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SRX2698600: UCE target enrichment of Dasylabris_sp_EX559: whole organism
1 ILLUMINA (Illumina HiSeq 2500) run: 1.5M spots, 448.8M bases, 265.8Mb downloads

Design: For all newly sampled taxa, we extracted DNA using Qiagen DNeasy Blood and Tissue kits (Qiagen Inc., Valencia, CA) and we fragmented up to 500 ng of input DNA to an average fragment distribution of 400-600 bp using a Qsonica Q800R sonicator (Qsonica LLC, Newton, CT). Following sonication, we constructed sequencing libraries using Kapa library preparation kits (Kapa Biosystems Inc., Wilmington, MA) and custom sample barcodes. We assessed success of library preparation following PCR amplification by measuring DNA concentration and visualizing libraries on an agarose gel. We purified reactions following PCR using 0.8 to 1.0X AMPure substitute. For UCE enrichment we pooled 6Đ10 libraries together at equimolar concentrations and adjusted pool concentrations to 147 ng/_l. For each enrichment we used a total of 500 ng of DNA (3.4 _l each pool), and we performed enrichments using a custom RNA bait library developed for Hymenoptera and synthesized by MYcroarray (MYcroarray, Ann Arbor, MI). The probe set includes 2,749 probes, targeting 1,510 UCE loci. We hybridized RNA bait libraries to sequencing libraries at 65źC for a period of 24 hours, and we enriched each pool following a standardized protocol (version 1.5; protocol available from http://ultraconserved.org). We verified enrichment success with qPCR (ViiA 7, Applied Biosystems, Waltham MA) by comparing amplification profiles of unenriched to enriched pools using PCR primers designed from several UCE loci. After verification, we used qPCR to measure the DNA concentration of each pool, and we combined all pools together at equimolar ratios to produce a final pool-of-pools. To remove overly large and small fragments, we size-selected the final pools to a range of 300Đ800 bp using a Blue Pippin size selection instrument (Sage Science, Beverly, MA). We mailed size-selected pools to either the UCLA Neuroscience Genomics Core or the Cornell University Biotechnology Resource Center (http://www.biotech.cornell.edu/brc/genomics-facility), where the samples were quality checked on a Bioanalyzer (Agilent Technologies, Santa Clara, CA), quantified with qPCR, and sequenced on an Illumina HiSeq 2500 (2x150 Rapid Run; Ilumina Inc, San Diego, CA).
Submitted by: University of Utah
Study: Phylogenomic insights into the evolution of stinging wasps and the origins of ants and bees
show Abstracthide Abstract
The stinging wasps (Hymenoptera: Aculeata) are an extremely diverse lineage of hymenopteran insects, encompassing over 70,000 described species and a diversity of life history traits, including ectoparasitism, cleptoparasitism, predation, pollen feeding (bees [Anthophila] and Masarinae) and eusociality (social vespid wasps, ants, and some bees) [1]. The most well-studied lineages of Aculeata are the ants, which are ecologically dominant in most terrestrial ecosystems [2], and the bees, the most important lineage of angiosperm-pollinating insects [3]. Establishing the phylogenetic affinities of ants and bees helps us understand and reconstruct patterns of social evolution as well as fully appreciate the biological implications of the switch from carnivory to pollen feeding (pollenivory). Despite recent advancements in aculeate phylogeny [4–11], considerable uncertainty remains regarding higher level relationships within Aculeata, including the phylogenetic affinities of ants and bees [5–7]. We used ultraconserved element (UCE) phylogenomics [7,12] to resolve relationships among stinging wasp families, gathering sequence data from > 800 UCE loci and 187 samples, including 30 out of 31 aculeate families. We analyzed the 187-taxon data set using multiple analytical approaches, and we evaluated several alternative taxon sets. We also tested alternative hypotheses for the phylogenetic positions of ants and bees. Our results present a highly supported phylogeny of the stinging wasps. Most importantly, we find unequivocal evidence that ants are the sister group to bees+apoid wasps (Apoidea) and that bees are nested within a paraphyletic Crabronidae. We also demonstrate that taxon choice can fundamentally impact tree topology and clade support in phylogenomic inference.
Sample: Specimen used for DNA extraction with a Qiagen kit.
SAMN06672442 • SRS2483221 • All experiments • All runs
Library:
Name: Dasylabris_sp_EX559
Instrument: Illumina HiSeq 2500
Strategy: WGA
Source: GENOMIC
Selection: Hybrid Selection
Layout: PAIRED
Runs: 1 run, 1.5M spots, 448.8M bases, 265.8Mb
Run# of Spots# of BasesSizePublished
SRR54061221,496,089448.8M265.8Mb2017-08-31

ID:
3893263

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