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98 results for “Targeted capture”
Target capture methods offer insight into the evolution of rapidly diverged taxa and resolve allopolyploid homeologs in the fern genus Polypodium s.s.
<p><span></span></p> <p>Like many fern lineages comprising reticulate species complexes, <em>Polypodium</em> s.s. (Polypodiacaeae) has a history shaped by rapid diversification, hybridization, and polyploidy that poses substantial challenges for phylogenetic inference with plastid and single-locus nuclear loci. Using target capture probes for 408 nuclear loci developed by the GOFlag project and a custom bioinformatic pipeline, SORTER, we constructed multi-locus nuclear datasets for diploid temperate and Mesoamerican species of <em>Polypodium</em> and five allotetraploid species belonging to the well-studied <em>Polypodium</em> <em>vulgare</em> complex. SORTER employs a clustering approach to separate putatively paralogous copies of targeted loci into orthologous matrices and haplotype phasing to infer allopolyploid haplotypes across loci, resulting in datasets amenable to both concatenated maximum likelihood and multi-species coalescent phylogenetic analyses. By comparing phylogenies derived from maximum likelihood and multi- species coalescent analyses of unphased and phased datasets, as well as evaluating discordance among gene trees and species trees, we recover support for incomplete lineage sorting within <em>Polypodium</em> s.s., novel relationships among diploid taxa of the <em>Polypodium</em> <em>vulgare</em> complex and its Mesoamerican sister clade, and the placement of several <em>Polypodium</em> species within other genera. Additionally, we were able to infer well-supported phylogenies that identified the hypothesized progenitors of the allotetraploid species, indicating that SORTER is an effective and accurate tool for reconstructing homeolog haplotypes of allopolyploids in fern taxa and other non-model organisms from target capture data.</p>
Supplementary Material for "Target-capture Phylogenetics of the Paper Daisy Stoebe clade (Gnaphalieae: Asteraceae) Using Compositae1061 Baits"
<p>This upload contains supporting information for a manuscript in preparation titled "Target-capture Phylogenetics of the Paper Daisy Stoebe clade (Gnaphalieae: Asteraceae) Using Compositae1061 Baits". The folder contains sequence alignments for the Stoebe clade of paper daisies (Gnaphalieae: Asteraceae), as well as species trees estimated using these data. Additional files are described in the accompanying README file.</p>
A new target capture phylogeny elucidates the systematics and evolution of wing coupling in sack‐bearer moths
<p>The frenulum is a wing coupling structure that is found on the wings of most families of Lepidoptera. It is a single bristle or set of bristles that originate from the base of the hindwing that often interlocks with the forewing during flight. This wing coupling mechanism is thought to have been a major evolutionary innovation that allowed for enhanced flight in Lepidoptera. The sack-bearer moths (Mimallonidae) are unusual among Lepidoptera in that not all species within the family have a frenulum. We test the hypothesis that the frenulum is not necessary and is therefore lost in mimallonids that have longer male forewings because such wings are perhaps better suited to be coupled by other means. To understand the evolution of the frenulum, we inferred the most taxonomically and genetically sampled anchored hybrid enrichment-based phylogeny of Mimallonidae, including 604 loci from all 41 genera and from 120 species, covering about 40% of the described species in the family. The maximum likelihood tree robustly supports major relationships within the family, and ancestral state reconstruction clearly recovers the frenulum as the plesiomorphic condition in Mimallonidae. Our results show that the frenulum is more often observed in species that have shorter, rather than longer, male forewings. The frenulum has historically been used as an important character for intrafamilial classification in Mimallonidae, but our results conclusively show that this character system is more variable than previously thought. Based on our results, we erect two new subfamilies, Roelofinae St Laurent & Kawahara, <b>subfam. n.</b> and Meneviinae St Laurent, Herbin, & Kawahara, <b>subfam. n.</b>, for four genera previously considered <i>incertae sedis.</i> In the predominantly frenulum-lacking clade Cicinninae, we describe a new genus, <i>Cerradocinnus </i>St Laurent, Mielke, & Kawahara, <b>gen. n.</b>, and the genus <i>Gonogramma </i><b>stat. rev.</b> is revalidated to include many species previously placed in <i>Cicinnus sensu lato</i>. With these changes, <i>Cicinnus </i>can now be considered monophyletic. Thirty-three species are transferred to <i>Gonogramma </i>from <i>Cicinnus sensu lato</i>.</p>
Targeted DNA methylation from cell free DNA using hybrid probe capture
<p>CSV files contain beta value and coverage per base & per region, as indicated in the file name.<br> Columns are samples, rows are CpGs or target region - depending on the file.</p> <p>Files were generated from our bismark/bsseq pipeline as described in the manuscript.</p> <p>Contact: dnbuckle@usc.edu</p>
Target-capture probes for phylogenomics of the Caenogastropoda
<p class="MsoNormal">Target-capture approaches have facilitated a rapid growth in the field of phylogenomics but few probe sets exist for mollusks, an exceptionally rich phylum with unparalleled ecological and morphological diversity. We designed and tested the first universal probe set using Phyluce to capture ultraconserved elements (UCEs) and exon loci from the Subclass Caenogastropoda – one of six major lineages of gastropods. The probe set consists of 29,441 probes (8,872 for UCEs and 20,569 for exons) designed to target 1,142 UCE loci and 1,933 exon loci (3,075 total). In silico analyses of our probe set yielded an average of 2,110 loci from genomes and 1,389 loci from transcriptomes of diverse caenogastropods, respectively. After screening these loci to remove those that matched multiple contigs, an average of 1,686 loci from genomes and 785 loci from transcriptomes were retained. Phylogenetic analyses of the loci extracted from transcriptomes produced well-supported trees very similar to those published based on transcriptomic analyses. Although there are few caenogastropod genomes to analyze, phylogenetic relationships estimated from the analysis of loci extracted from genomes recover similar phylogenetic relationships and indicate that the loci targeted with this probe set are informative for resolving deep phylogenetic relationships. An in vitro analysis of the probe set with the Epitoniidae, a diverse caenogastropod family of uncertain affinity and with poorly resolved evolutionary relationships, recovered an average of 1,710 loci and produced a well-resolved phylogeny. Although preliminary, the analysis of loci captured by our probe set for a small number of epitoniid taxa produced a well-resolved tree indicating that this probe set is also able to resolve relationships at shallower hierarchical scales. Together, the in silico and in vitro analyses indicate that target-capture enrichment with this probe set is a useful tool for reconstructing phylogenetic relationships across taxonomic levels and evolutionary time scales.</p>
Data from: Targeted sampling and target capture: assessing phylogeographic concordance with genome-wide data
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Target capture methods offer insight into the evolution of rapidly diverged taxa and resolve allopolyploid homeologs in the fern genus Polypodium s.s.
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Genome-scale target capture of mitochondrial and nuclear environmental DNA from water samples
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Validating a target-enrichment design for capturing uniparental haplotypes in ancient domesticated animals
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Data from: Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in gray wolves
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Target-capture probes for phylogenomics of the Caenogastropoda
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Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae)
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Data from: A target capture-based phylogeny of emerald moths (Lepidoptera: Geometridae: Geometrinae) provides new insights into tribal-level classification
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A new target capture phylogeny elucidates the systematics and evolution of wing coupling in sack‐bearer moths
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Data from: Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs
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Alignments from: Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae)
<p class="BodyA"><span><b>Background:</b> The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e., genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus <i>Hibiscus </i>L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. <i>Hibiscus </i>is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole genome duplication events, we tested three alternative scenarios describing different polyploidization events.</span></p> <p class="BodyA"><span><b>Results:</b> Using target sequence capture, we designed a new probe set for <i>Hibiscus </i>and generated 87 orthologous genes from four diploid species. We detected paralogues in >54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of <i>Hibiscus</i> sampled shared one genome duplication with <i>H. syriacus</i> and one whole genome duplication occurred along the branch leading to <i>H. syriacus</i>.</span></p> <p class="BodyA"><span><b>Conclusions:</b> Here, we corroborated the independent genome doubling previously found in the lineage leading to <i>H. syriacus </i>and a shared genome doubling of this lineage and the remainder of <i>Hibiscus</i>. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within <i>Hibiscus</i>) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.</span></p>
Data from: Comparison of taxon-specific versus general locus sets for targeted sequence capture for plant phylogenomics
Premise of the study: Targeted sequence capture can be used to efficiently gather sequence data for large numbers of loci, such as single-copy nuclear loci. Most published studies in plants have used taxon-specific locus sets developed individually for a clade using multiple genomic and transcriptomic resources. General locus sets can also be developed from loci that have been identified as single-copy and having orthologs in large clades of plants. Methods: We identify and compare a taxon-specific locus set and three general locus sets (COSII, APVO SSC, PPR) for targeted sequence capture in Buddleja (Scrophulariaceae) and outgroups. We evaluate their performance in terms of assembly success, sequence variability, and resolution and support of inferred phylogenetic trees. Results: The taxon-specific locus set had the most target loci. Assembly success was high for all locus sets in Buddleja samples. For outgroups, general locus sets had greater assembly success. Taxon-specific and PPR loci had the highest average variability. The taxon-specific dataset produced the best supported tree, but all datasets showed improved resolution over previous non-sequence capture datasets. Discussion: General loci can be a useful source of sequence capture targets, especially if multiple genomic resources are not available for a taxon.
Data from: Phylogenetics of moth-like butterflies (Papilionoidea: Hedylidae) based on a new 13-locus target capture probe set
The Neotropical moth-like butterflies (Hedylidae) are perhaps the most unusual butterfly family. In addition to being species-poor, this family is predominantly nocturnal and has anti-bat ultrasound hearing organs. Evolutionary relationships among the 36 described species are largely unexplored. A 13-gene anchored hybrid enrichment probe set ('BUTTERFLY2.0'), that includes standard markers used in butterfly phylogenetics, captured sequences from decades-old museum specimens, and appears to be a cost-effective technique to infer phylogenetic relationships of the butterfly tree of life. Our dataset comprises up to 10,898 aligned base pairs from each of the 22 species of Hedylidae and 19 outgroups. Eleven of the thirteen loci were captured from 100% of the taxa, and the remaining loci were captured from ≥94% of taxa. The inferred phylogeny had robust support at 80% of nodes. Our results are consistent with morphological work, with Macrosoma tipulata sister to all remaining hedylids, followed by M. semiermis sister to the remaining species in the genus. We tested the hypothesis that nocturnality evolved only once from diurnality in Hedylidae, and showed that the ancestral condition was likely diurnal, with a shift to nocturnality early in the diversification of this family.
Data from: Phylogenomics of horned lizards (genus: Phrynosoma) using targeted sequence capture data
New genome sequencing techniques are enabling phylogenetic studies to scale-up from using a handful of loci to hundreds or thousands of loci from throughout the genome. In this study, we use targeted sequence capture (TSC) data from 540 ultraconserved elements and 44 protein-coding genes to estimate the phylogenetic relationships among all 17 species of horned lizards in the genus Phrynosoma. Previous molecular phylogenetic analyses of Phrynosoma based on a few nuclear genes, restriction site associated DNA (RAD) sequencing, or mitochondrial DNA (mtDNA) have produced conflicting relationships. Some of these conflicts are likely the result of rapid speciation at the start of Phrynosoma diversification, whereas other examples of gene tree discordance appear to be caused by active and residual traces of hybridization. Concatenation and coalescent-based species tree phylogenetic analyses of these new TSC data support the same topology, and a divergence dating analysis suggests that the Phrynosoma crown group is up to 30 million years old. The new phylogenomic tree supports the recognition of four main clades within Phrynosoma, including Anota (P. mcallii, P. solare, and the P. coronatum complex), Doliosaurus (P. modestum, P. goodei, and P. platyrhinos), Tapaja (P. ditmarsi, P. douglasii, P. hernandesi, and P. orbiculare), and Brevicauda (P. braconnieri, P. sherbrookei, and P. taurus). The phylogeny provides strong support for the relationships among all species of Phrynosoma and provides a robust new framework for conducting comparative analyses.
Data from: Phylogenomic analyses of Sabal (Arecaceae) species relationships using targeted sequence capture
With the increasing availability of high-throughput sequencing, phylogenetic analyses are no longer constrained by the limited availability of a few loci. Here, we describe a sequence capture methodology, which we used to collect data for analyses of diversification within Sabal (Arecaceae), a palm genus native to the south-eastern USA, Caribbean, Bermuda and Central America. RNA probes were developed and used to enrich DNA samples for putatively low copy nuclear genes and the plastomes for all Sabal species and two outgroup species. Sequence data were generated on an Illumina MiSeq sequencer and target sequences were assembled using custom workflows. Both coalescence and supermatrix analyses of 133 nuclear genes were used to estimate species trees relationships. Plastid genomes were also analysed, yielding generally poor resolution with regard to species relationships. Species relationships described in both nuclear gene and plastome sequences largely reflect the biogeography of the group and, to a lesser extent, previous morphology-based hypotheses. Beyond the biological implications, this research validates a high-throughput methodology for generating a large number of genes for coalescence-based phylogenetic analyses in plant lineages.
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