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SRX1705956: UCE target enrichment of chondestes-grammacus-UWBM-103584 muscle tissue
1 ILLUMINA (Illumina MiSeq) run: 475,998 spots, 239M bases, 147.2Mb downloads

Design: We extracted genomic DNA from vouchered bird tissues using Qiagen DNeasy Blood & Tissue Kits (Qiagen Inc.), and we prepared sequencing libraries for Illumina sequencing using Nextera XT Library Preparation Kits (Illumina, Inc.). We generally followed the sequence capture workflow for Nextera-prepared libraries detailed in Faircloth et al. (2012), but we modified this protocol by using 1/4 aliquots of the required Nextera kit reagents and genomic DNA, and we pooled indexed libraries into groups of eight libraries, prior to enrichment. We enriched each pool using a set of 5,472 custom-designed probes (MYbaits, MYcroarray, Inc.) targeting 5,060 UCE loci (Faircloth et al. 2012) following an open-source protocol (see www.ultraconserved.org for the full protocol). Following enrichment and an 18 cycle PCR-recovery, we combined pooled libraries together in equimolar ratios to a final concentration of 10 然, and we sent the pooled libraries to the UCLA Genoseq Facility for 250 base-pair paired-end sequencing using two runs of an Illumina MiSeq.
Submitted by: Louisiana State University
Study: Target enrichment of thousands of ultraconserved elements sheds new light on early relationships within New World sparrows (Aves: Passerellidae)
show Abstracthide Abstract
Sparrows in the nine-primaried oscine family Passerellidae represent an attractive model for studying avian diversification across North and South America. However, the lack of phylogenetic resolution at the base of the New World sparrow tree has hampered the use of the existing sparrow phylogeny to test questions about the evolution of sparrow traits. We generated phylogenomic data from 1,063 ultraconserved elements to estimate phylogenetic relationships among the major clades of New World sparrows. Concatenated and species-tree analyses of 271,830 base pairs of sequence data converged on a well-supported phylogeny that differs from previous estimates. The resolved backbone of the sparrow phylogeny provides new insight into the biogeography of this radiation by suggesting both a tumultuous biogeographic history, with many colonizations of South America, and several independent ecological transitions to different habitat types.
Sample: Tissue:DHB 3910
SAMN04857243 • SRS1398108 • All experiments • All runs
Name: chondestes-grammacus-UWBM-103584
Instrument: Illumina MiSeq
Strategy: WGS
Selection: Hybrid Selection
Layout: PAIRED
Runs: 1 run, 475,998 spots, 239M bases, 147.2Mb
Run# of Spots# of BasesSizePublished


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