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210 results for “Bayesian inference”
Data from: Phylogeographic inference using Bayesian model comparison across a fragmented chorus frog species complex
Fragmented species complexes provide an interesting system for investigating biogeographic history and the present distribution of genetic variation. Recent advances in sequencing technology and statistical phylogeography enable the collection and rigorous analysis of large multilocus data sets, but designing studies that produce meaningful phylogeographic inferences remains challenging. We implemented a Bayesian model comparison approach to investigate previous biogeographic hypotheses while simultaneously inferring the presence of genetic structure in a chorus frog species complex. The Illinois chorus frog (Pseudacris illinoensis), originally described as a subspecies of the broadly distributed Strecker's chorus frog (Pseudacris streckeri), occurs in small, disjunct regions associated with scarce sand prairie habitats that have been impacted by human development. We used high-throughput sequencing to develop and collect a multitiered genetic data set comprised of three different marker types (23 anonymous nuclear sequence loci, four mitochondrial genes and 14 microsatellite loci) designed to address questions across different evolutionary timescales. Phylogenetic analyses uncovered a deep divergence between populations in the Edwards Plateau of central Texas and all other P. streckeri/P. illinoensis populations, but suggest the disjunct distribution of P. illinoensis occurred more recently. Our best-supported migration model is consistent with the hypothesis that central Texas represented a refugium from which populations expanded via multiple routes. This model also indicates that disjunct northern and southern regions of P. illinoensis should be considered genetically distinct management units. Our study provides an evolutionary context for future studies and conservation efforts in P. illinoensis and demonstrates the utility of model-based approaches for phylogeographic inference.
Data from: Bayesian inference of a historical bottleneck in a heavily exploited marine mammal
Emerging Bayesian analytical approaches offer increasingly sophisticated means of reconstructing historical population dynamics from genetic data, but have been little applied to scenarios involving demographic bottlenecks. Consequently, we analysed a large mitochondrial and microsatellite dataset from the Antarctic fur seal Arctocephalus gazella, a species subjected to one of the most extreme examples of uncontrolled exploitation in history when it was reduced to the brink of extinction by the sealing industry during the late eighteenth and nineteenth centuries. Classical bottleneck tests, which exploit the fact that rare alleles are rapidly lost during demographic reduction, yielded ambiguous results. In contrast, a strong signal of recent demographic decline was detected using both Bayesian skyline plots and approximate Bayesian computing, the latter also allowing derivation of posterior parameter estimates that were remarkably consistent with historical observations. This was achieved using only contemporary samples, further emphasizing the potential of Bayesian approaches to address important outstanding problems in conservation and evolutionary biology.
Data from: Bayesian phylogeographic inferences reveal contrasting colonization dynamics among European groundwater isopods
The potentially important role of northern microrefugia during postglacial dispersal is challenging the view of southern Europe as a refuge and source area of European biota. In groundwaters, large geographic ranges of presumably good dispersers are increasingly suspected to consist of assemblages of cryptic species with narrow ranges. Moreover, a large species range, even when confirmed by molecular evidence, tells us little about the spatiotemporal dynamics of dispersal. Here, we used phylogenetic inferences, species delineation methods and Bayesian phylogeographic diffusion models to test for the likelihood of postglacial colonization from distant refugia among five morphospecies of Proasellus (Isopoda, Asellidae). All morphospecies except one were monophyletic, but they comprised a total of 15–17 cryptic species. Three cryptic species retained ranges that spanned a distance >650 km, similar to that of the nominal morphospecies. Bayesian diffusion models based on mitochondrial markers revealed considerable spatiotemporal heterogeneity in dispersal rates, suggesting that short-time dispersal windows were instrumental in shaping species ranges. Only one species was found to experience a recent, presumably postglacial, range expansion. The Jura and Alpine foothills probably played a major role in maintaining diversity within Proasellus in northern regions by acting both as diversification hotspots and Pleistocene refugia. Gaining insight into the spatiotemporal heterogeneity of dispersal rates revealed contrasting colonization dynamics among species that were not consistent with a global postglacial colonization of Europe from distant refugia.
Data from: Taxonomic reassessment of Clevosaurus latidens Fraser, 1993 (Lepidosauria, Rhynchocephalia) and rhynchocephalian phylogeny based on parsimony and Bayesian inference
The Late Triassic rhynchocephalian Clevosaurus latidens Fraser, 1993 is known from the fissure deposits of Cromhall Quarry, England. Many studies have questioned its referral to the genus Clevosaurus and some phylogenetic analyses suggest a close relationship with herbivorous rhynchocephalians. We reexamine the type specimens and referred material of C. latidens to elucidate its taxonomic identity. Additionally, we provide new phylogenetic analyses of the Rhynchocephalia using both parsimony and Bayesian approaches. Our taxonomic review and both phylogenetic analyses reveal that C. latidens is not referable to Clevosaurus, but represents a new genus. We reassess C. latidens and provide an amended diagnosis for the new genus Fraserosphenodon gen. nov. Both parsimony and Bayesian analyses recover similar topologies and we propose formal names for two higher clades within Rhynchocephalia: Eusphenodontia and Neosphenodontia.
FIGURE 1. Bayesian tree inferred from SSU gene DNA sequences. Posterior probabilities exceeding 50 in A review of the genus Tripylina Brzeski, 1963 (Nematoda: Triplonchida), with descriptions of five new species from New Zealand
FIGURE 1. Bayesian tree inferred from SSU gene DNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species, GenBank numbers, locations are listed for each taxon if known.
FIGURE 2. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50 in A review of the genus Tripylina Brzeski, 1963 (Nematoda: Triplonchida), with descriptions of five new species from New Zealand
FIGURE 2. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species, GenBank numbers, locations are listed for each taxon if known.
FIGURE 5 Bayesian phylogenetic tree inferred from SSU gene DNA sequences. Posterior probabilities great than 50 in New Zealand species of the genus Tripyla Bastian, 1865 (Nematoda: Triplonchida: Tripylidae). I: A new species, a new record and key to long-tailed species
FIGURE 5 Bayesian phylogenetic tree inferred from SSU gene DNA sequences. Posterior probabilities great than 50% are given on appropriate clades. Nematode species, GenBank numbers, locations are listed for each taxon if known.
FIGURE 6 Bayesian phylogenetic tree inferred from LSU gene DNA sequences. Posterior probabilities greater than 50 in New Zealand species of the genus Tripyla Bastian, 1865 (Nematoda: Triplonchida: Tripylidae). I: A new species, a new record and key to long-tailed species
FIGURE 6 Bayesian phylogenetic tree inferred from LSU gene DNA sequences. Posterior probabilities greater than 50% are given on appropriate clades. Nematode species, GenBank numbers, locations are listed for each taxon if known.
FIGURE 7. Bayesian tree inferred from D2–D3 in Morphological and molecular characterization of Pratylenchoides persicus n. sp. (Nematoda: Merliniidae) and additional data on two other species of the genus from Iran
FIGURE 7. Bayesian tree inferred from D2–D3 region of the LSU rDNA gene. Posterior probabilities (pp) exceeding 0.5 are given on appropriate clades, bifurcations with pp above 0.95 are considered to be well-supported. Nematode species and GenBank numbers are listed for each taxon. In bold: newly generated D2–D3 LSU rDNA sequences.
FIGURE 6. Bayesian inference tree derived from 16S rRNA for all species. The nodal numbers are posterior probability values. Only values above 50 in Cophecheilus bamen, a new genus and species of labeonine fishes (Teleostei: Cyprinidae) from South China
FIGURE 6. Bayesian inference tree derived from 16S rRNA for all species. The nodal numbers are posterior probability values. Only values above 50% are given.
FIGURE 3 Bayesian tree inferred from SSU gene rDNA sequences. Posterior probabilities exceeding 50 in A review of the genus Trischistoma Cobb, 1913 (Nematoda: Enoplida), with descriptions of four new species from New Zealand
FIGURE 3 Bayesian tree inferred from SSU gene rDNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species, GenBank numbers are listed for each taxon.
FIGURE 4 Bayesian tree inferred from LSU gene rDNA sequences. Posterior probabilities exceeding 50 in A review of the genus Trischistoma Cobb, 1913 (Nematoda: Enoplida), with descriptions of four new species from New Zealand
FIGURE 4 Bayesian tree inferred from LSU gene rDNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species and GenBank numbers are listed for each taxon if known.
FIGURE 4. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50 in Laimaphelenchus persicus n. sp. (Nematoda: Aphelenchoididae) from Iran
FIGURE 4. Bayesian tree inferred from LSU gene DNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species and GenBank numbers are listed for each taxon.
FIGURE 1. Bayesian consensus tree inferred from D2 in Nematodes from galls on Myrtaceae. IV. Fergusobia from flat leaf galls on Eucalyptus and Corymbia, with descriptions of two new species
FIGURE 1. Bayesian consensus tree inferred from D2/D3 under TVM+I+G model (lnL=4053.8611; freqA=0.2908; freqC=0.1437; freqG=0.2386; freqT=0.3269; R(a)=0.8687; R(b)=3.4319; R(c)=1.9944; R(d)=0.4487; R(e)=3.4319; R(f)=1; Pinva=0.5164; Shape=0.5896). Posterior probability values exceeding 50% are given on appropriate clades.
FIGURE 1. Bayesian phylogenetic tree inferred from SSU gene DNA sequences. Posterior probabilities great than 50 in New Zealand species of the genus Tripyla Bastian, 1865 (Nematoda: Triplonchida: Tripylidae). II: Two new, a known species and key to species
FIGURE 1. Bayesian phylogenetic tree inferred from SSU gene DNA sequences. Posterior probabilities great than 50% are given on appropriate clades. Nematode species, GenBank numbers, locations are listed for each taxon if known.
FIGURE 4. Bayesian inference tree derived from cyt b in Molecular evidence for taxonomic status of the gudgeon genus Huigobio Fang, 1938 (Teleostei: Cypriniformes), with a description of a new species from Guangdong Province, South China
FIGURE 4. Bayesian inference tree derived from cyt b gene for the Armatogobionina of the subfamily Gobioninae. Nodal numbers are posterior probability values. Only values above 50% are given.
FIGURE 4. Bayesian inference analysis 50 in Description of Trichodorus iranicus sp. n. (Diphtherophorina, Trichodoridae) from Iran
FIGURE 4. Bayesian inference analysis 50% majority rule consensus tree as inferred from D2–D3 expansion segments of 28S rDNA sequence alignment under the GTR+G+I model. The newly–obtained sequence is in bold.
FIGURE 6. Bayesian inference analysis 50 in Rotylenchus castilloi n. sp. (Nematoda: Hoplolaimidae), a new species with long stylet from northern Iran
FIGURE 6. Bayesian inference analysis 50% majority rule consensus tree as inferred from ITS1 rDNA sequence alignment under the GTR+G+I model. Bayesian posterior probabilities and maximum likelihood bootstrap values more than 50% are given for appropriate clades in the form: BPP/ML BS. New sequences are in bold font.
FIGURE 5. Bayesian inference analysis 50 in Rotylenchus castilloi n. sp. (Nematoda: Hoplolaimidae), a new species with long stylet from northern Iran
FIGURE 5. Bayesian inference analysis 50% majority rule consensus tree as inferred from D2–D3 expansion segments of 28S rDNA sequence alignment under the GTR+G+I model. Bayesian posterior probabilities and maximum likelihood bootstrap values more than 50% are given for appropriate clades in the form: BPP/ML BS. New sequence is in bold font.
FIGURE 7. Bayesian phylogenetic tree inferred from SSU rRNA gene sequences. Posterior probabilities greater than 50 in Description of Trischistoma abharensis n. sp. (Nematoda: Trischistomatidae) and first record of Tripylella intermedia (Bütschli, 1873) Brzeski & Winiszewska-Ślipinska, 1993 (Nematoda: Tripylidae) from Iran
FIGURE 7. Bayesian phylogenetic tree inferred from SSU rRNA gene sequences. Posterior probabilities greater than 50% are given on appropriate clades. Nematode species, GenBank accession numbers, and locations are listed for each taxon if known. The accession no. AY284737 was originally deposited in GenBank as Paratripyla sp., but it was used as Tripylella sp. by van Megen et. al. (2009).
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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)
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DANDI Archive for NWB datasets
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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.