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SRX7386924: Double-digest RAD-Seq of American Crows (Corvus brachyrhynchos): Muscle and blood
1 ILLUMINA (Illumina HiSeq 2500) run: 3.1M spots, 139.5M bases, 87.3Mb downloads

Design: We generated reduced representation double digest restriction-associated DNA (ddRAD) libraries from blood and frozen tissue samples. We followed the ddRAD sequencing protocol of Peterson et al. (2012). We digested 350-500 ng of DNA with SbfI-HF and MspI rriction endonucleases (New England BioLabs, Ipswich, MA), pooled sets of 8 samples, and size-selected 415-515 bp DNA fragments on a BluePippin machine (Sage Science, Beverly, MA). We multiplexed 96 avian ddRAD libraries from this study and another study, obtaining two runs of single-end 50-bp reads from Illumina HiSeq 2500 at the Computational Genomics Research Laboratory at the University of California (Berkeley, CA). We used process_radtags in STACKS 1.42 (Catchen et al. 2013) with default settings to demultiplex reads, discard low-quality reads, discard reads with an uncalled base, rescue barcodes, and rescue SbfI RAD tags.
Submitted by: University of Washington
Study: Cryptic and extensive hybridization between ancient lineages of American crows
show Abstracthide Abstract
Most species and therefore most hybrid zones have historically been defined using phenotypic characters. However, both speciation and hybridization can occur with negligible morphological differentiation. Recently developed genomic tools provide the means to better understand cryptic speciation and hybridization. The Northwestern Crow (Corvus caurinus) and American Crow (Corvus brachyrhynchos) are continuously distributed sister taxa that lack reliable traditional characters for identification. In this study, our objective was to use genomic data and geographically robust sampling of American and Northwestern crows to better understand the evolutionary history of these presumptive species that lack well-defined phenotypic characters. Specifically, we set out to 1) assess whether Northwestern and American crows represent independently evolving evolutionary lineages, and, if so, 2) determine the extent to which they might hybridize or exhibit reproductive isolation, 3) test the role of specific geographic barriers in potentially structuring gene flow, and 4) better understand their evolutionary and biogeographic history.
Sample:
SAMN13608597 • SRS5835915 • All experiments • All runs
Library:
Name: yvr01
Instrument: Illumina HiSeq 2500
Strategy: RAD-Seq
Source: GENOMIC
Selection: Restriction Digest
Layout: SINGLE
Runs: 1 run, 3.1M spots, 139.5M bases, 87.3Mb
Run# of Spots# of BasesSizePublished
SRR107027063,099,513139.5M87.3Mb2020-02-19

ID:
9672219

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