today, the Vegetable Substances collection comprises more than 8000 surviving specimens/boxes and the original three-volume manuscript catalogue. This dataset includes a transcription of said manuscript and all 12,752 handwritten entries. At the core of these entries is information about what the object is, and from here, the level of detail is varied. This ranges from information about people and places, local uses of plants, margin annotations (which detail cabinet and drawer numbers where Sloane kept these things in his house) to bibliographic references, and modern determinations. Users are recommended to consult the 'Data description and change log' before using the resources provided here. A version of the transcription can also be found in the NHM library catalogue (Primo), together with images of the manuscript catalogue pages: https://nhm.primo.exlibrisgroup.com/permalink/44NHM_INST/16ehpmm/alma9936352402081. Please note: This dataset preserves the data in Sloane’s catalogue in their original form to retain authenticity and facilitate research. As such, some entries contain language that may be offensive and that is not acceptable nor appropriate in an inclusive environment. This work was supported by a grant from the Arts and Humanities Research Council Towards a National Collection Programme (Grant AH/W003457/1).
Victoria Pickering; Charles Jarvis; Mark Carine
This is the list of papers extracted from our literature searches, along with whether they were relevant (or not) and thus included in dataset **02_plastic-ingestion-data**. Full details of data collection are in the Supplementary Materials of the paper. In brief, papers were identified using Web of Science and/or Google Scholar searches using the following search terms: - “seabird* plastic OR debris OR pollution” - “plastic* gull OR shearwater OR albatross OR petrel OR penguin OR puffin OR auk OR guillemot OR murre* OR tern OR skua OR jaeger OR frigatebird OR booby OR gannet OR cormorant OR shag OR tropicbird OR merganser OR pelican OR phalarope OR scoter OR eider OR fulmar OR prion OR noddy OR gannet OR loon OR diver”. We considered peer-reviewed papers, research reports, conference proceedings and theses published to the end of 2024 and spanning 387 seabird species as defined by Gaston (2004), excluding eight extinct species (*Bulweria bifax, Camptorhynchus labradorius, Hydrobates macrodactylus, Mergus australis, Pinguinus impennis, Pterodroma caribbaea, Pterodroma rupinarum,* and *Urile perspicillatus*). We excluded articles and reports on species occurring only in freshwater, extinct species, captive populations, and studies reporting on cases of plastic entanglement or ingestion of non-plastic items, such as studies that pooled plastic with non-plastic marine debris (e.g., metal fishing hooks, natural fibres, artificially treated cellulose, rubber and glass). Both plastic-focused research and research where plastic was found incidentally, such as in traditional diet studies, were included. Plastics of all types (e.g., fragments, foam, sheets, fibres) and of all sizes were recorded. All publications discovered in literature searches were downloaded and recorded in **01_sources-for-plastic-ingestion-data**, but only relevant studies were added to the dataset **02_plastic-ingestion-data**. Column contents are as follows. - **Source**. Shortened name of the source, e.g. Author et al, YEAR. If not included in the main dataset **02_plastic-ingestion-data** this is set to "Not relevant". - **Used**. Indicates whether data from a particular source was used in the present study. Any papers labelled "Yes" were included in the **02_plastic-ingestion-data** dataset. Sources marked as "Not relevant" or anything other other than "Yes" were not included in **02_plastic-ingestion-data**. Reasons for papers being classed as "Not relevant" included irrelevance to the study's scope or redundancy with other sources. For example, sources may be excluded if they focus on topics like nest pollution, entanglement, distribution characterisation, or if they lack specificity regarding plastic ingestion. Duplicate information from other references was also a common reason for exclusion. * **Authors**. Authors of the paper. * **Year**. Year of publication. * **Link.plastic**. Link to the paper. * **Title**. Title of the paper. * **DOI**. DOI of the paper * **Comments**. Any comments added by data curators about the relevancy of the paper.
Full phylogeny without sampled ancestors used in diversification analyses in paper 2.
SPME GCMS data for bespoke conservation box
Solid phase microextraction (SPME) GCMS volatile compound data collected from a bespoke enclosure constructed from foamboard, acid-free card, plastazote foam, Tyvek and a final layer of bondina using a 85-μm CAR/PDMS SPME fiber. Five hours exposure time, desorbed for 10 minutes at 270 C on a DB-5 column.
NHM Botanical Types Georeferenced for China
This data contains the georeferenced locations of the Botanical TYPES held at the Natural History Museum that have been collected in China. Each location Lat and Long has been carefully georeferenced, using label information from the specimen, and collector research. All sources of information have been noted in the notes. The data can be downloaded and imported to ArcGIS Pro or Google Earth and shows the spatial location of NHM Botanical TYPES specimens held at the Natural History Museum, London.
A searchable csv file of all specimens examined for the monograph, including those from outside the specific area treated for widely distributed or introduced species. Column headings are: Herbarium = herbarium acronym acc. to Index Herbariorum; Category = specimen or photograph of specimen; SpecID = brahms specimen ID; Brahms = Brahms collection event ID; Accession = accession number of specimen; Barcode = barcode of specimen; Collector = principal collector; Prefix = collection number prefix (if applicable); Number = collection number; Suffix = collection number suffix (if applicable); AddColl = additional collectors; Type = type of type; Type of = type of what species; Day -= day of collection; Month = month of collection; Year = year of collection; DateRes = date resolution (if applicable); Family = plant family; Genus = genus name; Species = species epithet; Author = species author name(s); Country = country of collection; Majorarea = first political division; Minorarea = second political division; Gazetteer = nearby town or place; Locnotes = locality; Habitattxt = vegetation characteristics; Lat = latitude; NS = north or south; Longitude = longitude; EW = east or west; LLunit = coordinate units (DD = decimal degrees; DM = decimal minutes; DMS = degrees, minutes, seconds); LLres = coordinate resolution (4 = nearest minute; 7 = area centroid); LLorigin = origin of coordinates; LatLong = coordinates in DMS; LatDec = decimal latitude; LongDec = decimal longitude; Alt = elevation minimum; AltMax = elevation maximum; AltRes = elevation resolution; AltUnit = elevation units (all metres); AltRange = elevational range.
3D scans of ten Cetacean skulls collected between 1873 and 2007. The dataset contains both baleen and toothed whales including _Physeter macrocephalus_ (a sperm whale) the largest of the toothed whales and the largest toothed predator on Earth. Scanning was done by Kate Burton using a Creaform Go!Scan 50 structured light scanner and the scans were processed using Geomagic Wrap software. Specimen and context data was provided by Richard Sabin.
Richard C Sabin; Kaitlyn Burton; Natalie Cooper; Anjali Goswami
json file providing area codes and names (using UN M49 area codes for countries, interregions, subregions and regions).
NHM Botanical Types Georeferenced for Australia
The Herbarium of Samuel Dale M.D. (1659-1739)
Samuel Dale was born in 1659. He was apprenticed as an apothecary before moving to practice in Braintree, Essex in 1680. There, he befriended John Ray and began to pursue an interest in botany. Dale assisted Ray in the preparation of several publications and was became a correspondent of Sloane and Petiver. In 1693, he published Pharmacologia. He also contributed papers on natural history to the Philosophical Transactions of the Royal Society. In later life, Dale was licenced as a physician by the Royal College of Physicians. Dale assembled a herbarium that was bequeathed to the Society of Apothecaries following his death. It was kept at Chelsea Physic Garden as a discrete collection housed in specially made oak presses until 1869 when it was transferred to the British Museum. It was subsequently moved to South Kensington in 1881. Today, it forms part of the Herbarium of the Natural History Museum. Dale’s herbarium comprises 2827 specimens, 458 of which have another collector named. The remainder (2369 specimens) we consider to have been collected by Dale himself. The collections span the period from 1692 until 1739, the year of Dale’s death. Almost all of the dated specimens collected by Dale were made after 1709. Essex and Suffolk feature prominently among English localities although English gardens represent a more significant source of specimens. There are 435 specimens from Chelsea Physic Garden (collected between 1704 and 1738); 115 specimens from William Sherard’s garden in Eltham, most collected between 1722 and 1726; 41 from the Oxford Botanic Garden (collected in 1709); and 27 from Fulham Palace collected in 1711. Other notable gardens represented include those of Lord Petre (Old Thorndon Hall), Blathwayt (Dyrham Park), Jekyll (Hedingham), Fairchild (Hoxton), Collinson (Peckham), the Duchess of Beaufort (Chelsea), Uvedale (Enfield), Sir Charles Wager (Fulham) and DuBois (Mitcham). There are collections from Dale’s own garden and one specimen from the garden of John Ray. Thirty individuals other than Dale himself are named on labels. Isaac Rand, Curator of the Chelsea Physic Garden in 1712, its Keeper in 1719 and its first Director from 1725 is named on 124 specimens. There is a collection of 99 specimens from Mark Catesby, including material he collected in Virginia, Carolina, Jamaica and the Bahamas between 1713 and 1726, along with six specimens from the Bahamas collected by Francis Dale in 1730. Fifty eight specimens were contributed by the East India Company surgeon Edward Bulkley. Collected between 1700 and 1712, most are from Fort St George (= Chennai, India) where he was the company surgeon although some are from Ava (= Inwa) and Pegu (= Bago) in modern day Myanmar. Indian specimens collected by Alexander Brown in 1692 are also among the earliest dated specimens in the herbarium. Most specimens are accompanied by labels in Dale’s neat and careful hand, detailing names and synonyms that apply to the specimen. Fifteen specimens have more than one label including provenance information. Where there is a second label, we have transcribed the earliest; details of the second label can be seen in the 'Additional labels' data resource below. The specimens are mostly stored in the Botany Historic Collections Room (HCR) where they are curated in a family order. However, localised British material is stored in the British and Irish Herbarium in the main run. The determinations given for HCR specimens are largely the families in which the specimens are curated (albeit updated to reflect the names used elsewhere in the botany collections eg Fabaceae, Asteraceae etc). In some cases, a second determination is provided. The Catesby specimens have been determined to species as have the specimens in the British and Irish Herbarium. Imaging of the specimens is in progress.
Trait data extracted from BHL descriptions
Agilent data file of GCMS data from bespoke specimen enclosure.
Former British Petroleum microfossil collection data
Specimens referred by Sloane and his assistants to plant names described by John Ray in his Historia Plantarum (1686-1704) and to additional names recorded in the headers and footers.
Sloane's annotations in Ray's Historia Plantarum
An explanation of the data included in the dataset. We recommend reading this guide before using the dataset.
Former Aberystwyth Microfossil Collection
British and Irish 'Larger' Micro Moths Collection
The British and Irish 'Larger' Micro Moths Collection comprises the records of all the pinned material of Alucitidae, Cossidae, Limacodidae, Sesiidae and Zygaenidae housed in the British and Irish Lepidoptera Collection at the Natural History Museum, London at the time of project completion (January 2024). The British and Irish 'Larger' Micro Moths Collection was digitised to further complete work started during the iCollections project to digitise all British and Irish Lepidoptera material held at the Natural History Museum, London. Each specimen record has been published with an image capturing both the specimen and its associated labels and creating an inventory record with a unique identifier (Data Matrix barcode) and taxon information. The data resource generated by the project is available using the Data and Resources link. Please search for the relevant taxa as this dataset is part of a project covering a range of families.
Peter Wing; Louise Berridge; Emma Bonzo; Joseph Deane; Noelia Gahan; Daniel Hall; Krisztina Lohonya; Nicola Lowndes; Ying Luo; Skye Neal; Olga Sivell; Megan Squire; Glory Turnbull; Larissa Welton; Chrissy Williams; Janice Wu; Chiho Ikebe; Marla Spencer; Hillery Warner; Geoff Martin
Raw data from GBIF. Please cite GBIF if you use this data: > GBIF, GBIF Occurrence Download https://doi.org/10.15468/dl.ub7yfv. Accessed 21st April 2021. (2021). (reptiles)
Index of john Murray's type slides now housed at the NHM
Ray Bate Collection of mainly Cretaceous ostracods from West Africa
The dataset describes a named taxonomic reference collection of 311 slides of individual specimens as well as a listing of related assemblage slides covering 4 slide cabinets. Data has been enhanced by reference to various hard copy reports and logging sheets detailing the contents and stratigraphic metadata from the area.
Link to the Aphidoidea Slide Collection specimen records from the NHM catalogue, published as part of the wider NHM collection dataset.
The specimens collected by Samuel Browne
Marine Plastic Pollution Ingested by Flesh-Footed Shearwaters
# Introduction This image database is intended for the analysis of physical and colorimetric properties of plastic litter consumed by fledgling seabirds, but we hope that these images will also serve to highlight the seriousness of the threat to marine wildlife posed by plastic pollution, with some fledglings having ingested more than 200 pieces of plastic. This database was made available as part of the publication of a paper describing the methodology we developed for quantitative photography of plastic pollution, in the hope that it will improve the robustness and accuracy with which plastic pollution is measured in terms of size, shape, and colour of individual fragments. Details of the publication are as follows: # About the project Each image represents the plastic (and pumice) removed from the digestive system of a single Flesh-footed shearwater (Ardenna carneipes) fledgling during fieldwork undertaken by Alexander L Bond and Jennifer L Lavers in 2021 and 2022, as part of a long-term project studying trends in plastic consumption and effects on this highly-impacted marine species. Plastics were removed from the proventriculus and the gizzard of each bird and stored separately for imaging. An X-Rite colour reference card is included in each image for the purposes of calibration and scaling. # Image Acquisition and Processing The 2021 image set was acquired using a Canon EOS 4000D DSLR at the Natural History Museum in Tring, UK by Joseph Razzell Hollis. The 2022 image set was acquired using a Canon EOS 1500D DSLR at the University of Tasmania by Gabrielle Henderson. Both image sets were processed in Adobe LightRoom to remove lens distortion, and then colour-corrected using custom Python script written by Joseph Razzell Hollis. For a full description of methods and data analysis, see Razzell Hollis et al. (2023). # Acknowledgements We would like to acknowledge the Tasmanian Aboriginal people as the traditional owners and first scientists of the land where this research was conducted. JRH was funded by the European Union's Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 101030480. This research was approved by the Charles Sturt University Animal Ethics Committee (A22382), New South Wales Office of Environment and Heritage (SL100169), Lord Howe Island Board (LHIB 07/18), and the University of Tasmania Human Ethics Panel (H0028598).
Joseph Razzell Hollis; Gabrielle Henderson; Jennifer Lavers; Edward Rea; Valeriya Komyakova; Alexander Bond
Sceloporus climate data (clade comparisons)
Trait data extracted from Flora of North America descriptions
Phylogeny for baleen whales, containing only the species included in the analyses. The tree contains 105 taxa including those with zero length branches (ZBL).
Reference list for entries in the references column of the *Total-proxy-measurement-data.csv* dataset.
**Specimen number**: NHMUK 1876.2.16.1 **Specimen link**: http://data.nhm.ac.uk/object/bb92fdad-975e-42c3-9837-0301466f15de **Description**: _Caperea marginata_ -- Neobalaenidae;
Geography file for all taxa used in biogeography analyses in paper 2.
John Whittaker's collection of micropalaeontological slides from his archaeological studies
This is a listing of all of the unregistered slides from John Whittaker's work on Archaeological Sites from the UK. Each row represents an assemblage slide of mixed micropalaeontological materials (mainly Foraminifera and Ostracoda) from work done towards the end of his career at the NHM and during his retirement.
Fossil phylogeny for taxa used in biogeography analyses in paper 2.
As for "extra-data-sexed" but includes unsexed records. * **sex** = Female, Male or NA
British and Irish Agromyzidae (Diptera) Collection
The British and Irish Agromyzidae Collection comprises of the records of all pinned agromyzid material at the Natural History Museum, London at the time of project completion (July 2019). The aim of this project was to digitise the pinned agromyzid specimens using the ALICE workflow (Angled Label Image Capture and Extraction) to enable the national agromyzid expert to work remotely with this collection to extract data from the specimen labels and verify identifications. Each specimen record has been published with six standard images capturing the dorsal habitus, lateral habitus and four angled views of the specimen labels. The images created were attached to existing specimen records within the Collection Managment System. The data resource generated by the project is available using the link. This collection was digitised as part of the Museum's Digital Collections Programme.
Robyn Crowther; Elizabeth Devenish; Peter Wing; Louise Allan; James Ayre; Charlotte Barclay; Nigel Wyatt
Summary table of annual averages of pasture amount for each country, subregion and region.
Minchin et al (2024) British and Irish Botany ITS alignment.txt
Global seabird plastic ingestion database
**Data from the paper**: Global seabird plastic ingestion varies across phylogeny but not behavioural traits. 2026. Stephanie Avery-Gomm, Nia Potapova, Chrissie Potter, Alexander L. Bond, Stephanie B. Borrelle, Jennifer L. Lavers, Steven J. Portugal, Hugh P. Possingham, Jennifer F. Provencher, and Natalie Cooper. ADD LINK. Code for all analyses can be found on GitHub: https://github.com/nhcooper123/PhyloPlastics Archived data are as follows. Please click on individual files below for their associated metadata. ##Raw data * **01_sources-for-plastic-ingestion-data.csv**. The papers from our literature searches. * **02_plastic-ingestion-data.csv**. The raw plastic ingestion data extracted from papers in 01 * **03_trait-data.csv**. Species specific trait data taken from the literature. ## Cleaned data used in the analyses The raw data were cleaned and aggregated prior to analyses. See `analyses/data-preparation` and `01-data-preparation.qmd` at https://github.com/nhcooper123/PhyloPlastics for more details. * **plastic-data-aggregated_2026.csv**. Aggregated data used in analyses. * **seabird-tree-plastic-2026.csv**. Phylogeny of Claramunt et al 2025 pruned to only species with plastic ingestion data. * **full-species-list-2026.csv**. Summarised dataset for all seabird species indicating which are/are not part of our plastic ingestion dataset. Used in the creation of Figure S2. ## Taxonomy * **seabird-list-Clements2025.csv**. List of seabird species according to Clements et al 2025 taxonomy. The full taxonomy file can be found here: https://www.birds.cornell.edu/clementschecklist/download/. If you want to use the taxonomy please cite: > Clements, J. F., P. C. Rasmussen, T. S. Schulenberg, M. J. Iliff, T. A. Fredericks, J. A. Gerbracht, D. Lepage, A. Spencer, S. M. Billerman, B. L. Sullivan, M. Smith, and C. L. Wood. 2025. The eBird/Clements Checklist of Birds of the World: v2025. Downloaded from https://www.birds.cornell.edu/clementschecklist/download/. ## Phylogeny * **sea-bird-tree-2026.nex**. Phylogeny of Claramunt et al. 2025 pruned to seabird species only. * **family-tree-2026.nex**. Family level phylogeny of Claramunt et al. 2025 pruned to seabird families only. * **tips-to-add.csv**. Details of 39 species missing from Claramunt et al. 2025 and how these were added to the phylogeny. The full raw phylogeny file can be found here: https://raw.githubusercontent.com/evolucionario/BigBirdTree/refs/heads/main/RAGBackbone/BBtree3.tre. If you want to use the phylogeny please cite: > Claramunt, Santiago, Catherine Sheard, Joseph W. Brown, Gala Cortés-Ramírez, Joel Cracraft, Michelle M. Su, Brian C. Weeks, and Joseph A. Tobias. 2025. “A New Time Tree of Birds Reveals the Interplay between Dispersal, Geographic Range Size, and Diversification.” Current Biology 35 (16): 3883-3895.e4.
Stephanie Avery-Gomm; Nia Potapova; Chrissie Potter; Alexander Bond; Stephanie B. Borrelle; Jennifer L. Lavers; Steven J. Portugal; Hugh P. Possingham; Jennifer F. Provencher; Natalie Cooper
Concatenated four gene alignment of partial 18S rDNA, 28S rDNA, cox1 and cytb.
# List of seabirds from Clements taxonomy Citation: Clements, J. F., P. C. Rasmussen, T. S. Schulenberg, M. J. Iliff, T. A. Fredericks, J. A. Gerbracht, D. Lepage, A. Spencer, S. M. Billerman, B. L. Sullivan, M. Smith, and C. L. Wood. 2025. The eBird/Clements checklist of Birds of the World: v2025. Downloaded from https://www.birds.cornell.edu/clementschecklist/download/ Seabirds are defined as follows: 1. All Sphenisciformes (penguins) 1. All Procellariiformes (petrels, albatross etc.) 1. All Gaviiformes (divers/loons) 1. All Phaethontiformes (tropicbirds) 1. All Suliformes (gannets, boobies etc.) except Anhingidae (anhingas) 1. Within Pelecaniformes, Pelecanidae (pelicans) 1. Within Charadriiformes, Laridae (gulls), Alcidae (auks), Stercorariidae (skuas) and Phalaropodini (phalaropes) 1. Within Anseriformes, Mergini (diving ducks) We also exclude the extinct species *Bulweria bifax, Camptorhynchus labradorius, Hydrobates macrodactylus, Mergus australis, Pinguinus impennis, Pterodroma caribbaea, Pterodroma rupinarum,* and *Urile perspicillatus*
Phylogeny for baleen whales, containing only the species included in the analyses. This tree contains 83 taxa, excluding those with zero length branches (ZBL).
Plymouth University (Prof. Malcolm Hart) Microfossil Collection
This is a collections level description of 12 cabinets from the research collection of Malcolm hart, donated in 2022 to the NHM.
Summary table of annual averages of urban amount for each country, subregion and region.
**Specimen number**: NHMUK ZD 1992.42 **Specimen Link**: http://data.nhm.ac.uk/object/640cd2d8-ae5e-405d-9713-ab7a023414ca **Decription**: _Hyperoodon ampullatus_ -- Ziphiidae; Cetacea; Mammalia, male
The Herbarium of John Ray FRS (1627 – 1705)
John Ray F.R.S. (1627-1705) was the leading English naturalist of the 17th century. The son of a blacksmith, born in Black Notley in Essex, Ray was educated at Trinity College Cambridge, where he would also become a Fellow. Ray took holy orders in 1660 but subsequently resigned in 1662, unable to conform to the requirements of the Act of Uniformity. After leaving Cambridge, Ray travelled extensively, both through Britain and Europe, with his former student, friend and later patron, Francis Willughby. He made botanical collections during those travels. The bulk of the specimens in Ray’s herbarium are European, or from cultivation, collected during Ray’s European travels between 1663 and 1665 (Trimen, 1870), described by Ray in his Observations in the Low Countries (1673). There are, additionally, a number of specimens from England that Trimen suggests were probably collected during travels in 1667 and 1668. The plants gathered on his British tours were described in his Catalogus plantarum Angliae (1670). Ray's specimens were also used for his Methodus plantarum nova (1682) and the Historia generalis plantarum which he published in three volumes in 1686, 1688 and 1704. As Trimen (1870) noted, Ray’s botanical specimens are therefore of particular value in determining the identity of plants described in his publications. Ray’s herbarium comprises 523 sheets arranged in 20 lettered fascicles (A-Y but with no I, P, U, V or X) and with each fascicle comprising between 9 and 44 numbered sheets (although there are two sheets labelled F16, with the second distinguished by an asterisk, and one sheet in fascicle R is unnumbered). The sheets typically contain multiple specimens that are stitched to the paper on which they are mounted and that are labelled in the hand of Ray (or, possibly, Dale). The sheets were subsequently remounted after their transfer to BM. Typically, the original sheet is mounted onto the larger sheet but this is not always the case and in some instances only the specimens and labels were remounted. Not all of the specimens that originally formed part of Ray’s herbarium survive since a significant number of sheets have been cut and, in some cases, the past existence of specimens is evident only from plant fragments, stitch holes, discolouration, or the accompanying name. Upon his death in 1705, Ray bequeathed his herbarium to the apothecary Samuel Dale. While in Dale’s possession, he produced an alphabetically arranged catalogue to the herbarium that lists pre-Linnean polynomial names, sometimes with the place of publication and, more rarely, with synonyms. References to the sheets on which specimens referrable to that name are found are also provided. The catalogue collectively accounts for 1225 specimens, although no specimens from the 89 sheets that make up fascicles T, W or Y were catalogued by Dale. The dataset provided here contains two resources. The first is a transcription of Dale’s catalogue to the herbarium that serves as a taxonomic index. Links to images of the corresponding herbarium sheets and the relevant page from Dale's catalogue are included for each specimen entry. In the future, we aim to include modern determinations. The second comprises images of all 523 herbarium sheets. A digital edition of Dale's catalogue to Ray's herbarium is available on the Library and Archives archive viewer: https://nhm.primo.exlibrisgroup.com/discovery/delivery/44NHM_INST:44NHM_V1/12244210500002081 Reference: Trimen, H. (1870). Notes on Ray’s ‘Hortus Siccus’. Journal of Botany, British and foreign 8: 82—84.
The file contains a listing of a 311 slide taxonomic reference collection of mainly Cretaceous non-marine ostracods from West Africa as well as a listing of the contents of 4 slide cabinets holding associated assemblage materials. Items in red were added as the details were gathered from slides with more complete information. Items in green were added following a review of associated logging sheets and reports on file at the NHM.
The Plants of South Asia dataset comprises details of herbarium specimens from the South Asian region and includes botanical specimens Bangladesh, Bhutan, India, Maldives, Myanmar, Nepal, Pakistan, and Sri Lanka and reflects the extensive collections from the South Asian region held in the herbarium at the Natural History Museum. The dataset comprises over 70,000 specimens of which more than 10,000 are types or original material. The earliest specimens were collected in 1701 but collections from the 20th century account for nearly three quarters of the specimens for which collecting year is recorded. The majority of the specimens were gathered in India (49%). The collections are also particularly rich in specimens from Nepal (18%). The dataset comprises records generated from two main sources: 1. Records captured through the Global Plants Initiative types project and ‘business as usual’ databasing 2. Records from a number of broad-scale databasing and imaging projects focussed either specifically on collections from the South Asian region or on complete digitisation of groups of plants. The Natural History Museum V Factor Volunteer Programme enabled volunteers to contribute to mass-digitisation and was a major contributor of records. Funding from the Rutherford Fellowship Programme (funded by the Department of Business, Energy and Industrial Strategy, UK) and the Ministry of Environment, Forest and Climate Change, India, enabled scientists from the Botanical Survey of India (BSI) to make a substantial contribution to the programme. Records have also been contributed by colleagues from the Museum’s Digital Collections Programme. Mass digitisation projects have focussed on seed plants and consequently, seed plants are over-represented in the dataset with over 80% of specimens in the dataset from the Museum's seed plant collections. We would ask users to remember that the dataset is not comprehensive and it does not represent the full extent of South Asian material at BM. If you expect to find a specimen at BM but it is not in the dataset, it doesn’t mean we don’t have it. Please get in contact so that we can investigate further by contacting Ranee Prakash (r.prakash@nhm.ac.uk) in the first instance. Data completeness for records included in this dataset is variable, reflecting the different approaches to digitisation taken. While type digitisation and ‘BAU’ digitisation has typically generated records with detailed locality information, mass-digitisation programmes have generated records with more limited data. In the first instance, the records include only the taxon name, geographical region (South Asia) and an image of the specimen. An ongoing programme is in place to enhance those records with details of collector(s), collection date and collection number and country. The data enhancement work is also being supported by Natural History Museum Volunteers. Our hope is that the POSA dataset will be of value to the scientific community working on South Asian plants and will contribute towards knowledge of the floras of the countries of the region.
Jovita Yesilyurt; Shyam Biswa; Mark Carine; Felipe Dominguez Santana; Susan Higgins; Dr. Bhavana Joshi ; Dilip Kumar Roy; Gopal Krishna; Pushpa Kumari; Nicky Nicholl; Basant Kumar Singh; Hillery Warner; Ranee Om Prakash
Raw body size and sexual size dimorphism data. * **order** = order. * **family** = family. * **binomial** = species binomial. * **Nspecs** = number of specimens in the bias dataset.* **max_body_size_mm** = maximum recorded body size for the species, i.e. snout-vent-length (SVL) or for turtles carapace length. In mm. * **body_size_refs** = source of body size data. * **larger_sex** = which sex is larger. "Males", "Females" or "Neither". * **max_male** = maximum recorded body size for males of the species, i.e. snout-vent-length (SVL) or for turtles carapace length. In mm. * **max_female** = maximum recorded body size for females of the species, i.e. snout-vent-length (SVL) or for turtles carapace length. In mm. * **sex_size_ref** = source for sex disaggregated body size data. Full references can be found in `reference-list.csv`
A list of research publications by Dr John E. Whittaker covering his work as a Micropalaeontolgist at the Natural History Museum and subsequent to his retirement.
Searchable csv file of South American (incl. the Juan Fernández islands) morelloid specimens examined for this monograph. Suppl. Mat. 2 in Knapp et al. (2023). Column headings are: Herbarium = herbarium acronym according to Index Herbariorum; Category = specimen or photograph of specimen; SpecID = brahms specimen ID; Brahms = Brahms collection event ID; Accession = accession number of specimen; Barcode = barcode of specimen; Collector = principal collector; Prefix = collection number prefix (if applicable); Number = collection number; Suffix = collection number suffix (if applicable); AddColl = additional collectors; Type = type of type; Type of = type of what species; Day = day of collection; Month = month of collection; Year = year of collection; DateRes = date resolution (if applicable); Family = plant family; Genus = genus name; Species = species epithet; Author = species author name(s); Continent = TDWG continent; Region = TDWG region; Country = country of collection; Majorarea = first political division; Minorarea = second political division; Gazetteer = nearby town or place; Locnotes = locality; Plantdesc = description of the plant; Habitattxt = vegetation characteristics; Lat = latitude; NS = north or south; Long = longitude; EW = east or west; LLunit = coordinate units (DD = decimal degrees; DM = decimal minutes; DMS = degrees, minutes, seconds); LLres = coordinate resolution; LLorig = origin of coordinates; LatLong = coordinates in DMS; LatDec = decimal latitude; LongDec = decimal longitude; Alt = elevation minimum; AltMax = elevation maximum; AltRes = elevation resolution; AltUnit = elevation units (all metres); AltRange = elevational range; Vernacular = common name; Language = language of common name (if known).
Cultural and historical artefacts from The Natural History Museum
Geography file for extant taxa used in biogeography analyses in paper 2.
Submerged corridors of ancient gene flow in an insular caecilian amphibian
Many island archipelagos sit on shallow continental shelves. During the Pleistocene, these islands were often connected as global sea levels dropped following glaciation. Given a continental shelf only 30–60 m below sea level, the terrestrial biota of the Seychelles archipelago likely dispersed amongst now isolated islands during the Pleistocene. _Hypogeophis rostratus_ is a caecilian amphibian found on ten islands in the Seychelles. Despite the seemingly limited dispersal abilities of a terrestrial, salt-intolerant, and primarily fossorial amphibian, this broad geographical distribution suggests historic dispersal across now submerged continental shelf corridors. Here, we tested for the genetic signature of these historic corridors despite thousands of generations spent isolated on different islands. Using fine-scale genomic data (ddRADseq) we found that genomic clusters often did not correspond to islands in the archipelago. Additionally, isolation-by-distance patterns were more consistent with gene flow across a continuous landscape than isolated island populations. Using effective migration surfaces and ancestral range expansion prediction we found support for contemporary populations originating near the large southern island of Mahé and dispersing to northern islands via the isolated Frégate island, with additional historic migration across the flat expanse of the Seychelles bank. Collectively, our results suggest that biogeographic patterns can retain signals from Pleistocene ‘palaeo-islands’, and that present-day islands can be thought of as hosting bottlenecks or transient refugia rather than discrete genetic units. Thus, the signatures of gene flow associated with palaeo-islands may be stronger than the isolating effects of contemporary islands in terrestrial species distributed on continental shelf islands.
Miranda Sherlock; Mark Wilkinson; Simon Maddock; Julia Day; Jeffrey Streicher
The data set represents seed plants material stored in fluids, where several specimens have corresponding herbarium sheets in the General herbarium. The collections have been recently recurated with 70% IMS and are arranged jar-size wise. Although the collection is small with just over three thousand specimens, it is an important collection representing biodiversity around the world with some type specimens collected by several collectors spanning a time scale dating back to early 18th century. Those wishing to research and physically examine these collections are welcome to book an appointment with the curation team.
Seed plants fluid collections at the Natural History Museum
Records and images of the herbarium sheets contained in the Herbarium of John Ray. The data can be viewed as a table, with links to the images, in a list view which displays thumbnails of the image alongside the data for each sheet or as a gallery of images of herbarium sheets The following information is provided for each sheet: the fascicle; folio number; NHM registration number (a nine digit number with a BM prefix which should be used when citing an individual sheet); url for the image on the NHM dataportal. Images may be downloaded at the original resolution and used under a CC-BY licence (acknowledging the copyright The Trustees of the Natural History Museum). For further details see https://data.nhm.ac.uk/terms-conditions.
Screen shots of internally available Power BI dashboard. These cover statistics for the entire collection and have not been filtered. Filtering functionality allows to display results at any level from the entire museum to individual Collection Unit.
Screen shots of internally available Power BI dashboard
Clade III PCA file (Species delimitation)
Phylogeny for toothed whales, containing only the species included in the analyses. This tree contains 184 taxa, excluding those with zero length branches (ZBL).
SNAPPER input file ingroup (Fig. 2, Fig. S1A)
Median tree from metatree analyses used for all analyses in paper 2.
Link to the iCollections specimen records from the NHM catalogue, published as part of the wider NHM collection dataset.
Lycianthes (Solanaceae) of Australia, New Guinea & Oceania
Specimen data used in the publication: Knapp S (2022) A revision of _Lycianthes_ (Solanaceae) in Australia, New Guinea, and the Pacific. PhytoKeys 209: 1-134, https://doi.org/10.3897/phytokeys.209.87681. Abstract. The genus _Lycianthes_ (Dunal) Hassl. (Solanaceae) has in the past been treated as a section of the large genus _Solanum_ L., but is more closely related to _Capsicum_ L. The eighteen species of _Lycianthes_ occurring Australia, New Guinea (defined as the island of New Guinea, comprising Papua New Guinea [incl. Bougainville] and the Indonesian provinces of Papua Barat and Papua, plus the surrounding islands connected during the last glacial maximum) and the Pacific Islands are here treated in full, with complete descriptions, including synonymy, typifications and synonyms, distribution maps and illustrations. The history of taxonomic treatment of the genus in the region is also discussed. These taxa occupy a diverse range of forested habitats, and are in diverse in habit, from small shrubs to large canopy lianas to epiphytic shrubs. They are for the most part rarely collected, and many are endemic (14 of the 18 species treated here). Australia has a single endemic _Lycianthes_ species (_L. shanesii_ (F.Muell.) A.R.Bean). Nine species are found in both Indonesia and Papua New Guinea, one in Indonesia only, four in Papua New Guinea only, and _L. vitiensis_ (Seem). A.R.Bean is known from Bougainville (Papua New Guinea) and the south Pacific as far east as Samoa. _Lycianthes lucens_ S.Knapp sp. nov. is described from the islands of Lihir, New Ireland and the Louisiade Archipelago of Papua New Guinea. The cultivated _L. rantonnetii_ (Carrière) Bitter is also treated in full, in this region known currently only from Australia; it is native to southern South America. Preliminary conservation assessments are presented for all species except the cultivated _L. rantonnetii_.
Global maps of Biodiversity Intactness Index (Sanchez-Ortiz et al., 2019 - bioRxiv )
Global maps of biodiversity intactness for the year 2005 (Abundance-based BII and Richness-based BII). These high-resolution rasters were used to plot Figure 1 in "Land-use and related pressures have reduced biotic integrity more on islands than on mainlands" (Sanchez-Ortiz et al., 2019). We have updated methods previously used to estimate BII globally (Newbold et al., 2016) to allow pressure effects to differ between islands and mainlands, while also implementing some other recent improvements in modelling.
Katia Sanchez-Ortiz; Ricardo E Gonzalez; Adriana De Palma; Tim Newbold; Samantha L L Hill; Jason Tylianakis; Igor Lysenko; Luca Borger; Andy Purvis
Hans Sloane’s collection of dried plants (the Sloanean Herbarium): an inventory
From the early 1680s until his death in 1753, London physician Hans Sloane amassed a vast collection of objects, among which were the 121,000 plant specimens that formed his herbarium. Though most have been re-bound, and some other interventions have occurred, the plant collection is still largely organised as it was in 1753. It comprises 337 numbered horti sicci (‘dried gardens’), bound into 265 volumes. A small proportion were gathered by Sloane himself, either in and around London or in France in the early 1680s, or on his voyage to Jamaica from 1687 to 1688. However, the majority of the collection was either bought by, or bequeathed or given to Sloane by other collectors, and over 320 named individuals are represented in this herbarium. While a large proportion of the collection is European, it also includes tens of thousands of specimens from much further afield. Their geographical distribution largely reflects British trading and colonial interests, but also includes plants from parts of the Portuguese and Spanish empires, as well as from Japan and China. This dataset provides high-level metadata for the collection. At its core is a survey of the entire herbarium, which records key information for each folio. This includes the number of specimens, illustrations or ‘manuscripts’ present, together with an indication of the presence/absence of: specimen labels; cross references to Sloane’s annotated copy of John Ray’s Historia Plantarum; common/local names in any language; usage information; names of people or places; and any modern (binomial) determinations. To this have been added the people and places identified for any given folio in The Sloane Herbarium (1958), edited by James Dandy, together with some corrections and additions. Dandy (1958) The Sloane Herbarium has been digitised and can be accessed on Biodiversity Heritage Library: https://www.biodiversitylibrary.org/bibliography/137366 For a description of the data contained in the dataset, please read the Data Description and Change Log: https://shorturl.at/8h0Wg This work was supported by a grant from the Arts and Humanities Research Council Towards a National Collection Programme (Grant AH/W003457/1) and a doctoral studentship from the Arts and Humanities Research Council-funded London Arts and Humanities Programme Doctoral Training Partnership (Grant AH/R012679/1).
Brad Scott; Victoria Pickering; Mark Carine
Papilionoidea New Types Digitisation Project
The Papilionoidea type collection comprises the records of recently acquired (~last 20 years) Papilionoidea type material held within a synoptic collection at the Natural History Museum, London. This synoptic type collection was digitised to create specimen records and capture specimen metadata. Each specimen record has been published with an image capturing both the specimen (dorsal and ventral habitus) and its associated labels, and creating an inventory record with a unique identifier (Data Matrix barcode), taxon information, type status, determination date, taxonomic authority and country level collection locality. The data resource generated by the project is available using the link. This collection was digitised as part of the Museum's Digital Collections Programme.
Robyn Crowther; Louise Allan; Charlotte Barclay; Blanca Huertas
A csv file of all specimens examined for the monograph of Lycianthes in tropical Asia. Column headings are designed to be self explanatory.
Specimens of Lycianthes from tropical Asia
**Specimen number**: NHMUK 1986.116 **Specimen Link**: http://data.nhm.ac.uk/object/0b44593f-7375-4148-90c4-f9d9883e823d **Decription**: _Balaena mysticetus_ -- Balaenidae, Cetacea; Mammalia
Elliott J. R. Capp (University of Sheffield) Emma C. Hughes (University of Sheffield) Chris J. A. Moody (University of Sheffield) Lara O. Nouri (University of Sheffield) Zoë K. Varley (University of Sheffield)
The Mark My Bird dataset comprises 3D scans of bird bills from the ornithology collection of the Natural History Museum, London. Mark My Bird is part of a European Research Council (ERC) funded project based at the University of Sheffield. The project aims to contribute to our understanding of how and why bird species form and diversify. 3D scans of bills were taken primarily from the ornithological skins collections. The scans were uploaded to the markmybird.org citizen science website where they were analysed by both researchers from the University of Sheffield and volunteer citizen scientists. Analysis involved landmarking pre-defined features of the bill on computer visualisations of the scans. The dataset comprises records of 2028 specimens. Each specimen represents a different birds species and is typically a male. The dataset includes raw scan data in obj format, landmarks from 3-4 volunteers (and the average of those landmarks) for each specimen stored as txt files with three columns of XYZ coordinates. Mark My Bird usernames, documenting the contributing volunteer, are assigned to each landmark file. The dataset also includes a csv format file (MarkMyBird_manifest.csv) detaling taxonomy, museum accession number, and sex for each species.
Gavin H Thomas; Jen A Bright; Chris R Cooney
Summary table of annual averages of cropland amount for each country, subregion and region.
Occurrence and specimen data used in the publication: Knapp S, T. Särkinen & G.E Barboza (2023) A revision of the South American species of the Morelloid clade (Solanum L.; Solanaceae). PhytoKeys, in press. Abstract. The Morelloid clade, also known as the black nightshades or “Maurella” (Morella), is one of the 10 major clades within the mega-diverse genus _Solanum_ L. The clade is most diverse in the central to southern Andes, but species occur around the tropics and subtropics, some extending well into the temperate zone. Plants of the group vary from herbs to short-lived perennials to perennial shrubs that are distinctly woody at the base, and have small mostly white or purplish white flowers, and small juicy berries. Due to the complex morphological variation and weedy nature of these plants, coupled with the large number of published synonyms (especially for European taxa), our understanding of species limits and diversity in the Morelloid clade has lagged behind that of other clades in _Solanum_. Here we provide the last in a three-part series of monographic treatments of the morelloid solanums (see PhytoKeys vols. 106, 125), treating the 62 species occurring in South America. This region is by far the most diverse in the clade, both in terms of species number and morphological diversity. Distribution maps, and common names and uses are provided for all native species occurring in this region. We provide complete synonymy, nomenclatural details, including lecto- and neotypifications where needed, and morphological descriptions, illustrations to aid identification both in herbaria and in the field, and distribution maps for all native, non-cultivated species. We include a key to all species, a synoptic character list for the species treated here and links to synoptic online keys for all species of the Morelloid clade. Preliminary conservation assessments following IUCN guidelines are also provided for all native species.
Sandra Knapp; Tiina Särkinen; Gloria E. Barboza
Link to the British and Irish 'larger' micro moth specimen records from the NHM catalogue, published as part of the wider NHM collection dataset.
British and Irish 'larger' micro moth specimens
Sceloporus morphology data (clade comparisons)
Link to the Aleyrodoidea slide collection specimen records from the NHM catalogue, published as part of the wider NHM collection dataset.
What predicts gene flow during speciation? The relative roles of time, space, morphology, and climate
The processes that restrict gene flow between populations are fundamental to speciation. Here, we develop a simple framework for studying whether divergence in morphology, climatic niche, time, and space contribute to reduced gene flow among populations and species. We apply this framework to a model system involving a clade of spiny lizards (_Sceloporus_) occurring mostly in northeastern Mexico, which show striking variation in morphology and habitat among closely related species and populations. We developed a new time-calibrated phylogeny for the group using RADseq data from 152 individuals. This phylogeny identified 12 putative species-level clades including at least two undescribed species. We then estimated levels of gene flow among 21 geographically adjacent pairs of species and populations. We also estimated divergence in morphological and climatic-niche variables among these same pairs, along with divergence times and geographic distances. Using Bayesian generalized linear models, we found that gene flow between pairs of lineages is negatively related to divergence time and morphological divergence among them (which are uncorrelated), and not to geographic distance or climatic divergence. The framework used here can be applied to study speciation in many other organisms having genomic data but lacking direct data on reproductive isolation. We also found several other intriguing patterns in this system, including the parallel evolution of a strikingly similar montane blue-red morph from more dull-colored desert ancestors within two different, non-sister species.
Jeffrey Streicher; Shea Lambert; Fausto Méndez de la Cruz; Norberto Martínez-Méndez; Uri Omar García-Vázquez; Adrián Nieto Montes de Oca; John Wiens
Plymouth University Microfossil Collection.pdf
Cleaned and aggregated dataset used in the analyses. To get from the raw data to this dataset see details on GitHub in script **01-data-preparation**. In brief we: - recalculate median year of each study to give a decimal number - standardise body size with TWO standard deviations, as suggested by Gelman 2008 - merge trait and plastic datasets - convert all No/Yes variables to binary 0/1. - add a column called tips which is the Binomial name with "_" to match the tree - aggregate age class into just two life history stages: free-flying and not (i.e. nestbound). We exclude nestbound birds but keep mixed studies. - remove columns we don't need in the analyses - remove a small number of NAs which we aren't able to work with. We lose a few studies, which include few species each, and one species with no diet info. We also aggregated the data because some studies separate birds into small groups (i.e. within-study sampling locations). However, for the purposes of meta-analyses, we are treating all observations as exchangeable (i.e. as replicates) if they: - are collected by the same authors (Source) - in the same Marine Region - in the same Year Columns are as follows. * **clements2025_binomial**. Species name matched to Clements et al 2025 taxonomy. * **tips**. Species name matched to Clements et al 2025 taxonomy with _ to match the phylogeny. * **order**. Taxonomic order. * **family**. Taxonomic family. * **freeflying**. Freeflying (adult, subadult, adult/subadult age class) or mixed. 1 (freeflying) or NA (mixed). Nestbound birds have been removed. * **source**. Source name in the form Author et al, YEAR. This matches the Source column in 01_sources-for-plastic-ingestion-data and 02-plastic-ingestion-data. **date_median**. Median year the study covered. **marine_region**. Ocean basin of study site. Options are Arctic, Indian, North Atlantic, North Pacific, South Atlantic, South Pacific, or Southern oceans. * **sampling_method**. Primary way that plastic samples were obtained. Options are bolus, brushing, lavage, necropsy, regurgitation or scat. * **body_mass_g**. Body mass (g). * **body_mass_2sd**. Mean normalised body mass. * **main_diet**. Primary diet based on the dominant prey type. Options are: carrion and non-fish vertebrates, cephalopods, crustaceans, fish, or other invertebrates. * **carrion**. Presence or absence of carrion in the diet description. 0 (absence) or 1 (presence). * **fish**. Presence or absence of carrion in the diet description. 0 (absence) or 1 (presence). * **cephalopods**. Presence or absence of carrion in the diet description. 0 (absence) or 1 (presence). * **crustaceans**. Presence or absence of carrion in the diet description. 0 (absence) or 1 (presence). * **other_inverts**. Presence or absence of other invertebrates (i.e. not cephalopods or crustaceans) in the diet description. 0 (absence) or 1 (presence). * **as_fishery**. Presence or absence of carrion in the diet description. 0 (absence) or 1 (presence). * **as_agriculture**. Presence or absence of carrion in the diet description. 0 (absence) or 1 (presence). * **as_refuse**. Presence or absence of carrion in the diet description. 0 (absence) or 1 (presence). * **anthropogenic_subsidy**. Does the species use anthropogenic food sources? 0 (absence) or 1 (presence). * **pelagic_specialist**. Is the species a pelagic specialist? 0 (absence) or 1 (presence). * **feeding_method**. Primary feeding method for each species. Options are: aerial pursuit, bottom-feeding, diving, plunging (includes pursuit plunging and surface plunging), scavenging, skimming, or surface seizing (includes dipping and pattering). * **aerial_pursuit**. Presence or absence of aerial pursuit feeding. 0 (absence) or 1 (presence). * **bottom_feeding**. Presence or absence of bottom feeding. 0 (absence) or 1 (presence). * **diving**. Presence or absence of diving feeding. 0 (absence) or 1 (presence). * **plunging**. Presence or absence of plunging. 0 (absence) or 1 (presence). * **scavenging**. Presence or absence of scavenging. 0 (absence) or 1 (presence). * **skimming**. Presence or absence of skim feeding. 0 (absence) or 1 (presence). * **surface_seizing**. Presence or absence of surface seizing. 0 (absence) or 1 (presence). * **terrestrial_feeding**. Presence or absence of terrestrial feeding. 0 (absence) or 1 (presence). * **n_plastic**. Number of sampled birds that had ingested at least one piece of plastic. * **n_total**. Number of birds sampled. * **FO**. Frequency of occurrence of plastic. This is calculated as n_plastic / n_total.
Raw geography data for biogeography analyses in paper 2.
Species level record denoting the presence of a taxon in the Museum collection.
Catalogue records for Hans Sloane's vegetable and vegetable substances that survive in the botanical collections at the Natural History Museum.
Hans Sloane's Vegetables and Vegetable Substances
Data pertaining to the collection of John W. Murray's now housed at the NHM. This includes specimens, samples, residues, theses and published/unpublished data
The seed plants fluid collection at the Natural History Museum
This dataset represents over three thousand seed plants fluid collection at the Natural History Museum that have been recently recurated with 70% IMS (Industrial methylated spirit). The data can also be seen by using the link: https://data.nhm.ac.uk/search/expressly-active-dormouse. The collections are arranged as per jar size rather than taxonomically in order to maximise space. The collection ranges from early 19th century to the current era and it continues to grow with material incorporated with recent acquisitions. Over 150 families are represented with some important type specimens such as the world's largest flower-Rafflesia arnoldii R.Br collected by Raffles and Arnold. Other notable collections include several types of orchids collected by C.E. Carr from New Guinea during the second world war and John Gossweiler from Angola. The largest collection is from Nancy Garwood (over 700 bottles) which consists of some carpological material collected from Panama as well as seedlings. Several collections have corresponding herbarium sheets in the General Herbarium. By curating these collections, we have now made these collections accessible. We hope that more people interested in these collections will be able to make use of these collections for their research and help us to update the collections by way of adding determinations. The data will be eventually ingested in KE-Emu, the Museum's database in due course. A paper on "Re-curation of the seed plants fluid collection at the Natural History Museum" has been published by Prakash, R.O., Gilliat, G., Dart, G., and Campion, K. in Journal of Natural Science Collections, Volume 13, pages 54 - 62.
Ranee Om Prakash; Geoff Dart; Gabriella Gilliat; Kathryn Campion; Ranee Om Prakash
Participants survey kelp on the shoreline by running a monthly survey at a given location at the lowest tide of the month. The survey consists of: Taking a photo of the kelp patch from a distance. Heading down to the kelp patch and completing three surveys at different points within the patch by counting kelp within a quadrat. If the patch is large enough, a fourth quadrat may also be surveyed. A photo and latitude/longitude is required for each quadrat. Data is submitted to an online form.
Angiosperm functional traits extracted from botanical descriptions
This dataset provides a large-scale compilation of plant functional traits automatically extracted from published taxonomic descriptions of flowering plants. The taxonomic backbone comprises all accepted angiosperm species names sourced from World Flora Online (WFO). Each accepted species was systematically searched across multiple textual sources, including the Biodiversity Heritage Library (BHL; OCR-derived biodiversity literature), eFloras (including Flora of North America, Flora of China, and related online floras), and the Ecological Flora Database (Ecoflora). Where botanical descriptions were identified, natural language processing methods were used to extract structured trait information. Trait extraction was implemented using the [ADEPT](https://github.com/NaturalHistoryMuseum/ADEPT) pipeline, which combines machine-learning classification of botanical descriptions, ontology-driven terminology matching, named-entity recognition for numeric traits, syntactic parsing, and rule-based semantic interpretation to associate traits with plant structures and standardise measurements. The dataset includes trait information for 59,369 angiosperm species, comprising 888,328 extracted trait values spanning vegetative, reproductive, and ecological characteristics such as growth form, plant height, leaf morphology, floral traits, fruit and seed traits, dispersal attributes, and cytological information where available. Trait coverage varies among taxa and trait types, reflecting differences in descriptive detail, taxonomic practice, and source availability. Separate files are provided for each source dataset alongside a combined dataset, enabling users to assess provenance and tailor analyses. This resource supports large-scale studies of plant functional diversity, ecological strategy, conservation risk, and biodiversity modelling by mobilising trait information historically embedded in taxonomic literature.
Full phylogeny for taxa used in biogeography analyses in paper 2.
An inventory of the Sloane Herbarium, including details of people and places listed in Dandy (1958)
Data for numbers of Items, Collection Units and Reporting Count, broken down by section.
Look-up lists for Item Type and Preservation Method used in the 2018 survey. Please note that these were not published in the original paper as current work external to the museum as part of the Collection Descriptions work led by TDWG means that these are likely to need updating.
Micropalaeontology student thesis collection
The NHM holds micropalaeontology thesis slide collections from the University of Hull, University College London, Imperial College London and University College of Wales, Aberystwyth along with other theses relating to students supervised by staff or other donated collections. Most of these collections are unregistered so a listing is posted here to draw attention to their availability. All of these theses are registered in the library catalogue and a link to each library catalogue record is provided. A small number of theses listed do not have associated slide collections in our holdings.
The Psylloidea slide collection comprises the records of all the slide-mounted psyllid material at the Natural History Museum, London at the time of project completion (September 2018). Each specimen record has been published with an image capturing both the specimen and its associated labels and creating an inventory record with a unique identifier (Data Matrix barcode), taxon information, type status and country level collection locality. Some specimens will have additional images capturing the reverse side of labels and/or the paper envelopes that house the slides. High resolution images were taken of specimens marked as a primary type. The data resource generated by the project is available using the link. Please search for the relevant taxa as this dataset if part of a larger project covering a range of Orders and Superfamilies. This collection was digitised as part of the Museum's Digital Collections Programme.
Robyn Crowther; Elizabeth Devenish; Phaedra Kokkini; Nicola Lowndes; Peter Wing; Louise Allan; Charlotte Barclay; Paul Andrew Brown
Full references for the body size and sexual dimorphism data in `body-size-herps-SA-NC-2022-02-09.csv`
Description of each of the fields used in the dataset
A csv file of all collections seen of Lycianthes (Solanaceae) species native outside of the Americas (Asia, New Guinea and the Pacific). This comprises all species treated in PhytoKeys 209 and xxx. Column headings are designed to be self explanatory.
Collection events for Lycianthes native outside the Americas
Slimehead size through time: testing the temperature-size relationship in Late Cretaceous Trachichthyidae
As global temperatures rise, fish are predicted to become smaller. Body size is a fundamental trait that impacts many aspects of an animal's life history and ecology, and understanding how it may respond to climate change in particular fish groups, especially commercial or keystone species, is critical. The slimeheads (Family Trachichthyidae) include several commercially important species, but because they are deep‐dwelling, long‐lived fish that reproduce slowly, directly testing the temperature–size relationship in this family is challenging. Fortunately, Trachichthyidae have a long evolutionary history beginning in the Cretaceous, and their fossil record provides empirical data on the response of this family to past climate change events. In this study, we leveraged the extensive fossil record of the Late Cretaceous trachichthyid genus Hoplopteryx from the British Chalk Group of southern England, United Kingdom, to test whether its size declined at higher temperatures. Standard Lengths were measured from complete individuals and estimated from partial remains. Seawater palaeotemperature estimates were derived from oxygen stable isotope values (𝛿18O) of the bulk chalk rock surrounding the fossils using standard techniques and assumptions. Individual fish ranged from 56.3 to 262.6 mm in length, and measured seawater temperature estimates ranged from 19.5°C to 27.1°C. Multiple linear regression analyses revealed that the estimated seawater temperature was a significant negative predictor of Standard Length in the most common species, Hoplopteryx lewesiensis, supporting the prediction that higher temperatures led to smaller body size in fish. In addition, carbon stable isotope values (𝛿13C) also significantly negatively predicted the Standard Lengths of Hoplopteryx spp., suggesting that other environmental factors, such as primary productivity and/or the burial of organic matter, may also have affected body size.
Chloe Victoria Griffiths; James Witts; Emma Bernard; Julie C.S. Brown; Richard John Twitchett
Searchable csv file of all specimens examined for this monograph, including Africa, Asia, Australia, Europe, the Caribbean, North and Central America, the Pacific and South America. Suppl. Mat. 3 in Knapp et al. (2023). Column headings are: Herbarium = herbarium acronym according to Index Herbariorum; Category = specimen or photograph of specimen; SpecID = brahms specimen ID; Brahms = Brahms collection event ID; Accession = accession number of specimen; Barcode = barcode of specimen; Collector = principal collector; Prefix = collection number prefix (if applicable); Number = collection number; Suffix = collection number suffix (if applicable); AddColl = additional collectors; Type = type of type; Type of = type of what species; Day = day of collection; Month = month of collection; Year = year of collection; DateRes = date resolution (if applicable); Family = plant family; Genus = genus name; Species = species epithet; Author = species author name(s); Continent = TDWG continent; Region = TDWG region; Country = country of collection; Majorarea = first political division; Minorarea = second political division; Gazetteer = nearby town or place; Locnotes = locality; Plantdesc = description of the plant; Habitattxt = vegetation characteristics; Lat = latitude; NS = north or south; Long = longitude; EW = east or west; LLunit = coordinate units (DD = decimal degrees; DM = decimal minutes; DMS = degrees, minutes, seconds); LLres = coordinate resolution; LLorig = origin of coordinates; LatLong = coordinates in DMS; LatDec = decimal latitude; LongDec = decimal longitude; Alt = elevation minimum; AltMax = elevation maximum; AltRes = elevation resolution; AltUnit = elevation units (all metres); AltRange = elevational range; Vernacular = common name; Language = language of common name (if known).
Link to the “Papilionoidea New Type” specimen records from the NHM catalogue, published as part of the wider NHM collection dataset.
Trait data extracted from Flora of China descriptions
Site-level summaries in zipped CSV format
A transcription of the catalogue to the John Ray Herbarium produced by Samuel Dale (1659-1739). Updated on 23/12/2025 to include links to images of corresponding pages in Samuel Dale's catalogue to the herbarium.
Phylogeny for Cetacea excluding Archaeocetes, containing only the species included in the analyses. The tree contains 322 taxa including those with zero length branches (ZBL)
This resource contains candidate original material for names yet to be typified.
Diffuse infrared reflectance of CY carbonaceous chondrites
Thermal (~5 - 50 µm) infrared diffuse reflectance of the Y-86720, Y-86789 and B-7904 CY carbonaceous chondrite meteorites.
Micropalaeontology Collection citations and visitor numbers
A dataset to support the figures in a publication in Revue de Micropaleontologie on the Natural History Museum Microfossil Collection. Data derived mainly from annotations in museum specimen registers and museum visitor books to the Foraminifera and fossil Ostracoda collections . These have been added to with more recent citations for collections yet to be fully digitised.
A list of masters and PhD theses relating to the micropalaeontology collections at the Natural History Museum. Most of these correspond to unregistered slides or other materials but a very small number do not have corresponding material. Degree awarding universities include mainly UCL, Imperial College, Hull, Aberystwyth and Southampton.
A full copy of the UK Species Inventory, including all tables. This gives the ultimate in functionality but does require a copy of Microsoft Access (or similar database environment) and skills in joining and querying complex table relationships. Although this dataset includes the source checklists, these are NOT to be reproduced without the permission of their creators. The manual is provided here but please contact me if you think you need access to the data itself.
R code used to simulate species description rates
A pdf file listing all specimens examined for the monograph organised alphabetically by first collector and number. A shorter list is part of the publication itself and lists only specimens from the area treated.
Exsiccatae list for all specimens examined (SM1)
Listing of HMS Challenger Sediment Collection
This is a dataset to accompany a paper published in 2025 in the journal Historical Biology: Miller, C. Giles and Jouet-Sarkany, Monique M. H. 2025. Sir John Murray’s H.M.S. Challenger Sedimentary Deposits Collection at the Natural History Museum, London. https://doi.org/10.1080/08912963.2025.2506185. A description of the fields is available via this link and the abstract for the paper copied: The Natural History Museum holds 4,713 bottles, tubes, boxes and slides containing sediment and derived preparations from the voyage of H.M.S. Challenger (1873-1876). The sediment collections include manganese nodules, pumice, and various marine vertebrates and invertebrates from all the major oceans of the world. A complete online database of the collection is presented to include all of the associated collecting and preparation data from the oceanic dredges, trawls, soundings and anchor mud collections alongside shallower water collections previously undocumented in the Challenger Deep Sea Deposits Report of Murray and Renard (1891). The dataset allows assessment of other Challenger sediment collections in museums and private collections. A historical account of the collection follows; collecting and studying onboard, studying in Edinburgh post cruise, donation by Sir John Murray’s family to the British Museum (Natural History) and accounts of the collection’s historical housing at the museum. The historical context and presented dataset are intended to aid future users of the collection to select suitable materials for study or display. A review of previous scientific and exhibition uses of the collection is followed by suggestions for the future storage and potential for illuminating the debate on anthropologically driven climate, biodiversity and atmospheric changes.
Species-specific data on behavioural and life-history traits were collected for each seabird species from Handbook of Birds of the World, 2025 and Dunning et al 2007. We focused on traits that have previously been used to explain observed patterns in plastic ingestion and traits which we theorised could increase vulnerability to plastic ingestion. These were diet, use of anthropogenic subsidies, foraging method, whether a species is a pelagic specialist, and body mass. Diet was categorised based on the presence or absence of prey types in the published diet descriptions: ‘carrion and non-fish vertebrates’, ‘cephalopods’, ‘crustaceans’, ‘fish’, or ‘other invertebrates’. Species were classified as using anthropogenic subsidies in the form of agricultural sources (i.e. following farm machinery of workers etc.), refuse (i.e. association with landfills etc.), or fisheries (i.e., attending trawlers, foraging on fisheries discards or offal, fish farms etc.). Foraging method was categorised based on the presence or absence of foraging methods: ‘aerial pursuit’, ‘bottom-feeding’, ‘diving’ (i.e. moving through the water powered by feet or wings), ‘plunging’ (including pursuit plunging and surface plunging from any height, or any submersion of head/body while feeding on the water's surface), ‘terrestrial-feeding’ (hunting live prey or scavenging on land), ‘scavenging’ (either terrestrially or on the water), ‘skimming’ (including hydroplaning), or ‘surface seizing’ (including dabbling, dipping, and pattering). Species were classified as pelagic specialists if they predominantly forage in the pelagic zone. Columns contain the following. * **HBWv8.1_Binomial**. Species name following Handbook of Birds of the World (HBW) v8.1 taxonomy. Note taxonomy is updated to Clements et al 2025 in the data cleaning stages. * **Link_species**. Link to the HBW species account. * **Feeding.Method.Simple**. Primary feeding method for each species. Options are: aerial pursuit, bottom-feeding, diving, plunging (includes pursuit plunging and surface plunging), scavenging, skimming, or surface seizing (includes dipping and pattering). Taken from the HBW species account. * **Diet**. Primary diet based on the dominant prey type. Options are: carrion and non-fish vertebrates, cephalopods, crustaceans, fish, or other invertebrates. Taken from the HBW species account. * **Diet_description**. Verbatim copy of HBW species account diet information. * **Anthropogenic.subsidy.search.word**. * **Anthropogenic.subsidy.simple**. * **Fish**. Presence or absence of fish in the diet description in HBW. * **Cephalopods**. Presence or absence of cephalopods in the diet description in HBW. * **Crustaceans**. Presence or absence of crustaceans in the diet description in HBW. * **Other.Inverts**. Presence or absence of other invertebrates (i.e. not cephalopods or crustaceans) in the diet description in HBW. * **Carrion.NonFishVertebrates**. Presence or absence of carrion or non fish vertebrates in the diet description in HBW. * **Anthropogenic.Subsidy**. Does the species use anthropogenic food sources? Yes/No. Species were classified as using anthropogenic resources if diet descriptions included mention of an association with landfills, fisheries (i.e., attending trawlers, foraging on fisheries discards or offal) fish farms or other human food sources. * **pelagic_specialist_CR**. Does the species predominantly forage in the pelagic zone? Yes/No. * **Body.Mass.g**. Species body mass (g). If more than one value given, we used the average for Male and Female. * **scaled.body.mass**. Mean normalised body mass. * **Source_Body.Mass.g**. Source of body mass data, primarily Dunning JB Jr. 2007 CRC Handbook of Avian Body Masses, Second Edition. 2nd edn. Boca Raton: CRC Press. See https://www.crcpress.com/CRC-Handbook-of-Avian-Body-Masses-Second-Edition/Dunning-Jr/p/book/9781420064445. * **AS.Fishery**. Presence or absence of feeding on fisheries discards or attending trawlers in the diet description in HBW. * **AS.Refuse**. Presence or absence of feeding on refuse in the diet description in HBW. * **AS.Agriculture**. Presence or absence of feeding on agricultural sources, e.g. attending fields in the diet description in HBW. * **aerial_pursuit**. Presence or absence of aerial pursuit feeding in the feeding behaviour description in HBW. * **bottom_feeding**. Presence or absence of bottom feeding in the feeding behaviour description in HBW. * **diving**. Presence or absence of diving in the feeding behaviour description in HBW. * **plunging**. Presence or absence of plunging (including pursuit plunging and surface plunging) in the feeding behaviour description in HBW. * **scavenging**. Presence or absence of scavenging in the feeding behaviour description in HBW. * **skimming**. Presence or absence of skimming or hydroplaning in the feeding behaviour description in HBW. * **surface_seizing**. Presence or absence of surface seizing (including dabbling, dipping, and pattering) in the feeding behaviour description in HBW. * **terrestrial_feeding**. Presence or absence of terrestrial-feeding (hunting live prey or scavenging on land) in the feeding behaviour description in HBW. * **feeding_method_notes**. Notes taken from HBW species accounts used to determine the feeding method.
iCollections: British and Irish Pyraloidea (Moths) Collection
The Pyraloidea collection comprises the records of all British and Irish material at the Natural History Museum, London at the time of project completion (August 2019). It includes the main collection and recently acquired (2019) material from the J.M. Jaques collection. The Pyraloidea collection was digitised to complete the iCollections dataset (British and Irish Lepidoptera) and to create specimen records and capture specimen metadata. Each specimen record has been published with an image capturing both the specimen (dorsal habitus) and its associated labels, and creating an inventory record with a unique identifier (Data Matrix barcode), taxon information and locality within the collection. Some specimens will have additional images capturing the reverse side of labels. The data resource generated by the project is available using the link. This collection was digitised as part of the Museum's Digital Collections Programme.
Robyn Crowther; Elizabeth Devenish; Phaedra Kokkini; Nicola Lowndes; Peter Wing; Louise Allan; James Ayre; Charlotte Barclay; Geoff Martin
Raw total length data, for living and fossil species, taken from the literature. * (super)Family - Superfamily (ends 'oidea') or family (ends 'idae') the species belongs to * Genus - genus name * Species - species name * TL (mm) - total length (in millimetres) * Reference - study which estimation was sourced from * Age - geological Epoch specimen is from (extant = still living) * Notes - additional information about species where necessary *NA - Not applicable/no data* #### Abbreviations * NHM - Natural History Museum * HMM - Handbook of Marine Mammals * PRSB - Proceedings of the Royal Society B
The John Chainey Lepidoptera Collection comprises the records of all the pinned material donated by John Chainey to the Lepidoptera Collection at the Natural History Museum, London at the time of project completion (July 2025). The John Chainey Lepidoptera Collection was digitised to improve access and support research into British and Irish Lepidoptera Each specimen record has been published with an image capturing a dorsal view of the specimen and its associated labels, creating an inventory record with a unique identifier (Data Matrix barcode) taxon information, and location in the collection. The data resource generated by the project is available using the Data and Resources link.
Glory Turnbull; Louise Berridge; Emma Bonzo; Leo Le Good; Roisin Mackie; Skye Neal; Kathryn Royce Schronk; Larissa Welton; Peter Wing; Hillery Warner; Chiho Ikebe; Geoff Martin; Robyn Crowther
Extant phylogeny used in diversification analyses in paper 2.
Summary table of annual averages of secondary vegetation amount for each country, subregion and region.
A Darwin Core export of all of the records on the NHM Data Portal relating to the Ocean Bottom Deposits Collection. Each line in the data may refer to multiple items. Sometimes these may have been allocated separate records that need to be searched for in the data portal. Please contact the dataset curator if you are interested to know about material available for any of these samples.
Molecular phylogenetic analyses reveal both underestimation and overestimation of species diversity in northern rain frogs (Craugastor)
Among direct-developing rain frogs of the genus _Craugastor_ is a clade of 19 described species (_bocourti_ series) that occur in Mexico and northern Central America. Many of these 19 species have been described based on subtle morphological differences and have never been examined using molecular data. Here, we used a multilocus dataset (one mitochondrial (mtDNA) and four nuclear (nDNA) gene fragments; totaling 3,048 concatenated base pairs) to investigate species limits and phylogenetic relationships among 60 northern rain frogs referable to 12 species with a focus on species from Guatemala. We inferred phylogenies using maximum likelihood and Bayesian analyses on separate mtDNA and nDNA datasets. Concatenated and coalescent species-tree analyses support the monophyly of multiple species, with interspecific relationships mostly unresolved. These mtDNA and nDNA trees were often incongruent with morphology-based taxonomy. For example, two genetically shallow clades contained individuals referable to at least five described species, whereas a single described species contained deep divergences indicative of multiple cryptic species. These findings indicate that morphology-based taxonomy has both overestimated and underestimated actual species diversity (depending on the species), an interpretation supported by two molecular species-delimitation procedures. Based on these findings we synonymize _C. glaucus_ (Lynch, 1967) and _C. stuarti_ (Lynch, 1967) with _C. xucanebi_ (Stuart, 1941). We also synonymize _C. nefrens_ (Smith, 2005) and _C. cyanochthebius_ McCranie & Smith, 2006 with _C. campbelli_ (Smith, 2005). The molecular data also support multiple undescribed species, notably within _C. decoratus_ (Taylor, 1942). Overall, we show how morphology-based species delimitation can both underestimate and overestimate species richness in morphologically conservative groups.
Jeffrey Streicher; John Wiens; Merlijn Jocqué; Uri García-Vázquez; Eric Smith
Phylogeny for Cetacea excluding species for which we had to imput total length data, containing only the species included in the analyses. The tree contains 258 taxa including those with zero length branches (ZBL)
This represents the ct scan dataset from a paper entitled "Reassessing the HMS Challenger collection as a late 19th century surface ocean indicator using X-ray microcomputed tomography" by Stergios Zarkogiannis, Thomas Wood, C. Giles Miller, Stephen Stukins and Brett Clark. Plankton tow net samples collected during the HMS Challenger expedition (1872–1876) have highlighted the potential to provide an unique window into past oceanic conditions. This study aims to assess the suitability of HMS Challenger sediment samples as indicators of late 19th century surface oceanic conditions using X-ray micro-computed tomography (mCT). We used mCT to examine all 21 available Challenger samples from the global ocean that were labelled as ‘tow-net at dredge’, ‘weights’, or ‘trawl’. Our analysis reveals that most samples contain benthic foraminifera shells, along with high concentrations of foraminiferal fragments and detrital quartz grains, while the remaining samples consist of sedimentary material devoid of calcareous microfossils. These findings suggest that these tow-net samples include resuspended bottom sediments rather than exclusively surface-derived material. This distinction is critical because it demonstrates that two types of Challenger tow-net samples exist: surface ocean samples and deep-water tow-net samples that incorporate seafloor material. The surface tow-net samples were recently located and are referenced in this study. These findings highlight the importance of re-evaluating historical sediment collections with modern analytical techniques to ensure accurate paleoceanographic interpretations. Furthermore, the study demonstrates the effectiveness of mCT as a non-destructive tool for sediment analysis, allowing for the detailed examination of collections without the need for washing or wet sieving.
Stergios Zarkogiannis; Thomas Wood; Giles Miller; Stephen Stukins; Brett Clark
Phylogeny for Cetacea excluding species for which we had to imput total length data, containing only the species included in the analyses. This tree contains 216 taxa, excluding those with zero length branches (ZBL)
Imperial College Royal School of Mines Micropalaeontology Collection
Prof. Richard J. Aldridge conodont collection
File explaining where to add missing species to the taxonomy of Claramunt et al 2025. Column contents are as follows. * **Species**. Name of missing species. * **Simple**. Is the taxon simple to add to the tree, i.e. can it just be added to an existing tip (yes) or does it require more complicated coding (no)? YES/NO. * **Tip**. For simple additions, the name of the tip that the missing species should be grafted onto. Otherwise the name of the group the missing species needs to be grafted onto. * **Branch**. The divergence time for the branch length of the new branch added when the missing species is grafter to the tree. * **Justification**. Justification for decisions in the previous columns. * **Source**. Reference for the decision.
**Specimen number**: NHMUK 1915.7.20.1 **Specimen Link**: http://data.nhm.ac.uk/object/65a406e1-bc62-45bc-a0fb-dea543e4e2d9 **Decription**: _Ziphius cavirostris_ -- Ziphiidae
Phylogeny for Cetacea, containing only the species included in the analyses. The tree contains 345 taxa including those with zero length branches (ZBL).
Contains an introduction to the project and its historical perspective, methodological notes and a list of publications resulting from the dataset.
Helper file used as a placeholder half way through the data wrangling script. See https://github.com/nhcooper123/sex-bias-herps for more details.
Link to the “Thysanoptera Slide Collection” specimen records from the NHM catalogue, published as part of the wider NHM collection dataset.
Ceratopogonidae Slide Collection Specimens
Phylogeny for Cetacea from Lloyd & Slater (2021). This tree belongs to the "Safe" dataset in the paper, and contains 494 taxa including the ones with zero branch lengths (ZBL). All other trees are based on this tree.
Collection-level records describing the holdings of the Natural History Museum as of April 2025. See the dataset description and the other resources in this repository for more detail on navigating and interpreting this data: - [Data dictionary](https://data.nhm.ac.uk/dataset/join-the-dots-collection-level-descriptions/resource/09b2f07b-9e77-44b7-8645-ddcba1266629) - [Join the Dots user manual](https://data.nhm.ac.uk/dataset/join-the-dots-collection-level-descriptions/resource/6920d9c9-6ea4-415c-95c8-54512a70346c)
Raw data for total length proxy measurements taken from extant specimens at Natural History Museum London (NHMUK). * Specimen number - registered accession number of specimen in holding institution * Family - family name * Genus - genus name * Species - species name * TL (mm) - total length (in millimetres) * CBL (mm) - condylobasal length (in millimetres) * BIZYG (mm) - bizygomatic width (in millimetres) * EXOC (mm) - exoccipital width (in millimetre * OCB (mm) - occipital condyle breadth (in millimetres) * AON (mm) - distance between antorbital notches (in millimetres) * NFW (mm) - narial fossa width (in millimetres) * BNW (mm) - binasal width (width across the two nasal bones) (in millimetres) * AAFW (mm) - width of the articular facets of the atlas vertebra (in millimetres) * HL (mm) - humerus length (in millimetres) * Notes - additional information about species where necessary #### Abbreviations * C - Natural History Museum mammal collection designation * ZD - Natural History Museum zoology department designation * SW - Natural History Museum collection designation * SK - Natural History Museum collection designation
As for "all-specimen-data" but also includes: * **Nspecs** = number of specimens. * **max_body_size_mm** = maximum body size for the species in mm. Size is snout-vent length (SVL) for most species except turtles for which this is carapace length. * **body_size_refs** = Reference for maximum body size data. * **max_size_certainty** = Certainty level of maximum body size data. * **larger_sex** = which sex is larger - Female, Male or Neither. * **max_male** = maximum body size for males of the species in mm. * **max_female** = maximum body size for females of the species in mm. * **sex_size_ref** = Reference for maximum sex specific body size data. * **sex_size_certainty** = Certainty level of sex specific body size data. Raw body size and sexual size dimorphism data are in `body-size-herps-SA-NC-2022-02-09.csv` and the full references for each data point are in `reference-list.csv`
Summary table of annual averages of primary amount for each country, subregion and region.
Data mobilisation for IUCN conservation assessments of global freshwater bioindicators
The project "Data mobilisation for IUCN conservation assessments of global freshwater bioindicators" involved the rehousing, imaging and label data transcription of all the Ephemeroptera, Plecoptera and Trichoptera specimens belonging at the Natural History Museum, London at the time of project completion (March 2022). In addition, it included the label data transcription of the slide mounted and wet material of specimens of the families mentioned above, creating a valuable resource for bioindication and conservation assessments. The output of this project is part of a much larger dataset with the same name, to which two other European institutions also contribute. This collection was digitised as part of the Museum's Digital Collections Programme and was funded by Synthesys+ Virtual Access.
Katharine Holub-Swindell; Katharine Holub-Swindell; Robyn Crowther; Elizabeth Devenish; Daniel Hall; Abbie Herdman; Phaedra Kokkini; Nicola Lowndes; Krisztina Lohonya; Larissa Welton; Peter Wing; Louise Allan; Marla Spencer; Benjamin Price
All angiosperm species names accepted in the December 2023 update of World Flora Online (www.wfo.org). These data are licensed CC0.
Cleaned and anonymised data from the Earthworm Watch citizen science project run by the Natural History Museum, London and Earthwatch Institute (Europe) April 2016 to August 2018. Includes imputed fertiliser data used for the submitted manuscript paper Earthworm Watch: modelling the functional distribution of UK earthworms using a matched pair citizen science survey.
Annual country-level summaries of BII and land use (2001-2012) for tropical and subtropical forests
Here we provide machine-readable (csv files) and human readable (pdf files) tables of country, subregion and region averages for the Biodiversity Intactness Index (BII) and land use (primary vegetation, secondary vegetation, cropland, pasture and urban) for countries that include tropical or subtropical forest biomes, for each year from 2001-2012. These data are taken from De Palma et al (2021) Annual changes in the Biodiversity Intactness Index in tropical and subtropical forest biomes, 2001-2012, _Scientific Reports_.
Adriana De Palma; Andrew Hoskins; Ricardo E Gonzalez; Luca Borger; Tim Newbold; Katia Sanchez-Ortiz; Simon Ferrier; Andy Purvis
This is the data used for analyses in paper 1. * species - species name * tl - total length (in centimetres) of individual * cbl - condylobasal length (in millimetres) * bizyg - bizygomatic width (in millimetres) * exoc - exoccipital width (in millimetres) * ocb - occipital condyle breadth (in millimetres) * aon - distance between antorbital notches (in millimetres) * nfw - narial fossa width (in millimetres) * bnw - binasal width (width across the two nasal bones) (in millimetres) * aafw - width of the articular facets of the atlas vertebra (in millimetres) * hl - humerus length (in millimetres) * type - whether species is extant (living) or fossil Note that raw data with specimen numbers and literature references is provided in separate files in this repo.
Clade II STRUCTURE file (Species delimitation)
World and European Brassicales Collection
The World and European Brassicales collections comprises the records of all the sheet-mounted material at the Natural History Museum, London at the time of project completion (April 2019). Each specimen record has been published with an image capturing both the specimen and its associated labels and creating an inventory record with a unique identifier (barcode), taxon information and geographical locality. The data resource generated by the project is available using the link. This collection was digitised as part of the Museum's Digital Collections Programme and V Factor programme.
Peter Baker; Clare Booth-Downs; Yoke-Shum Broom; Robyn Crowther; Melis Erdem; Pauline Heathcote; Neil Ireland; Phaedra Kokkini; Renee Miller; Ranee Om Prakash; Sarah Price; Judith Rose; Judith Shorter; Michelle Sutton; Hillery Warner; Peter Wing; Jovita C. Yesilyurt; Louise Allan
A document formulated to help define Collections Units within the Join the Dots collections assessment exercise at the Natural History Museum.
Collection Unit Definition and Guidlines
Details of additional labels attached to specimens in the Dale Herbarium recording collector, location and or date, in addition to the label data captured in the main dataset.
The Aleyrodoidea slide collection comprises the records of all the slide-mounted whitefly material at the Natural History Museum, London at the time of project completion (November 2018). Each specimen record has been published with an image capturing both the specimen and its associated labels and creating an inventory record with a unique identifier (Data Matrix barcode), taxon information, type status and country level collection locality. Some specimens will have additional images capturing the reverse side of labels and/or the paper envelopes that house the slides. The data resource generated by the project is available using the link. Please search for the relevant taxa as this dataset if part of a larger project covering a range of Orders and Superfamilies. This collection was digitised as part of the Museum's Digital Collections Programme.
Robyn Crowther; Elizabeth Devenish; Nicola Lowndes; Peter Wing; Louise Allan; Charlotte Barclay; Paul Andrew Brown
**Specimen number**: NHMUK 1862.7.18.1 **Specimen Link**: http://data.nhm.ac.uk/object/cac65e48-4615-43c1-915d-d5a572fc5260 **Decription**: _Balaenoptera physalus_ -- Balaenopteridae;
Trait data extracted from Ecoflora descriptions
Full phylogeny used in diversification analyses in paper 2.
This dataset provides a complete catalogue of the diatoms samples preserved dried on paper, glass and mica sheets and stored in packets glued to herbarium sheets. Each specimen has been databased to capture, minimally, its registration number (barcode) and the 'filed as' name, which may or may not be the currently accepted name. Most of these specimens have images associated with them, such as a photograph of the herbarium sheet.
Data from the "Back to the water" project
Data from papers published as part of Leverhulme Trust Research Project Grant (RPG-2019-323): Back to the water: macroevolutionary dynamics of secondarily aquatic tetrapods. These data have been used in two papers. > **Paper 1**: Burin, G., Park, T., James, T.D, Slater, G.J. & Cooper, N. 2023. The dynamic adaptive landscape of cetacean body size. Current Biology, 33, 1787–1794. DOI: 10.1016/j.cub.2023.03.014. See `README_PAPER1.md` and https://github.com/gburin/bodysize-evolution-cetacea for more details. > **Paper 2**: Park, T., Burin, G., Lazo-Cancino, D., Rees, J.P.G., Rule, J.P., Slater, G.J., Cooper, N. 2024. Charting the course of pinniped evolution: insights from molecular phylogeny and fossil record integration. Evolution, 78, 1212-1226. DOI: 10.1093/evolut/qpae061. See `README_PAPER2.md` and https://github.com/nhcooper123/pinniped-macro for more details.
Travis Park; Gustavo Burin; Graham J Slater; Natalie Cooper
**Specimen number**: NHMUK 1873.3.3.1 **Specimen Link**: http://data.nhm.ac.uk/object/357d83dc-7861-4ee9-a8f6-77aa3c3ae6e7 **Decription**: _Eubalaena australis_ -- Balaenidae; Cetacea; Mammalia
Link to the “Convolvulaceae Digitisation” specimen records from the NHM catalogue, published as part of the wider NHM collection dataset.
Link to the Castniidae specimen records from the NHM catalogue, published as part of the wider NHM collection dataset.
The Atlas of Living Malaysia project comprises the records of pre-selected pinned insect specimens at the Natural History Museum, London. It includes representatives of over 5,000 species that occur in Malaysia and the surrounding regions, including material collected by Alfred Russel Wallace along with his personal collection. Pinned insect specimens from the following 13 Orders were digitised: Blattodea, Coleoptera, Dermaptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera, Mantodea, Neuroptera, Odonata, Orthoptera, Phasmatodea, and Trichoptera. Each specimen record has been published with an image capturing both the specimen and its associated labels and creating an inventory record with a unique identifier (Data Matrix barcode), taxon information and country level collection locality. Some specimens will have additional images capturing the reverse side of labels and/or additional views of the specimen (ventral and/or lateral). The data resource is available using the link. Please search for the relevant taxa. This collection was digitised as part of the Museum's Digital Collections Programme and the non-governmental organisation ECOMY (Ecotourism and Conservation Society of Malaysia).
Robyn Crowther; Phaedra Kokkini; Peter Wing; Louise Allan; Charlotte Barclay; Laurence Livermore
Cleaned and anonymised data from the Earthworm Watch citizen science project run by the Natural History Museum, London and Earthwatch Institute (Europe) April 2016 to August 2018. Includes reshaped data on functional groups used for the submitted manuscript paper Earthworm Watch: modelling the functional distribution of UK earthworms using a matched pair citizen science survey.
Full details are available in the Supplementary Material of the paper. In brief, for each relevant publication in **01_sources-for-plastic-ingestion-data** we extracted information on the age class of sampled birds, sample size of birds, year(s) in which sampling was conducted, sampling method (bolus, brushing, lavage, necropsy, regurgitation or scat) and ocean basin (Arctic, Indian, North Atlantic, North Pacific, South Atlantic, South Pacific, or Southern oceans). We categorised the reported age class of sampled individuals as ‘adult’, ‘subadult’, ‘adult/subadult’, ‘nest-bound’ (i.e., chicks or fledglings), and ‘mixed’. If birds were collected at sea and age class was not reported, sampled birds were categorised as ‘adult/subadult’ because they were not nest-bound. When multiple age classes were pooled (e.g., chicks and adults) or when age class could not be discerned, we categorised age class as ‘mixed’. Data from each source was divided to ensure separate sampling units for each combination of source, year, site, species, age class, and sampling method, depending on how much detail on data collection was provided in the paper. Literature that failed to report sample sizes of birds examined for plastic ingestion and/or sample sizes of birds found with plastic was not included in the dataset. Duplicate data from secondary research was removed as long as they were specified as such by the authors. Column contents are as follows. * **HBWv8.1_Binomial**. Species name matched to Handbook of Birds of the World v8.1 taxonomy. Note that the data cleaning steps prior to the analyses update these to the Clements et al 2025 taxonomy. * **UniqueID_Plastic.study**. A unique ID for the combination of source*year*site*species*ageclass. This number is not linked to the Source. * **Source**. Source name in the form Author et al, YEAR. This matches the Source column in **01_sources-for-plastic-ingestion-data** . * **Common.name_Plastic.study**. Common name of the species as stated in the source. * **Sci.name_Plastic.study**. Scientific name of the species as stated in the source. * **Site**. Study site name, as per the Source. Include Country. * **lat**. Latitude (DMS) of study site. * **lon**. Longitude (DMS) of study site. * **MarineRegion**. Ocean basin of site. Options are Arctic, Indian, North Atlantic, North Pacific, South Atlantic, South Pacific, or Southern oceans. * **Age.Class**. Age class of sampled birds. Options are adult, subadult, adult/subadult, nest-bound (i.e., chicks or fledglings), or mixed. If birds were collected at sea and age class was not reported, sampled birds were categorised as adult/subadult because they were not nest-bound. When multiple age classes were pooled (e.g., chicks and adults) or when age class could not be discerned, we categorised age class as mixed. * **Date_Text**. Date as text. If relevant this was the range of dates the study covered. * **Date_FirstYR**. First year the study covered. * **Date_LastYR**. Last year the study covered. * **Date_MedianYR**. Median year the study covered. * **Study.Duration** . Study duration in years. * **n**. Number of birds sampled. * **n_plastic**. Number of sampled birds that had ingested at least one piece of plastic. * **FO**. Frequency of occurrence of plastic. This is calculated as *n_plastic / n*. * **Plastic**. Did any of the sampled birds ingest at least one piece of plastic? Yes/No. * **Sampling_method**. Primary way that plastic samples were obtained. Options are bolus, brushing, lavage, necropsy, regurgitation or scat. * **Added_by**. Data curator who added the data. Primarily Steph Avery-Gomm (SA-G), Nia Potapova (NP) or Chrissie Potter (CP). * **Comments**. Any comments, queries or notes made by the data curators.
A collections level dataset of fossil and recent ostracods in the collections at the Natural History Museum.
The oceans are experiencing extraordinary human-induced threats from global climate change, overfishing, pollution and an increase in invasive non-native species. Seaweeds create the largest vegetated marine habitats on the planet, which underpin global marine function but are threatened by the impacts of environmental change. Despite the importance of seaweeds, and the threats they face, they are afforded inadequate conservation measures, a major gap which urgently needs to be addressed. The state of the world’s seaweeds has come about as a result of this need. It provides the evidence-base which will inform a ‘Seaweed Breakthrough’, a potentially powerful means of protecting seaweeds and seaweed habitats through the UNFCCC High Level Climate Champion 2030 Breakthrough Agenda. Through setting global targets to halt habitat loss, protect and restore habitats and secure sustainable investment, Breakthroughs falling under the overarching goal for Marine Conservation aim to achieve significant change to reach a resilient, zero carbon future by 2030 across every sector of the global economy. We have compiled an up-to-date overview on the state of the world’s seaweeds. Through a series of chapters covering information on seaweed distribution, habitats, ecosystem services, as well as how they are threatened, protected and restored, we have identified knowledge gaps and drafted ambitious high-level targets that will form the basis of expert-led workshops to support the Seaweed Breakthrough. This review demonstrates how important seaweeds and their habitats are in the functioning of marine ecosystems, global fisheries, food security, valuable materials for industrial and pharmaceutical uses and, therefore, livelihoods. It documents what is known. For example, we now have quantitative evidence for the severity of losses and degradation that kelp forests are suffering in many regions around the world. Less is known about most other seaweed habitats, as they have received far less attention. For example, rhodolith beds, habitats formed by free-living calcified red seaweeds, are extensive in many parts of the world and are still being discovered. However, they are threatened by pollution, habitat degradation, climate change, ocean acidification and trawling. Deep-water seaweed habitats have also only been studied in a tiny fraction of the oceans yet are likely to hold diversity that is still to be discovered.
Sophie Corrigan; Elizabeth J, Cottier-Cook; Phaik Eem Lim; Juliet Brodie
Helper file used as a placeholder half way through the data wrangling script for all sexed and unsexed specimens. See https://github.com/nhcooper123/sex-bias-herps for more details.
This table indicates which box the individual specimen tray labels have been stored in. It also include notes indicating labels that were not allocated and suggested updates for the data
Global Asteroidea Occurrence Dataset.csv
Global species hotspots and COI barcoding cold spots of marine Gastropoda
This compressed repository contains the processed datasets of species occurrence records (from GBIF) that were taxon-matched (WoRMS/LifeWatch) and analysed in the manuscript "Global species hotspots and COI barcoding cold spots of marine Gastropoda," as well as the R script used for analysis and visualisation. The datasets contain species occurrence metadata of both dated/undated and geotagged/ungeotagged records, taxonomic information of the accepted extant marine gastropod species, and the metadata of COI barcodes (deposited in BOLD) and of available complete mitochondrial genomes (NCBI). The raw species occurrence dataset compiling all recorded, present (i.e., non-absent) occurrences of gastropods (N = 11,085,172) can be downloaded at the GBIF portal (https://doi.org/10.15468/dl.qgsn2b).
Andrew Torres; Owen Wangensteen; Willem Renema; Christopher Meyer; Ian Kendrich Fontanilla; Jonathan Todd
This is a ZIP file containing five CSVs: documents_view, observations_matrix, questions_view, samples_view. *__Documents_view__: A list of the image files that show survey locations and their associated sample ID and file name. *__Observations_matrix__: the number of observations per survey (sample_ID). *__Questions_view__: Contains the name of the survey location. *__Samples_view__: For each quadrat (sample) surveyed, there is the following information: sample_start_datetime, sample_end_datetime, submission_datetime, first_name last_name, sample_observers_number, sample_location_latitude, sample_location_longitude, sample_location_region, verification_completion_status *__Taxon_view__*: Contains the sample IDs for each individual quadrat, along when the data was submitted, the number of kelp counted in the quadrat, the number of photos of the quadrat and a link to an image file.
Geography file for fossil taxa used in biogeography analyses in paper 2.
*The output was too large for the supplemental materials so we include it here instead.* The metadata for the processed file was copied from the FabricPostProcessor manual for BayesTraits v4.0.0, which can be found in the link http://www.evolution.reading.ac.uk/FabricPostProcessorV1.0.0/Files/FabricPostProcessor.pdf * ID: ID for each node * Branch: Length Branch length from phylogenetic tree * Height: Height of the node, with the root having the largest height * Height Mid-Point: Height of the node at its mid-point * Sum BL: Sum of all branches that contained within the node * No Descendants: Number of descendant nodes, 0 for a tip, 2 for binary node * No Concurrent Linages Start: Number of concurrent lineages at the start of the node. * No Concurrent Linages Mid-point: Number of concurrent lineages at the mid-point of the node. * No Concurrent Linages End: Number of concurrent lineages at the end of the node. * Mean (Beta * BL): Mean beta * SD (Beta * BL): Beta standard deviation * Mean (Beta * BL) NZ: Mean beta excluding samples when the beta is set to zero. Note: we recommend that this should be used for estimating the size of the directional effect. * SD (Beta * BL) NZ: Standard deviation excluding samples when the beta is set to zero * Sample Size: Number of samples in the MCMC posterior * P < 0: Probability beta is less than 0 * P == 0: Probability beta is 0 * P > 0: Probability beta is greater than 0 * P (Beta * BL): The probability of Beta * BL, given the prior and threshold value * Observed P (Beta * BL): The observed probability of Beta * BL in the Markov chain * SD Observed P(Beta * BL): The standard deviation of observed P (Beta * BL) * Z (Beta * BL): The Z score of Beta * BL * Sig (Beta * BL): 1 if the Z scores is significant (Z >= 2), 0 otherwise * Mean Evolvability Scalar: The mean scalar * SD Scalar: The standard deviation of the scalar * Mean Non 1 Scalar: The mean scalar excluding samples when it is 1. Note: we recommend that this should be used for estimating the size of the evolvability effect. * Median Non 1: The median scalar excluding samples when it is 1. Worth checking to see if the mean and median agree. Lack of agreement indicates a skewed posterior. * SD Non 1 Scalar: The standard deviation of the scalar excluding samples when it is 1 * P < 1: The probability the scalar is less than one * P == 1: The probability the scalar is one * P > 1: The probability the scalar is greater than one * P Scalar: The probability of an evolvability scalar, given the prior and threshold value * Observed P Scalar: The observed probability of the evolvability scalar * SD Observed P Scalar: The standard deviation of observed P evolvability scalar * Z Scalar: The Z score of the evolvability scalar * Sig Scalar: 1 if the Z scores is significant (Z >= 2), 0 otherwise * Prop beta followed by a variance scalar: The probability of a beta followed by an evolvability scalar * No Beta or Node: Number of times the sample has a beta or evolvability scalar * Prop Variance scalar followed by a beta: The probability of an evolvability scalar followed by a beta * Prop Beta on Dec Nodes: The probability of a beta on a descendant node * MD5 Sum: An MD5 check sum based on the taxa names that define the node, sorted into alphabetical order. * No Taxa: Number of taxa which define the node * Taxa List: A list of taxa names which define the node
The Malvales collection comprises the records of all the sheet-mounted material at the Natural History Museum, London at the time of project completion (June 2022). Each specimen record has been published with an image capturing both the specimen and its associated labels and creating an inventory record with a unique identifier (barcode), taxon information and geographical locality. The data resource generated by the project is available using the link. This collection was digitised as part of the Museum's Digital Collections Programme.
Jovita C. Yesilyurt; Larissa Welton; Krisztina Lohonya; Peter Wing; Hillery Warner; Louise Berridge; Phaedra Kokkini; Nicola Lowndes; Leo Le Good; Ashleigh Whittaker; Daniel Hall; Ranee Om Prakash; Joseph Deane; Clare Booth-Downs; Judith Shorter; Marianne Rueffer Turner; Melis Erdem; Neil Ireland; Sarah Price; Louise Allan
The Coccoidea slide collection comprises the records of all the slide-mounted scale insect material housed at the Natural History Museum, London at the time of project completion (August 2020). Each specimen record has been published with an image capturing both the specimen and its associated labels and creating an inventory record with a unique identifier (Data Matrix barcode), taxon information, type status and country level collection locality. Some specimens will have additional images capturing the reverse side of labels and/or the paper envelopes that house the slides. The data resource generated by the project is available using the link. Please search for the relevant taxa as this dataset if part of a larger project covering a range of Orders and Superfamilies. This collection was digitised as part of the Museum's Digital Collections Programme.
Robyn Crowther; Elizabeth Devenish; Phaedra Kokkini; Krisztina Lohonya; Nicola Lowndes; Peter Wing; Louise Allan; Charlotte Barclay; Paul Andrew Brown
## Introduction This image database is intended primarily for taxonomists and other researchers, but the historical importance of the specimens portrayed is such that we hope they will attract a broader audience. The database contains images of the butterfly specimens upon which Linnaeus based his descriptions. Linnaeus described 305 taxa under the name _Papilio_. Of these, 241 refer to currently valid butterfly species names and two to subspecies. This site has been developed as an adjunct to a paper published on Linnaeus's butterflies, and makes images of type specimens and their labels available. Details of the publication are as follows: Linnaeus's butterflies (Lepidoptera: Papilionoidea and Hesperioidea). _Zoological Journal of the Linnean Society_, 2001, **132**: 277-399, by [Martin R. Honey](https://www.nhm.ac.uk/about-us/contact-enquiries/forms/emailform.jsp?recip=m.honey&business_title=M.Honey&email_title=Linnaean+Type+Specimens+website+enquiry) and [Malcolm J. Scoble](https://www.nhm.ac.uk/about-us/contact-enquiries/forms/emailform.jsp?recip=m.scoble&business_title=M.Scoble&email_title=Linnaean+Type+Specimens+website+enquiry). ## Sources of specimens The specimens on which Linnaeus based his descriptions are housed in several institutions. Most were found either in his personal collection, now in the Linnean Society of London, or in that of Queen Ludovica Ulrica, now in the Zoological Museum of the University of Uppsala, Sweden. Further material was examined from the collections of Carl Clerck and Charles De Geer, both housed in the Naturhistoriska Riksmuseet, Stockholm, and from the material of James Petiver, which forms part of the collection of Sir Hans Sloane, in the Natural History Museum, London. ## About the project The project was carried out at the Natural History Museum, London, in association with [The Linnean Society of London](https://www.linnean.org/), and was supported by a grant from [The Leverhulme Trust](https://www.leverhulme.ac.uk/). It is hoped that eventually all the existing primary types will be illustrated on this site. Initially, nearly all those from The Linnean Society of London have been posted. ## Labels The small labels associated with the images are by Linnaeus, while the larger ones were added subsequently by Sir James Edward Smith, who purchased Linnaeus's collection. ## Acknowledgements The authors thank the Natural Environmental Research Council for a publications grant (administered by The Linnean Society of London) that enabled this website to be developed. ## Related resources [The Cockayne database of UK butterflies](https://www.nhm.ac.uk/research-curation/projects/cockayne/). --- _This data was originally hosted at [https://www.nhm.ac.uk/research-curation/research/projects/linntypes/](https://www.nhm.ac.uk/research-curation/research/projects/linntypes/) but has been moved to the NHM Data Portal._
Fossil phylogeny without sampled ancestors used in diversification analyses in paper 2.
The Chrysopidae collection comprises the records of all the pinned material at the Natural History Museum, London at the time of project completion (June 2023). Each specimen record has been published with an image capturing both the specimen and its associated labels and creating an inventory record with a unique identifier (Data Matrix barcode), taxon information and type status. The data resource generated by the project is available using the Data and Resources link, please search for the relevant taxa.
Peter Wing; Louise Berridge; Emma Bonzo; Skye Neal; Glory Turnbull; Louise Allan; Chiho Ikebe; Marla Spencer; Daniel Hall; Benjamin Price
Moonlight, PW, Baldaszti, L, Cardoso, D, Elliott, A, Särkinen, T, Knapp, S (2024) Twenty years of big plant genera. Proceedings of the Royal Soiety B 291: 20240702, http://doi.org/10.1098/rspb.2024.0702. Summary: We use data from the World Flora Online (WFO) to provide an updated list of big (>500 species) and megadiverse (>1,000 species) flowering plant genera and highlight changes since the last review in 2004. The number of big genera has increased from 57 to 86; today one of every four plant species is classified as a member of a big genus, with 14% in just 28 megadiverse genera. Most (71%) of the growth in big genera since 2000 is the result of new species description, not generic re-circumscription. More than 15% of all currently accepted flowering plant species described in the last two decades are in big genera, suggesting that groups previously considered intractable are now being actively studied taxonomically. Despite this rapid growth in big genera, they remain a significant yet understudied proportion of plant diversity. Code version: R version 4.3.3 Four files included: 1. R code used in simulations (as R file; Big Genera Simulations.R) 2. Accepted genera of flowering plants from December 2023 World Flora Online download (WFO_genera Accepted genera and sizes Dec 2023 update.csv) includes all accepted flowering plant genera from the World Flora Online 3. Accepted species names in flowering plants from December 2023 World Flora Online download (WFO_species_Angiosperm Species Level Names Accepted Dec 2023 Update.csv) includes all accepted species from World Flora Online 4. New species names coined in flowering plants since the year 2000 (IPNI_species_described post 2000.csv) includes all species described in flowering plants since the year 2000
Peter Moonlight; Ludwig Baldaszti; Domingos Cardoso; Alan Elliott; Tiina Särkinen; Sandra Knapp
**Specimen number**: NHMUK ZD.2007.100 **Specimen Link**: http://data.nhm.ac.uk/object/fc5f2fd6-b92f-464e-92e3-0a095bf6f790 **Decription**: _Physeter macrocephalus_ -- Physeteridae;
Listing of unregistered slides from John Whittaker's Archaeological Studies. Assemblage slides containing mainly Foraminifera and Ostracoda from sites studied in from the South of England.
Link to the Wheat Through the Ages Project specimen records from the NHM catalogue, published as part of the wider NHM collection dataset.
Specimen and tissue region with the different chemical analysis done. For EDS whole maps of the dental plates/teeth are marked with an X. Reports the number of measurement points per tissue/specimen are shown for X-ray diffraction and Raman analysis
An Excel file created to aid scoring of individual Collections Units as part of the "Join The Dots" collections exercise. Currently this contains example data from the 2016 pilot exercise.
Supplementary figures and tables to support Griffiths et al. (2025)
Micropalaeontology collections citation and visitor data
Catalysts for change: museum gardens in a planetary emergency
A csv file containing collector and identification records for herbarium specimens found that have been collected in the Museum grounds. Dates range from 1865 to 2022. As the Natural History Museum herbarium (BM) is imaged and digitised we are likely to find more collections, particularly from the early 20th century. Current plant records in the gardens are observational only and can be found in the resources mentioned in the text. More specimens will be available as we encounter them via the search function on the NHM Data Portal (https://data.nhm.ac.uk/).
Anonymised data from participants who registered for the Earthworm Watch citizen science project which ran from April 2016 to August 2018. This data was used for the paper Who watches the worms? Motivation and participation in a contributory citizen science project
This is a species-level pruned tree matched to the seabird list from Clements 2025 taxonomy. All species are present in this tree, except four species of *Sterna* with uncertain taxonomic placement. The original trees come from Claramunt et al 2025: BBtree3. Available from: https://raw.githubusercontent.com/evolucionario/BigBirdTree
A transcription of Hans Sloane's three-volume catalogue to his Collection of Vegetables and Vegetable Substances. File updated 17 June 2024
Transcription of Hans Sloane's Catalogue of Vegetables and Vegetable Substances.xlsx
Clade IV STRUCTURE file (Species delimitation)
Data for wild sex ratios comparisons in supplementary materials. * **class** = taxonomic class * **order** = order * **family** = family * **binomial** = species binomial name * **skew** = which sex is usually more abundant in a population. Either "Male biased", "Female biased" or "Variable/Equal". * **notes** = any notes about the above * **source** = data source. * **female** = % female specimens for the main dataset
A tif file illustrating the Moisture Index Map, calculated according to the Splash algorithm, at a 30 arcsec spatial resolution (c. 1 km) used in the analyses (Supplementary Material 4 file)
Tree with node numbers for use in interpreting `DEC-all-node-probabilities.csv` and `DECJ-all-node-probabilities.csv`
"Join the dots" collections assessment exercise
The files submitted here form the backbone to a 2018 collections assessment exercise at the Natural History Museum and support a methodology paper submitted to Museum Management and Curatorship. They include: a document to help define collections units, an Excel spread sheet for gathering data about each unit, a Manual for scorers, a document listing and illustrating cabinet types with their suggested scores to aid consistent scoring, some screen shots of the internally available Power BI dashboard, item type and preservation look-ups and a list of numbers of specimens in the museum broken down to sectional level.
Link to the Birdwing Butterfly Collection specimen records from the NHM catalogue, published as part of the wider NHM collection dataset.
These are the data used to create the labels.
Join the Dots collection-level descriptions
The records in this dataset provide a high-level summary of the Natural History Museum's collection and encompass the material managed by its Life Sciences, Earth Sciences and Library & Archives departments. The data has been gathered, structured and published with the intention of providing some level of visibility into the scope, nature and composition of the Museum's holdings, the majority of which have yet to be digitised. The 2,800+ records in this dataset represent the majority of the NHM collection, approximately 78 million items, and should be treated as an index or discovery tool: they are an indicative view of the Museum's holdings, a source of high-level figures and a signpost towards the relevant curatorial team to contact for more in-depth information. ## Descriptive fields Each record in the **JtD collection-level records** table describes a group of objects, referred to as a 'collection unit'. Collection units can range in size from a handful of objects to several million and are defined by a set of high-level characteristics common to the objects within them (e.g., taxonomy, straitgraphy, item type, preservation method). Controlled vocabularies and external authority lists underpin descriptive fields wherever possible: see **Data dictionary** for field-level definitions and guidance for all fields used in this dataset. ## Collection metrics The count fields indicate the scale of each collection unit in terms of the estimated quantity of 'items' (specimen-level or equivalent) and 'curatorial units' (objects physically managed during curation activities, such as jars or boxes) it holds. The 'reporting count' field should be used when aggregating multiple units and is the default collection size metric used by the Museum both internally and externally. Assessment scores are allocated by curatorial teams and are an attempt to indicate subjective or mutable qualities of each collection unit, such as outreach potential, scope and significance, physical accessibility and level of information available. See **Data dictionary** and **Join the Dots User Manual** for scoring definitions and examples. Scores are updated on an annual basis and are best viewed as a benchmark of the state of a collection unit/group of units: they are intended to allow us to track the impact of collection care, development and management activities over time and are not intended for use as a comparative measure between different areas of the collection. ## Join the Dots Framework The criteria underpinning collection units and the methodology by which they are quantified and assessed is defined in the Join the Dots (JtD) cross–disciplinary collection assessment framework, developed and used at the NHM since 2018. For details on the full JtD framework see **Join the Dots User Manual** and the summary paper referenced below. Note that not all fields referenced in the JtD specification are included in this dataset: a subset is presented to avoid compromising the security of the collection and to provide a level of detail relevant to an external audience. ## Further references - [NHM main website collection pages](https://www.nhm.ac.uk/our-science/collections.html) - [Library & Archives Discovery Layer](https://www.nhm.ac.uk/our-science/departments-and-staff/library-and-archives.html) - [Archives Catalogues](https://www.nhm.ac.uk/CalmView/default.aspx) - [Specimen-level collection dataset](https://doi.org/10.5519/0002965) - [Join the Dots: assessing a collection of 80 million items at The Natural History Museum, London, 2022](https://www.tandfonline.com/doi/full/10.1080/09647775.2021.2023900) - currently paywalled: contact the dataset curator for a copy
Herbarium specimens of Begonia occurring in Peru, downloaded from the Begonia Resource Centre xx/xx/2021
The database provides information on discrete sub-collections within the conodont collection housed at the Natural History Museum, London. It includes generic, specific and subspecific names, and links to images are included with some collections.
Sex biases and the scarcity of sex metadata in global herpetology collections
Data from paper: **Sex biases and the scarcity of sex metadata in global herpetology collections**. https://academic.oup.com/biolinnean/article/142/3/308/7287291. > Tara Wainwright, Morwenna Trevenna, Sarah R. Alewijnse, Patrick D. Campbell, Marc E.H. Jones, Jeff W. Streicher & Natalie Cooper. 2024. Sex biases and the scarcity of sex metadata in global herpetology collections. Biological Journal of the Linnean Society. 142, 308-318. DOI: 10.1093/biolinnean/blad129. The analyses require the two tidied datasets `all-specimen-data.csv` (unzipped) and `all-extra-data.csv`. Raw data sources used to build these are listed in the metadata. More details can be found at https://github.com/nhcooper123/sex-bias-herps.
Tara Wainwright; Morwenna Trevenna; Sarah R. Alewijnse; Patrick Campbell; Marc Jones; Natalie Cooper
Databased specimens from South Asia in the BM Herbarium
Clade II PCA file (Species delimitation)
The Bee Land-use Change Project dataset comprises the records of all pinned Bombus hortorum, B.hypnorum, B.lapidarius, B.muscorum, B.pascuorum, B.ruderatus and B.sylvarum material collected in the UK and housed at the Natural History Museum, London. The dataset comprises 6753 specimens. Specimen labels were removed from each specimen and imaged alongside the specimen. Dorsal images were taken of each specimen. Each specimen record has been published with a unique identifier (barcode), taxon information, label metadata transcription, locality georeferencing and an image capturing both the specimen and its associated labels. This collection was digitised as part of the Museum's Digital Collections Programme and funded by NERC award NE/P012914/1 "Bee sensitivity to a century of agricultural land-use change".
A description of the datasets and details of changes made.
Phylogeny for toothed whales containing only the species included in the analyses. The tree contains 217 taxa including those with zero length branches (ZBL).
The 2016 release of the PREDICTS database [SUPERSEDED]
__IMPORTANT NOTICE: THIS VERSION OF THE DATABASE HAS BEEN SUPERSEDED__ Data review in 2021-2023 has resulted in some changes and additions to the database. The new version (version 1.1), is available for non-commercial use [https://data.nhm.ac.uk/dataset/the-2016-release-of-the-predicts-database-v1-1]. A dataset of 3,250,404 measurements, collated from 26,114 sampling locations in 94 countries and representing 47,044 species. The data were collated from 480 existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database was assembled as part of the [PREDICTS project](https://www.nhm.ac.uk/our-science/our-work/biodiversity/predicts.html) - Projecting Responses of Ecological Diversity In Changing Terrestrial Systems. The taxonomic identifications provided in the original data sets are those determined at the time of the original research, and so will not reflect subsequent taxonomic changes. This dataset is described in [10.1002/ece3.2579](http://dx.doi.org/10.1002/ece3.2579). A description of the way that this dataset was assembled is given in [10.1002/ece3.1303](http://dx.doi.org/10.1002/ece3.1303). * `columns.csv`: Description of data extract columns * `database.zip`: Database in zipped CSV format * `database.rds`: Database in RDS format * `sites.zip`: Site-level summaries in compressed CSV format * `sites.rds`: Site-level summaries in RDS format * `references.csv`: Data references in CSV format * `references.bib`: Data references in BibTeX format
Lawrence Hudson; Tim Newbold; Sara Contu; Samantha L L Hill; Igor Lysenko; Adriana De Palma; Helen Phillips; Tamera I Alhusseini; Felicity E Bedford; Dominic J Bennett; Hollie Booth; Victoria Burton; Wen Ting Charlotte Chng; Argyrios Choimes; David L P Correia; Julie Day; Susy Echeverría-Londoño; Susan R Emerson; Di Gao; Morgan Garon; Michelle L K Harrison; Daniel J Ingram; Martin Jung; Victoria Kemp; Lucinda Kirkpatrick; Callum Martin; Yuan Pan; Gwilym Pask-Hale; Edwin L Pynegar; Alexandra N Robinson; Katia Sanchez-Ortiz; Rebecca A Senior; Benno Simmons; Hannah J White; Hanbin Zhang; Job Aben; Stefan Abrahamczyk; Gilbert B Adum; Virginia Aguilar-Barquero; Marcelo A Aizen; Belén Albertos; E L Alcala; Maria del Mar Alguacil; Audrey Alignier; Marc Ancrenaz; Alan N Andersen; Enrique Arbeláez-Cortés; Inge Armbrecht; Víctor Arroyo-Rodríguez; Tom Aumann; Jan C Axmacher; Badrul Azhar; Adrián B Azpiroz; Lander Baeten; Adama Bakayoko; András Báldi; John E Banks; Sharad K Baral; Jos Barlow; Barbara I P Barratt; Lurdes Barrico; Paola Bartolommei; Diane M Barton; Yves Basset; Péter Batáry; Adam J Bates; Bruno Baur; Erin M Bayne; Pedro Beja; Suzan Benedick; Åke Berg; Henry Bernard; Nicholas J Berry; Dinesh Bhatt; Jake E Bicknell; Jochen H Bihn; Robin J Blake; Kadiri S Bobo; Roberto Bóçon; Teun Boekhout; Katrin Böhning-Gaese; Kevin J Bonham; Paulo A V Borges; Sérgio H Borges; Céline Boutin; Jérémy Bouyer; Cibele Bragagnolo; Jodi S Brandt; Francis Q Brearley; Isabel Brito; Vicenç Bros; Jörg Brunet; Grzegorz Buczkowski; Christopher M Buddle; Rob Bugter; Erika Buscardo; Jörn Buse; Jimmy Cabra-García; Nilton C Cáceres; Nicolette L Cagle; María Calviño-Cancela; Sydney A Cameron; Eliana M Cancello; Rut Caparrós; Pedro Cardoso; Dan Carpenter; Tiago F Carrijo; Camila R Cassano; Anelena L Carvalho; Helena Castro; Alejandro A Castro-Luna; Rolando Cerda B; Alexis Cerezo; Kim Alan Chapman; Matthieu Chauvat; Morten Christensen; Francis M Clarke; Daniel F R Cleary; Giorgio Colombo; Stuart P Connop; Michael D Craig; Leopoldo Cruz-López; Saul A Cunningham; Biagio D'Aniello; Neil D'Cruze; Pedro Giovâni da Silva; Martin Dallimer; Emmanuel Danquah; Ben Darvill; Jens Dauber; Adrian L V Davis; Jeff Dawson; Claudio de Sassi; Benoit de Thoisy; Olivier Deheuvels; Alain Dejean; Jean-Louis Devineau; Tim Diekötter; Jignasu V Dolia; Erwin Domínguez; Yamileth Dominguez-Haydar; Silvia Dorn; Isabel Draper; Niels Dreber; Bertrand Dumont; Simon G Dures; Mats Dynesius; Lars Edenius; Paul Eggleton; Felix Eigenbrod; Zoltán Elek; Martin H Entling; Karen J Esler; Ricardo F de Lima; Aisyah Faruk; Nina Farwig; Tom M Fayle; Antonio Felicioli; Annika M Felton; Roderick J Fensham; Ignacio C Fernandez; Catarina C Ferreira; Gentile F Ficetola; Cristina Fiera; Bruno K C Filgueiras; Hüseyin K Fırıncıoğlu; David Flaspohler; Andreas Floren; Steven J Fonte; Anne Fournier; Robert E Fowler; Markus Franzén; Lauchlan H Fraser; Gabriella M Fredriksson; Geraldo B Freire-Jr; Tiago L M Frizzo; Daisuke Fukuda; Dario Furlani; René Gaigher; Jörg U Ganzhorn; Karla P García; Juan C Garcia-R; Jenni G Garden; Ricardo Garilleti; Bao-Ming Ge; Benoit Gendreau-Berthiaume; Philippa J Gerard; Carla Gheler-Costa; Benjamin Gilbert; Paolo Giordani; Simonetta Giordano; Carly Golodets; Laurens G L Gomes; Rachelle K Gould; Dave Goulson; Aaron D Gove; Laurent Granjon; Ingo Grass; Claudia L Gray; James Grogan; Weibin Gu; Moisès Guardiola; Nihara R Gunawardene; Alvaro G Gutierrez; Doris L Gutiérrez-Lamus; Daniela H Haarmeyer; Mick E Hanley; Thor Hanson; Nor R Hashim; Shombe N Hassan; Richard G Hatfield; Joseph E Hawes; Matt W Hayward; Christian Hébert; Alvin J Helden; John-André Henden; Philipp Henschel; Lionel Hernández; James P Herrera; Farina Herrmann; Felix Herzog; Diego Higuera-Diaz; Branko Hilje; Hubert Höfer; Anke Hoffmann; Finbarr G Horgan; Elisabeth Hornung; Roland Horváth; Kristoffer Hylander; Paola Isaacs-Cubides; Hiroaki Ishida; Masahiro Ishitani; Carmen T Jacobs; Víctor J Jaramillo; Birgit Jauker; F Jiménez Hernández; McKenzie Johnson; Virat Jolli; Mats Jonsell; Nur Juliani S; Thomas S. Jung; Vena Kapoor; Heike Kappes; Vassiliki Kati; Eric Katovai; Klaus Kellner; Michael Kessler; Kathryn R Kirby; Andrew M Kittle; Mairi E Knight; Eva Knop; Florian Kohler; Matti Koivula; Annette Kolb; Mouhamadou Kone; Ádám Kőrösi; Jochen Krauss; Ajith Kumar; Raman Kumar; David J Kurz; Alex S Kutt; Thibault Lachat; Victoria Lantschner; Francisco Lara; Jesse R Lasky; Steven C Latta; William F Laurance; Patrick Lavelle; Violette Le Féon; Gretchen LeBuhn; Jean-Philippe Légaré; Valérie Lehouck; María V Lencinas; Pia E Lentini; Susan G Letcher; Qi Li; Simon A Litchwark; Nick Littlewood; Yunhui Liu; Nancy França Lo Man Hung; Carlos A López-Quintero; Mounir Louhaichi; Gabor L Lövei; Manuel Esteban Lucas-Borja; Victor H Luja; Matthew S Luskin; M Cristina MacSwiney G; Kaoru Maeto; Tibor Magura; Neil Aldrin Mallari; Louise A Malone; Patrick K Malonza; Jagoba Malumbres-Olarte; Andreia Salvador; Inger E Måren; Erika Marin-Spiotta; Charles J Marsh; E J P Marshall; Eliana Martínez; Guillermo Martínez Pastur; David Moreno Mateos; Margaret M Mayfield; Vicente Mazimpaka; Jennifer L McCarthy; Kyle P McCarthy; Quinn S McFrederick; Sean McNamara; Nagore G Medina; Rafael Medina; Jose L Mena; Estefania Mico; Grzegorz Mikusinski; Jeffrey C Milder; James R Miller; Daniel R Miranda-Esquivel; Melinda L Moir; Carolina L Morales; Mary N Muchane; Muchai Muchane; Sonja Mudri-Stojnic; Nur Munira A; Antonio Muñoz-Alonso; B F Munyekenye; Robin Naidoo; A Naithani; Michiko Nakagawa; Akihiro Nakamura; Yoshihiro Nakashima; Shoji Naoe; Guiomar Nates-Parra; Dario A Navarrete Gutierrez; Luis Navarro-Iriarte; Paul K Ndang'ang'a; Eike L Neuschulz; Jacqueline T Ngai; Violaine Nicolas; Sven G Nilsson; Norbert Holstein; Olivia Norfolk; Jorge Ari Noriega; David A Norton; Nicole M Nöske; A Justin Nowakowski; Catherine Numa; Niall O'Dea; Patrick J O'Farrell; William Oduro; Sabine Oertli; Caleb Ofori-Boateng; Christopher Omamoke Oke; Vicencio Oostra; Lynne M Osgathorpe; Samuel Eduardo Otavo; Navendu V Page; Juan Paritsis; Alejandro Parra-H; Luke Parry; Guy Pe'er; Peter B Pearman; Nicolás Pelegrin; Raphaël Pélissier; Carlos A Peres; Pablo L Peri; Anna S Persson; Peta Angela Hayes; Marcell K Peters; Rohan S Pethiyagoda; Ben Phalan; T Keith Philips; Finn C Pillsbury; Jimmy Pincheira-Ulbrich; Eduardo Pineda; Joan Pino; Jaime Pizarro-Araya; A J Plumptre; Santiago L Poggio; Natalia Politi; Pere Pons; Katja Poveda; Eileen F Power; Steven J Presley; Vânia Proença; Marino Quaranta; Carolina Quintero; Romina Rader; B R Ramesh; Martha P Ramirez-Pinilla; Jai Ranganathan; Claus Rasmussen; Nicola A Redpath-Downing; J Leighton Reid; Yana T Reis; José M Rey Benayas; Juan Carlos Rey-Velasco; Chevonne Reynolds; Danilo Bandini Ribeiro; Miriam H Richards; Barbara A Richardson; Michael J Richardson; Rodrigo Macip Ríos; Richard Robinson; Carolina A Robles; Jörg Römbke; Luz Piedad Romero-Duque; Matthias Rös; Loreta Rosselli; Stephen J Rossiter; Dana S Roth; T'ai H Roulston; Laurent Rousseau; André V Rubio; Jean-Claude Ruel; Jonathan Sadler; Szabolcs Sáfián; Romeo A Saldaña-Vázquez; Katerina Sam; Ulrika Samnegård; Joana Santana; Xavier Santos; Jade Savage; Nancy A Schellhorn; Menno Schilthuizen; Ute Schmiedel; Christine B Schmitt; Nicole L Schon; Christof Schüepp; Katharina Schumann; Oliver Schweiger; Dawn M Scott; Kenneth A Scott; Jodi L Sedlock; Steven S Seefeldt; Ghazala Shahabuddin; Graeme Shannon; Douglas Sheil; Frederick H Sheldon; Eyal Shochat; Stefan J Siebert; Fernando A B Silva; Javier A Simonetti; Eleanor M Slade; Jo Smith; Allan H Smith-Pardo; Navjot S Sodhi; Eduardo J Somarriba; Ramón A Sosa; Grimaldo Soto Quiroga; Martin-Hugues St-Laurent; Brian M Starzomski; Constanti Stefanescu; Ingolf Steffan-Dewenter; Philip C Stouffer; Jane C Stout; Ayron M Strauch; Matthew J Struebig; Zhimin Su; Marcela Suarez-Rubio; Shinji Sugiura; Keith S Summerville; Yik-Hei Sung; Hari Sutrisno; Jens-Christian Svenning; Tiit Teder; Caragh G Threlfall; Anu Tiitsaar; Jacqui H Todd; Rebecca K Tonietto; Ignasi Torre; Béla Tóthmérész; Teja Tscharntke; Edgar C Turner; Jason Tylianakis; Marcio Uehara-Prado; J Nicolas Urbina-Cardona; Denis Vallan; Adam Vanbergen; Heraldo L Vasconcelos; Kiril Vassilev; Hans A F Verboven; Maria João Verdasca; José R Verdú; Carlos H Vergara; Pablo M Vergara; Jort Verhulst; Massimiliano Virgilio; Lien Van Vu; Edward M Waite; Tony R Walker; Hua-Feng Wang; Yanping Wang; James I Watling; Britta Weller; Konstans Wells; Catrin Westphal; Edward D Wiafe; Christopher Williams; Michael R Willig; John C Z Woinarski; Jan H D Wolf; Volkmar Wolters; Ben A Woodcock; Jihua Wu; Joseph M Wunderle; Yuichi Yamaura; Satoko Yoshikura; Douglas W Yu; Andrey S Zaitsev; Juliane Zeidler; Fasheng Zou; Ben Collen; Rob M Ewers; Georgina M Mace; Drew W Purves; Jorn Scharlemann; Andy Purvis
The 2016 release of the PREDICTS database V1.1
__This is an updated version of the 2016 release of the PREDICTS database. __ Data review in 2021-2023 has resulted in some changes and additions to the database. One source (consisting of three studies) has changed ID. 24 studies have an additional blocking structure that was mistakenly omitted in the original database release. Three studies have additional blocks and records, as data from additional years have been included in this extract. We recommend using this updated version of these data, rather than the original 2016 release. A dataset of 3,278,056 measurement, collated from 26,194 sampling locations in 94 countries and representing 47,089 species. The data were collated from 480 existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database was assembled as part of the [PREDICTS project](https://www.nhm.ac.uk/our-science/our-work/biodiversity/predicts.html) - Projecting Responses of Ecological Diversity In Changing Terrestrial Systems. The taxonomic identifications provided in the original data sets are those determined at the time of the original research, and so will not reflect subsequent taxonomic changes. This dataset is described in [10.1002/ece3.2579](http://dx.doi.org/10.1002/ece3.2579). A description of the way that this dataset was assembled is given in [10.1002/ece3.1303](http://dx.doi.org/10.1002/ece3.1303). * `columns.csv`: Description of data extract columns * `database.zip`: Database in zipped CSV format * `database.rds`: Database in RDS format * `sites.zip`: Site-level summaries in compressed CSV format * `sites.rds`: Site-level summaries in RDS format * `references.csv`: Data references in CSV format * `references.bib`: Data references in BibTeX format
Lawrence Hudson; Tim Newbold; Sara Contu; Samantha L L Hill; Igor Lysenko; Adriana De Palma; Helen Phillips; Tamera I Alhusseini; Felicity E Bedford; Dominic J Bennett; Hollie Booth; Victoria Burton; Wen Ting Charlotte Chng; Argyrios Choimes; David L P Correia; Julie Day; Susy Echeverría-Londoño; Susan R Emerson; Di Gao; Morgan Garon; Michelle L K Harrison; Daniel J Ingram; Martin Jung; Victoria Kemp; Lucinda Kirkpatrick; Callum Martin; Yuan Pan; Gwilym Pask-Hale; Edwin L Pynegar; Alexandra N Robinson; Katia Sanchez-Ortiz; Rebecca A Senior; Benno Simmons; Hannah J White; Hanbin Zhang; Job Aben; Stefan Abrahamczyk; Gilbert B Adum; Virginia Aguilar-Barquero; Marcelo A Aizen; Belén Albertos; E L Alcala; Maria del Mar Alguacil; Audrey Alignier; Marc Ancrenaz; Alan N Andersen; Enrique Arbeláez-Cortés; Inge Armbrecht; Víctor Arroyo-Rodríguez; Tom Aumann; Jan C Axmacher; Badrul Azhar; Adrián B Azpiroz; Lander Baeten; Adama Bakayoko; András Báldi; John E Banks; Sharad K Baral; Jos Barlow; Barbara I P Barratt; Lurdes Barrico; Paola Bartolommei; Diane M Barton; Yves Basset; Péter Batáry; Adam J Bates; Bruno Baur; Erin M Bayne; Pedro Beja; Suzan Benedick; Åke Berg; Henry Bernard; Nicholas J Berry; Dinesh Bhatt; Jake E Bicknell; Jochen H Bihn; Robin J Blake; Kadiri S Bobo; Roberto Bóçon; Teun Boekhout; Katrin Böhning-Gaese; Kevin J Bonham; Paulo A V Borges; Sérgio H Borges; Céline Boutin; Jérémy Bouyer; Cibele Bragagnolo; Jodi S Brandt; Francis Q Brearley; Isabel Brito; Vicenç Bros; Jörg Brunet; Grzegorz Buczkowski; Christopher M Buddle; Rob Bugter; Erika Buscardo; Jörn Buse; Jimmy Cabra-García; Nilton C Cáceres; Nicolette L Cagle; María Calviño-Cancela; Sydney A Cameron; Eliana M Cancello; Rut Caparrós; Pedro Cardoso; Dan Carpenter; Camila R Cassano; Tiago F Carrijo; Anelena L Carvalho; Helena Castro; Alejandro A Castro-Luna; Rolando Cerda B; Alexis Cerezo; Kim Alan Chapman; Matthieu Chauvat; Morten Christensen; Francis M Clarke; Daniel F R Cleary; Giorgio Colombo; Stuart P Connop; Michael D Craig; Leopoldo Cruz-López; Saul A Cunningham; Biagio D'Aniello; Neil D'Cruze; Pedro Giovâni da Silva; Martin Dallimer; Emmanuel Danquah; Ben Darvill; Jens Dauber; Adrian L V Davis; Jeff Dawson; Claudio de Sassi; Benoit de Thoisy; Olivier Deheuvels; Alain Dejean; Jean-Louis Devineau; Tim Diekötter; Jignasu V Dolia; Erwin Domínguez; Yamileth Dominguez-Haydar; Silvia Dorn; Isabel Draper; Niels Dreber; Bertrand Dumont; Simon G Dures; Mats Dynesius; Lars Edenius; Paul Eggleton; Felix Eigenbrod; Zoltán Elek; Martin H Entling; Karen J Esler; Ricardo F de Lima; Aisyah Faruk; Nina Farwig; Tom M Fayle; Antonio Felicioli; Annika M Felton; Roderick J Fensham; Ignacio C Fernandez; Catarina C Ferreira; Gentile F Ficetola; Cristina Fiera; Bruno K C Filgueiras; Hüseyin K Fırıncıoğlu; David Flaspohler; Andreas Floren; Steven J Fonte; Anne Fournier; Robert E Fowler; Markus Franzén; Lauchlan H Fraser; Gabriella M Fredriksson; Geraldo B Freire-Jr; Tiago L M Frizzo; Daisuke Fukuda; Dario Furlani; René Gaigher; Jörg U Ganzhorn; Karla P García; Juan C Garcia-R; Jenni G Garden; Ricardo Garilleti; Bao-Ming Ge; Benoit Gendreau-Berthiaume; Philippa J Gerard; Carla Gheler-Costa; Benjamin Gilbert; Paolo Giordani; Simonetta Giordano; Carly Golodets; Laurens G L Gomes; Rachelle K Gould; Dave Goulson; Aaron D Gove; Laurent Granjon; Ingo Grass; Claudia L Gray; James Grogan; Weibin Gu; Moisès Guardiola; Nihara R Gunawardene; Alvaro G Gutierrez; Doris L Gutiérrez-Lamus; Daniela H Haarmeyer; Mick E Hanley; Thor Hanson; Nor R Hashim; Shombe N Hassan; Richard G Hatfield; Joseph E Hawes; Matt W Hayward; Christian Hébert; Alvin J Helden; John-André Henden; Philipp Henschel; Lionel Hernández; James P Herrera; Farina Herrmann; Felix Herzog; Diego Higuera-Diaz; Branko Hilje; Hubert Höfer; Anke Hoffmann; Finbarr G Horgan; Elisabeth Hornung; Roland Horváth; Kristoffer Hylander; Paola Isaacs-Cubides; Hiroaki Ishida; Masahiro Ishitani; Carmen T Jacobs; Víctor J Jaramillo; Birgit Jauker; F Jiménez Hernández; McKenzie Johnson; Virat Jolli; Mats Jonsell; Nur Juliani S; Thomas S. Jung; Vena Kapoor; Heike Kappes; Vassiliki Kati; Eric Katovai; Klaus Kellner; Michael Kessler; Kathryn R Kirby; Andrew M Kittle; Mairi E Knight; Eva Knop; Florian Kohler; Matti Koivula; Annette Kolb; Mouhamadou Kone; Ádám Kőrösi; Jochen Krauss; Ajith Kumar; Raman Kumar; David J Kurz; Alex S Kutt; Thibault Lachat; Victoria Lantschner; Francisco Lara; Jesse R Lasky; Steven C Latta; William F Laurance; Patrick Lavelle; Violette Le Féon; Gretchen LeBuhn; Jean-Philippe Légaré; Valérie Lehouck; María V Lencinas; Pia E Lentini; Susan G Letcher; Qi Li; Simon A Litchwark; Nick Littlewood; Yunhui Liu; Nancy França Lo Man Hung; Carlos A López-Quintero; Mounir Louhaichi; Gabor L Lövei; Manuel Esteban Lucas-Borja; Victor H Luja; Matthew S Luskin; M Cristina MacSwiney G; Kaoru Maeto; Tibor Magura; Neil Aldrin Mallari; Louise A Malone; Patrick K Malonza; Jagoba Malumbres-Olarte; Andreia Salvador; Inger E Måren; Erika Marin-Spiotta; Charles J Marsh; E J P Marshall; Eliana Martínez; Guillermo Martínez Pastur; David Moreno Mateos; Margaret M Mayfield; Vicente Mazimpaka; Jennifer L McCarthy; Kyle P McCarthy; Quinn S McFrederick; Sean McNamara; Nagore G Medina; Rafael Medina; Jose L Mena; Estefania Mico; Grzegorz Mikusinski; Jeffrey C Milder; James R Miller; Daniel R Miranda-Esquivel; Melinda L Moir; Carolina L Morales; Mary N Muchane; Muchai Muchane; Sonja Mudri-Stojnic; Nur Munira A; Antonio Muñoz-Alonso; B F Munyekenye; Robin Naidoo; A Naithani; Michiko Nakagawa; Akihiro Nakamura; Yoshihiro Nakashima; Shoji Naoe; Guiomar Nates-Parra; Dario A Navarrete Gutierrez; Luis Navarro-Iriarte; Paul K Ndang'ang'a; Eike L Neuschulz; Jacqueline T Ngai; Violaine Nicolas; Sven G Nilsson; Norbert Holstein; Olivia Norfolk; Jorge Ari Noriega; David A Norton; Nicole M Nöske; A Justin Nowakowski; Catherine Numa; Niall O'Dea; Patrick J O'Farrell; William Oduro; Sabine Oertli; Caleb Ofori-Boateng; Christopher Omamoke Oke; Vicencio Oostra; Lynne M Osgathorpe; Samuel Eduardo Otavo; Navendu V Page; Juan Paritsis; Alejandro Parra-H; Luke Parry; Guy Pe'er; Peter B Pearman; Nicolás Pelegrin; Raphaël Pélissier; Carlos A Peres; Pablo L Peri; Anna S Persson; Peta Angela Hayes; Marcell K Peters; Rohan S Pethiyagoda; Ben Phalan; T Keith Philips; Finn C Pillsbury; Jimmy Pincheira-Ulbrich; Eduardo Pineda; Joan Pino; Jaime Pizarro-Araya; A J Plumptre; Santiago L Poggio; Natalia Politi; Pere Pons; Katja Poveda; Eileen F Power; Steven J Presley; Vânia Proença; Marino Quaranta; Carolina Quintero; Romina Rader; B R Ramesh; Martha P Ramirez-Pinilla; Jai Ranganathan; Claus Rasmussen; Nicola A Redpath-Downing; J Leighton Reid; Yana T Reis; José M Rey Benayas; Juan Carlos Rey-Velasco; Chevonne Reynolds; Danilo Bandini Ribeiro; Miriam H Richards; Barbara A Richardson; Michael J Richardson; Rodrigo Macip Ríos; Richard Robinson; Carolina A Robles; Jörg Römbke; Luz Piedad Romero-Duque; Matthias Rös; Loreta Rosselli; Stephen J Rossiter; Dana S Roth; T'ai H Roulston; Laurent Rousseau; André V Rubio; Jean-Claude Ruel; Jonathan Sadler; Szabolcs Sáfián; Romeo A Saldaña-Vázquez; Katerina Sam; Ulrika Samnegård; Joana Santana; Xavier Santos; Jade Savage; Nancy A Schellhorn; Menno Schilthuizen; Ute Schmiedel; Christine B Schmitt; Nicole L Schon; Christof Schüepp; Katharina Schumann; Oliver Schweiger; Dawn M Scott; Kenneth A Scott; Jodi L Sedlock; Steven S Seefeldt; Ghazala Shahabuddin; Graeme Shannon; Douglas Sheil; Frederick H Sheldon; Eyal Shochat; Stefan J Siebert; Fernando A B Silva; Javier A Simonetti; Eleanor M Slade; Jo Smith; Allan H Smith-Pardo; Navjot S Sodhi; Eduardo J Somarriba; Ramón A Sosa; Grimaldo Soto Quiroga; Martin-Hugues St-Laurent; Brian M Starzomski; Constanti Stefanescu; Ingolf Steffan-Dewenter; Philip C Stouffer; Jane C Stout; Ayron M Strauch; Matthew J Struebig; Zhimin Su; Marcela Suarez-Rubio; Shinji Sugiura; Keith S Summerville; Yik-Hei Sung; Hari Sutrisno; Jens-Christian Svenning; Tiit Teder; Caragh G Threlfall; Anu Tiitsaar; Jacqui H Todd; Rebecca K Tonietto; Ignasi Torre; Béla Tóthmérész; Teja Tscharntke; Edgar C Turner; Jason Tylianakis; Marcio Uehara-Prado; J Nicolas Urbina-Cardona; Denis Vallan; Adam Vanbergen; Heraldo L Vasconcelos; Kiril Vassilev; Hans A F Verboven; Maria João Verdasca; José R Verdú; Carlos H Vergara; Pablo M Vergara; Jort Verhulst; Massimiliano Virgilio; Lien Van Vu; Edward M Waite; Tony R Walker; Hua-Feng Wang; Yanping Wang; James I Watling; Britta Weller; Konstans Wells; Catrin Westphal; Edward D Wiafe; Christopher Williams; Michael R Willig; John C Z Woinarski; Jan H D Wolf; Volkmar Wolters; Ben A Woodcock; Jihua Wu; Joseph M Wunderle; Yuichi Yamaura; Satoko Yoshikura; Douglas W Yu; Andrey S Zaitsev; Juliane Zeidler; Fasheng Zou; Ben Collen; Rob M Ewers; Georgina M Mace; Drew W Purves; Jorn Scharlemann; Andy Purvis
Phylogeny for Cetacea excluding living taxa, containing only the species included in the analyses. The tree contains 256 taxa including those with zero length branches (ZBL)
Unexpected high taxonomic diversity in the bryozoan family Horneridae (order Cyclostomatida), with morphomolecular recognition of new species and a new genus in the southern Zealandian region
The taxonomically challenging cyclostome bryozoan family Horneridae is abundant and diverse in the waters around Aotearoa New Zealand. Using a combination of molecular and morphological approaches, we developed diagnostic characters for species of hornerids, describing eleven species (seven of which are new) in three genera (one of which is new, and one reinstated) from the seafloor around southern New Zealand between Cook Strait at ~42°S and the subantarctic islands at ~55°S. Gracilohornera n. gen. comprises five small, gracile species: the type species G. currieae, as well as G. granolineata n. sp., G. taitonga n. sp., G. retrosa n. sp. and G. tumida n. sp. The reticulate genus Retihornera is revived and includes R. squamosa and R. foliacea which are compared with the type species R. corbicula. In the genus Hornera, we describe the pinnate and palmate branching species H. girvanae n. sp., H. polaris n. sp. and H. querciformis n. sp., comparing them to Hornera robusta. In contrast to other regions, hornerid cyclostomes in Aotearoa New Zealand have flourished and diversified; indeed, many more hornerid species may await discovery in New Zealand waters.
Abigail Smith; Peter Batson; Helen Jenkins; Paul Taylor; Andrea Waeschenbach
This is a species-level pruned tree matched to the seabird list from Clements 2025 taxonomy, containing **ONLY** the 240 species we collated data from in *02-plastic-ingestion-data*. **This is the tree used in most of the analyses.** Trees come from Claramunt et al 2025: BBtree3. Available from: https://raw.githubusercontent.com/evolucionario/BigBirdTree