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115 results for “ultraconserved elements”
Disentangling Historical Relationships Within Poeciliidae (Teleostei: Cyprinodontiformes) Using Ultraconserved Elements
<p>The present dataset contains alignments and trees associated with the article "<strong>Disentangling Historical Relationships Within Poeciliidae (Teleostei: Cyprinodontiformes) Using Ultraconserved Elements</strong>". Raw reads can be found at http://www.ncbi.nlm.nih.gov/bioproject/992473 </p>
Ultraconserved elements resolve the phylogeny and corroborate patterns of molecular rate variation in herons (Aves: Ardeidae)
<p>Thoroughly sampled and well-supported phylogenetic trees are essential to taxonomy and to guide studies of evolution and ecology. Despite extensive prior inquiry, a comprehensive tree of heron relationships (Aves: Ardeidae) has not yet been published. As a result, the classification of this family remains unstable, and their evolutionary history remains poorly studied. Here, we sample genome-wide ultraconserved elements (UCEs) and mitochondrial DNA sequences (mtDNA) of >90% of extant species to estimate heron phylogeny using a combination of maximum likelihood (ML), coalescent, and Bayesian inference (BI) methods. The UCE and mtDNA trees are mostly concordant with one another, providing a topology that resolves relationships among the five heron subfamilies and indicates that the genera <em>Gorsachius</em>, <em>Botaurus</em>, <em>Ardea</em>, and <em>Ixobrychus</em> are not monophyletic. We also present the first genetic data from the Forest Bittern <em>Zonerodius</em> <em>heliosylus</em>, an enigmatic species of New Guinea; our results suggest that it is a member of the genus <em>Ardeola</em> and not the Tigrisomatinae (tiger herons), as previously thought. Lastly, we compare molecular rates between heron clades in the UCE tree with those in previously constructed mtDNA and DNA-DNA hybridization trees. We show that rate variation in the UCE tree corroborates rate patterns in the previously constructed trees, i.e., that bitterns (<em>Ixobrychus</em> and <em>Botaurus</em>) evolved comparatively faster, and some tiger herons (<em>Tigrisoma</em>) and the Boat-billed Heron (<em>Cochlearius</em>) more slowly, than other heron taxa. </p>
Fig. 4. A. Dorsal, B in Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family
Fig. 4. A. Dorsal, B, lateral and C. ventral view of the skull of Micrelaps muelleri (SMNH.R 17777). D. Ectopterygoid of the same specimen in ventral view. E. Ventral and F. lateral views of the palatomaxillary arch.
Fig. 1. A. ASTRAL and B. wASTRAL-hybrid species trees for the superfamily Elapoidea from the 50 in Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family
Fig. 1. A. ASTRAL and B. wASTRAL-hybrid species trees for the superfamily Elapoidea from the 50 % complete dataset, consisting of 4561 loci. Circles on the branch represent a local posterior probability support of 0.95 to 1.0. Abbreviations – AT – Atractaspidinae, CL – Cyclocoridae, EL – Elapidae, LM – Lamprophiinae, MC – Micrelapidae fam. nov., OG – outgroup, PD – Pseudaspidinae, PR – Prosymninae, PS – Psammophiinae, PX – Pseudoxyrhophiinae.
Fig. 3 in Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family
Fig. 3. Time calibrated phylogeny (50 % complete dataset) of elapoid snakes, estimated with the Maximum Likelihood implementation of the RelTime method (with lognormal node calibration densities). Values on the branches indicate the estimated divergence times. The blue bar represents the 95 % confidence intervals around the estimated divergence times.
Fig. 2. Maximum Likelihood species tree from the concatenated 50 in Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family
Fig. 2. Maximum Likelihood species tree from the concatenated 50 % complete dataset consisting of 4561 loci. Values on the branch indicate Shimodaira Hasegawalike approximate likelihood ratio test and ultrafast bootstrap. Abbreviations as in Fig. 1.
To design, or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe design
<p>This repository contains Materials and designed UCE probe sets for the manuscript entitled "To design or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe design".</p>
Ultraconserved elements resolve the phylogeny and corroborate patterns of molecular rate variation in herons (Aves: Ardeidae)
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Phylogenomics of bivalvia using ultraconserved elements (UCEs) reveal new topologies for Pteriomorphia and Imparidentia
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Data from: A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements
Molecular phylogenetics has transitioned into the phylogenomic era, with data derived from next-generation sequencing technologies allowing unprecedented phylogenetic resolution in all animal groups, including understudied invertebrate taxa. Within the most diverse harvestmen suborder, Laniatores, most relationships at all taxonomic levels have yet to be explored from a phylogenomics perspective. Travunioidea is an early-diverging lineage of laniatorean harvestmen with a Laurasian distribution, with species distributed in eastern Asia, eastern and western North America, and south-central Europe. This clade has had a challenging taxonomic history, but the current classification consists of ~77 species in three families, the Travuniidae, Paranonychidae, and Nippononychidae. Travunioidea classification has traditionally been based on structure of the tarsal claws of the hind legs. However, it is now clear that tarsal claw structure is a poor taxonomic character due to homoplasy at all taxonomic levels. Here, we utilize DNA sequences derived from capture of ultraconserved elements (UCEs) to reconstruct travunioid relationships. Data matrices consisting of 317–677 loci were used in maximum likelihood, Bayesian, and species tree analyses. Resulting phylogenies recover four consistent and highly supported clades; the phylogenetic position and taxonomic status of the enigmatic genus Yuria is less certain. Based on the resulting phylogenies, a revision of Travunioidea is proposed, now consisting of the Travuniidae, Cladonychiidae, Paranonychidae (Nippononychidae is synonymized), and the new family Cryptomastridae Derkarabetian & Hedin, fam. n., diagnosed here. The phylogenetic utility and diagnostic features of the intestinal complex and male genitalia are discussed in light of phylogenomic results, and the inappropriateness of the tarsal claw in diagnosing higher-level taxa is further corroborated.
Ultraconserved element data for phylogenomic placement of the jumping spider genus Iranattus Prószyński, 1992 (Salticidae, Plexippini, Plexippina)
<p>The jumping spider genus <em>Iranattus</em> Prószyński, 1992 has been placed in the Harmochirina based on morphology. We use phylogenomic evidence based on ultraconserved element (UCE) data to show that it belongs instead in the subtribe Plexippina.</p>
Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non-model organisms
<p>Despite the increasing accessibility of high-throughput sequencing, obtaining high-quality genomic data on non-model organisms without proximate well-assembled and annotated genomes remains challenging. Here we describe a workflow that takes advantage of distant genomic resources and ingroup transcriptomes to select and jointly enrich long open reading frames (ORFs) and ultraconserved elements (UCEs) from genomic samples for integrative studies of microevolutionary and macroevolutionary dynamics. This workflow is applied to samples of the African unionid bivalve tribe Coelaturini (Parreysiinae) at basin and continent-wide scales. Our results indicate that ORFs are efficiently captured without prior identification of intron-exon boundaries. The enrichment of UCEs was less successful but nevertheless produced substantial datasets. Exploratory continent-wide phylogenetic analyses with ORF supercontigs (> 515,000 parsimony informative sites) resulted in a fully resolved phylogeny, the backbone of which was also retrieved with UCEs (> 11,000 informative sites). Variant calling on ORFs and UCEs of Coelaturini from the Malawi Basin produced ~2,000 SNPs per population pair. Estimates of nucleotide diversity and population differentiation were similar for ORFs and UCEs. They were low compared to previous estimates in mollusks, but comparable to those in recently diversifying Malawi cichlids and other taxa at an early stage of speciation. Skimming off-target sequence data from the same enriched libraries of Coelaturini from the Malawi Basin, we reconstructed the maternally-inherited mitogenome, which displays the gene order inferred for the most recent common ancestor of Unionidae. Overall, our workflow and results provide exciting perspectives for integrative genomic studies of microevolutionary and macroevolutionary dynamics in non-model organisms.</p>
Unraveling the myotis norass: Ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble
<p>Using sequences from 2615 UCE loci and multiple methodologies we inferred phylogenies for the largest genetic dataset of New World Myotis to date. The resulting phylogenetic trees were populated with short branch lengths and widespread conflict, hallmarks consistent with rapid adaptive radiations. The degree of conflict observed in Myotis has likely contributed to difficulties disentangling deeper evolutionary relationships. Unlike earlier phylogenies based on 1-2 gene sequences, this UCE dataset places M. brandtii outside the New World clades. Introgression testing of a small subset of our samples revealed evidence of historical but not contemporary gene flow, suggesting that hybridization occurs less frequently in the Neotropics than in the Nearctic. We identified several instances of cryptic lineages within described species as well as several instances of potential taxonomic over-splitting. Evidence from Central and South American localities suggests that diversity in those regions is not fully characterized. In light of the accumulated evidence of the evolutionary complexity in Myotis and our survey of the taxonomic implications from our phylogenies it is apparent that the definition of species and regime of species delimitation need to be re-evaluated for Myotis. This will require substantial collaboration and sample sharing between geneticists and taxonomists to build a system that is both robust and applicable in a genus as diverse as Myotis.</p>
Data from: Ultraconserved elements improve resolution of marmot phylogeny and offer insights into biogeographic history
<p class="MsoNormal"><span>Marmots (<em>Marmota</em> spp.) comprise a lineage of large-bodied ground squirrels that diversified rapidly in the Pleistocene, when the planet quickly transitioned to a drier, colder, and highly seasonal climate—particularly at high latitudes. Fossil evidence indicates the genus spread from North America, across Beringia, and into the European Alps over the course of only a few million years, beginning in the late Pliocene. Marmots are highly adapted to survive long and severely cold winters, and this likely favored their expansion and diversification over this time period. Previous phylogenetic studies have identified two major subgenera of marmots, but the timing of important speciation events and some species relationships have been difficult to resolve. Here we use ultraconserved elements and mitogenomes, with samples from all 15 extant species, to more precisely retrace how and when marmots came to inhabit a vast Holarctic range. Our results indicate marmots arose in North America in the mid Miocene (~16.3 Mya) and dispersed across the Bering Land Bridge in the late Pliocene (~3-4 Mya); in addition, our fossil-calibrated timeline is suggestive of the rise and spread of open grasslands as being particularly important to marmot diversification. The woodchuck (<em>M. monax</em>) and the Alaska marmot (<em>M. broweri</em>) are found to be more closely related to the Eurasian species than to the other North American species. Paraphyly is evident in the bobak marmot (<em>M. bobak</em>) and the hoary marmot (<em>M. caligata</em>), and in the case of the latter the data are highly suggestive of a second, cryptic species in the Cascade Mountains of Washington.</span></p>
Ultraconserved elements support the elevation of a new avian family, Eurocephalidae, the white-crowned shrikes
<p>In this study, we infer genus-level relationships within shrikes (Laniidae), crows (Corvidae), and their allies using ultraconserved elements (UCEs). We confirm previous results of the Crested Shrikejay (<em>Platylophus</em> <em>galericulatus</em>) as comprising its own taxonomic family and find strong support for its sister relationship to laniid shrikes. We also find strong support that the African-endemic genus <em>Eurocephalus</em>, which comprises two allopatric species (<em>E. ruppelli </em>and<em> E. anguitimens</em>), are not shrikes. We propose elevating the white-crowned shrikes to their own family, Eurocephalidae. </p>
Supplementary material: Ultraconserved elements improve the resolution of difficult nodes within the rapid radiation of neotropical sigmodontine rodents (Cricetidae: Sigmodontinae)
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Data from: A phylogenomic perspective on the biogeography of skinks in the Plestiodon brevirostris group inferred from target enrichment of ultraconserved elements
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Phasing in and out of phytophagy: Phylogeny and evolution of the family Eurytomidae (Hymenoptera: Chalcidoidea) based on Ultraconserved Elements
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Data from: Diversification in Amazonian <em>Hypocnemis</em> antbirds (Aves: Thamnophilidae) inferred from Ultraconserved Elements (UCEs)
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Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non-model organisms
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International Brain Laboratory public data
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OpenNeuro
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