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115 results for “Multi-locus”
Data from: Understanding the mechanisms of anti-tropical divergence in the seabird White-faced Storm-petrel (Procellariiformes: Pelagodroma marina) using a multi-locus approach
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Data from: Assessing models of speciation under different biogeographic scenarios; an empirical study using multi-locus and RNA-seq analyses
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Data from: Deciphering the genomic architecture of the stickleback brain with a novel multi-locus gene-mapping approach
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Data from: Multi-locus analyses reveal four giraffe species instead of one
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Data from: Simultaneous delimitation of species and quantification of interspecific hybridization in Amazonian peacock cichlids (genus Cichla) using multi-locus data
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Data from: Detecting genotypic changes associated with selective mortality at sea in Atlantic salmon: polygenic multi-locus analysis surpasses genome scan
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Data from: An integrative approach to phylogeography: investigating the effects of ancient seaways, climate, and historical geology on multi-locus phylogeographic boundaries of the arboreal salamander (Aneides lugubris)
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DNA barcodes combined with multi-locus data of representative taxa can generate reliable higher-level phylogenies
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Data from: Multi-locus sequence data reveal a new species of coral reef goby (Teleostei: Gobiidae: Eviota), and evidence of Pliocene vicariance across the Coral Triangle
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Data from: Multi-locus analysis of Pristionchus pacificus on La Réunion Island reveals an evolutionary history shaped by multiple introductions, constrained dispersal events, and rare out-crossing
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Data from: Multi-locus sequence data illuminate demographic drivers of Pleistocene speciation in semi-arid southern Australian birds (Cinclosoma spp.)
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Figure 1 from: Saba M, Haelewaters D, Pfister DH, Khalid AN (2020) New species of Pseudosperma (Agaricales, Inocybaceae) from Pakistan revealed by morphology and multi-locus phylogenetic reconstruction. MycoKeys 69: 1-31. https://doi.org/10.3897/mycokeys.69.33563
Figure 1 The best-scoring ML tree (-lnL = 27210.474) of the Rimosae s.s. and Inosperma clades, reconstructed from the concatenated ITS–nrLSU–mtSSU dataset. ML bootstraps (if ≥ 70) are presented above or in front of the branch leading to each node. Thick branches have maximum support (ML BS = 100). Subclade designations within sect. Rimosae s.s. follow Larsson et al. (2009) in the strict sense. Newly-described species are in boldface.
Figure 6 from: Saba M, Haelewaters D, Pfister DH, Khalid AN (2020) New species of Pseudosperma (Agaricales, Inocybaceae) from Pakistan revealed by morphology and multi-locus phylogenetic reconstruction. MycoKeys 69: 1-31. https://doi.org/10.3897/mycokeys.69.33563
Figure 6 Pseudosperma triaciculare: A Basidiomata of paratype collection (FH 00304561) B–F microscopic characters: B Basidia C cheilocystidia D caulocystidia E basidiospores F pileipellis. Scale bars: 1 cm (A), 10 µm (B, E), 30 µm (C, D, F).
Figure 3 from: Saba M, Haelewaters D, Pfister DH, Khalid AN (2020) New species of Pseudosperma (Agaricales, Inocybaceae) from Pakistan revealed by morphology and multi-locus phylogenetic reconstruction. MycoKeys 69: 1-31. https://doi.org/10.3897/mycokeys.69.33563
Figure 3 The best-scoring ML tree (-lnL = 5704.951) of Rimosae s.s. subclade A, complemented with recently-described species within sect. Rimosae s.s., reconstructed from the nrLSU dataset. ML bootstraps (if ≥ 70) are presented above or in front of the branch leading to each node. Thick branches have maximum support (ML BS = 100). Newly-described species are in boldface.
Figure 2 from: Saba M, Haelewaters D, Pfister DH, Khalid AN (2020) New species of Pseudosperma (Agaricales, Inocybaceae) from Pakistan revealed by morphology and multi-locus phylogenetic reconstruction. MycoKeys 69: 1-31. https://doi.org/10.3897/mycokeys.69.33563
Figure 2 The best-scoring ML tree (-lnL = 9359.879) of Rimosae s.s. subclade A, reconstructed from the concatenated ITS–nrLSU–mtSSU dataset. ML bootstraps (if ≥ 70) are presented above or in front of the branch leading to each node. Thick branches have maximum support (ML BS = 100). Well-supported clades that represent described species within Rimosae s.s. subclade A are named. Newly-described species are in boldface.
Figure 5 from: Saba M, Haelewaters D, Pfister DH, Khalid AN (2020) New species of Pseudosperma (Agaricales, Inocybaceae) from Pakistan revealed by morphology and multi-locus phylogenetic reconstruction. MycoKeys 69: 1-31. https://doi.org/10.3897/mycokeys.69.33563
Figure 5 Pseudosperma pinophilum: A Basidiomata of holotype collection (FH 00304582) B–E microscopic characters: B basidia C cheilocystidia D basidiospores E pileipellis. Scale bars: 1 cm (A), 10 µm (B, D), 30 µm (C, E).
Figure 4 from: Saba M, Haelewaters D, Pfister DH, Khalid AN (2020) New species of Pseudosperma (Agaricales, Inocybaceae) from Pakistan revealed by morphology and multi-locus phylogenetic reconstruction. MycoKeys 69: 1-31. https://doi.org/10.3897/mycokeys.69.33563
Figure 4 Pseudosperma brunneoumbonatum: A Basidiomata of holotype collection (LAH 310032) B–E microscopic characters: B basidia C cheilocystidia D basidiospores E pileipellis. Scale bars: 1 cm (A), 10 µm (B), 30 µm (C, E), 20 µm (D).
Multi-locus microsatellite genotypes of Pocillopora acuta (Scleractinia: Pocilloporidae) in the Bolinao-Anda Reef Complex, Philippines
<p>This repository contains genotype data and sampling metadata used for the manuscript "Shifts in coral clonality along a gradient of disturbance: insights on reproduction and dispersal of <em>Pocillopora acuta</em>". The dataset contains genotypes of 428 <em>P. acuta </em>colonies using 16 polymorphic microsatellite loci, colony sizes, in-transect locations of each coral, and geographic coordinates of reef sites. These were used to examine clonal richness and structure, population genetic differentiation, and demographic and genetic connectivity within the reef system. In the study, we estimated the relative contribution of sexual and asexual modes of reproduction to population maintenance, and inferred the species' spatial scale of realized dispersal all against a backdrop of varying levels of wave exposure. </p>
Data from: Addressing gene tree discordance and non-stationarity to resolve a multi-locus phylogeny of the flatfishes (Teleostei: Pleuronectiformes)
Non-homogeneous processes and, in particular, base compositional non-stationarity have long been recognized as a critical source of systematic error. But only a small fraction of current molecular systematic studies methodically examine and effectively account for the potentially confounding effect of non-stationarity. The problem is especially overlooked in multi-locus or phylogenomic scale analyses, in part because no efficient tools exist to accommodate base composition heterogeneity in large data sets. We present a detailed analysis of a data set with 20 genes and 214 taxa to study the phylogeny of flatfishes (Pleuronectiformes) and their position among percomorphs. Most genes vary significantly in base composition among taxa and fail to resolve flatfish monophyly and other emblematic groups, suggesting that non-stationarity may be causing systematic error. We show a strong association between base compositional bias and topological discordance among individual gene partitions and their inferred trees. Phylogenetic methods applying non-homogeneous models to accommodate non-stationarity have relatively minor effect to reduce gene tree discordance, suggesting that available computer programs applying these methods do not scale up efficiently to the data set of modest size analysed in this study. By comparing phylogenetic trees obtained with species tree (STAR) and concatenation approaches, we show that gene tree discordance in our data set is most likely due to base compositional biases than to incomplete lineage sorting. Multi-locus analyses suggest that the combined phylogenetic signal from all loci in a concatenated data set overcomes systematic biases induced by non-stationarity at each partition. Finally, relationships among flatfishes and their relatives are discussed in the light of these results. We find support for the monophyly of flatfishes and confirm findings from previous molecular phylogenetic studies suggesting their close affinity with several carangimorph groups (i.e., jack and allies, barracuda, archerfish, billfish and swordfish, threadfin, moonfish, beach salmon, and snook and barramundi).
Data from: Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution
Over half of all vertebrates are "fishes", which exhibit enormous diversity in morphology, physiology, behavior, reproductive biology, and ecology. Investigation of fundamental areas of vertebrate biology depend critically on a robust phylogeny of fishes, yet evolutionary relationships among the major actinopterygian and sarcopterygian lineages have not been conclusively resolved. Although a consensus phylogeny of teleosts has been emerging recently, it has been based on analyses of various subsets of actinopterygian taxa, but not on a full sample of all bony fishes. Here we conducted a comprehensive phylogenetic study on an unprecedented combination of broad taxonomic sampling of actinopterygian and sarcopterygian lineages (with a chondrichthyan outgroup) using a molecular data set of 21 independent loci. These data yielded a resolved phylogenetic hypothesis for extant Osteichthyes, including 1) reciprocally monophyletic Sarcopterygii and Actinopterygii, as currently understood, with polypteriforms as the first diverging lineage within Actinopterygii; 2) a monophyletic group containing gars and bowfin (= Holostei) as sister group to Teleostei; and 3) the earliest diverging lineage among teleosts being Elopomorpha, rather than Osteoglossomorpha. Relaxed-clock dating analysis employing a set of 24 newly applied fossil calibrations reveals divergence times that are more consistent with paleontological estimates than previous studies. Establishing a new phylogenetic pattern with accurate divergence dates for bony fishes illustrates several areas where the fossil record is incomplete and provides critical new insights on diversification of this important vertebrate group.
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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.