Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
549
datasets available to search
ShareScore release 0.9.0
Dataset results
549 results for “species extinction”
Molecular and Taxonomic Reevaluation of the Digitaria filiformis Complex (Poaceae) including a Globally Extinct, Single Site Endemic from New Hampshire, USA, and a New Species from Mexico
<p>We examine the <em>Digitaria filiformis </em>complex, to determine the proper taxonomic rank and rarity of each taxon. The taxonomy of the <em>D. filiformis </em>complex is highly debated and includes two widespread species, <em>D. filiformis </em>and <em>D. villosa</em>; a possibly extinct species endemic to a single-site in New Hampshire, <em>D. laeviglumis</em>; and a rare species of southern Florida and the West Indies, <em>D.</em><em> dolichophylla. </em>We conducted morphologic comparisons and molecular analysis of the four members of the <em>D. filiformis</em> complex, together with specimens from Mexico and Venezuela purportedly identified as <em>D. laeviglumis</em> (morphology only). Based on results of phylogenetic analyses of plastid and nuclear ITS sequences and morphologic comparisons, we recognize five species in the <em>D. filiformis </em>complex, including a newly described Mexican endemic <em>D. glabrifloris. </em>After field investigation we have moved the global rank of <em>D. laeviglumis </em>from globally historical (GH) to extinct (GX), as there is virtually no likelihood of rediscovery. <em>Digitaria</em><em> dolichophylla </em>is much rarer than previously recognized, moving from secure (T5) to imperiled with extinction (G2).</p>
Species diversity and extinction risk of vertebrate pollinators in India
<p>This repository includes the data compiled and used for the study of <strong>‘Species diversity and extinction risk of vertebrate</strong><br><strong>pollinators in India’</strong>. If you use these data, please cite them along with our manuscript:</p> <blockquote> <p>Kallivalappil R., Grattarola F., de Alwis Pitts D., Cotter S.C. & Pincheira-Donoso D. (2024). Species diversity and extinction risk of vertebrate<br>pollinators in India. <em>Biodiversity and Conservation</em>. https://doi.org/10.1007/s10531-024-02848-3</p> </blockquote> <p> </p> <h2>Abstract</h2> <p>Animal pollinators underpin the functioning and persistence of ecosystems globally. However, the vital role of pollination is being progressively eroded by the worldwide decline of pollinator species caused by human-induced environmental degradation, resulting in rising costs to biodiversity, agriculture, and economy. Most studies quantifying pollinator diversity and declines have focused on insects, whereas vertebrate pollinators remain comparatively neglected. Here, we<br>present the first comprehensive study quantifying the macroecological patterns of species richness and extinction risk of bird and mammal pollinators in India, a region of extremely high biodiversity and increasing anthropogenic pressure. Our results reveal that hotspots of mammal pollinator diversity are restricted to the south of the Western Ghats, whereas bird pollinator diversity hotspots are scattered throughout the country. Analyses of hotspots of threatened species<br>(based on the IUCN Red List) show that only mammal pollinators are currently classified as threatened in India, whereas multiple hotspots of population declines were observed for birds, and primarily in the Southwest for mammal pollinators. Our analyses failed to identify a role for species traits as drivers of these patterns, whereas most pollinators appear to be threatened by agriculture, logging and hunting for food, and medicinal purposes. Pollinator endangerment has widescale<br>ecological and economic implications such as reduced food production, plant extinction, loss of functional and genetic diversity, and economic damage. We suggest protection of vertebrate pollinators should be emphasised in active conservation agendas in India.</p> <p> </p> <h2>Files</h2> <h3>Spatial</h3> <ul> <li><code>india.gpkg</code></li> <li><code>birds.gpkg</code></li> <li><code>mammals.gpkg</code></li> <li><code>how_to_read_gpkg_data.R</code></li> </ul> <h3>Phylogenetic</h3> <ul> <li><code>PGLS_phylogeny_birds.nex</code></li> <li><code>PGLS_phylogeny_mammals.nex</code></li> </ul> <h3>Tables</h3> <ul> <li><code>all_bird_traits.csv</code></li> <li><code>all_mammals_traits.csv</code></li> <li><code>threatened_mammals_traits.csv</code></li> <li><code>plant_pollinator_dataset.csv</code></li> <li><code>pollinator_plant_dataset.csv</code></li> <li><code>references.txt</code></li> </ul>
Chromosomal-level genome assembly of the scimitar‐horned oryx: insights into diversity and demography of a species extinct in the wild
<p>Captive populations provide a valuable insurance against extinctions in the wild. However, they are also vulnerable to the negative impacts of inbreeding, selection and drift. Genetic information is therefore considered a critical aspect of conservation management. Recent developments in sequencing technologies have the potential to improve the outcomes of management programmes; however, the transfer of these approaches to applied conservation has been slow. The scimitar‐horned oryx (<i>Oryx dammah)</i> is a North African antelope that has been extinct in the wild since the early 1980s and is the focus of a large‐scale and long‐term reintroduction project. To enable the selection of suitable founder individuals, facilitate post‐release monitoring and improve captive breeding management, comprehensive genomic resources are required. Here, we used 10X Chromium sequencing together with Hi‐C contact mapping to develop a chromosomal‐level genome assembly for the species. The resulting assembly contained 29 chromosomes with a scaffold N50 of 100.4 Mb, and displayed strong chromosomal synteny with the cattle genome. Using resequencing data from six additional individuals, we demonstrated relatively high genetic diversity in the scimitar‐horned oryx compared to other mammals, despite it having experienced a strong founding event in captivity. Additionally, the level of diversity across populations varied according to management strategy. Finally, we uncovered a dynamic demographic history that coincided with periods of climate variation during the Pleistocene. Overall, our study provides a clear example of how genomic data can uncover valuable insights into captive populations and contributes important resources to guide future management decisions of an endangered species.</p>
FIGURE 6 in A new and presumably extinct species of Ptychochromoides (Teleostei: Perciformes: Cichlidae) from central Madagascar
FIGURE 6. Ptychochromoides vondrozo, holotype, UMMZ 235297, adult female, 182.0 mm SL; Madagascar: Fianarantsoa Province: Ramanara River. Right side illustrated due to distortion of specimen (image reversed). Photograph by Heok Hee Ng.
FIGURE 4 in A new and presumably extinct species of Ptychochromoides (Teleostei: Perciformes: Cichlidae) from central Madagascar
FIGURE 4. Ptychochromoides betsileanus, lectotype, BMNH 1882.2.25: 69, adult male, 159.6 mm SL; Madagascar: Betsileo region. Right side illustrated due to damage to left side (image reversed).
Fig. 22 in The Extinct Fauna of Stingless Bees (Hymenoptera: Apidae: Meliponini) in Dominican Amber: Two New Species and Redescription of the Male of Proplebeia dominicana (Wille and Chandler)
Fig. 22. Photomicrographs of Proplebeia vetusta, sp. n., worker, paratype, AMNHDR141440. Scale = 1.0 mm.
Fig. 21 in The Extinct Fauna of Stingless Bees (Hymenoptera: Apidae: Meliponini) in Dominican Amber: Two New Species and Redescription of the Male of Proplebeia dominicana (Wille and Chandler)
Fig. 21. Photomicrograph of Proplebeia tantilla, sp. n., male, holotype, AMNHDR141439. Scale = 1.0 mm.
Fig. 20 in The Extinct Fauna of Stingless Bees (Hymenoptera: Apidae: Meliponini) in Dominican Amber: Two New Species and Redescription of the Male of Proplebeia dominicana (Wille and Chandler)
Fig. 20. Proplebeia tantilla, sp. n., holotype, male, AMNHDR141439, detail of pregenital sterna and genitalia, ventral view.
Figs. 15–19 in The Extinct Fauna of Stingless Bees (Hymenoptera: Apidae: Meliponini) in Dominican Amber: Two New Species and Redescription of the Male of Proplebeia dominicana (Wille and Chandler)
Figs. 15–19. Proplebeia tantilla, sp. n. 15–17. holotype, male, AMNHDR141439, head, forewing, and tibia and tarsus III. 18, 19. paratype, worker, same amber piece, fragments of tibia and tarsus III, detail of rastellum, and mandible, detail of denticles.
Figs. 8–10 in The Extinct Fauna of Stingless Bees (Hymenoptera: Apidae: Meliponini) in Dominican Amber: Two New Species and Redescription of the Male of Proplebeia dominicana (Wille and Chandler)
Figs. 8–10. Forewing, worker; 8. Proplebeia vetusta, sp.n., holotype, specimen, AMNHDR14854; 9. Proplebeia dominicana, specimen AMNHDR141175; 10. Proplebeia tantilla, sp. n., paratype, specimen AMNHDR14911. Scale = 1.0 mm.
Figs. 6, 7 in The Extinct Fauna of Stingless Bees (Hymenoptera: Apidae: Meliponini) in Dominican Amber: Two New Species and Redescription of the Male of Proplebeia dominicana (Wille and Chandler)
Figs. 6, 7. Proplebeia dominicana, genitalia of male, posterior view and profile, specimen AMNHDR14954; S5–S7 = 5th–7th metasomal sterna, respectively. Scale = 1.0 mm.
Figs. 3, 4. Proplebeia dominicana, tibia III. 3 in The Extinct Fauna of Stingless Bees (Hymenoptera: Apidae: Meliponini) in Dominican Amber: Two New Species and Redescription of the Male of Proplebeia dominicana (Wille and Chandler)
Figs. 3, 4. Proplebeia dominicana, tibia III. 3. outer surface, specimen AMNHDR141179; 4. inner surface, detail of the keirotrichiate area and rastellum, specimen AMNHDR141175. Scale = 1.0 mm.
Figs. 11–13 in The Extinct Fauna of Stingless Bees (Hymenoptera: Apidae: Meliponini) in Dominican Amber: Two New Species and Redescription of the Male of Proplebeia dominicana (Wille and Chandler)
Figs. 11–13. Proplebeia vetusta, sp. n., holotype, AMNHDR141481, head, detail of mandible, tibia and tarsus III, detail of penicillum and rastellum. Minor scale bar = 1.0 mm (fig. 11), large scale bar = 1.0 mm (figs. 12–13).
How to render species comparable taxonomic units through deep time: A case study on intraspecific osteological variability in extant and extinct lacertid lizards
<p>Generally, the species is considered to be the only naturally occurring taxon. However, species recognized and defined using different species delimitation criteria cannot readily be compared, impacting studies of biodiversity through Deep Time. This comparability issue is particularly marked when comparing extant with extinct species because the only available data for species delimitation in fossils are derived from their preserved morphology, which is generally restricted to osteology in vertebrates. Here, we quantify intraspecific, intrageneric, and intergeneric osteological variability in extant species of lacertid lizards using pairwise dissimilarity scores based on a data set of 253 discrete osteological characters for 99 specimens referred to 24 species. Variability is always significantly lower intraspecifically than between individuals belonging to distinct species of a single genus, which is in turn significantly lower than intergeneric variability. Average values of intraspecific variability and associated standard deviations are consistent (with few exceptions), with an overall average within a species of 0.208 changes per character scored. Application of the same methods to six extinct lacertid species (represented by 40 fossil specimens) revealed that intraspecific osteological variability is inconsistent, which can at least in part be attributed to different researchers having unequal expectations of the skeletal dissimilarity within species units. Such a divergent interpretation of intraspecific and interspecific variability among extant and extinct species reinforces the incomparability of the species unit. Lacertidae is an example where extant species recognized and defined based on a number of delimitation criteria show comparable and consistent intraspecific osteological variability. Here, as well as in equivalent cases, application of those skeletal dissimilarity values to paleontological species delimitation potentially provides a way to ameliorate inconsistencies created by the use of morphology to define species.</p>
Figures 1–10. Termitodius species dorsal habitus and lateral pronotum. 1–2 in Extinct or extant? A new species of Termitodius Wasmann, 1894, (Coleoptera: Scarabaeidae: Aphodiinae: Rhyparini) with a short review of the genus
Figures 1–10. Termitodius species dorsal habitus and lateral pronotum. 1–2) T. coronatus, cotype. 3–4) T. araujoi. 5–6) T. chaki, paratype. 7–8) T. woodruffi, copal paratype. 9–10) T. woodruffi, holotype.
Figures 17–25 in Extinct or extant? A new species of Termitodius Wasmann, 1894, (Coleoptera: Scarabaeidae: Aphodiinae: Rhyparini) with a short review of the genus
Figures 17–25. Images of Termitodius and host. 17) T. woodruffi, paratype, cut open in copal processing, note genitalia inside body (arrow). After photographing, genitalia removed for study. 18–19) T. araujoi male genitalia, caudal and lateral view. 20–21) T. woodruffi male genitalia of paratype in Fig. 17, caudal and lateral view. 22) T. woodruffi with worker host termite. 23) Soldier termite with T. woodruffi. 24–25) T. woodruffi, individual paratypes.
Figures 27–32. Some smaller copal pieces containing T in Extinct or extant? A new species of Termitodius Wasmann, 1894, (Coleoptera: Scarabaeidae: Aphodiinae: Rhyparini) with a short review of the genus
Figures 27–32. Some smaller copal pieces containing T. woodruffi paratypes, host termites and other inclusions. 27) CMNC. 28) REWC. 29–30) CEMT. Scale line = 1 mm. 31) IAvH-E. 32) FSCA (ex. RLBC), arrow indicates male with genitalia extracted, see Fig. 17. Photos for Figures 29–30 by Vinícius Costa-Silva (CEMT).
Figures 11–16 in Extinct or extant? A new species of Termitodius Wasmann, 1894, (Coleoptera: Scarabaeidae: Aphodiinae: Rhyparini) with a short review of the genus
Figures 11–16. Termitodius woodruffi, recent specimen, holotype. 11) Dorsal habitus. 12) Ventral habitus. 13) Lateral habitus. 14) Elytra apex, caudal view. 15) Head, anterior view. 16) Labels.
Monitoring demography of resurrected populations of locally extinct and extant species to investigate drivers of species loss
<p>Extinctions are predicted to rise by an order of magnitude over the next century. Although contemporary documented extinctions are uncommon, local extirpations likely provide hints about global extinction risks. Comparing responses to global change of locally extinct versus extant species pairs in a phylogenetic framework could highlight why certain species are more vulnerable to extinction than others and which anthropogenic changes are most relevant to their decline. As anthropogenic changes likely interact to affect population declines, demographic studies partitioning the effects of multifactorial stressors are needed but remain rare. I examine demographic responses to nitrogen addition and deer herbivory, two major drivers of species losses in grasslands, in experimental reintroductions of fourteen locally extinct and extant confamilial native plants from Michigan prairies. Nitrogen consistently reduces survival, especially in locally extinct species, and growth of locally extinct species benefits less from nitrogen than growth of extant species. Nitrogen reduces population growth rates, largely via reductions in survival. Deer herbivory, meanwhile, had inconsistent effects on vital rates among species and did not affect population growth. Nitrogen and herbivory rarely interacted to affect vital rates. These results link community-level patterns of species loss under nitrogen addition to the population-level processes underlying those losses.</p>
Fig. 4 in A New Species Of The Extinct Ant Genus Electromyrmex (Hymenoptera, Formicidae)
Fig. 4. Electromyrmex wheeleri sp. n., line drawing of holotype male based on photo, body in lateral view.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.