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.
21
datasets available to search
ShareScore release 0.9.0
Dataset results
21 results for “phylogenetic dispersion”
Cryptic species can be phylogenetically old despite strong sex-biased dispersal
Open the record for dataset details and reuse information.
Molecular phylogenetic analyses reveal multiple long-distance dispersal events and extensive cryptic speciation in Nervilia (Orchidaceae), an isolated basal Epidendroid genus
Open the record for dataset details and reuse information.
Data from: Avoiding impacts of phylogenetic tip-state-errors on dispersal and extirpation rates in alpine plant biogeography
Open the record for dataset details and reuse information.
Environment filtering and dispersal limitation jointly shaped the taxonomic and phylogenetic beta diversity of natural forests in southern China
Open the record for dataset details and reuse information.
How did subterranean amphipods cross the Adriatic Sea? Phylogenetic evidence for the dispersal-vicariance interplay mediated by marine regression-transgression cycles
Open the record for dataset details and reuse information.
Tropical niche conservatism and dispersal limitation jointly determine taxonomic and phylogenetic β-diversities of Odonata in Eastern China
Open the record for dataset details and reuse information.
Data from: Quantifying species contributions to ecosystem processes: a global assessment of functional trait and phylogenetic metrics across avian seed-dispersal networks
Quantifying the role of biodiversity in ecosystems not only requires understanding the links between species and the ecological functions and services they provide, but also how these factors relate to measurable indices, such as functional traits and phylogenetic diversity. However, these relationships remain poorly understood, especially for heterotrophic organisms within complex ecological networks. Here, we assemble data on avian traits across a global sample of mutualistic plant–frugivore networks to critically assess how the functional roles of frugivores are associated with their intrinsic traits, as well as their evolutionary and functional distinctiveness. We find strong evidence for niche complementarity, with phenotypically and phylogenetically distinct birds interacting with more unique sets of plants. However, interaction strengths—the number of plant species dependent on a frugivore—were unrelated to evolutionary or functional distinctiveness, largely because distinct frugivores tend to be locally rare, and thus have fewer connections across the network. Instead, interaction strengths were better predicted by intrinsic traits, including body size, gape width and dietary specialization. Our analysis provides general support for the use of traits in quantifying species ecological functions, but also highlights the need to go beyond simple metrics of functional or phylogenetic diversity to consider the multiple pathways through which traits may determine ecological processes.
Data from: Bayesian phylogenetic estimation of clade ages supports trans-atlantic dispersal of cichlid fishes
Divergence-time estimation based on molecular phylogenies and the fossil record has provided insights into fundamental questions of evolutionary biology. In Bayesian node dating, phylogenies are commonly time calibrated through the specification of calibration densities on nodes representing clades with known fossil occurrences. Unfortunately, the optimal shape of these calibration densities is usually unknown and they are therefore often chosen arbitrarily, which directly impacts the reliability of the resulting age estimates. As possible solutions to this problem, two non-exclusive alternative approaches have recently been developed, the "fossilized birth-death" model and "total-evidence dating". While these approaches have been shown to perform well under certain conditions, they require including all (or a random subset) of the fossils of each clade in the analysis, rather than just relying on the oldest fossils of clades. In addition, both approaches assume that fossil records of different clades in the phylogeny are all the product of the same underlying fossil sampling rate, even though this rate has been shown to differ strongly between higher-level taxa. We here develop a flexible new approach to Bayesian age estimation that combines advantages of node dating and the fossilized birth-death model. In our new approach, calibration densities are defined on the basis of first fossil occurrences and sampling rate estimates that can be specified separately for all clades. We verify our approach with a large number of simulated datasets, and compare its performance to that of the fossilized birth-death model. We find that our approach produces reliable age estimates that are robust to model violation, on par with the fossilized birth-death model. By applying our approach to a large dataset including sequence data from over 1000 species of teleost fishes as well as 147 carefully selected fossil constraints, we recover a timeline of teleost diversification that is incompatible with previously assumed vicariant divergences of freshwater fishes. Our results instead provide strong evidence for trans-oceanic dispersal of cichlids and other groups of teleost fishes.
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 2. Phylogenetic relationships among Viverra tangalunga inferred from mtDNA haplotypes from the concatenated 797 in The distribution of the Malay civet Viverra tangalunga (Carnivora: Viverridae) across Southeast Asia: natural or human-mediated dispersal?
Figure 2. Phylogenetic relationships among Viverra tangalunga inferred from mtDNA haplotypes from the concatenated 797-bp mitochondrial control region and cytochrome b sequences. Trees for each of the three analyses (neighbour joining, maximum likelihood, and Bayesian inference) had similar topologies. Numbers above the branches represent bootstrap support, with only values> 60% shown. Numbers in parentheses represent the number of individuals sharing the same haplotype; haplotype codes are listed in Appendix S3.
A global analysis of mosses reveals low phylogenetic endemism and highlights the importance of long-distance dispersal
<p><span><span><span><span><span><span><span><span><span><span><span><u>Aim:</u> </span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>Digitization of herbarium specimens and DNA sequencing efforts in the past decade have enabled integrative analyses of patterns of diversity and endemism in a phylogenetic context. Here, we compare the best available floristic databases to a comprehensive specimen database to examine spatial patterns of moss phylogenetic assembly. We test the hypotheses that 1) mosses exhibit phylogenetic regionalization, 2) islands contain significantly high phylogenetic diversity, and 3) that moss phylogenetic endemism is low on a global scale.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><u>Location:</u> </span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>Global</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><u>Taxon:</u> </span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>Mosses</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><u>Methods:</u> </span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>We developed a phylogeny of 3,654 moss species using 25 markers and compiled a global specimen database from online repositories. We calculated floristic and phylogenetic measures of diversity and endemism and performed randomizations to test for significant deviations from expectations. We use rarefaction and extrapolation to alleviate substantial differences in sampling effort across the globe. We used both phylogenetic and floristic methods to test for spatial regionalization. We compare our specimen-based results to those obtained using a floristic dataset. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><u>Results:</u></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span> Phylogenetic diversity is more robust to missing data than species richness. Mean phylogenetic distance was significantly higher than expected in areas with high species richness, indicating that reported richness in these areas is likely a product of repeated colonization. Phylogenetic endemism is low globally. Phylogenetic regionalizations cluster into a Holarctic/Holantarctic temperate region, a pantropical region, and a region composed of Australia, New Zealand, and South Africa.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><u>Main Conclusions:</u></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span> Future efforts for collecting, sequencing, and databasing moss species should focus on the tropics, particularly Africa and Southeast Asia. We provide further evidence to support several important theories developed in moss biogeography, including the role of long-distance dispersal in shaping floristic patterns, the dominance of anagenesis in driving patterns of island diversity, and the role of climatic instability in driving patterns of assembly in the Holarctic.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: The influence of historical dispersal on the phylogenetic structure of tree communities in the tropical Andes
We test for evidence of the Tropical Niche Conservatism or the Out of The Tropics hypotheses in structuring patterns of tree community composition along a 2000+ meter elevational gradient in the northern tropical Andes. By collecting and integrating data on the presence-absence of tree species within plots with phylogenetic information, we analyzed: 1) patterns of phylogenetic dispersion and species diversity along the elevational gradient based on indexes of net relatedness, nearest taxon relatedness, and species richness (α-diversity); and 2) the replacement of lineages along the gradient using the PhyloSorensen metric (β-diversity). More specifically, we established 20 0.25-ha permanent tree inventory plots between 750 and 2802 m asl where all individuals with Diameter at Breast Height (DBH) ≥ 10 cm were measured and identified. We then used a series of linear models to test for changes in α and β diversity between plots in relation to elevation. Neither the net relatedness index nor the nearest taxon index showed a significant relationship with elevation. However, there was greater phylogenetic over-dispersion at intermediate elevations; this likely reflects the mixing of species with contrasting origins from tropical and temperate lineages. β-diversity between plots was negatively related to the corresponding difference in elevation, indicating that closely related lineages occupy similar ranges of elevation and temperature. We conclude that the immigration of lineages from extra-tropical regions have significant effects in determining the phylogenetic structure of tree communities in tropical Andean forests.
Data from: Bayesian phylogenetic estimation of clade ages supports trans-atlantic dispersal of cichlid fishes
Open the record for dataset details and reuse information.
Data from: Quantifying species contributions to ecosystem processes: a global assessment of functional trait and phylogenetic metrics across avian seed-dispersal networks
Open the record for dataset details and reuse information.
Data from: The influence of historical dispersal on the phylogenetic structure of tree communities in the tropical Andes
Open the record for dataset details and reuse information.
A global analysis of mosses reveals low phylogenetic endemism and highlights the importance of long-distance dispersal
Open the record for dataset details and reuse information.
Data from: Why close relatives make bad neighbors: phylogenetic conservatism in niche preferences and dispersal disproves Darwin’s Naturalization Hypothesis in the thistle tribe
Open the record for dataset details and reuse information.
Data from: Logging increases the functional and phylogenetic dispersion of understorey plant communities in tropical lowland rainforest
Open the record for dataset details and reuse information.
Phylogenetically under‐dispersed gut microbiomes are not correlated with host genomic heterozygosity in a genetically diverse reptile community
Open the record for dataset details and reuse information.
Data from: Molecular phylogenetics and biogeography of galaxiid fishes (Osteichthyes: Galaxiidae): dispersal, vicariance, and the position of Lepidogalaxias salamandroides
The galaxiid fishes exhibit a gondwanan distribution. We use mitochondrial DNA sequences to test conflicting vicariant and dispersal biogeographic hypotheses regarding the southern hemisphere range of this freshwater group. Although phylogenetic resolution of cytochrome b and 16S rRNA sequences is largely limited to more recent divergences, our data indicate that the radiation can be interpreted as a number of relatively recent dispersal events superimposed on an ancient gondwanan radiation. Genetic relationships contradict the findings of recent morphological analyses of galaxioid fishes. In particular, a number of hypotheses regarding phylogenetic placement of the enigmatic Lepidogalaxias are examined. While most workers consider Lepidogalaxias to be an unusual scaled member of the southern hemisphere galaxioids, it has also been suggested that this species is related to the northern hemisphere esocoids. Our data strongly suggest that this species is not a galaxiid; the alternative hypothesised esocoid relationship cannot be rejected. The species-rich genus Galaxias is shown to be polyphyletic and the generic taxonomy of the Galaxiinae is reassessed in the light of phylogenetic relationships. Juvenile saltwater-tolerance is phylogenetically distributed throughout the Galaxiinae and the loss of this migratory phase may be a major cause of speciation.
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.