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SRX2729549: UCE target enrichment of Fistularia tabacaria: muscle tissue
1 ILLUMINA (NextSeq 500) run: 889,883 spots, 268.7M bases, 114.7Mb downloads

Design: We extracted DNA from ethanol-preserved tissues following a modified Qiagen DNeasy protocols. We quantified all DNA extracts with a Qubit Fluorometer, assessed each extract for quality by electrophoresis, and then sheared extracts by sonication to a target size of 600bp on a Bioruptor (Diagenode, Inc.). Library preparation and targeted enrichment for UCEs followed protocols described in detail by McGee et al. (2016, http://dx.doi.org/10.1098/rspb.2015.1413), which are also available online (http://ultraconserved.org). In brief, we prepared libraries from sheared DNA using commercially available library preparation regents (Kapa Biosystems), a generic SPRI substitute and custom adapters (Glenn et al., 2016, BioRxiv 049114). Following amplification, we grouped libraries into pools of eight based on taxonomic similarity, and we enriched pooled libraries for UCE targets using Mycoarray MYbaits UCE Capture Kits designed to target approximately 1,340 highly conserved loci across acanthomorph fishes. We determined the size of enriched and purified pools with a Bioanalyzer (Agilent Technologies, Inc.) and we quantified enriched libraries by qPCR (Kapa Biosystems) prior to sequencing. We sequenced libraries using approximately 2/3 of an Illumina NextSeq PE150 run (Georgia Genomics Facility). We demultiplexed and converted reads for downstream processing using bcl2fastq2 conversion software (v02.14.01.07. Illumina Inc.). These are the raw, untrimmed reads.
Submitted by: University of California, Davis
Study: Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements
show Abstracthide Abstract
Phylogenetics is undergoing a revolution as large-scale molecular datasets reveal unexpected but repeatable rearrangements of clades that were previously thought to be disparate lineages. One of the most unusual clades of fishes that has been recovered by large-scale molecular datasets is an expanded Syngnathiformes including traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), as well as a diverse set of largely benthic-associated fishes (Callionymoidei, Dactylopteridae, Mullidae, Pegasidae) that were previously dispersed across three orders. The monophyly of this surprising clade of fishes has been upheld by recent studies utilizing both nuclear and mitogenomic data, but the relationships among major lineages within Syngnathiformes remain ambiguous; previous analyses have recovered inconsistent topologies and are plagued by low support at deep divergences between the major lineages. In this study, we use a dataset of ultraconserved elements (UCEs) to conduct the first phylogenomic study of Syngnathiformes. UCEs have been shown to be effective markers for resolving deep phylogenetic relationships in fishes and, combined with increased taxon sampling, we expected UCEs to resolve problematic syngnathiform relationships. Overall, UCEs were effective at resolving relationships within Syngnathiformes at a range of evolutionary timescales. We find consistent support for the monophyly of traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), which better agrees with morphological hypotheses than previously published topologies from molecular data. This result was recovered in all Bayesian and maximum likelihood analyses, was robust to differences in matrix completeness and potential sources of bias, and was also recovered with high support from ASTRAL coalescent-based analyses when matrices were filtered to contain the most phylogenetically informative loci. While Bayesian and maximum likelihood analyses found support for a monophyletic benthic-associated clade (Callionymidae, Dactylopteridae, Mullidae, and Pegasidae) as sister to the long-snouted clade, this result was not replicated in the ASTRAL analyses. The base of our phylogeny is characterized by short internodes separating major syngnathiform lineages and is consistent with the hypothesis of an ancient rapid radiation at the base of Syngnathiformes. Syngnathiformes therefore present an exciting opportunity to study patterns of morphological variation and functional innovation arising from rapid but ancient radiation.
Sample:
SAMN06563074 • SRS2117565 • All experiments • All runs
Library:
Name: fistularia_tabacaria_CEO87
Instrument: NextSeq 500
Strategy: WGS
Source: GENOMIC
Selection: Hybrid Selection
Layout: PAIRED
Runs: 1 run, 889,883 spots, 268.7M bases, 114.7Mb
Run# of Spots# of BasesSizePublished
SRR5439646889,883268.7M114.7Mb2017-04-13

ID:
3932939

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