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.
1,344
datasets available to search
ShareScore release 0.9.0
Dataset results
1,344 results for “phylogenomics”
Code and sequence data pertaining to: A phylogenomic perspective on interspecific competition
Open the record for dataset details and reuse information.
Data for: Ancient rapid radiation explains most conflicts among gene trees and well-supported phylogenomic trees of nostocalean cyanobacteria
Open the record for dataset details and reuse information.
Data from: Forget-me-not phylogenomics: Improving the resolution and taxonomy of a rapid island and mountain radiation in Aotearoa New Zealand (Myosotis; Boraginaceae)
Open the record for dataset details and reuse information.
Data from: Phylogenomics resolves key relationships in Rumex and uncovers a dynamic history of independently evolving sex chromosomes
Open the record for dataset details and reuse information.
Saguaro cactus within-species phylogenomics
Open the record for dataset details and reuse information.
Data for: Phylogenomics and historical biogeography of Hydrangeeae (Hydrangeaceae) elucidate the effects of geologic and climatic dynamics on diversification
Open the record for dataset details and reuse information.
Phylogenomics of the tetraploid Hawaiian lobeliads: Implications for their origin, dispersal history, and adaptive radiation
Open the record for dataset details and reuse information.
Data from: A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses
Open the record for dataset details and reuse information.
Phylogenomics and comparative genomics of two of the largest genera of angiosperms, Piper and Peperomia (Piperaceae)
Open the record for dataset details and reuse information.
Phylogenomics and contrasting modes of genome evolution in Ascomycota
<p>332 Saccharomycotina assemblies <br> 761 Pezizomycotina assemblies<br> 14 Taphrinomycotina assemblies<br> 6 Basidiomycota (outgroup) assemblies</p> <p>Proteomes of 1,107 Ascomycota</p>
Data from: Phylogenomic data reveal reticulation and incongruence among mitochondrial candidate species in Dusky Salamanders (Desmognathus)
<p>Gene flow between evolutionarily distinct lineages is increasingly recognized as a common occurrence. Such processes distort our ability to diagnose and delimit species, as well as confound attempts to estimate phylogenetic relationships. A conspicuous example is Dusky Salamanders (<i>Desmognathus</i>), a common model-system for ecology, evolution, and behavior. Only 22 species are described; 7 in the last 40 years. However, mitochondrial datasets indicate the presence of up to 45 "candidate species" presenting a complex history of reticulation. Some authors have even suggested that the search for species boundaries in the group may be in vain. Here, we analyze nuclear and mitochondrial data containing 161 individuals from at least 49 distinct evolutionary lineages that we treat as candidate species. Concatenated and species-tree methods fail to provide satisfactory resolution for relationships among these taxa. Comparing topologies and applying methods for estimating phylogenetic networks, we find strong support for numerous instances of hybridization throughout the history of the group. We suggest that these processes may be more common than previously thought across the phylogeography-phylogenetics continuum, and that while the search for species boundaries in <i>Desmognathus</i> may not be in vain, it will be complicated by factors such as crypsis, parallelism, and gene-flow.</p>
Data from: The origin of the legumes is a complex paleopolyploid phylogenomic tangle closely associated with the Cretaceous-Paleogene (K-Pg) mass extinction event
The consequences of the Cretaceous-Paleogene (K-Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastrichtian or early Paleocene and that, apart from the Detarioideae WGD, paleopolyploidy occurred close to the KPB. We conclude that the early evolution of the legumes followed a complex history, in which multiple auto- and/or allopolyploidy events coincided with rapid diversification and in association with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic.
Data from: Parallel evolution of bower-building behavior in two groups of bowerbirds suggested by phylogenomics
<p>The bowerbirds in New Guinea and Australia include species that build the largest and perhaps most elaborately decorated constructions outside of humans. The males use these courtship bowers, along with their displays, to attract females. In these species, the mating system is polygynous and the females alone incubate and feed the nestlings. The bowerbirds also include 10 species of the socially monogamous catbirds in which the male participates in most aspects of raising the young. How the bower-building behavior evolved has remained poorly understood, as no comprehensive phylogeny exists for the family. It has been assumed that the monogamous catbird clade is sister to all polygynous species. We here test this hypothesis using a newly developed pipeline for obtaining homologous alignments of thousands of exonic and intronic regions from genomic data to build a phylogeny. Our well-supported species tree shows that the polygynous, bower-building species are not monophyletic. The result suggests either that bower-building behavior is an ancestral condition in the family that was secondarily lost in the catbirds, or that it has arisen in parallel in two lineages of bowerbirds. We favor the latter hypothesis based on an ancestral character reconstruction showing that polygyny but not bower-building is ancestral in bowerbirds, and on the observation that <em>Scenopoeetes dentirostris</em>, the sister species to one of the bower-building clades, does not build a proper bower but constructs a court for male display. This species is also sexually monomorphic in plumage despite having a polygynous mating system. We argue that the relatively stable tropical and subtropical forest environment in combination with low predator pressure and rich food access (mostly fruit) facilitated the evolution of these unique life-history traits. </p>
Data from: Phylogenomic analysis of Wolbachia strains reveals patterns of genome evolution and recombination
<p><i>Wolbachia</i> are widespread intracellular bacteria that mediate many important biological processes in arthropod species. In this study, we identified 210 conserved single-copy genes in 33 genome-sequenced <i>Wolbachia</i> strains in the A, B, C, D, E and F supergroups. Phylogenomic analysis with these core genes indicate that all 33 <i>Wolbachia</i> strains maintain the supergroup relationship classified previously based on the multilocus sequence typing (MLST) genes. Using an interclade recombination screening method, 14 inter-supergroup recombination events were discovered in six genes (2.9%) among 210 single copy orthologs. This finding suggests a relatively low frequency of intergroup recombination. Interestingly, they have occurred not only between A and B supergroups (9 events), but also between A and E supergroups (5 events). Maintenance of such transfers suggests possible roles in <i>Wolbachia</i> infection related functions. Comparisons of strain divergence using the five genes of the MLST system show a high correlation (Pearson correlation coefficient r = 0.98) between MLST and whole genome divergences, indicating that MLST is a reliable method for identifying related strains when whole genome data are not available. The phylogenomic analysis and the identified core gene set in our study will serve as a valuable foundation for strain identification and the investigation of recombination and genome evolution in <i>Wolbachia</i>.</p>
Data from: Uneven missing data skew phylogenomic relationships within the lories and lorikeets
<p>Inlcuded is the supplementary data for Smith, B. T., Mauck, W. M., Benz, B., & Andersen, M. J. (2018). Uneven missing data skews phylogenomic relationships within the lories and lorikeets. <em>BioRxiv</em>, 398297. </p> <p>The resolution of the Tree of Life has accelerated with advances in DNA sequencing technology. To achieve dense taxon sampling, it is often necessary to obtain DNA from historical museum specimens to supplement modern genetic samples. However, DNA from historical material is generally degraded, which presents various challenges. In this study, we evaluated how the coverage at variant sites and missing data among historical and modern samples impacts phylogenomic inference. We explored these patterns in the brush-tongued parrots (lories and lorikeets) of Australasia by sampling ultraconserved elements in 105 taxa. Trees estimated with low coverage characters had several clades where relationships appeared to be influenced by whether the sample came from historical or modern specimens, which were not observed when more stringent filtering was applied. To assess if the topologies were affected by missing data, we performed an outlier analysis of sites and loci, and a data reduction approach where we excluded sites based on data completeness. Depending on the outlier test, 0.15% of total sites or 38% of loci were driving the topological differences among trees, and at these sites, historical samples had 10.9x more missing data than modern ones. In contrast, 70% data completeness was necessary to avoid spurious relationships. Predictive modeling found that outlier analysis scores were correlated with parsimony informative sites in the clades whose topologies changed the most by filtering. After accounting for biased loci and understanding the stability of relationships, we inferred a more robust phylogenetic hypothesis for lories and lorikeets.</p>
Exploration of plastid phylogenomic conflict yields new insights into the deep relationships of Leguminosae
<p>Phylogenomic analyses have helped resolve many recalcitrant relationships in the angiosperm tree of life, yet phylogenetic resolution of the backbone of the Leguminosae, one of the largest and most economically and ecologically important families, remains poor due to generally limited molecular data and incomplete taxon sampling of previous studies. Here, we resolve many of the Leguminosae's thorniest nodes through comprehensive analysis of plastome-scale data using multiple modified coding and noncoding datasets of 187 species representing almost all major clades of the family. Additionally, we thoroughly characterize conflicting phylogenomic signal across the plastome in light of the family's complex history of plastome evolution. Most analyses produced largely congruent topologies with strong statistical support, and provided strong support for resolution of some long-controversial deep relationships among the early diverging lineages of the subfamilies Caesalpinioideae and Papilionoideae. The robust phylogenetic backbone reconstructed in this study establishes a framework for future studies on legume classification, evolution, and diversification. However, conflicting phylogenetic signal was detected and quantified at several key nodes that prevents the confident resolution of these nodes using plastome data alone.</p>
Disentangling sources of gene tree discordance in phylogenomic datasets: testing ancient hybridizations in Amaranthaceae s.l.
<p>Gene tree discordance in large genomic datasets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization events within the plant family Amaranthaceae s.l. that was previously supported by morphological, ecological, and Sanger-based molecular data. The dataset included seven genomes and 88 transcriptomes, 17 generated for this study. We examined gene-tree discordance using coalescent-based species trees and network inference, gene tree discordance analyses, site pattern tests of introgression, topology tests, synteny analyses, and simulations. We found that a combination of processes might have generated the high levels of gene tree discordance in the backbone of Amaranthaceae s.l. Furthermore, we found evidence that three consecutive short internal branches produce anomalous trees contributing to the discordance. Overall, our results suggest that Amaranthaceae s.l. might be a product of an ancient and rapid lineage diversification, and remains, and probably will remain, unresolved. This work highlights the potential problems of identifiability associated with the sources of gene tree discordance including, in particular, phylogenetic network methods. Our results also demonstrate the importance of thoroughly testing for multiple sources of conflict in phylogenomic analyses, especially in the context of ancient, rapid radiations. We provide several recommendations for exploring conflicting signals in such situations.</p>
Data from: Phylogenomics, biogeography, and evolution of the blue- or white-fruited dogwoods
<p>In this study, we combined data from RAD-seq, morphology, fossils, and ecological niche to understand species relationships, biogeographic history, ecological niche and morphological evolution of the blue- or white-fruited dogwoods, the largest of the four major clades of Cornus. Our phylogenomic analyses with RAxML and MrBayes recovered a strongly supported and well-resolved phylogeny of the BW group with three intercontinental disjunct clades in east Asia/Eurasia and North America - of which two in subg. Kraniopsis are newly identified. Divergence time analyses with BEAST and treePL and DEC-based total evidence analysis resolved an ancestral range of the BW crown in eastern Asia or Eurasia in the Late Cretaceous and ancestral ranges of the three disjunct clades in Eurasia and North America during the Miocene, suggesting dispersal via the North Atlantic and Bering land bridges. Character mapping and comparison of ecological niche, morphospace, and rate of evolution shows evidence of different divergence patterns in morphology, ecological niche, and molecules of the disjunct sisters. The overall diversity bias towards EA cannot be explained by a greater net diversification rate but rather an early diversification of subg. Kraniopsis in EA. Although morphological stasis was observed in most of the characters across the disjuncts, evolutionary changes in vegetative, fruit, and habit traits may be attributed to continental differences in temperature, precipitation, and elevation. These findings in conjunction with previous studies suggest the EA-ENA disjunct floras are an assembly of lineages descended from the boreotropical or mesophytic flora through taxon-specific evolutionary pathways.</p>
Repeated parallel losses of inflexed stamens in Moraceae: phylogenomics and generic revision of the tribe Moreae and the reinstatement of the tribe Olmedieae (Moraceae)
<p><span><span><span><span><span><span><span><span><span><span><span>We present a densely-sampled phylogenomic study of the mulberry tribe (Moreae, Moraceae), an economically important clade with a global distribution, revealing multiple losses of inflexed stamens, a character traditionally used to circumscribe Moreae. Inflexed stamens facilitate ballistic pollen release and are associated with wind pollination, and the results presented here suggest that losses of this character state may have evolved repeatedly in Moraceae. Neither Moreae nor several of its major genera (<i>Morus</i>, <i>Streblus</i>, <i>Trophis</i>) were found to be monophyletic. A revised system for a monophyletic Moreae is presented, including the reinstatement of the genera <i>Ampalis, Maillardia, Taxotrophis, </i>and <i>Paratrophis</i>, and the recognition of the new genus <i>Afromorus</i>. <i>Pseudostreblus </i>is reinstated and transferred to the Parartocarpeae, and <i>Sloetiopsis </i>is reinstated and transferred to the Dorstenieae. The tribe Olmediae is reinstated, replacing the Castilleae, owing to the reinstatement of the type genus <i>Olmedia, </i>and its exclusion from Moreae. <i>Streblus </i>s.s. is excluded from Moreae and transferred to the Olmediae, which is characterized primarily by involucrate inflorescences without regard to stamen position. Eight new combinations are made.</span></span></span></span></span></span></span></span></span></span></span></p>
Phylogenomic species delimitation, taxonomy, and "bird guide" identification for the Neotropical ant genus Rasopone (Hymenoptera: Formicidae)
<p><i>Rasopone</i> Schmidt & Shattuck is a poorly known lineage of ants that live in Neotropical forests. Informed by phylogenetic results from thousands of ultraconserved elements (UCEs) and mitochondrial DNA barcodes, we revise the genus, providing a new morphological diagnosis and a species-level treatment. Analysis of UCE data from many <i>Rasopone</i> samples and select outgroups revealed non-monophyly of the genus. Monophyly of <i>Rasopone</i> was restored by transferring several species to the unrelated genus <i>Mayaponera </i>Schmidt & Shattuck. Within <i>Rasopone</i>, species are morphologically very similar, and we provide a "bird guide" approach to identification rather than the traditional dichotomous key. Species are arranged by size in a table, along with geographic range and standard images. Additional diagnostic information is then provided in individual species accounts. We recognize a total of 15 named species, of which the following are described as <b>new species</b>: <i>R. costaricensis</i>, <i>R. cryptergates</i>,<i> R. cubitalis</i>,<i> R. guatemalensis</i>,<i> R. mesoamericana</i>,<i> R. pluviselva</i>,<i> R. politognatha</i>, <i>R. subcubitalis</i>, and <i>R. titanis</i>. An additional 12 morphospecies are described but not formally named due to insufficient material. <i>Rasopone panamensis</i> (Forel, 1899) is <b>removed from synonymy</b> and <b>elevated to species</b>. The following species are removed from <i>Rasopone</i> and made <b>new combinations</b> in <i>Mayaponera</i>: <i>M. arhuaca</i> (Forel, 1901), <i>M. becculata</i> (Mackay & Mackay, 2010), <i>M. cernua</i> (Mackay & Mackay, 2010), <i>M. conicula</i> (Mackay & Mackay, 2010), <i>M. longidentata</i> (Mackay & Mackay, 2010), and <i>M. pergandei</i> (Forel, 1909).</p>
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.