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.
501
datasets available to search
ShareScore release 0.7.1
Dataset results
501 results for “Phylogenetic tree”
Data from: Phylogenetic tree shape and the structure of mutualistic networks
Species community composition is known to alter the network of interactions between two trophic levels, potentially affecting its functioning (e.g. plant pollination success) and the stability of communities. Phylogenies vary in shape with regard to the rate of evolutionary change across a tree (influencing tree balance) and variation in the timing of branching events (affecting the distribution of node ages in trees), both of which may influence the structure of species interaction networks. Because related species are likely to share many of the traits that regulate interactions, the shape of phylogenetic trees may provide some insights into the distribution of traits within communities, and hence the likelihood of interaction among species. However, little attention has been paid to the potential effects of changes in phylogenetic diversity (PD) on interaction networks. Phylogenetic diversity is influenced by species diversity within a community, but also how distantly-related the constituent species are from one another. Here, we evaluate the relationship between two important measures of phylogenetic diversity (tree shape and age of nodes) and the structure of plant-pollinator interaction networks using empirical and simulated data. Whereas the former allows us to evaluate patterns in real communities, the latter allows us to evaluate more systematically the relationship between tree shape and network structure under three different models of trait evolution. In empirical networks, less balanced plant phylogenies were associated with lower connectance in interaction networks indicating that communities with the descendants of recent radiations are more diverged and specialized in their partnerships. In simulations, tree balance and the distribution of nodes through time were included in the best models for modularity, and the second best models for connectance and nestedness. In models assuming random evolutionary change through time (i.e., Brownian motion), less balanced trees and trees with nodes near the tips exhibited greater modularity, whereas in models with an early burst of radiation followed by relative stasis (i.e. early-burst models) more balanced trees and trees with nodes near roots had greater modularity. Synthesis: Overall, these results suggest that the shape of phylogenies can influence the structure of plant-pollinator interaction networks. However, the mismatch between simulations and empirical data indicate that no simple model of trait evolution mimics that observed in real communities.
Data from: The local-clock permutation test: a simple test to compare rates of molecular evolution on phylogenetic trees
Rates of molecular evolution vary substantially between lineages, and a growing research effort is directed at uncovering the causes and consequences of this variation. Comparing local-clocks (rates of molecular evolution estimated from sets of branches of a phylogenetic tree) is a common tool in this research effort. Here, I show that a commonly used test (the Likelihood Ratio Test, LRT) will not be statistically valid for comparing local-clocks in most cases. Instead, I propose the local-clock permutation test (LCPT), a simple test which can be used to test the significance of differences between local-clocks. The LCPT could also be used to test for differences between any parameter that can be assigned to individual branches on a phylogenetic tree. Using simulated data, I show that the LCPT has good power to detect differences between local-clocks.
Concatenated DNA matrix and BEAST tree used for phylogenetic, dating, biogeographic and diversification analyses of Caribbean Podocarpus
<p><b>Aim </b>The Progression Rule, that older lineages inhabit older islands and colonize newer ones as they emerge, has seldom been tested in the Caribbean due to its geological complexity. Here we use the conifer genus <i>Podocarpus</i> to explore this hypothesis. We infer the evolutionary history, biogeography, and diversification rates of this genus under a hypothesis testing framework.</p> <p><b>Location</b> The Caribbean archipelago (Antilles)</p> <p><b>Methods</b> We present the most comprehensive sampling for Caribbean <i>Podocarpus</i> to date in a Bayesian dated phylogenetic tree using a genotyping by sequencing DNA matrix of 67,589 bp. We inferred ancestral ranges and inter-island divergence patterns using several models available. We explored diversification rates associated with island colonization, and checked for diversification rate shifts in the phylogeny.</p> <p><b>Results</b> Caribbean <i>Podocarpus</i> is the result of colonization from the Andes during the Eocene to Oligocene (ca. 45-31 Ma). Lesser Antillean species originated during the Oligocene from the Andes or the Greater Antilles, depending on the model of choice. Vicariance can explain the divergence of Cuban and Hispaniolan species, with subsequent dispersals into Jamaica. Despite the availability of new habitat opportunities, which might promote cladogenesis, insular <i>Podocarpus</i> did not show higher diversification rates than continental taxa.</p> <p><b>Main</b> <b>conclusions </b>The conditions for progression rule were not met because colonization of younger islands (Lesser Antilles) occurred from the continent, or because suitable habitat in the partially emerged younger islands was likely present at the time older islands (Greater Antilles) were colonized. An improved paleogeographic knowledge of the Caribbean will allow testing this hypothesis in multiple lineages. Our finding that diversification rates did not increase with island colonization might be common in other Caribbean lineages. Genotyping by sequencing proved promising to reveal complex historical assembly processes of vicariance and dispersal at a fine phylogenetic scale.</p> <p> </p>
Figure 13 in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle
Figure 13. Amphibioplana onnisi. Schematic horizontal reconstruction of the copulatory apparatus.
Figure 9. A phylogenetic tree shows the genetic relationship between the C. sphaerospermum isolate 9 in Morphological and molecular identification of Cladosporium sphaerospermum isolates collected from tomato plant residues
Figure 9. A phylogenetic tree shows the genetic relationship between the C. sphaerospermum isolate 9 investigated in this study as indicated by red dote (●), and the C. sphaerospermum isolates available in NCBI.
Fig. 3. A neighbor-joining phylogenetic tree reconstructed from a in Report of two unrecorded yeast species in the class Tremellomycetes
Fig. 3. A neighbor-joining phylogenetic tree reconstructed from a comparative analysis of 26S rRNA gene sequences showing the relationships of strain DJ2-14-10C with closely related species. Bootstrap values (>70%) based on neighbor-joining methods are shown at the branch nodes. Bar, 0.01 substitutions per nucleotide position (Trees, 1987).
FIGURE 6. Phylogenetic tree for I in Redescription, molecular features, and neotype deposition of Rhipicephalus pusillus Gil Collado and Ixodes ventalloi Gil Collado (Acari, Ixodidae)
FIGURE 6. Phylogenetic tree for I. ventalloi based on 16S rDNA.
FIGURE 3. Phylogenetic tree for R in Redescription, molecular features, and neotype deposition of Rhipicephalus pusillus Gil Collado and Ixodes ventalloi Gil Collado (Acari, Ixodidae)
FIGURE 3. Phylogenetic tree for R. pusillus based on 16S rDNA.
Figures 5-6 from: Yang H-M, Sluys R, Kawakatsu M, Min G-S (2018) New molecular sequences for two genera of marine planarians facilitate determination of their position in the phylogenetic tree, with new records for two species (Platyhelminthes, Tricladida, Maricola). ZooKeys 781: 1-17. https://doi.org/10.3897/zookeys.778.26324
Figures 5-6 Paucumaratrigonocephala. 5ZMA V.Pl. 7279.1, microphotograph of sagittal section of the copulatory apparatus; anterior to the left 6 Dorsal view of live specimen from Lake Hi-numa, Japan. Scale bar not available.
Figures 10-11 from: Yang H-M, Sluys R, Kawakatsu M, Min G-S (2018) New molecular sequences for two genera of marine planarians facilitate determination of their position in the phylogenetic tree, with new records for two species (Platyhelminthes, Tricladida, Maricola). ZooKeys 781: 1-17. https://doi.org/10.3897/zookeys.778.26324
Figures 10-11 Obrimoposthiawandeli. 10 NIBRIV0000813547, microphotograph of sagittal section of the copulatory apparatus; anterior to the left 11ZMA V.Pl. 951.5, microphotograph of transverse section through the bursal canal and gonopore.
Figure 1 from: Yang H-M, Sluys R, Kawakatsu M, Min G-S (2018) New molecular sequences for two genera of marine planarians facilitate determination of their position in the phylogenetic tree, with new records for two species (Platyhelminthes, Tricladida, Maricola). ZooKeys 781: 1-17. https://doi.org/10.3897/zookeys.778.26324
Figure 1 Maximum-likelihood tree based on 18S ribosomal DNA sequences. Numbers on nodes represent support values for Maximum-Likelihood (bootstrap –BO) and Bayesian Inference (posterior probability – PP): BO/PP. Scale bar indicates number of nucleotide substitutions per site.
Figures 2-3 from: Yang H-M, Sluys R, Kawakatsu M, Min G-S (2018) New molecular sequences for two genera of marine planarians facilitate determination of their position in the phylogenetic tree, with new records for two species (Platyhelminthes, Tricladida, Maricola). ZooKeys 781: 1-17. https://doi.org/10.3897/zookeys.778.26324
Figures 2-3 Paucumaratrigonocephala. 2 Dorsal view of live specimen from South Korea. Scale bar not available 3ZMA V.Pl. 7279.1, microphotograph of eye lens; anterior to the left.
Figure 9 from: Yang H-M, Sluys R, Kawakatsu M, Min G-S (2018) New molecular sequences for two genera of marine planarians facilitate determination of their position in the phylogenetic tree, with new records for two species (Platyhelminthes, Tricladida, Maricola). ZooKeys 781: 1-17. https://doi.org/10.3897/zookeys.778.26324
Figure 9 Obrimoposthiawandeli. NIBRIV0000813547, sagittal reconstruction of the copulatory apparatus; anterior to the left.
Figures 7-8 from: Yang H-M, Sluys R, Kawakatsu M, Min G-S (2018) New molecular sequences for two genera of marine planarians facilitate determination of their position in the phylogenetic tree, with new records for two species (Platyhelminthes, Tricladida, Maricola). ZooKeys 781: 1-17. https://doi.org/10.3897/zookeys.778.26324
Figures 7-8 Obrimoposthiawandeli. 7 Dorsal view of preserved specimen from King George Island. Scale bar not available 8 NIBRIV0000813547, microphotograph of sagittal section of penis papilla; anterior to the left.
Figures 12-13 from: Yang H-M, Sluys R, Kawakatsu M, Min G-S (2018) New molecular sequences for two genera of marine planarians facilitate determination of their position in the phylogenetic tree, with new records for two species (Platyhelminthes, Tricladida, Maricola). ZooKeys 781: 1-17. https://doi.org/10.3897/zookeys.778.26324
Figures 12-13 Obrimoposthiawandeli. 12 MZUPL 00290-A163, microphotograph of sagittal section of copulatory apparatus of holotype of Procerodessanderi; anterior to the left 13 MZU PL. 00291(nos. A788-821), sagittal reconstruction of the copulatory apparatus of presumed specimen of Procerodessanderi.
Figure 4 from: Yang H-M, Sluys R, Kawakatsu M, Min G-S (2018) New molecular sequences for two genera of marine planarians facilitate determination of their position in the phylogenetic tree, with new records for two species (Platyhelminthes, Tricladida, Maricola). ZooKeys 781: 1-17. https://doi.org/10.3897/zookeys.778.26324
Figure 4 Paucumaratrigonocephala. ZMA V.Pl. 7279.1, sagittal reconstruction of the copulatory apparatus; anterior to left.
Fig. 5. Phylogenetic tree including Ornithodoros huajianensis n in Ornithodoros (Ornithodoros) huajianensis sp. nov. (Acari, argasidae), a new tick species from the Mongolian marmot (Marmota bobak sibirica), Gansu province in China
Fig. 5. Phylogenetic tree including Ornithodoros huajianensis n. sp. and other selected species of Ixodes based on 16S rDNA. The alignment was produced using Clustal X and the tree was inferred by means of the MP method with 500 replicates of random addition. The species Otobius megnini was used as outgroup. The Bayesian support (posterior probability) values are derived from 1,000,000 replicates.
Fig. 2. Mid-point phylogenetic trees using SAG3 in Toxoplasma gondii infection in Amami spiny rat on Amami-Oshima Island, Japan
Fig. 2. Mid-point phylogenetic trees using SAG3 (A), GRA6 (B), and ROP18 (C) sequences of Toxoplasma gondii detected from the Amami spiny rat specimen and the references available in the public databases. *, type I strain; **, type II strain; ***, type III strain; ****, atypical strain. Bars represents the number of nucleotide substitutions per site.
Figure 8. Phylogenetic tree for 12S in New insight into the systematic position of the endemic Madagascan genus Amberiana (Hemiptera: Heteroptera: Dinidoridae) using 12S rDNA sequences
Figure 8. Phylogenetic tree for 12S rDNA sequences of 28 species used in this study generated by using the neighbor-joining method. Bootstrap support is indicated at nodes; the frame shows the clade consisting of Amberiana montana and Sehirus luctuosus.
Figure 2. A neighbour-joining tree using 604 cytochrome c oxidase subunit I in Phylogenetic relationship among slender loris species (Primates, Lorisidae: Loris) in Sri Lanka based on mtDNA CO1 barcoding
Figure 2. A neighbour-joining tree using 604 cytochrome c oxidase subunit I (CO1) sequences from 7 different slender loris (Loris) taxas found in Sri Lanka with their external appearance.
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.