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91 results for “evolutionary radiation”
Data from: Compensatory adaptation and diversification subsequent to evolutionary rescue in a model adaptive radiation
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Data from: Quantifying morphological change during an evolutionary radiation of Devonian trilobites
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Data from: Extinction vs. rapid radiation: the juxtaposed evolutionary histories of coelotine spiders support the Eocene–Oligocene orogenesis of the Tibetan Plateau
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Supplementary material for: Phylogenomic analysis of ultraconserved elements reveals the recent evolutionary radiation of the fairy wrasses (Teleostei: Labridae: Cirrhilabrus)
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Data from: Evolutionary origin of the Scombridae (tunas and mackerels): members of a Paleogene adaptive radiation with 14 other pelagic fish families
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Data from: Disentangling the complex evolutionary history of the Western Palearctic blue tits (Cyanistes spp.) – phylogenomic analyses suggest radiation by multiple colonisation events and subsequent isolation
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Data from: Evolutionary radiations of Proteaceae are triggered by the interaction between traits and climates in open habitats
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Evolutionary radiation in canids following continental colonizations
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A highly conserved ontogenetic limb allometry and its evolutionary significance in the adaptive radiation of Anolis lizards
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Data from: The ecology of a continental evolutionary radiation: Is the radiation of sigmodontine rodents adaptive?
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Data from: Ecological and evolutionary determinants for the adaptive radiation of the Madagascan vangas
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Data from: Evidence for past and present hybridization in three Antarctic icefish species provides new perspectives on an evolutionary radiation
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Data from: Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L.
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Reconstructing the complex evolutionary history of the Papuasian Schefflera radiation through herbariomics
<p>The Papuasia floristic region, comprising New Guinea and its surrounding islands, represents an ideal natural experiment in biogeography due to its high plant endemism, complex geological past, and location between the Southeast Asian archipelago and the Australian continent. However, the evolutionary history of Papuasian plants remains poorly understood because herbarium specimens from the region are scarce and scattered (limiting the usefulness of morphological analyses) and often several decades old (resulting in fragmented DNA that is unsuitable for traditional Sanger sequencing approaches). Our study capitalises on these historical herbarium specimens and novel high-throughput sequencing technology (Hyb-Seq, a combined target capture and genome skimming approach) to produce the first ever time-calibrated phylogeny for a mostly Papuasian plant lineage.</p> <p>1_trim: Reads trimmed with Trimmomatic</p> <p>2_1kp: Sequences from OneKP</p> <p>2_caps: Nuclear sequences captured with HybPiper</p> <p>2_genbank: Sequences downloaded from GenBank</p> <p>2_ITS: ITS sequences captured with HybPiper</p> <p>3_sequences: Sequences distributed according to gene region</p> <p>4a_raw_alignments: Sequences aligned with UPP</p> <p>4b_trimmed_alignments: Alignments trimmed with optrimAl</p> <p>5_gene_trees: Gene trees inferred with IQ-Tree</p> <p>6a_shrunk_taxa: Taxa removed from gene trees by TreeShrink</p> <p>6b_shrunk_trees: Gene trees after taxa removed by TreeShrink</p> <p>7a_raw_reduced_alignments: Alignments after taxa removed by TreeShrink re-aligned with UPP</p> <p>7b_trimmed_reduced_alignments: Re-aligned alignments trimmed with optrimAl</p> <p>8a_raw_reduced_trees: Gene trees inferred by IQ-Tree from re-aligned alignments</p> <p>8b_shrunk_reduced trees: Gene trees inferred by IQ-Tree from re-aligned alignments after taxa removed by TreeShrink</p> <p>9_species_trees: Species trees inferred with ASTRAL</p> <p>dating_area_code: Coded geographical regions used for BEAST divergence time estimation and ancestral area reconstruction</p> <p>Schefflera_dating: Sequences aligned with UPP and trimmed with optrimAl, used for BEAST divergence time estimation and ancestral area reconstruction</p>
Data from: Analysis of a rapid evolutionary radiation using ultraconserved elements (UCEs): Evidence for a bias in some multi-species coalescent methods
Rapid evolutionary radiations are expected to require large amounts of sequence data to resolve. To resolve these types of relationships many systematists believe that it will be necessary to collect data by next-generation sequencing (NGS) and use multispecies coalescent ("species tree") methods. Ultraconserved element (UCE) sequence capture is becoming a popular method to leverage the high throughput of NGS to address problems in vertebrate phylogenetics. Here we examine the performance of UCE data for gallopheasants (true pheasants and allies), a clade that underwent a rapid radiation 10–15 Ma. Relationships among gallopheasant genera have been difficult to establish. We used this rapid radiation to assess the performance of species tree methods, using ∼600 kilobases of DNA sequence data from ∼1500 UCEs. We also integrated information from traditional markers (nuclear intron data from 15 loci and three mitochondrial gene regions). Species tree methods exhibited troubling behavior. Two methods [Maximum Pseudolikelihood for Estimating Species Trees (MP-EST) and Accurate Species TRee ALgorithm (ASTRAL)] appeared to perform optimally when the set of input gene trees was limited to the most variable UCEs, though ASTRAL appeared to be more robust than MP-EST to input trees generated using less variable UCEs. In contrast, the rooted triplet consensus method implemented in Triplec performed better when the largest set of input gene trees was used. We also found that all three species tree methods exhibited a surprising degree of dependence on the program used to estimate input gene trees, suggesting that the details of likelihood calculations (e.g., numerical optimization) are important for loci with limited phylogenetic information. As an alternative to summary species tree methods we explored the performance of SuperMatrix Rooted Triple - Maximum Likelihood (SMRT-ML), a concatenation method that is consistent even when gene trees exhibit topological differences due to the multispecies coalescent. We found that SMRT-ML performed well for UCE data. Our results suggest that UCE data have excellent prospects for the resolution of difficult evolutionary radiations, though specific attention may need to be given to the details of the methods used to estimate species trees.
Data from: Iterative ecological radiation and convergence during the evolutionary history of damselfishes (Pomacentridae)
Coral reef fishes represent one of the most spectacularly diverse assemblages of vertebrates on the planet, but our understanding of their mode of diversification remains limited. Here we test whether the diversity of the damselfishes (Pomacentridae), one of the most species-rich families of reef-associated fishes, was produced by a single or multiple adaptive radiation(s) during their evolutionary history. Tests of the tempo of lineage diversification using a time-calibrated phylogeny including 208 species revealed that crown pomacentrid diversification has not slowed through time as expected under a scenario of a single adaptive radiation resulting from an early burst of diversification. Evolutionary modeling of trophic traits similarly rejected the hypothesis of early among-lineage partitioning of ecologically important phenotypic diversity. Instead, damselfishes are shown to have experienced iterative convergent radiations wherein subclades radiate across similar trophic strategies (i.e., pelagic feeders, benthic feeders, intermediate) and morphologies. Regionalization of coral reefs, competition, and functional constraints may have fueled iterative ecological radiation and convergent evolution of damselfishes. Through the Pomacentridae, we illustrate that radiations may be strongly structured by the nature of the constraints on diversification.
Data from: Integrating genomic and phenotypic data to evaluate alternative phylogenetic and species delimitation hypotheses in a recent evolutionary radiation of grasshoppers
Although resolving phylogenetic relationships and establishing species limits is a primary goal of systematics, these tasks remain challenging at both conceptual and analytical levels. Here, we integrated genomic and phenotypic data and employed a comprehensive suite of coalescent-based analyses to develop and evaluate competing phylogenetic and species delimitation hypotheses in a recent evolutionary radiation of grasshoppers (Chorthippus binotatus group) composed of two species and eight putative subspecies. To resolve the evolutionary relationships within this complex, we first evaluated alternative phylogenetic hypotheses arising from multiple schemes of genomic data processing and contrasted genetic-based inferences with different sources of phenotypic information. Second, we examined the importance of number of loci, demographic priors, number and kind of phenotypic characters, and sex-based trait variation for developing alternative species delimitation hypotheses. The best-supported topology was largely compatible with phenotypic data and showed the presence of two clades corresponding to the nominative species groups, one including three well-resolved lineages and the other comprising a four-lineage polytomy and a well-differentiated sister taxon. Integrative species delimitation analyses indicated that the number of employed loci had little impact on the obtained inferences but revealed the higher power provided by an increasing number of phenotypic characters and the usefulness of assessing their phylogenetic information-content and differences between sexes in among-taxa trait variation. Overall, our study highlights the importance of integrating multiple sources of information to test competing phylogenetic hypotheses and elucidate the evolutionary history of species complexes representing early-stages of divergence where conflicting inferences are more prone to appear.
Figure 1 from: Eben A, Espinosa A (2013) Tempo and mode of evolutionary radiation in Diabroticina beetles (genera Acalymma, Cerotoma, and Diabrotica). ZooKeys 332: 207-231. https://doi.org/10.3897/zookeys.332.5220
Figure 1 - Phylogenetic tree recovered from Bayesian inference showing posterior provability values at the nodes. The genera Acalymma and Cerotoma are recovered as monophyletic lineages. Diabrotica, however, is paraphyletic unless some species of Amphelasma and Paratriarius are renamed as Diabrotica. The general evolutionary scenario for changes in diet spectrum is mapped in the phylogeny.
Figure 2 from: Eben A, Espinosa A (2013) Tempo and mode of evolutionary radiation in Diabroticina beetles (genera Acalymma, Cerotoma, and Diabrotica). ZooKeys 332: 207-231. https://doi.org/10.3897/zookeys.332.5220
Figure 2 - Chronogram inferred from a coalescence analysis. The blue lines at the nodes indicate the 95% confidence range for the estimated split times. Letters A to G pinpoint at key nodes in the evolutionary history of Diabroticina beetles (see Table 3 for further detail). The evolutionary scenario for the acquisition of main plant hosts is presented.
Data from: Replicated evolutionary inhibition of a complex ancestral behaviour in an adaptive radiation
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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.