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.
5,864
datasets available to search
ShareScore release 0.9.0
Dataset results
5,864 results for “species diversity”
Data from: Cryptic species diversity reveals biogeographic support for the 'mountain passes are higher in the tropics' hypothesis
The 'mountain passes are higher in the tropics' (MPHT) hypothesis posits that reduced climate variability at low latitudes should select for narrower thermal tolerances, lower dispersal and smaller elevational ranges compared with higher latitudes. These latitudinal differences could increase species richness at low latitudes, but that increase may be largely cryptic, because physiological and dispersal traits isolating populations might not correspond to morphological differences. Yet previous tests of the MPHT hypothesis have not addressed cryptic diversity. We use integrative taxonomy, combining morphology (6136 specimens) and DNA barcoding (1832 specimens) to compare the species richness, cryptic diversity and elevational ranges of mayflies (Ephemeroptera) in the Rocky Mountains (Colorado; approx. 40°N) and the Andes (Ecuador; approx. 0°). We find higher species richness and smaller elevational ranges in Ecuador than Colorado, but only after quantifying and accounting for cryptic diversity. The opposite pattern is found when comparing diversity based on morphology alone, underscoring the importance of uncovering cryptic species to understand global biodiversity patterns.
Data from: Molecular phylogenetics, species diversity, and biogeography of the Andean lizards Proctoporus (Squamata: Gymnophthalmidae)
The family Gymnophthalmidae comprises ca. 220 described species of Neotropical lizards distributed from southern Mexico to Argentina. It includes 36 genera, among them Proctoporus, which contains six currently recognized species occurring across the yungas forests and wet montane grasslands of the Amazonian versant of the Andes from central Peru to central Bolivia. Here, we investigate the phylogenetic relationships and species limits of Proctoporus and closely related taxa by analyzing 2121 base pairs of mitochondrial (12S, 16S, and ND4) and nuclear (c-mos) genes. Our taxon sampling of 92 terminals includes all currently recognized species of Proctoporus and 15 additional species representing the most closely related groups to the genus. Maximum parsimony, maximum likelihood and Bayesian phylogenetic analyses recovered a congruent, fully resolved, and strongly supported hypothesis of relationships that challenges previous phylogenetic hypotheses and classifications, and biogeographic scenarios. Our main results are: (i) discovery of a strongly supported clade that includes all species of Proctoporus and within which are nested the monotypic Opipeuter xestus (a genus that we consider a junior synonym of Proctoporus), and two species of Euspondylus, that are therefore transferred to Proctoporus; (ii) the paraphyly of Proctoporus bolivianus with respect to P. subsolanus, which is proposed as a junior synonym of P. bolivianus; (iii) the detection of seven divergent and reciprocally monophyletic lineages (five of them previously assigned to P. bolivianus) that are considered confirmed candidate species, which implies that more candidate species are awaiting formal description and naming than currently recognized species in the genus; (iv) rejection of the hypothesis that Proctoporus diversified following a south to north pattern parallel to the elevation of the Andes; (v) species diversity in Proctoporus is the result of in situ diversification through vicariance in the grasslands of the high Andes, with at least five dispersals contributing to montane forest species.
Data from: Standing genetic diversity and selection at functional gene loci are associated with differential invasion success in two non-native fish species
Invasive species are expected to experience a unique combination of high genetic drift due to demographic factors while also experiencing strong selective pressures. The paradigm that reduced genetic diversity should limit the evolutionary potential of invasive species and thus their potential for range expansion has received little empirical support, possibly due to the choice of genetic markers. Our goal was to test for effects of genetic drift and selection at functional genetic markers as they relate to the invasion success of two paired invasive goby species, one widespread (successful) and one with limited range expansion (less successful). We genotyped fish using two marker types: single nucleotide polymorphisms (SNPs) in known-function, protein-coding genes and microsatellites to contrast the effects of neutral genetic processes. We identified reduced allelic variation in the invaded range for the less-successful tubenose goby. SNPs putatively under selection were responsible for the observed differences in population structure between marker types for round goby (successful) but not tubenose goby (less successful). A higher proportion of functional loci experienced divergent selection for round goby, suggesting increased evolutionary potential in invaded ranges may be associated with round goby's greater invasion success. Genes involved in thermal tolerance were divergent for round goby populations but not tubenose goby, consistent with the hypothesis that invasion success for fish in temperate regions is influenced by capacity for thermal tolerance. Our results highlight the need to incorporate functional genetic markers in studies to better assess evolutionary potential for the improved conservation and management of species.
FIGURE 3. 50 in Species diversity and phylogeny of the deep-sea genus Pseudomma (Crustacea: Mysida)
FIGURE 3. 50% consensus tree from maximum parsimony analysis based on 57 conventional characters treated as unordered. Circled numbers above nodes are bootstrap values>50%. Numbers below nodes indicate majority rules percentages. Numbers in italics are decay indexes for congruent nodes from a separate maximum parsimony analysis based on the 204 GFC subcharacters.
FIGURE 2 in Species diversity and phylogeny of the deep-sea genus Pseudomma (Crustacea: Mysida)
FIGURE 2. Pseudomma morphology of characters used in the phylogenetic analyses. A, 1st maxilliped; B, P. roseum, detail of cusps on nail; C, P. truncatum, detail of dactylus' medial setae; D, 1st male pleopod; E, 4th male pleopod; F, 4th female pleopod; G, uropod; H, telson. Prop = propodus, Dac = dactylus, Endo = endopod, Exo = exopod.
FIGURE 4 in Species diversity and phylogeny of the deep-sea genus Pseudomma (Crustacea: Mysida)
FIGURE 4. Most parsimonious tree from analysis based on 57 conventional characters treated as ordered. Circled numbers above nodes indicate bootstrap values>50%. Open values below nodes are decay indexes for the conventional characters. Numbers in italics are decay indexes for congruent nodes from a separate maximum parsimony analysis based on the 204 GFC subcharacters.
FIGURE 1 in Species diversity and phylogeny of the deep-sea genus Pseudomma (Crustacea: Mysida)
FIGURE 1. Pseudomma morphology of characters used in the phylogenetic analyses. A, ocular plate; B, P. truncatum, antenna; C, P. belgicae, mandibles; D, mandible palp; E, P. belgicae, medial view of mandible palp; F, P. belgicae, lateral view of mandible palp; G, maxillule; H, P. frigidum, cuspidate setae on maxillule basis; I, P. truncatum, teeth arming posterior rim of basis; J, maxilla; K, P. frigidum, detail of coxal endites dorsal surface.
Data from: Environmental factors influence both abundance and genetic diversity in a widespread bird species
Genetic diversity is one of the key evolutionary variables that correlate with population size, being of critical importance for population viability and the persistence of species. Genetic diversity can also have important ecological consequences within populations, and in turn, ecological factors may drive patterns of genetic diversity. However, the relationship between the genetic diversity of a population and how this interacts with ecological processes has so far only been investigated in a few studies. Here, we investigate the link between ecological factors, local population size, and allelic diversity, using a field study of a common bird species, the house sparrow (Passer domesticus). We studied sparrows outside the breeding season in a confined small valley dominated by dispersed farms and small-scale agriculture in southern France. Population surveys at 36 locations revealed that sparrows were more abundant in locations with high food availability. We then captured and genotyped 891 house sparrows at 10 microsatellite loci from a subset of these locations (N = 12). Population genetic analyses revealed weak genetic structure, where each locality represented a distinct substructure within the study area. We found that food availability was the main factor among others tested to influence the genetic structure between locations. These results suggest that ecological factors can have strong impacts on both population size per se and intrapopulation genetic variation even at a small scale. On a more general level, our data indicate that a patchy environment and low dispersal rate can result in fine-scale patterns of genetic diversity. Given the importance of genetic diversity for population viability, combining ecological and genetic data can help to identify factors limiting population size and determine the conservation potential of populations.
Data from: Species pool functional diversity plays a hidden role in generating β-diversity
Functional trait diversity is used as a way to infer mechanistic processes that drive community assembly. While functional diversity within communities is often viewed as a response variable, here we present and test a framework for how functional diversity among taxa in the regional species pool drive the assembly of communities among habitats. We predicted that species pool functional diversity should work with environmental heterogeneity to drive β-diversity. We tested these predictions by modeling empirical patterns in invertebrate communities from 570 streams in 52 watersheds. Our analysis of the field data provided strong support for the inclusion of both functional diversity and environmental heterogeneity in the models, and our predictions were supported when the community was analyzed all together. However, analyses within individual functional feeding guilds revealed strong context dependency in the relative importance of functional diversity, γ-richness, and environmental heterogeneity on β-diversity. We interpret the results to mean that functional diversity can play an important role in driving β-diversity; however, within guilds the nature of interspecific interactions and species pool size complicate the relationship. Future research should test this conceptual model across different ecosystems and in experimental settings using metacommunity mecocosms to enhance our understanding the role that functional variation plays in generating spatial biodiversity patterns.
Data from: Global patterns in helminth host specificity: phylogenetic and functional diversity of regional host species pools matter
Host specificity has a major influence on a parasite's ability to shift between human and animal host species. Yet there is a dearth of quantitative approaches to explore variation in host specificity across biogeographical scales, particularly in response to the varying community compositions of potential hosts. We built a global dataset of intermediate host associations for nine of the world's most widespread helminth parasites (all of which infect humans). Using hierarchical models, we asked if realised parasite host specificity varied in response to regional variation in the phylogenetic and functional diversities of potential host species. Parasites were recorded in 4-10 zoogeographical regions, with some showing considerable geographical variation in observed versus expected host specificity. Parasites generally exhibited the lowest phylogenetic host specificity in regions with the greatest variation in prospective host phylogenetic diversity, namely the Neotropical, Saharo-Arabian and Australian regions. Globally, we uncovered notable variation in parasite host shifting potential. Observed host assemblages for Hydatigera taeniaeformis and Hymenolepis diminuta were less phylogenetically diverse than expected, suggesting limited potential to spillover into unrelated hosts. Host assemblages for Echinococcus granulosus, Mesocestoides lineatus and Trichinella spiralis were less functionally diverse than expected, suggesting limited potential to shift across host ecological niches. By contrast, Hydatigera taeniaeformis infected a higher functional diversity of hosts than expected, indicating strong potential to shift across hosts with different ecological niches. We show that the realised phylogenetic and functional diversities of infected hosts are determined by biogeographical gradients in prospective host species pools. These findings emphasise the need to account for underlying species diversity when assessing parasite host specificity. Our framework to identify variation in realised host specificity is broadly applicable to other host-parasite systems and will provide key insights into parasite invasion potential at regional and global scales.
Data from: Revisiting comparisons of genetic diversity in stable and declining species: assessing genome-wide polymorphism in North American bumble bees using RAD sequencing
Genetic variation is of key importance for a species' evolutionary potential, and its estimation is a major component of conservation studies. New DNA sequencing technologies have enabled the analysis of large portions of the genome in nonmodel species, promising highly accurate estimates of such population genetic parameters. Restriction site-associated DNA sequencing (RADseq) is used to analyse thousands of variants in the bumble bee species Bombus impatiens, which is common, and Bombus pensylvanicus, which is in decline. Previous microsatellite-based analyses have shown that gene diversity is lower in the declining B. pensylvanicus than in B. impatiens. RADseq nucleotide diversities appear much more similar in the two species. Both species exhibit allele frequencies consistent with historical population expansions. Differences in diversity observed at microsatellites thus do not appear to have arisen from long-term differences in population size and are either recent in origin or may result from mutational processes. Additional research is needed to explain these discrepancies and to investigate the best ways to integrate next-generation sequencing data and more traditional molecular markers in studies of genetic diversity.
FIGURE 10 in Diversity of Manota Williston (Diptera: Mycetophilidae) in a Malaysian rainforest: description of twenty-seven new sympatric species
FIGURE 10. Apical part of gonostylus, dorsal view. A. Manota procera sp. n. (holotype). B. Manota calcarata sp. n. (paratype). C. Manota transversa sp. n. (holotype). Scale 0.05 mm.
FIGURE 17 in Diversity of Manota Williston (Diptera: Mycetophilidae) in a Malaysian rainforest: description of twenty-seven new sympatric species
FIGURE 17. Manota plusiochaeta sp. n. (A, C, D paratypes; B holotype). A. Flagellomere 4. B. Hypopygium, ventral view. C. Hypopygium, dorsal view. D. Apical part of gonocoxa, dorsal view. Scale for A 0.05 mm; for B, C, and D 0.10 mm.
FIGURE 6. Antennal flagellomere 4 in Diversity of Manota Williston (Diptera: Mycetophilidae) in a Malaysian rainforest: description of twenty-seven new sympatric species
FIGURE 6. Antennal flagellomere 4, lateral view (A, D); hypopygium, dorsal view (B, F) and ventral view (E); and gonostylus, dorsal view (C). A, B, C. Manota biloba sp. n. (holotype). D, E, F. Manota heptacantha sp. n. (D, F paratype; E holotype). Scale for A and D 0.05 mm; for B, C, E, and F 0.10 mm.
FIGURE 9. Antennal flagellomere 4 in Diversity of Manota Williston (Diptera: Mycetophilidae) in a Malaysian rainforest: description of twenty-seven new sympatric species
FIGURE 9. Antennal flagellomere 4, lateral view (A and C); hypopygium, ventral (B and D) and dorsal view (E). A, B. Manota procera sp. n. (holotype). C, D, E. Manota transversa sp. n. (holotype). Scale for A and D 0.05 mm; for B, C, E, and F 0.10 mm.
FIGURE 13. Antennal flagellomere 4 in Diversity of Manota Williston (Diptera: Mycetophilidae) in a Malaysian rainforest: description of twenty-seven new sympatric species
FIGURE 13. Antennal flagellomere 4, lateral view (A, C); hypopygium, dorsal (B, E) and ventral view (D). A, B. Manota globigera sp. n. (holotype). C, D, E. Manota curvata sp. n. (D holotype, E paratype). Scale for A and C 0.05 mm; for B, D, and E 0.10 mm.
FIGURE 1 in Diversity of Manota Williston (Diptera: Mycetophilidae) in a Malaysian rainforest: description of twenty-seven new sympatric species
FIGURE 1. Left palp, dorsal view (A); apical part of palpomere 3, lateral view (B, C, D); and apical part of tibia 1 with basal part of tarsomere 1, prolateral view (E). A, C. Manota heptacantha sp. n (paratypes). B. Manota pappi sp. n. (paratype). D. Manota spadix sp. n. (paratype). E. Manota angustata sp. n. (paratype). Scale 0.1 mm. 1 = palpomere 1, 2 = palpomere 2, 3 = palpomere 3, 4 = palpomere 4, 5 = palpomere 5, 6 = sensory pit, 7 = curved sensillum, 8 = bluntended sensillum, 9 = seta, 10 = parasegment.
FIGURE 8. Antennal flagellomere 4 in Diversity of Manota Williston (Diptera: Mycetophilidae) in a Malaysian rainforest: description of twenty-seven new sympatric species
FIGURE 8. Antennal flagellomere 4, lateral view (A, D); hypopygium, ventral (B and E) and dorsal view (C and F). A, B, C. Manota clausa sp. n. (A, B holotype; C paratype). D, E, F. Manota calcarata sp. n. (D, E holotype; F paratype). Scale for A and D 0.05 mm; for B, C, E, and F 0.10 mm.
FIGURE 12. Antennal flagellomere 4 in Diversity of Manota Williston (Diptera: Mycetophilidae) in a Malaysian rainforest: description of twenty-seven new sympatric species
FIGURE 12. Antennal flagellomere 4, lateral view (A, C); hypopygium, ventral (B, D) and dorsal view (E). A, B. Manota fera sp. n. (holotype). C, D, E. Manota ferrata sp. n. (C, D holotype; E paratype). Scale for A and C 0.05 mm; for B, D, and E 0.10 mm.
FIGURE 3. Antennal flagellomere 4 in Diversity of Manota Williston (Diptera: Mycetophilidae) in a Malaysian rainforest: description of twenty-seven new sympatric species
FIGURE 3. Antennal flagellomere 4, lateral view (A, C); hypopygium ventral (B) and dorsal (C) view; and cerci, dorsal view (E). A, B. Manota spadix sp. n. (holotype). C, D, E. Manota roslii sp. n. (holotype). Scale for A and C 0.05 mm; for B, D, and E 0.10 mm. For abbreviations, see under Material and methods.
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.