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SRX879681: RAD library sequences for C. cyanus flavipectus, sample Ccya (sorted per sample, MID removed, PCR duplicates removed)
1 ILLUMINA (Illumina HiSeq 2000) run: 6.5M spots, 1.3G bases, 799.2Mb downloads

Design: We prepared paired-end restriction site-associated DNA (RAD) libraries following Baird et al. (2008) and Etter et al. (2011) with the following modifications. We considered no RNase A treatment necessary; DNA fragments were sheared with a Bioruptor Standard UCD-200 (Diagenode) and selected to a size range comprising 150–750 bp (length excluding adapters); PCR reactions were set up at 50 μl with 16 μl RAD library template running 16 cycles. Such protocol, with more library template and fewer cycles, leads to more P2–P2 fragments but fewer PCR clones. We used the restriction enzyme SbfI and multiplexed 16 samples per library; each library was then sequenced on one HiSeq 2000 (Illumina) channel at BGI, Hong Kong.
Submitted by: Lund University
Study: Disentangling the complex evolutionary history of the Western Palearctic blue tits (Cyanistes spp.) – phylogenomic analyses suggest radiation by multiple colonisation events and subsequent isolation
show Abstracthide Abstract
Isolated islands and their often unique biota continue to play key roles for understanding the importance of drift, genetic variation, and adaptation in the process of population differentiation and speciation. One island system that has inspired and intrigued evolutionary biologists is the blue tit complex (Cyanistes spp.) in Europe and Africa, in particular the complex evolutionary history of the multiple genetically distinct taxa of the Canary Islands. Understanding Afrocanarian colonisation events is of particular importance because of recent unconventional suggestions that these island populations acted as source of the widespread population in mainland Africa. We investigated the relationship between mainland and island blue tits using a combination of Sanger sequencing at a population level (20 loci; 12,500 nucleotides) and next generation sequencing of single population representatives (>3,200,000 nucleotides), analysed in coalescence and phylogenetic frameworks. We found (i) that Afrocanarian blue tits are monophyletic and represent four major clades, (ii) that the blue tit complex has a continental origin, and that the Canary Islands were colonised three times, (iii) that all island populations have low genetic variation, indicating low long-term effective population sizes, and (iv) that populations on La Palma and in Libya represent relicts of an ancestral North African population. Further, demographic reconstructions revealed (v) that the Canary Islands, conforming to traditional views, hold sink populations, which have not served as source for back colonisation of the African mainland. Our study demonstrates the importance of complete taxon sampling and an extensive multi-marker study design to obtain robust phylogeographical inferences.
Sample: Cyanistes cyanus flavipectus, sample Ccya
SAMN03352167 • SRS847055 • All experiments • All runs
Library:
Instrument: Illumina HiSeq 2000
Strategy: OTHER
Source: GENOMIC
Selection: Restriction Digest
Layout: PAIRED
Spot descriptor:
forward94  reverse

Pipeline: show...hide...
ProgramVersion
Stacks: process_radtags, clone_filter1.17
Runs: 1 run, 6.5M spots, 1.3G bases, 799.2Mb
Run# of Spots# of BasesSizePublished
SRR18106466,506,9161.3G799.2Mb2015-02-27

ID:
1261645

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