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 12 in Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae)
FIGURE 12. Male genital structures of S. tarascum sp.n. holotype (A–C); S. planum (D–F); S. macrophallicum paratype #234 (G–I); and S. minimum (J–L). For all taxa left squares show epiphallus (I) and ectophallus (II) in dorsal view, and endophallus in lateral view (III); meddle squares show ectophallus in posterior view; and right squares show a close up of ectophallus in lateral view (Scale bars = 1mm).
FIGURE 14 in Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae)
FIGURE 14. Type specimens of S. rugosum: lectotype m (A) and paralectotype f (B); S. barrettii: lectotype m (C); S. borrei: lectotype m (D) and paralectotype f (E); S. bruneri lectotype m (F) and paralectotype f (G); S. variabile: holotype m (H) (Scale bars = 1cm).
FIGURE 2 in Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae)
FIGURE 2. Bayesian phylogeny of Sphenarium based on a concatenated analysis of 2527 nucleotide positions from five loci and 145 terminals (129 ingroup and 16 outgroup terminals). Higher-level phylogenetic relationships are shown on left-top box and ingroup relationships are magnified outside. Voucher and locality identifier numbers of the analysed specimens are indicated in bold characters in terminals names, except for those cases in which genetic information was retrieved from the GenBank. Different branch colours highlight the three mayor clades within the genus (brown, Clade 1; red, Clade 2; and purple, Clade 3). Different colours of the Sphenarium terminals represent the 17 taxa identified during the morphologic analysis. Black circles behind the nodes indicate PP values ± 95%. For some important nodes we also showed the PP values in bold numbers. Black bottom bars in all cases are equal to 0.03 substitutions per site.
FIGURE 10 in Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae)
FIGURE 10. Male genital structures of S. purpurascens: morphotype 1 (A–C), morphotype 2 (D–F), morphotype 3 (G–I); and S. zapotecum sp.n. holotype (J–l). For all taxa left squares show epiphallus (I) and ectophallus (II) in dorsal view, and endophallus in lateral view (III); meddle squares show ectophallus in posterior view; and right squares show a close up of ectophallus in lateral view (Scale bars = 1mm).
FIGURE 4 in Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae)
FIGURE 4. External morphologic characters of Sphenarium and Prosphena: antennae filiform (A) or weakly ensiform (B); head subtriangular-compresed (C), subtriangular-elongated (D) or conical (E, F); tegmina spatula-like (G), strap-like (H) or tongue-like (I); subgenital plate of males tapered (J) or rounded moderately (K) or notably (L) developed posteriorly; dorsal ovipositor valves rounded (M), moderately lanceolate (N) or notably elongated (O).
FIGURE 7 in Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae)
FIGURE 7. Geographic distribution of Sphenarium species. Numbers within parenthesis in front of taxa names indicate the number of identified morphotype within the species. White surrounded areas and upper case abbreviations denote the Mexican biogeographic provinces. AC, Altos de Chiapas; AL, Altiplano Sur; BRB, Balsas River Basin; GMC, Gulf of Mexico Coast; MVB, Mexican Volcanic Belt; PC, Pacific Coast; SMOC, Sierra Madre Occidental; SMOR, Sierra Madre Oriental; SMS, Sierra Madre Sur; SO, Soconusco; and SOX, Sierra de Oaxaca.
FIGURE 11 in Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae)
FIGURE 11. Bayesian phylogeny of Sphenarium species based on CO1 sequences of Pedraza-Lara et al. (2015) and this study. The analysis was conducted using the substitution model estimated previously and under the same conditions above specified for the concatenated phylogenetic analysis in methods section. Terminals of different colours represent the 17 recognized species in this study. Black dots behind the nodes indicate PP values greater than 95%. Black bottom bars are equal to 0.04 substitutions per site.
FIGURE 3 in Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae)
FIGURE 3. Species phylogeny and approximate divergence times between Sphenarium lineages. The consensus tree is shown in dark grey; whereas other possible trees are denoted in light grey. Numbers behind the nodes indicate their PP values (left numbers in bold) and mean divergence time (Ma) (right numbers in italics). Empty bars in the middle of the nodes indicate the 95% HDP interval values for the divergence time estimations.
FIGURE 9 in Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae)
FIGURE 9. External morphology of S. purpurascens: morphotype 1 m (A) and f (B), morphotype 2 m (C) and f (D), and morphotype 3 m (E) and f (F); S. zapotecum sp.n. holotype m (G) and paratype f #23 (H); S. tarascum sp.n. holotype m (I) and paratype f #2 (J,); S. planum m (K) and f (L); S. macrophallicum paratype m #230 (M) and f (N); S. minimum m (O) and f (P); S. infernalis sp.n. holotype m (Q) and paratype f #2 (R); S. rugosum morphotype 1 m (S) and f (T) (Scale bars = 1cm).
FIGURE 1 in Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae)
FIGURE 1. Sampled localities (bold numbers in map) for the genetic analysis and geographic distribution of the identified morphologic taxa in Sphenarium (different symbols) in Mexico. Numbers within parenthesis in front of taxon names indicate the different morphotypes identified within the respective taxa. White surrounded areas and upper case abbreviations denote the Mexican biogeographic provinces. AC, Altos de Chiapas; AL, Altiplano Sur; BRB, Balsas River Basin; GMC, Gulf of Mexico Coast; MVB, Mexican Volcanic Belt; PC, Pacific Coast; SMOC, Sierra Madre Occidental; SMOR, Sierra Madre Oriental; SMS, Sierra Madre Sur; SO, Soconusco; and SOX, Sierra de Oaxaca.
FIGURE 6 in Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae)
FIGURE 6. General colour traits of Sphenarium grasshoppers: T1, fastigium; T2, lateral postocular bands; T3, longitudinal lines of eyes; T4, dorsomedial line; T5, dorsal shades; T6, lateral shades: T7, lateral bands of blotches; T8, lateral light blotches of the 1st abdominal segment; T9 ventral bands of pronotum; T10, lateral carinas of pronotum; T11, mesonotum; T12, lateral segments of mesonotum and metanotum; T13, upper medial area of hind femora hind femora; T14, lower medial area of hind femora hind femora; T15, lower marginal area of hind femora hind femora; T16, knees of hind femora; and T17 hind tibia.
FIGURE 5 in Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae)
FIGURE 5. Male genitalia of Sphenarium: epiphallus in dorsal view (A); ectophallus in dorsal (B), lateral (C) and posterior (D) view; and endophallus in lateral (E) and dorsal (F) view. A, appendix of epiphallus; AC, apodemal plate of cingulum; AP, anterior projection of epiphallus; AS, aedeagal sclerites; ASA, apical spine of aedeagus; AV, aedeagal valve; B, bridge of epiphallus; BAS, base of aedeagal sclerites; BC, basal thickening of cingulum; BE, basal emargination of cingulum; CM, central membrane; CV, cingulum valve; DI, dorsal inflection of endophallic apodeme; EA, endophallic apodeme; ISR, inflection of supraramus; L, lophus of epiphallus; LBR, lateral borders of ramus of cingulum; LP, lateral plate of epiphallus; PZ, pseudoarch of ectophallus; RC, ramus of cingulum; S, sheath of ectophallus; SS, spermatophore sac; SZ, suprazygomal plate of cingulum; VC, ventral cleft of cingulum; VI, ventral inflection of endophallic apodeme; VMA, ventral margins of aedeagal valves; VP, ventral process of cingulum; VTC, ventral transverse thickening of cingulum; Z, zygoma of cingulum; I, length of bridge of epiphallus; II, length of lateral plate of epiphallus; III, interspace between apodemal plates of cingulum; IV, width of base of aedeagal sclerites; V, length of dorsal inflections of endophallus; VI, length of aedeagal sclerites and valves together (from the tip of aedeagus to the base of aedeagal sclerites).
FIGURE 8 in Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae)
FIGURE 8. Type specimens of S. purpurascens: lectotype m (A) and paralectotype f (B); S. planum: lectotype m (C) and paralectotype f (D); S. macrophallicum: holotype m (E) and allotype f (F); S. minimum lectotype m (G); S. affine lecototype m (H) (Scale bars = 1cm).
Phylogenetically under‐dispersed gut microbiomes are not correlated with host genomic heterozygosity in a genetically diverse reptile community
<p>We are providing semi-processed datasets relevant to the paper "Phylogenetically under-dispersed gut microbiomes across a range of host genetic diversity in a reptile community point to structuring by conserved host genes." Specifically, we include VCF files of RADseq data from host individuals, which are processed versions of the raw reads available at NCBI's Short Read Archive under PRJA744273. These data were processed for heterozygosity calculation using an adapted of the pipeline presented in Singhal et al. 2017, "Genetic diversity is largely unpredictable but scales with museum occurrences in a species-rich clade of Australian lizards."</p> <p>In addition, we include a database of 16S sequences from gut microbiome amplicon sequencing from the same host animals. The raw reads are available at NCBI's Short Read Archive under PRJNA746253. The sequences accessioned here are a curated, cleaned set of reference reads to which we realigned reads from each individual host.</p>
FIGURE 1 in Moss diversity: A molecular phylogenetic analysis of genera
FIGURE 1. The optimal maximum likelihood tree of the combined rps4/nad5/nuc26S data set under the general timereversible model with site rate variation (GTR+I+Γ: -ln likelihood = 54575.7; optimal parameters: A/C = 1.1166, A/G = 5.0600, A/T = 0.2165, C/G = 1.0611, C/T = 5.6457, G/T =1(fixed); f(A) = 0.3360, f(C) = 0.1836, f(G) = 0.1781, f(T) = 0.3027; α = 0.5730; pinvar = 0.3410). Nodes support by>95% posterior probability are highlighted. Taxonomic labels are applied to clades at the lowest rank applicable to the clade following the classification of Buck and Goffinet (2000): A) acrocarpous mosses - the two exemplars marked with an asterisk were originally labeled Hymenostylium recurvirostre and Pottia truncata and subsequently identified as Ceratodon purpureus, B) pleurocarpous mosses - part 1, C) pleurocarpous mosses - part 2.
Fig. 3 in Genomics Reveals Exceptional Phylogenetic Diversity Within a Narrow-Range Flightless Insect
Fig. 3. Phylogenetic reconstruction reveals three well-supported Zelandoperla maungatuaensis clades. (a) Bayesian maximum likelihood consensus phylogeny illustrating the relationships among Z. maungatuaensis lineages based on the mitochondrial COI gene. Posterior probability values are noted above each node. Outgroups (Zelandoperla agnetis and Zelandoperla denticulata) are excluded for diagrammatic clarity. (b) Midpoint rooted maximum likelihood phylogeny illustrating genome-wide relationships among Z. maungatuaensis lineages, based on 10,429 SNP markers. IQTREE ultrafast bootstrap values ≥ 90 are indicated at each node.
Fig. 2 in Genomics Reveals Exceptional Phylogenetic Diversity Within a Narrow-Range Flightless Insect
Fig. 2. Striking genetic substructuring across the narrow geographic range of Zelandoperla maungatuaensis. (a) Collection localities (coloured circles) for Z. maungatuaensis across the Maungatua range.White crosses indicate sites where Z. maungatuaensis has not been found. (b) Principal component analysis, based on 10,429 genome-wide SNPs, illustrating the genetic differentiation among Northern, Southern, and Central Z. maungatuaensis lineages.
Fig. 1. A in Genomics Reveals Exceptional Phylogenetic Diversity Within a Narrow-Range Flightless Insect
Fig. 1. A portion of southeastern South Island, illustrating the topographic isolation of the Maungatua Range, where the flightless stonefly Zelandoperla maungatuaensis (inset) is found.
Dataset and code for the manuscript "Plant indirect interactions reduce species richness but increase phylogenetic diversity"
<p>This Zenodo repository contains the original data set and code for replicating the result published in the paper "<strong>Plant indirect interactions reduce species richness but increase phylogenetic diversity</strong>"</p><p> </p><ol><li>The "BD.xlsx" data frame contains the original data. The first column, "ID," is an ID for each one of the patches (i.e., vegetation units containing one or more individuals for the same or different species separated from other patches by bare ground). The second and third columns, "localidad" and "suelo", inform about the location where patches are found. The "species" column identifies the different species present at each patch.</li><li> The "Comb1.xlsx" data frame contains the possible combination of 4 species for each ID (concatenation of "localidad" and "suelo") for all the species found in the sampling. Besides "ID", there is one column for each of the species included in interactions ("spA", "spB", "spC", "spD") that contains the name of the species.</li><li>The "phylo.xlsx" data frame contains the taxonomic information of the species found during the sampling. For each species recorded in column "species" we assign its genus (column "genus") and family (column "family")</li><li> "ALL_IN.xlsx" is a data frame containing for each "ID" (proxy of location), the species involved in interactions ("spA", "spB", "spC" & "spD"), the "interaction sign" indicating if a given interaction is positive or negative (results based on simulation) and "Order" indicating the number of species involved in the interactions(from two to four).</li><li>"Code.R" provides the R code necessary to obtain the results. As statistics is based on simulation, every run can provide slightly different results, although differences do not affect interpretation. Please note that running time can be elevated depending on the computer used.</li></ol><p> </p>
Supplementary material 1 from: Gioria M, Carta A, Balogianni V, Fornara D, Pyšek P, Osborne BA (2023) Changes in the functional and phylogenetic diversity of above- and below-ground plant communities invaded by two alien herbs. NeoBiota 88: 75-101. https://doi.org/10.3897/neobiota.88.109185
Species lists, list of traits, and results of Bayesian phylogenetic generalized linear mixed models of species richness and abundance data in the vegetation and the soil seed bank
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.