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1,344 results for “: phylogenomics”
Rapid radiation and rampant reticulation: Phylogenomics of South American Liolaemus lizards
<p>Understanding the factors that cause heterogeneity among gene trees can increase the accuracy of species trees. Discordant signals across the genome are commonly produced by incomplete lineage sorting (ILS) and introgression, which in turn can result in reticulate evolution. Species tree inference using the multispecies coalescent is designed to deal with ILS and is robust to low levels of introgression, but extensive introgression violates the fundamental assumption that relationships are strictly bifurcating. In this study, we explore the phylogenomics of the iconic Liolaemus subgenus of South American lizards, a group of over 100 species mostly distributed in and around the Andes mountains. Using mitochondrial DNA (mtDNA) and genome-wide restriction site-associated DNA sequencing (RADseq; nDNA hereafter), we inferred a time-calibrated mtDNA gene tree, nDNA species trees, and phylogenetic networks. We found high levels of discordance between mtDNA and nDNA, which we attribute in part to extensive ILS resulting from rapid diversification. These data also reveal extensive and deep introgression, which combined with rapid diversification, explain the high level of phylogenetic discordance. We discuss these findings in the context of Andean orogeny and glacial cycles that fragmented, expanded, and contracted species distributions. Finally, we use the new phylogeny to resolve long-standing taxonomic issues in one of the most studied lizard groups in the New World.</p>
Fig. 5 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)
Fig. 5. Mesosomal structure of fully alate (A) vs. brachypterous (B) queen.
Phylogenomics resolves the invasion history of Acacia auriculiformis in Florida
<p><b>Aim:</b> <span>Understanding the genetic structure of plants in their native range is crucial when reconstructing the invasion history of weeds. This information allows researchers to pin-point the provenance of invasive plants, and to test the importance of genetic admixture in facilitating invasion success.</span> We assessed genetic structuring across the native range of <i>A. auriculiformis</i>, to determine whether genetic admixture contributes to the success of this weed in its introduced range, and test for rapid adaptation to environmental conditions in the invasive lineage.</p> <p><b>Location:</b> Australia, Papua New Guinea, Florida</p> <p><b>Taxon: </b><i>Acacia auriculiformis</i></p> <p><b>Methods: </b>We sampled <i>A. auriculiformis </i>from across its entire native distribution (northern Australia, Papua New Guinea) and its invasive range in Florida, and used Genotyping-by-sequencing (GBS) to assess population structuring.</p> <p><b>Results:</b> Principal component analysis, based on 9,591 SNPs, indicated significant differentiation among samples from Papua New Guinea, the Northern Territory (Australia), and north Queensland (Australia). Florida samples also formed a distinct cluster, with these samples most closely related to samples from the Northern Territory. These results indicate that the Florida <i>A. auriculiformis </i>lineage most likely originates from the Northern Territory, with no evidence that plants were introduced from different parts of the native range. We found evidence of allelic shifts in the Florida population, suggesting rapid adaptation to environmental conditions may contribute the success of the invasive lineage.</p> <p><b>Main conclusions: </b>Two well-known biogeographic barriers – the Carpentaria Gap and Torres Strait – have caused genome-wide divergence among <i>A. auriculiformis</i> plants from north Queensland, Northern Territory, and Papua New Guinea. The taxonomic status of these allopatric populations should be further assessed. As the Florida lineage originated in the Northern Territory the search for potential biological control agents should be focused in this region. Our results also demonstrate how artificial selection and strong genetic drift may cause introduced plants to have a unique genetic make-up not found in the native range.</p>
Figure 2 from: Duan L, Han L-N, Sirichamorn Y, Wen J, Compton JA, Deng S-W, Arslan E, Ertuğrul K, Schrire B, Chen H-F (2021) Proposal to recognise the tribes Adinobotryeae and Glycyrrhizeae (Leguminosae subfamily Papilionoideae) based on chloroplast phylogenomic evidence. PhytoKeys 181: 65-77. https://doi.org/10.3897/phytokeys.181.71259
Figure 2 Bayesian maximum clade credibility tree of the GAW clade and related groups based on chloroplast CDSs. Bayesian posterior probabilities are given above branches, Maximum Likelihood bootstrap values below branches. Asterisks indicate PP = 1 and LBS = 100%. W. nieuwenhuisii indicates Whitfordiodendron nieuwenhuisii.
Figure 1 from: Duan L, Han L-N, Sirichamorn Y, Wen J, Compton JA, Deng S-W, Arslan E, Ertuğrul K, Schrire B, Chen H-F (2021) Proposal to recognise the tribes Adinobotryeae and Glycyrrhizeae (Leguminosae subfamily Papilionoideae) based on chloroplast phylogenomic evidence. PhytoKeys 181: 65-77. https://doi.org/10.3897/phytokeys.181.71259
Figure 1 Representative plants of Adinobotryeae and Glycyrrhizeae. Inflorescences (A) and fruits (B) of Adinobotrys atropurpureus; inflorescence (C) and infructescence (D) of Glycyrrhiza pallidiflora; inflorescence (E) and infructescence (F) of Glycyrrhiza uralensis; fruits (G) of Glycyrrhiza inflata; inflorescence (H) and part of dried infructescence [I; photographed on herbarium specimen: A. Eustace 31 (E!)] of Glycyrrhizopsis flavescens.
Detecting and removing sample contamination in phylogenomic data: An example and its implications for Cicadidae phylogeny (Insecta: Hemiptera)
<p class="MsoNormal">Contamination of a genetic sample with DNA from one or more non-target species is a continuing concern of molecular phylogenetic studies, both Sanger sequencing studies and Next-Generation Sequencing (NGS) studies. We developed an automated pipeline for identifying and excluding likely cross-contaminated loci based on detection of bimodal distributions of patristic distances across gene trees. When the contamination occurs between samples within a dataset, comparisons between a contaminated sample and its contaminant taxon will yield bimodal distributions with one peak close to zero patristic distance. Here we present an automated pipeline for identifying and excluding likely cross-contaminated loci based on detection of these bimodal distributions of patristic distances between taxa across gene trees. This new method does not rely on <em>a priori</em> knowledge of taxon relatedness nor does it determine the process(es) that caused the contamination. Exclusion of putatively contaminated loci from a dataset generated for the insect family Cicadidae showed that these sequences were affecting some topological patterns and branch supports, although the effects were sometimes subtle, with some contamination-influenced relationships exhibiting strong bootstrap support. Long tip branches and outlier values for one anchored phylogenomic pipeline statistic (AvgNHomologs) were correlated with the presence of contamination. While the AHE markers used here, which target hemipteroid taxa, proved effective in resolving deep and shallow level Cicadidae relationships in aggregate, individual markers contained inadequate phylogenetic signal, in part probably due to short length. The cleaned dataset, consisting of 90 genera representing 44 of 56 current Cicadidae tribes, and 429 loci, supported three of the four sampled Cicadidae subfamilies in concatenated-matrix (IQ-TREE ML) and multispecies coalescent-based (ASTRAL-III) species tree analyses, with the fourth subfamily weakly supported in the ML trees. No well-supported patterns from previous family-level Sanger sequencing studies of Cicadidae phylogeny were contradicted. One taxon (<em>Aragualna plenalinea</em>) did not fall with its current subfamily in the genetic tree, and this genus and its tribe Aragualnini is reclassified to Tibicininae following morphological re-examination. Only subtle differences were observed in trees after removal of loci for which divergent base frequencies were detected. Greater success may be achieved by increased taxon sampling and developing a probe set targeting a more recent common ancestor and longer loci. Searches for contamination are an essential step in phylogenomic analyses of all kinds and our pipeline is an effective solution.</p>
Supplementary material 2 from: Liu L, Liu Q, Gao T (2022) Genome-wide survey reveals the phylogenomic relationships of Chirolophis japonicus Herzenstein, 1890 (Stichaeidae, Perciformes). ZooKeys 1129: 55-72. https://doi.org/10.3897/zookeys.1129.91543
Maximum likelihood phylogenomic tree of Chirolophis japonicus
FIGURE 74 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 74. Mantidactylus inaudax in life, in dorsolateral and ventral view. (a,b) Adult male from a forest fragment west of Lake Alaotra, photographed in 2008. (c,d,e) Adult female from a forest fragment west of Lake Alaotra, photographed in 2008, and femoral gland closeup (e). (f,g) Adult male from a forest fragment west of Lake Alaotra, photographed in 2008. (h,i) Adult male from a forest fragment west of Lake Alaotra, photographed in 2008. (j,k,l) Adult female from Fierenana, photographed in 2003, and femoral gland closeup (l). (m,n,o) Adult male from Fierenana, photographed in 2003, and femoral gland closeup (o). All of these specimens correspond to collected voucher specimens but cannot be reliably assigned to specific voucher numbers.
FIGURE 64 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 64. Audiospectrogram and corresponding oscillogram of a 1000 ms section of a series of advertisement calls (five calls figured) of Mantidactylus biporus recorded on 31 October 2007 at Betampona (19°C air temperature).
FIGURE 44 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 44. Mantidactylus kortei sp. nov. from Andohahela in life, in dorsolateral and ventral view. All photographs taken in 2005. (a,b) Adult male (holotype ZSM 205/2005 = FGZC 2376). (c,d) Adult female (ZSM 204/2005 = FGZC 2375). (e) Female specimen (probably preserved in UADBA). Note the relatively broad and short head of the first two specimens and the more pointed head of the third specimen in (e) which however showed no difference to the other two specimens in the molecular markers analysed.
FIGURE 23 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 23. Preserved holotype specimens of M. steinfartzi sp. nov., the single newly named species in the M. ulcerosus clade. Scale bars equal 5 mm.
FIGURE 36 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 36. Mantidactylus noralottae from the Isalo massif in life, in dorsolateral and ventral view. (a,b) Adult female (tissue ACZC 7948; FAZC 14340). (c,d) Adult male (tissue ACZC 7947; FAZC 14339).
FIGURE 45 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 45. Audiospectrogram and corresponding oscillogram of one advertisement call tentatively assigned to Mantidactylus kortei, recorded on 27 January 2006 at Andohahela National Park (17.6°C air temperature). Recording bandpass-filtered at 500– 4000 Hz.
FIGURE 55 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 55. Mantidactylus marintsoai sp. nov. in life, in dorsolateral, dorsal and ventral view. (a) Unsexed adult (tissue THT 204, not collected). (b,c) Adult female (THT282, not collected). (d,e) Adult female (CURSA-A036/2021 = THC354). (f,g) Adult male (holotype CURSA-A033/2021 = THC301).
FIGURE 12 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 12. Audiospectrogram and corresponding oscillogram of two advertisement calls from a regular call series of Mantidactylus alutus, recorded on 21 January 2003 near Antoetra (20.5–21.0°C air temperature). Recording highpass-filtered at 375 Hz.
FIGURE 9 in An inordinate fondness for inconspicuous brown frogs: integration of phylogenomics, archival DNA analysis, morphology, and bioacoustics yields 24 new taxa in the subgenus Brygoomantis (genus Mantidactylus) from Madagascar
FIGURE 9. Preserved holotypes of newly named species and subspecies in the M. curtus clade. Scale bars equal 5 mm.
Supplementary material 4 from: Lou Y-L, Ma D-K, Jin Z-T, Wang H, Lou L-H, Jin S-H, Liu K, Liu B-B (2022) Phylogenomic and morphological evidence reveal a new species of spider lily, Lycoris longifolia (Amaryllidaceae) from China. PhytoKeys 210: 79-92. https://doi.org/10.3897/phytokeys.210.90391
Figure S4
Supplementary material 2 from: Lou Y-L, Ma D-K, Jin Z-T, Wang H, Lou L-H, Jin S-H, Liu K, Liu B-B (2022) Phylogenomic and morphological evidence reveal a new species of spider lily, Lycoris longifolia (Amaryllidaceae) from China. PhytoKeys 210: 79-92. https://doi.org/10.3897/phytokeys.210.90391
Figure S2
Supplementary material 5 from: Lou Y-L, Ma D-K, Jin Z-T, Wang H, Lou L-H, Jin S-H, Liu K, Liu B-B (2022) Phylogenomic and morphological evidence reveal a new species of spider lily, Lycoris longifolia (Amaryllidaceae) from China. PhytoKeys 210: 79-92. https://doi.org/10.3897/phytokeys.210.90391
Figure S5
Supplementary material 6 from: Lou Y-L, Ma D-K, Jin Z-T, Wang H, Lou L-H, Jin S-H, Liu K, Liu B-B (2022) Phylogenomic and morphological evidence reveal a new species of spider lily, Lycoris longifolia (Amaryllidaceae) from China. PhytoKeys 210: 79-92. https://doi.org/10.3897/phytokeys.210.90391
Figure S6
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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.