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115 results for “Ultraconserved elements”
Data from: Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales
Comparative genetic studies of non-model organisms are transforming rapidly due to major advances in sequencing technology. A limiting factor in these studies has been the identification and screening of orthologous loci across an evolutionarily distant set of taxa. Here, we evaluate the efficacy of genomic markers targeting ultraconserved DNA elements (UCEs) for analyses at shallow evolutionary timescales. Using sequence capture and massively parallel sequencing to generate UCE data for five co-distributed Neotropical rainforest bird species, we recovered 776–1516 UCE loci across the five species. Across species, 53–77% of the loci were polymorphic, containing between 2.0 and 3.2 variable sites per polymorphic locus, on average. We performed species tree construction, coalescent modeling, and species delimitation, and we found that the five co-distributed species exhibited discordant phylogeographic histories. We also found that species trees and divergence times estimated from UCEs were similar to the parameters obtained from mtDNA. The species that inhabit the understory had older divergence times across barriers, contained a higher number of cryptic species, and exhibited larger effective population sizes relative to the species inhabiting the canopy. Because orthologous UCEs can be obtained from a wide array of taxa, are polymorphic at shallow evolutionary timescales, and can be generated rapidly at low cost, they are an effective genetic marker for studies investigating evolutionary patterns and processes at shallow timescales.
Data from: Analysis of a rapid evolutionary radiation using ultraconserved elements (UCEs): Evidence for a bias in some multi-species coalescent methods
Rapid evolutionary radiations are expected to require large amounts of sequence data to resolve. To resolve these types of relationships many systematists believe that it will be necessary to collect data by next-generation sequencing (NGS) and use multispecies coalescent ("species tree") methods. Ultraconserved element (UCE) sequence capture is becoming a popular method to leverage the high throughput of NGS to address problems in vertebrate phylogenetics. Here we examine the performance of UCE data for gallopheasants (true pheasants and allies), a clade that underwent a rapid radiation 10–15 Ma. Relationships among gallopheasant genera have been difficult to establish. We used this rapid radiation to assess the performance of species tree methods, using ∼600 kilobases of DNA sequence data from ∼1500 UCEs. We also integrated information from traditional markers (nuclear intron data from 15 loci and three mitochondrial gene regions). Species tree methods exhibited troubling behavior. Two methods [Maximum Pseudolikelihood for Estimating Species Trees (MP-EST) and Accurate Species TRee ALgorithm (ASTRAL)] appeared to perform optimally when the set of input gene trees was limited to the most variable UCEs, though ASTRAL appeared to be more robust than MP-EST to input trees generated using less variable UCEs. In contrast, the rooted triplet consensus method implemented in Triplec performed better when the largest set of input gene trees was used. We also found that all three species tree methods exhibited a surprising degree of dependence on the program used to estimate input gene trees, suggesting that the details of likelihood calculations (e.g., numerical optimization) are important for loci with limited phylogenetic information. As an alternative to summary species tree methods we explored the performance of SuperMatrix Rooted Triple - Maximum Likelihood (SMRT-ML), a concatenation method that is consistent even when gene trees exhibit topological differences due to the multispecies coalescent. We found that SMRT-ML performed well for UCE data. Our results suggest that UCE data have excellent prospects for the resolution of difficult evolutionary radiations, though specific attention may need to be given to the details of the methods used to estimate species trees.
Data from: A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs)
Ray-finned fishes constitute the dominant radiation of vertebrates with over 32,000 species. Although molecular phylogenetics has begun to disentangle major evolutionary relationships within this vast section of the Tree of Life, there is no widely available approach for efficiently collecting phylogenomic data within fishes, leaving much of the enormous potential of massively parallel sequencing technologies for resolving major radiations in ray-finned fishes unrealized. Here, we provide a genomic perspective on longstanding questions regarding the diversification of major groups of ray-finned fishes through targeted enrichment of ultraconserved nuclear DNA elements (UCEs) and their flanking sequence. Our workflow efficiently and economically generates data sets that are orders of magnitude larger than those produced by traditional approaches and is well-suited to working with museum specimens. Analysis of the UCE data set recovers a well-supported phylogeny at both shallow and deep time-scales that supports a monophyletic relationship between Amia and Lepisosteus (Holostei) and reveals elopomorphs and then osteoglossomorphs to be the earliest diverging teleost lineages. Our approach additionally reveals that sequence capture of UCE regions and their flanking sequence offers enormous potential for resolving phylogenetic relationships within ray-finned fishes.
Supplementary material 2 from: Jasso-Martínez JM, Brady SG, Kula RR (2023) Phylogenetic affinities of the non-cyclostome subfamilies Amicrocentrinae and Dirrhopinae (Hymenoptera, Braconidae) confirmed by ultraconserved element data. Journal of Hymenoptera Research 96: 1017-1030. https://doi.org/10.3897/jhr.96.111012
Maximum likelihood tree resulting from the 25% complete matrix
Enigmas no longer: using Ultraconserved Elements to place several unusual hawk taxa and address the non-monophyly of the genus Accipiter (Accipitriformes: Accipitridae)
<p>Alignment and tree data associated with the paper:<strong> </strong><span>Enigmas no longer: using Ultraconserved Elements to place several unusual hawk taxa and address the non-monophyly of the genus <em>Accipiter </em>(Accipitriformes: Accipitridae)</span></p>
Data from: Ultraconserved elements anchor thousands of genetic markers for target enrichment spanning multiple evolutionary timescales
Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with non-model organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota, because UCEs and phylogenetic relationships are well known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2,030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2,386 UCE-anchored loci from nine, non-model avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels.
Figure 7 from: Derkarabetian S, Starrett J, Tsurusaki N, Ubick D, Castillo S, Hedin M (2018) A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements. ZooKeys 760: 1-36. https://doi.org/10.3897/zookeys.760.24937
Figure 7 Representative penis morphology of Travunioidea. Clockwise from left: Trojanella serbica redrawn from Karaman (2005), Travunia hofferi redrawn from Karaman (2005), Cryptomaster behemoth adapted from Starrett et al. (2016), Holoscotolemon jaqueti redrawn from Martens (1978), Briggsus hamatus, Yuria pulcra, Paranonychus brunneus, Metanonychus setulus navarrus, Nippononychus japonicus redrawn from Suzuki (1975), Kaolinonychus coreanus coreanus redrawn from Suzuki (1975), Izunonychus ohruii, Zuma acuta. All Travuniidae and Cladonychiidae are drawn in ventral view; Cryptomastridae, Yuria, and Paranonychidae drawn in lateral. For simplicity, not all travunioid genera are included.
Figure 5 from: Derkarabetian S, Starrett J, Tsurusaki N, Ubick D, Castillo S, Hedin M (2018) A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements. ZooKeys 760: 1-36. https://doi.org/10.3897/zookeys.760.24937
Figure 5 Phylogenomic relationships among travunioid genera. Left: 70% SVDQuartets. Right: 70% ASTRAL. Nodes are fully supported (100% bootstrap), unless indicated.
Figure 3 from: Derkarabetian S, Starrett J, Tsurusaki N, Ubick D, Castillo S, Hedin M (2018) A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements. ZooKeys 760: 1-36. https://doi.org/10.3897/zookeys.760.24937
Figure 3 Phylogenetic relationships among major laniatorean lineages. Lower phylogenies correspond to results presented in this study. Nodes are fully supported (100% bootstrap or 1.0 posterior probability), unless indicated otherwise. Numbers in lower left phylogeny correspond to support values from 50% RAxML concatenated (top), and from 70% RAxML partitioned (bottom) analyses. Numbers in ASTRAL phylogeny based on 50% (top) and 70% (bottom) matrices.
Figure 2 from: Derkarabetian S, Starrett J, Tsurusaki N, Ubick D, Castillo S, Hedin M (2018) A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements. ZooKeys 760: 1-36. https://doi.org/10.3897/zookeys.760.24937
Figure 2 Geographic distribution of travunioid genera. Colors correspond to classification proposed in this study. Abbreviations: wNA = western North America, eNA = eastern North America, EUR = central and southern Europe, JPN/KOR = Japan and South Korea.
Figure 1 from: Derkarabetian S, Starrett J, Tsurusaki N, Ubick D, Castillo S, Hedin M (2018) A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements. ZooKeys 760: 1-36. https://doi.org/10.3897/zookeys.760.24937
Figure 1 Photographs of live travunioid harvestmen. A Theromaster brunneus B Erebomaster sp. C Cryptomaster leviathan D Holoscotolemon lessiniense E Peltonychia leprieurii F Trojanella serbica G Briggsus sp. H Isolachus spinosus I Speleonychia sengeri J Yuria pulcra K Paranonychus brunneus L Sclerobunus nondimorphicus M Metanippononychus sp. N Zuma acuta O Kainonychus akamai. All photos by MH, except D, E (courtesy of and copyright A. Schönhofer), and F (courtesy of and copyright I. Karaman).
Figure 4 from: Derkarabetian S, Starrett J, Tsurusaki N, Ubick D, Castillo S, Hedin M (2018) A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements. ZooKeys 760: 1-36. https://doi.org/10.3897/zookeys.760.24937
Figure 4 Phylogenomic relationships among travunioid genera. Left: RAxML and 50% BEAST concatenated topologies, with bootstrap support from the partitioned analysis. All nodes in the BEAST topology have posterior probability of 1.0. Abbreviations indicate placement in classification at the time of Kury et al. (2014): Tt = Travuniidae, Travuniinae; Tc = Travuniidae, Cladonychiinae; Tb = Travuniidae, Briggsinae; Pp = Paranonychidae, Paranonychinae; Ps = Paranonychidae, Sclerobuninae; N = Nippononychidae. Right: 70% BEAST concatenated. Nodes are fully supported (100% bootstrap or 1.0 posterior probability), unless indicated.
Figure 6 from: Derkarabetian S, Starrett J, Tsurusaki N, Ubick D, Castillo S, Hedin M (2018) A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements. ZooKeys 760: 1-36. https://doi.org/10.3897/zookeys.760.24937
Figure 6 Morphology of Cryptomastridae. A) male Cryptomaster, arrow denotes sexually dimorphic swelling diagnostic of Cryptomastridae; B) Speleomaster, habitus; C) Scanning electron micrograph of tibial swelling, from Starrett et al. (2016); D) Cryptomastrid distribution.
Supplementary material 2 from: Derkarabetian S, Starrett J, Tsurusaki N, Ubick D, Castillo S, Hedin M (2018) A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements. ZooKeys 760: 1-36. https://doi.org/10.3897/zookeys.760.24937
Figures : Explanation note:
Data from: Sequence capture of ultraconserved elements from bird museum specimens
New DNA sequencing technologies are allowing researchers to explore the genomes of the millions of natural history specimens collected prior to the molecular era. Yet, we know little about how well specific next-generation sequencing (NGS) techniques work with the degraded DNA typically extracted from museum specimens. Here, we use one type of NGS approach, sequence capture of ultraconserved elements (UCEs), to collect data from bird museum specimens as old as 120 years. We targeted 5060 UCE loci in 27 western scrub-jays (Aphelocoma californica) representing three evolutionary lineages that could be species, and we collected an average of 3749 UCE loci containing 4460 single nucleotide polymorphisms (SNPs). Despite older specimens producing fewer and shorter loci in general, we collected thousands of markers from even the oldest specimens. More sequencing reads per individual helped to boost the number of UCE loci we recovered from older specimens, but more sequencing was not as successful at increasing the length of loci. We detected contamination in some samples and determined that contamination was more prevalent in older samples that were subject to less sequencing. For the phylogeny generated from concatenated UCE loci, contamination led to incorrect placement of some individuals. In contrast, a species tree constructed from SNPs called within UCE loci correctly placed individuals into three monophyletic groups, perhaps because of the stricter analytical procedures used for SNP calling. This study and other recent studies on the genomics of museum specimens have profound implications for natural history collections, where millions of older specimens should now be considered genomic resources.
Data from: Ultraconserved element (UCE) probe set design: base genome and initial design parameters critical for optimization
Targeted capture and enrichment approaches have proven effective for phylogenetic study. Ultraconserved elements (UCEs) in particular have exhibited great utility for phylogenomic analyses, with the software package phyluce being among the most utilized pipelines for UCE phylogenomics, including probe design. Despite the success of UCEs, it is becoming increasing apparent that diverse lineages require probe sets tailored to focal taxa in order to improve locus recovery. However, factors affecting probe design and methods for optimizing probe sets to focal taxa remain underexplored. Here, we use newly available beetle (Coleoptera) genomic resources to investigate factors affecting UCE probe set design using phyluce. In particular, we explore the effects of stringency during initial design steps, as well as base genome choice on resulting probe sets and locus recovery. We found that both base genome choice and initial bait design stringency parameters greatly alter the number of resultant probes included in final probe sets and strongly affect the number of loci detected and recovered during in silico testing of these probe sets. In addition, we identify attributes of base genomes that correlated with high performance in probe design. Ultimately, we provide a recommended workflow for using Phyluce to design an optimized UCE probe set that will work across a targeted lineage, and use our findings to develop a new, open‐source UCE probe set for beetles of the suborder Adephaga.
Fig. 4 in To design, or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe
Fig. 4. The proportion of different types of loci targeted by scarab and hydrophiloid probe sets.
Data from: Advancing mite phylogenomics: designing ultraconserved elements for Acari phylogeny
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Data from: Ultraconserved element (UCE) probe set design: base genome and initial design parameters critical for optimization
Open the record for dataset details and reuse information.
Data from: Ultraconserved elements anchor thousands of genetic markers for target enrichment spanning multiple evolutionary timescales
Open the record for dataset details and reuse information.
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