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.
29
datasets available to search
ShareScore release 0.9.0
Dataset results
29 results for “diversification analyses”
Fig. 3 in Molecular and cytogenetic analyses of cryptic species within the Synbranchus marmoratus Bloch, 1795 (Synbranchiformes: Synbranchidae) grouping: species delimitations, karyotypic evolution and intraspecific diversification
Fig. 3. Representative ideograms of the analyzed karyomorphs of Synbranchus marmoratus showing the heterochromatic blocks, as determined by C-banding, and hybridization patterns of ribosomal sites.
Fig. 1. A in Molecular and cytogenetic analyses of cryptic species within the Synbranchus marmoratus Bloch, 1795 (Synbranchiformes: Synbranchidae) grouping: species delimitations, karyotypic evolution and intraspecific diversification
Fig. 1. A map showing the Synbranchus marmoratus specimen collection sites. Numbers indicate the sample locality, whereas symbols represent the karyomorphs found at each locality.
Fig. 4. A in Molecular and cytogenetic analyses of cryptic species within the Synbranchus marmoratus Bloch, 1795 (Synbranchiformes: Synbranchidae) grouping: species delimitations, karyotypic evolution and intraspecific diversification
Fig. 4. A dendrogram representing the relationship between the sampled Synbranchus marmoratus specimens based on the mitochondrial 16S, COI and Cyt B genes. The colors represent each of the characterized karyomorphs, and the groups (IA, IB, IC, ID and II) used as references are shown on the right side. Bootstrap support (>50%) are given above the branches. Diploid numbers of the samples are given along the branches. 2n=46* Diploid number of Ophisternon aenigmaticum (Nirchio et al., 2011).
Deep learning from phylogenies for diversification analyses
<p>Birth-death models are widely used in combination with species phylogenies to study past diversification dynamics. Current inference approaches typically rely on likelihood-based methods. These methods are not generalizable, as a new likelihood formula must be established each time a new model is proposed; for some models, such a formula is not even tractable. Deep learning can bring solutions in such situations, as deep neural networks can be trained to learn the relation between simulations and parameter values as a regression problem. In this paper, we adapt a recently developed deep learning method from pathogen phylodynamics to the case of diversification inference, and we extend its applicability to the case of the inference of state-dependent diversification models from phylogenies associated with trait data. We demonstrate the accuracy and time efficiency of the approach for the time-constant homogeneous birth-death model and the Binary-State Speciation and Extinction model. Finally, we illustrate the use of the proposed inference machinery by reanalyzing a phylogeny of primates and their associated ecological role as seed dispersers. Deep learning inference provides at least the same accuracy as likelihood-based inference while being faster by several orders of magnitude, offering a promising new inference approach for deployment of future models in the field.</p>
Deep learning from phylogenies for diversification analyses
Open the record for dataset details and reuse information.
Data from: Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record
<p>Echinoids are key components of modern marine ecosystems. Despite a remarkable fossil record, the emergence of their crown group is documented by few specimens of unclear affinities, rendering their early history uncertain. The origin of sand dollars, one of its most distinctive clades, is also unclear due to an unstable phylogenetic context. We employ eighteen novel genomes and transcriptomes to build a phylogenomic dataset with a near-complete sampling of major lineages. With it, we revise the phylogeny and divergence times of echinoids, and place their history within the broader context of echinoderm evolution. We also introduce the concept of a chronospace—a multidimensional representation of node ages—and use it to explore methodological decisions involved in time calibrating phylogenies. We find the choice of clock model to have the strongest impact on divergence times, while the use of site-heterogeneous models and alternative node prior distributions showing minimal effects. The choice of loci has an intermediate impact, affecting mostly deep Paleozoic nodes, for which clock-like genes recover dates more congruent with fossil evidence. Our results reveal that crown group echinoids originated in the Permian and diversified rapidly in the Triassic, despite the relative lack of fossil evidence for this early diversification. We also clarify the relationships between sand dollars and their close relatives and confidently date their origins to the Cretaceous, implying ghost ranges spanning approximately 50 million years, a remarkable discrepancy with their rich fossil record.</p>
Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere
<p>Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus <em>Malus</em> sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of <em>Malus</em> s.l. (including <em>Docynia</em>); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (<em>Malus doumeri)</em> and one recent event (<em>Malus</em> coronaria) were detected in <em>Malus</em> s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian-western North American origin of <em>Malus</em> s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming datasets.</p>
Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere
Open the record for dataset details and reuse information.
Data for: Phylogenomic and population genomic analyses of ultraconserved elements reveal deep coalescence and introgression shaped diversification patterns in Lamprologine cichlids of the Congo River
Open the record for dataset details and reuse information.
Data from: Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record
Open the record for dataset details and reuse information.
Data from: Species diversification in the sky islands of southwestern China revealed by genomic, introgression and demographic analyses of Asian shrew moles
Open the record for dataset details and reuse information.
Data from: The effects of cryptic diversity on diversification dynamics analyses in Crocodylia
Open the record for dataset details and reuse information.
Genome-wide analyses reveal drivers of penguin diversification
Penguins are the only extant family of flightless diving birds. They currently comprise at least 18 species, distributed from polar to tropical environments in the Southern Hemisphere. The history of their diversification and adaptation to these diverse environments remains controversial. We used 22 new genomes from 18 penguin species to reconstruct the order, timing, and location of their diversification, to track changes in their thermal niches through time, and to test for associated adaptation across the genome. Our results indicate that the penguin crown-group originated during the Miocene in New Zealand and Australia, not in Antarctica as previously thought, and thatAptenodytesis the sister group to all other extant penguin species. We show that lineage diversification in penguins was largely driven by changing climatic conditions and by the opening of the Drake Passage and associated intensification of the Antarctic Circumpolar Current (ACC). Penguin species have introgressed throughout much of their evolutionary history, following the direction of the ACC, which might have promoted dispersal and admixture. Changes in thermal niches were accompanied by adaptations in genes that govern thermoregulation and oxygen metabolism. Estimates of ancestral effective population sizes (Ne) confirm that penguins are sensitive to climate shifts, as represented by three different demographic trajectories in deeper time, the most common (in 11 of 18 penguin species) being an increasedNebetween 40 and 70 kya, followed by a precipitous decline during the Last Glacial Maximum. The latter effect is most likely a consequence of the overall decline in marine productivity following the last glaciation.
FIGURE 8. Allozyme analyses. A in Morphological and molecular diversification of slender salamanders (Caudata: Plethodontidae: Batrachoseps) in the southern Sierra Nevada of California with descriptions of two new species
FIGURE 8. Allozyme analyses. A. Minimum evolution tree showing the relationships of 14 populations based on Nei's (1978) D (Table 4) for 27 variable loci included in allozyme study 1. The topology of the neighbor-joining tree is identical. B. Multidimensional scaling of Nei's (1978) D (Table 5) for eight populations from the nigriventris group based on allozyme study 2. Note the intermediate position of the Cannell Creek (CAN) population between B. bramei from Fairview (FAI) and B. simatus from Erskine Creek (ERS). See Table 5 for abbreviations. Sampling localities are listed in Table 3.
Supplementary Datasets for "Analyses of the effects of selfing on lineage diversification across multiple genera"
<p><span>The datasets contain the mating system character states, sequence supermatrices and phylogenies used in the study “Analyses of the effects of selfing on lineage diversification across multiple genera”. Please read the "datasets_description.doc" file for a detailed description of the datasets.</span></p>
Data from: Evolutionary and structural analyses uncover a role for solvent interactions in the diversification of cocoonases in butterflies
Open the record for dataset details and reuse information.
Data from: Oligocene odyssey: Molecular phylogenetic analyses describe the origin and diversification of freshwater Gammarus in eastern North America
Open the record for dataset details and reuse information.
Genome-wide analyses reveal drivers of penguin diversification
Open the record for dataset details and reuse information.
A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses
<p>Phylogenetic trees provide a powerful framework for testing macroevolutionary hypotheses, but it is becoming increasingly apparent that inferences derived from extant species alone can be highly misleading. Trees incorporating living and extinct taxa are are needed to address fundamental questions about the origins of diversity and disparity but it has proved challenging to generate robust, species--rich phylogenies that include large numbers of fossil taxa. As a result, most studies of diversification dynamics continue to rely on molecular phylogenies. Here, we extend and apply a recently developed meta-analytic approach for synthesizing previously published phylogenetic studies to infer a well-resolved set of species level, time-scaled phylogenetic hypotheses for extinct and extant cetaceans (whales, dolphins and allies). Our trees extend sampling from the $\sim 90$ extant species to over 500 living and extinct species, and therefore allow for more robust inference of macroevolutionary dynamics. While the diversification scenarios we recover are broadly concordant with those inferred from molecular phylogenies they differ in critical ways, notably in the relative contributions of extinction and speciation rate shifts in driving rapid radiations. The metatree approach provides the most immediate route for generating higher level phylogenies of extinct taxa, and opens the door to re-evaluation of macroevolutionary hypotheses derived only from extant taxa.</p>
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>
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.