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SRX583039: Coturnix chinensis UCE reads
1 ILLUMINA (Illumina HiSeq 1500) run: 2.4M spots, 362.2M bases, 234.9Mb downloads

Design: We prepared Nextera sequencing libraries using the manufacturer’s protocol (Illumina Inc., San Diego CA). We pooled libraries into groups of 8 taxa, enriched each library pool for 5060 UCE loci (Faircloth et al. 2012), amplified the enriched pools using limited-cycle PCR (18 cycles), quantified the resulting pools using qPCR (Kapa Biosystems), and sequenced the enriched libraries using a single Illumina HiSeq 2000 lane (PE75 reads generated at the UC Irvine Genomics High-Throughput Facility).
Submitted by: UNIVERSITY OF CALIFORNIA
Study: The evolution of peafowl and other taxa with ocelli (eyespots): A phylogenomic approach
show Abstracthide Abstract
The most striking feature of peafowl (Pavo) is the males' elaborate train, which exhibits ocelli (ornamental eyespots) that are under sexual selection. Two additional genera (Polyplectron and Argusianus) exhibit ocelli, but there is substantial variation among genera in the appearance and location of eyespots, raising the question of whether ocelli are homologous. Within Polyplectron, ocelli appear to be ancestral, suggesting ocelli may have evolved even earlier, prior to the divergence of different genera. However, it remains unclear whether Pavo, Polyplectron, and Argusianus form a clade. We estimated the phylogeny of ocellated species and their likely relatives using sequences from 1966 ultraconserved elements (UCEs) and three mitochondrial regions. The phylogeny suggested that the three ocellated genera are in the same clade, but also that each ocellated genus is sister to at least one genus without ocelli. Indeed, Polyplectron and Galloperdix, a genus not previously suggested to be related to any ocellated taxon, were found to be sister genera. The close relationship between taxa with and without ocelli suggests either that ocelli have been lost repeatedly, or gained independently. Although independent gains may be considered unlikely, this could reflect a pre-existing bias for eye-like structures among females and/or the existence of a simple mutational pathway for the development of ocelli.
Sample:
SAMN02848453 • SRS631263 • All experiments • All runs
Library:
Name: coturnix_chinensis
Instrument: Illumina HiSeq 1500
Strategy: WGA
Source: GENOMIC
Selection: Hybrid Selection
Layout: PAIRED
Spot descriptor:
forward76  reverse

Experiment attributes:
nextera_tag: i7-N705,i5-N505
Runs: 1 run, 2.4M spots, 362.2M bases, 234.9Mb
Run# of Spots# of BasesSizePublished
SRR13656442,414,739362.2M234.9Mb2014-06-11

ID:
828365

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