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.
727
datasets available to search
ShareScore release 0.9.0
Dataset results
727 results for “phylogenetic diversity”
Figure 1 in Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes)
Figure 1. Accumulation curve of the original descriptions of current valid genera of Characidae s.l. highlighting the three periods of active descriptions of genera: (i) 1777–1900, (ii) 1900–1955, and (iii) 1955–present.
Figure 5 in Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes)
Figure 5. Phylogeny of Acestrorhamphidae and subfamilies Oxybryconinae, Trochilocharacinae, Stygichthyinae, Megalamphodinae, and Stichonodontinae based on 1348 nuclear loci of ultraconserved elements (538 472 bp). Numbers near nodes represent bootstrap support.
Data from: Phylogenetic diversity reveals hidden patterns related to population source and species pools during restoration
A phylogenetic perspective of community assembly can reveal new insights into how variation within dominant species interacts with the local species pool to influence the structure of restored plant communities. Many studies have examined the effect of dominant species in structuring plant communities, but few have investigated their effect on phylogenetic diversity (PD). We established grassland in a post-agricultural field using two population sources (cultivars and local ecotypes) of three dominant grasses (Sorghastrum nutans, Andropogon gerardii and Schizachyrium scoparium) with three unique pools of subordinate species that varied in PD but not taxonomic or life-form diversity. We tested the effect of the population source treatment on two metrics of community PD (net relatedness index [NRI] and nearest taxon index [NTI]) during the first 4 years of restoration. The NRI measures the overall pairwise phylogenetic distance between all pairs of taxa in a community. By contrast, NTI measures the pairwise distance between closely related taxa in a community. Population sources had a transitory effect on community phylogenetic structure over time. Local ecotypes decreased the abundance of closely related eudicots, monocots (low +NRI and +NTI values) and volunteer species (−NTI) more than cultivars. However, population sources did not affect ecologically conservative species (i.e. species with intermediate-to-poor ecological tolerance and a high degree of fidelity to prairie habitats). Thus, cultivars might have a positive effect on community phylogenetic diversity more than local ecotypes by decreasing the abundance of a phylogenetically diverse community of less closely related volunteer species. Differences in PD of seed mixes were maintained in the community of high-fidelity species, but did not affect PD of the unsown (volunteer) species in the assembling community. Synthesis and applications. This is the first experiment to show consequences of using different seed sources on phylogenetic diversity (PD) in grassland restoration. Phylogenetics can reveal the effects of population sources on the abundance of volunteer species not evident through traditional analyses of species diversity. The PD of seed mixes or establishing communities, or other assessments of phylogenetic relationships, by restoration practitioners is recommended as a metric to allow consequences of the evolutionary patterns among species to be included in conservation planning. Increased accessibility of phylogenetic tools will allow the application of PD in restoration monitoring.
Data from: Tree phylogenetic diversity promotes host–parasitoid interactions
Evidence from grassland experiments suggests that a plant community's phylogenetic diversity (PD) is a strong predictor of ecosystem processes, even stronger than species richness per se. This has, however, never been extended to species-rich forests and host–parasitoid interactions. We used cavity-nesting Hymenoptera and their parasitoids collected in a subtropical forest as a model system to test whether hosts, parasitoids, and their interactions are influenced by tree PD and a comprehensive set of environmental variables, including tree species richness. Parasitism rate and parasitoid abundance were positively correlated with tree PD. All variables describing parasitoids decreased with elevation, and were, except parasitism rate, dependent on host abundance. Quantitative descriptors of host–parasitoid networks were independent of the environment. Our study indicates that host–parasitoid interactions in species-rich forests are related to the PD of the tree community, which influences parasitism rates through parasitoid abundance. We show that effects of tree community PD are much stronger than effects of tree species richness, can cascade to high trophic levels, and promote trophic interactions. As during habitat modification phylogenetic information is usually lost non-randomly, even species-rich habitats may not be able to continuously provide the ecosystem process parasitism if the evolutionarily most distinct plant lineages vanish.
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: 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.
FIG UR E 3 (a) Dated phylogeny of the genus Theodoxus constructed in BEAST based on COI, 16S and ATPα. Node labels denote divergence times in millions of years ago (Ma); node bars indicate the 95% credibility interval around these dates. Small squares at nodes indicate significant support of divergence events found with BEAST and other phylogenetic analyses (see Figures S2.1 and S2.2), as explained through the key. Where MOTUs (A–R) show conspecifics among a number of morphospecies, species names are given in order of their year of description. Morphospecies, incorporated from GenBank, where determination was potentially dubious are highlighted by an asterisk. Clades (C) and subclades (SC) are demarcated by dashed lines between MOTUs. (b) LTT plots indicating the build‐up of lineages in Theodoxus over geological time. Dashed lines surrounding the solid LTT lines indicate the 95% confidence intervals. Where intra‐ and interspecific diversity diverge, interspecific diversity is highlighted in blue and intraspecific diversity in red. Transitions in geological ages are highlighted by narrow grey lines, while the grey bar marks the period of pronounced glacial cycles (last 900 kyr) [Colour figure can be viewed at wileyonlinelibrary.com] in Contributions of biogeographical functions to species accumulation may change over time in refugial regions
FIG UR E 3 (a) Dated phylogeny of the genus Theodoxus constructed in BEAST based on COI, 16S and ATPα. Node labels denote divergence times in millions of years ago (Ma); node bars indicate the 95% credibility interval around these dates. Small squares at nodes indicate significant support of divergence events found with BEAST and other phylogenetic analyses (see Figures S2.1 and S2.2), as explained through the key. Where MOTUs (A–R) show conspecifics among a number of morphospecies, species names are given in order of their year of description. Morphospecies, incorporated from GenBank, where determination was potentially dubious are highlighted by an asterisk. Clades (C) and subclades (SC) are demarcated by dashed lines between MOTUs. (b) LTT plots indicating the build‐up of lineages in Theodoxus over geological time. Dashed lines surrounding the solid LTT lines indicate the 95% confidence intervals. Where intra‐ and interspecific diversity diverge, interspecific diversity is highlighted in blue and intraspecific diversity in red. Transitions in geological ages are highlighted by narrow grey lines, while the grey bar marks the period of pronounced glacial cycles (last 900 kyr) [Colour figure can be viewed at wileyonlinelibrary.com]
Island area, not isolation, drives taxonomic, phylogenetic and functional diversity of ants on land-bridge islands
<p><b>Aim:</b> To explore the impact of island area and isolation on multiple dimensions of ant biodiversity (taxonomic, phylogenetic, and functional diversity) and the underlying processes of community assembly on islands.</p> <p><b>Location:</b> Thousand Island Lake, Zhejiang, China, created by dam construction in 1959.</p> <p><b>Taxon:</b> Ants.</p> <p><b>Methods:</b> We sampled ants on 33 islands, built a species-level phylogenetic tree and measured five morphological traits of all species collected to estimate taxonomic, phylogenetic, and functional diversity. We used multiple linear regression models and null models to examine the relationships between diversity metrics and island variables (area and isolation).</p> <p><b>Results</b>: We recorded 97 ant species on the study islands. We verified positive diversity–area relationships for species richness, phylogenetic diversity, and functional diversity. However, although functional and phylogenetic community structure were indistinguishable from random communities, phylogenetic structure tended to be clustered, whereas functional structure tended to be over dispersed. Additionally, we found the structure of ant communities shifted from phylogenetic and functional clustering on smaller islands to phylogenetic and functional overdispersion on larger islands.</p> <p><b>Main conclusions:</b> Our results support the hypothesis that environmental filtering is the dominant process structuring ant communities on smaller islands, and that competitive exclusion becomes more important on larger islands. Thus, island area acts as an important filter even though ant community structure on the study islands was indistinguishable from random communities. Moreover, our results show that environmental filtering influences phylogenetic community structure of ants, whereas competitive exclusion influences functional community structure of ants. These findings highlight the need to examine both phylogenetic and functional diversity in order to understand the mechanisms that govern the assembly of natural communities on islands.</p>
Phylogenetic diversity rankings in the face of extinctions: The robustness of the fair proportion index
<p>Planning for the protection of species often involves difficult choices about which species to prioritize, given constrained resources.<br> One way of prioritizing species is to consider their "evolutionary distinctiveness'', i.e. their relative evolutionary isolation on a phylogenetic tree. Several evolutionary isolation metrics or phylogenetic diversity indices have been introduced in the literature, among them the so-called Fair Proportion index (also known as the "evolutionary distinctiveness" score). This index apportions the total diversity of a tree among all leaves, thereby providing a simple prioritization criterion for conservation. </p> <p>Here, we focus on the prioritization order obtained from the Fair Proportion index and analyze the effects of species extinction on this ranking. More precisely, we analyze the extent to which the ranking order may change when some species go extinct and the Fair Proportion index is re-computed for the remaining taxa. We show that for each phylogenetic tree, there are edge lengths such that the extinction of one leaf per cherry completely reverses the ranking. Moreover, we show that even if only the lowest ranked species goes extinct, the ranking order may drastically change. <br> We end by analyzing the effects of these two extinction scenarios (extinction of the lowest ranked species and extinction of one leaf per cherry) for a collection of empirical and simulated trees. In both cases, we can observe significant changes in the prioritization orders, highlighting the empirical relevance of our theoretical findings.</p>
Spatial phylogenetics of butterflies in relation to environmental drivers and angiosperm diversity across North America
<p>Broad-scale quantitative assessments of biodiversity and the factors shaping it remain particularly poorly explored in insects. Here, we undertook a spatial phylogenetic analysis of North American butterflies via assembly of a time-calibrated phylogeny of the region coupled with a unique, complete range assessment for ~75% of the known species. We utilized a suite of phylodiversity metrics and associated environmental data to test whether climate stability and temperature gradients have shaped North American butterfly phylogenetic diversity and endemism. We also undertook the first direct, quantitative comparisons of spatial phylogenetic patterns between butterflies and flowering plants in North America. We expected concordance between butterflies and angiosperms based on both shared historical environmental drivers and presumed strong butterfly-host plant specializations. We instead found that biodiversity patterns in butterflies are strikingly different from flowering plants in some regions of the continent. In particular, the warm desert regions of the southwestern United States and Mexico showed surprisingly high butterfly phylogenetic diversity and endemism, in contrast to much lower values for angiosperms. Butterflies did not show patterns of phylogenetic clustering as found in flowering plants, suggesting differences in habitat conservation between the two groups. Finally, we found weak relationships and spatially structured biases in relative branching timing between angiosperms and butterflies. These results suggest that shared biogeographic histories and trophic associations do not necessarily assure similar diversity outcomes. The work has applied value in conservation planning, documenting warm deserts as an important North American butterfly biodiversity hotspot.</p>
FIGURE 5. A in Morphological diversity and phylogenetic relationships within a South-American clade of iguanian lizards (Liolaemidae: Phymaturus)
FIGURE 5. A—Phymaturus laurenti (MCN 2841). Character 172-0 subdigtal lamellae of fifth toe with smooth surfaces with inconspicuous keels. B—P. antofagastensis FML 1861 (Character 172-1) subdigital lamellae of fifth toe strongly keeled (four to six keels). Scales= 3 mm. C—Corneal surface of parietal eye translucent, P. dorsimaculatus 1569 (character 174-0). Scales= 2 mm. D—Parietal eye with white opaque coloration conspicuous under corneal surface, P. palluma MCN 3131 (character 174- 1). E—Second chinshields widely separated one from the other, P. palluma MCN 3131 (character 177-0). Scales= 5 mm. F— Contact in the midline of second chinshields, P. dorsimaculatusMCN 1569 (character 177-1).
FIGURE 7. A in Morphological diversity and phylogenetic relationships within a South-American clade of iguanian lizards (Liolaemidae: Phymaturus)
FIGURE 7. A—Ossified secondary coracoid fenestra, Phymaturus mallimaccii MCN 1484 (character 56-0).Scale= 3 mm. B— Incomplete rings in the distal third of trachea of P. antofagastensis FML 1861-11 (character 37, continuous character). Scale= 1 mm. C—Scleral ossicles of P. patagonicus MCN 1285 (character 183-1). Scale= 1 mm. D—Lower jaw of Phymaturus extrilidus MCN 2666 exhibiting Meckel´s groove opened (character 192-0) and P. indistinctus MCN 686 with dentary enclosing Meckel´s groove. (character 192-1). Scale= 2 mm. E—Absence of a ceratohyal process in P. extrilidus MCN 2665 (character 186-0). F—With a conspicuous ceratohyal process in P. indistinctus MCN 686 (character 186-2).Scales= 1 mm.
FIGURE 4. A in Morphological diversity and phylogenetic relationships within a South-American clade of iguanian lizards (Liolaemidae: Phymaturus)
FIGURE 4. A—Black "eye" in the center of scapular spot in a male of Phymaturus querque (character 140-1). Scale= 10 mm. B—P. excelsus (MCN 1386). Character 164-1 three to seven enlarged scales on the anterior margin of auditive meatus. C— Dorsal view of P. etheridgei´s head (MCN 3110). Character 165-1 enlarged scales on the anterior border of auditory meatus situated perpendicular to temporal scales. D—Posterior supralabials enlarged and projected over oral commissure P. sp.1 MCN 2107(Character 169-1).Scale= 2 mm. E—Internasal region convex, P. antofagastensis MCN 1436 (character 168-0). Scale= 2 mm. F—Internasal region concave, P. etheridgei MCN 3109 (Character 168-1). Scale= 2 mm.
FIGURE 2 in Morphological diversity and phylogenetic relationships within a South-American clade of iguanian lizards (Liolaemidae: Phymaturus)
FIGURE 2. Morphological diversity found among species of the lizard genus Phymaturus. A—Main sources of discrete characters (75%) used in this study for analyzing phylogenetic relationships within Phymaturus. B—Frequency distribution of different types of continuous characters. For more detail see text.
FIGURE 8. A in Morphological diversity and phylogenetic relationships within a South-American clade of iguanian lizards (Liolaemidae: Phymaturus)
FIGURE 8. A—Unicusped premaxillary teeth in Phymaturus laurenti MCN 318 (character 191-0). B—Tricuspid premaxillary teeth in P. laurenti MCN 321 (character 191-1). Example of a binary polymorphic character. Scales= 0.5 mm. C—Fenestra hipoischial present in P. laurenti MCN 326 (character 196-1). Scale= 3 mm. D—Multiple sternal fenestra, and four sternal ribs in P. antofagastensis FML 2019-13 (characters 195-1 and 204-1). Scale= 3 mm. E—Processus dorsalis of premaxilla projected beyond the level of anterior margins of nasals in P. sp.8 MCN 2817 (character 201-0), Scale= 2 mm. F—Processus dorsalis of premaxilla shorter not reaching that level in P. sp1 MCN 2708 (character 201-1), Scale= 2 mm.
FIGURE 13 in Morphological diversity and phylogenetic relationships within a South-American clade of iguanian lizards (Liolaemidae: Phymaturus)
FIGURE 13. Historical biogeographic hypothesis of palluma and patagonicus groups and subclades based on K3 topology showing the proposed pattern of vicariance processes that gave rise of actual diversity and speciation in Phymaturus.
FIGURE 1 in Morphological diversity and phylogenetic relationships within a South-American clade of iguanian lizards (Liolaemidae: Phymaturus)
FIGURE 1. Distribution of Phymaturus. Light blue: patagonicus group (17 spp.); orange: palluma group (15 spp. and 9 unnamed populations).
FIGURE 6. A in Morphological diversity and phylogenetic relationships within a South-American clade of iguanian lizards (Liolaemidae: Phymaturus)
FIGURE 6. A—Number of dorsal ocelli between hind limbs and shoulders, Phymaturus spectabilis MCN 1207 (character 129-2) and the same character in P. payuniae MCN 2878 (character 129-1). Scale= 10 mm. Color in life of males of three species of P. of the puna subclade: B—P. laurenti; Character 132-1 males with yellow as dorsal background colour; Character 138 scapular spot absent; Character 159-0 vertebral stripe absent; Character 171-1 dorsal melanism of neck incomplete. C—P. sp.8; Character 159-1 vertebral stripe present (light gray); Character 138-1 scapular spot present; Character 171-1 dorsal melanism of neck incomplete; Character 178-1 dorsum and flanks with oxidum ferric coloration. D—P.sp.9. Character 138-0 absence of scapular spot; Character 159-2 vertebral stripe present (dark gray); Character 171-0 dorsal melanism of neck complete. Scales= 20 mm.
FIGURE 12 in Morphological diversity and phylogenetic relationships within a South-American clade of iguanian lizards (Liolaemidae: Phymaturus)
FIGURE 12. Comparison of topologies recovered by Espinoza et al. (2004), Morando (2004) and the one obtained in this study analyzing DNA data only (7 terminals) with our morphological or/and total evidence analysis (same K3 tree- fig. 9).
FIGURE 11 in Morphological diversity and phylogenetic relationships within a South-American clade of iguanian lizards (Liolaemidae: Phymaturus)
FIGURE 11. Alternative hypotheses of relationships within the palluma group found applying different values of constant of weighting K.
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.