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86 results for “UCE”
Using UCEs to track the influence of sea-level change on leafy seadragon populations
<p>Data and code used in bioinformatic processing, bathymetry calculations, population genetic analyses and their output files. Ultraconserved Elements (UCEs) were sequenced in 68 individuals of leafy seadragons (<em>Phycodurus eques</em>, Syngnathidae) sampled across their range along the southern Australian coast.</p> <p>The repository contains</p> <p>A) Scripts to process the sequence data and the resulting</p> <ul> <li>BAM read mapping files</li> <li>VCF files with SNPs before and after filtering</li> </ul> <p> </p> <p>B) Scripts, input files, and output files for the analyses to</p> <ul> <li>reconstruct shallow water areas at different sea levels</li> <li>estimate population structure (PCA, DAPC, Structure, SVDquartets), and spatial genetic patterns (IBD plots, EEMS)</li> <li>calculate genetic diversity (individual-level heterozygosity, population-level heterozygosity, Tajima's D)</li> <li>perform phylogeographic modeling (DIYABC).</li> </ul>
Data from: Cryptic diversity in the Mexican highlands: thousands of UCE loci help illuminate phylogenetic relationships, species limits and divergence times of montane rattlesnakes (Viperidae: Crotalus)
With the continued adoption of genome-scale data in evolutionary biology comes the challenge of adequately harnessing the information to make accurate phylogenetic inferences. Coalescent-based methods of species tree inference have become common, and concatenation has been shown in simulation to perform well, particularly when levels of incomplete lineage sorting are low. However, simulation conditions are often overly simplistic, leaving empiricists with uncertainty regarding analytical tools. We use a large ultraconserved element (UCE) data set (>3000 loci) from rattlesnakes of the Crotalus triseriatus group to delimit lineages and estimate species trees using concatenation and several coalescent-based methods. Unpartitioned and partitioned maximum-likelihood and Bayesian analysis of the concatenated matrix yield a topology identical to coalescent analysis of a subset of the data in bpp. ASTRAL analysis on a subset of the more variable loci also result in a tree consistent with concatenation and bpp, whereas the SVDquartets phylogeny differs at additional nodes. The size of the concatenated matrix has a strong effect on species-tree inference using SVDquartets, warranting additional investigation on optimal data characteristics for this method. Species-delimitation analyses suggest up to 16 unique lineages may be present within the C. triseriatus group, with divergences occurring during the Neogene and Quaternary. Network analyses suggest hybridization within the group is relatively rare. Altogether, our results reaffirm the Mexican highlands as a biodiversity hotspot and suggest that coalescent-based species-tree inference on data subsets can provide a strongly supported species tree consistent with concatenation of all loci with a large amount of missing data.
Evaluating UCE data adequacy and integrating uncertainty in a comprehensive phylogeny of ants
<p>Data from manuscript "Evaluating UCE data adequacy and integrating uncertainty in a comprehensive phylogeny of ants". Includes assembled contigs, unaligned and aligned ultraconserved element loci (UCE) and concatenated matrices, input and output of phylogenetic analyses, custom scripts used.</p>
UCE phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) elucidates genus boundaries, species boundaries, and the vicariant history of a temperate-tropical disjunction
<p><span><span><span><span><span><span><span><span><span><span><span>The genus <i>Cryptopone</i> Emery contains 25 species of litter and soil ants, 5 of which occur in the Americas. <i>Cryptopone</i><i>gilva </i>occurs in the southeastern U.S.A. and cloud forests of Mesoamerica, exhibiting an uncommon biogeographic disjunction observed most often in plants. We used phylogenomic data from ultraconserved elements (UCEs), as well as mitogenomes and legacy markers, to investigate phylogenetic relationships, species boundaries, and divergence dates among New World <i>Cryptopone</i>. Species delimitation was conducted using a standard approach and then tested using model-based molecular methods (SNAPP, BPP, SODA, and bPTP). We found that <i>Cryptopone</i> as currently constituted is polyphyletic, and that all the South American species belong to <i>Wadeura</i> Weber, a separate genus unrelated to <i>Cryptopone</i>. A single clade of true <i>Cryptopone</i> occurs in the Americas, restricted to North and Central America. This clade is composed of four species that originated ~4.2 million years ago. One species from the mountains of Guatemala is sister to the other three, favoring a vicariance hypothesis of diversification. The taxonomy of the New World <i>Cryptopone</i>and <i>Wadeura</i> are revised. Taxonomic changes are: <i>Wadeura</i> Weber is <b>resurrected</b>, with <b>new combinations</b> <i>W. guianensis</i>Weber, <i>W. holmgreni</i> (Wheeler), and <i>W. pauli</i> (Fernandes & Delabie); <i>C. guatemalensis</i> (Forel) (<b>rev. stat.</b>) is raised to species, and includes <i>C. obsoleta</i> (Menozzi) (<b>syn. nov.</b>). The following <b>new species</b> are described: <i>Cryptopone gilvagrande</i>, <i>C. gilvatumida</i>, and <i>Wadeura holmgrenita</i>. <i>Cryptopone hartwigi</i> is transferred to <i>Fisheropone</i> (<b>n. comb.</b>). <i>Cryptopone mirabilis</i> (Mackay & Mackay 2010) is a junior synonym of <i>Centromyrmex brachycola</i> (Roger) (<b>syn. nov.</b>).</span></span></span></span></span></span></span></span></span></span></span></p>
UCE Phylogenomics resolves major relationships among Ectaheteromorph ants (Hymenoptera: Formicidae: Ectatomminae, Heteroponerinae): A new classification for the subfamilies and the description of a new genus
<p>Uncovering the evolutionary history of the subfamilies Ectatomminae and Heteroponerinae, or ectaheteromorphs, is key to understanding a major branch of the ant tree of life. Despite their diversity and ecological importance, phylogenetic relationships in the group have not been well explored. One particularly suitable tool for resolving phylogeny is the use of ultraconserved elements (UCEs), which have been shown to be ideal markers at a variety of evolutionary time scales. In the present study, we enriched and sequenced 2,127 UCEs from 135 specimens of ectaheteromorph ants and investigated phylogeny using a variety of model-based phylogenomic methods. Trees recovered from partitioned maximum-likelihood and species-tree analyses were well resolved and largely congruent. The results are consistent with an expanded concept of Ectatomminae that now includes the subfamily Heteroponerinae new synonym and its single tribe Heteroponerini new combination. Eleven monophyletic groups are recognized as genera: Acanthoponera, Alfaria status revived, Boltonia Camacho and Feitosa new genus, Ectatomma, Gnamptogenys, Heteroponera, Holcoponera status revived, Poneracantha status revived, Rhytidoponera, Stictoponera status revived, and Typhlomyrmex. The new phylogenetic framework and classification proposed here will shed light on the study of Ectatomminae taxonomy and systematics, as well as on the morphological evolution of the groups that it comprises.</p>
Phylogenomic placement of a new genus and species of jumping spiders (Araneae: Salticidae: Spartaeini) based on UCE data
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Expanded phylogeny of Nomadinae (Hymenoptera: Apidae) with integration of UCE and DNA barcode sequence data
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UCE phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) elucidates genus boundaries, species boundaries, and the vicariant history of a temperate-tropical disjunction
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Data from: Diversification in Amazonian <em>Hypocnemis</em> antbirds (Aves: Thamnophilidae) inferred from Ultraconserved Elements (UCEs)
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Data from: Cryptic diversity in the Mexican highlands: thousands of UCE loci help illuminate phylogenetic relationships, species limits and divergence times of montane rattlesnakes (Viperidae: Crotalus)
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UCE Phylogenomics resolves major relationships among Ectaheteromorph ants (Hymenoptera: Formicidae: Ectatomminae, Heteroponerinae): A new classification for the subfamilies and the description of a new genus
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Data from: Ultraconserved yet informative for species delimitation: UCEs resolve long-standing systematic enigma in Central European bees
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Fig. 7 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a
Fig. 7. Shape of third abdominal sternite, Cryptopone vs.Wadeura. Cryptopone gilvagrande (CASENT064143), lateral view (A), oblique ventral view (B). Wadeura guianensis (CASENT0640149), lateral view (C), oblique ventral view (D). Scale bars are 0.2 mm.
Fig. 6 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a
Fig. 6. Biogeography of the Cryptopone gilva complex within Central America. Chronogram inferred using BEAST2, 300 UCE loci, and a fixed topology (all UCE samples and SWSC-EN partitioning). Only results for the C. gilva complex are shown (see Supp Fig. 6 [online only] for the full results). Numbers on nodes are mean ages in millions of years ago and node bars are 95% Highest Posterior Densities (HPD).The map inset shows the distribution of C. gilva-clade samples within Central America. Colored dots match tip labels of the chronogram. Sites where specimens were identified by morphology alone (no sequencing) are shown as x for C. gilvagrande and a small black dot for C. guatemalensis. Samples of true C. gilva from the United States are not shown in the map.
Fig. 14 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a
Fig. 14. Wadeura species, petiole lateral views. (A) W. guianensis (CASENT0640150). (B) W. pauli (CASENT0637806). (C) W. holmgreni (CASENT0373370). (D) W. holmgrenita (CASENT0637779). Scale bars are 0.2 mm.
Fig. 5 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a
Fig. 5. Species tree and species delimitation in the Cryptopone gilva complex.The species tree was inferred using SNP data and the Bayesian program SNAPP, with the resulting tree set displayed using DensiTree.The SNAPP densitree shows at least four clearly differentiated species-level lineages. Species delimitation using the programs BPP, SODA, and bPTP, recovered between 4 and 17 species.The results for the UCE samples only are mapped onto the SNAPP densitree result. The connected red bars represent single species that were not monophyletic in the SNAPP phylogeny. The colored boxes and blue species names represent the final species delimitation and taxonomy.
Fig. 3. Relationships among samples within the C in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a
Fig. 3. Relationships among samples within the C. gilva complex based on analysis of 2,199 UCE loci and the SWSC-EN partitioning scheme. Four main clades were recovered and these were delimited as species using an integrative approach. Support values are UFB/SH-aLRT with maximum supports (100/100) not shown.The photo inset is of C. guatemalensis (CASENT0646802; Credit: John Longino).The same tree with support values is available in Supp Fig. 2 (online only).
Fig. 15 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a
Fig. 15. Holotype of Wadeura holmgrenita (CASENT0637779), lateral and dorsal views. Scale is the same for both images.
Fig. 3 in Understanding UCEs: A Comprehensive Primer on Using Ultraconserved Elements for Arthropod Phylogenomics
Fig. 3. Breakdown of the phylogenetic programs used by arthropod UCE-based publications (as of July 2019).
Fig. 1 in Understanding UCEs: A Comprehensive Primer on Using Ultraconserved Elements for Arthropod Phylogenomics
Fig. 1. Breakdown of the number of arthropod UCEs-based publications per year (as of July 2019) by taxonomic group and taxonomic hierarchy.
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