Parallel signatures of selection in temporally-isolated lineages of pink salmon.

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Parallel signatures of selection in temporally-isolated lineages of pink salmon.

Mol Ecol. 2014 Apr 25;

Authors: Seeb LW, Waples RK, Limborg MT, Warheit KI, Pascal CE, Seeb JE

Abstract
Studying the effect of similar environments on diverse genetic backgrounds has long been a goal of evolutionary biologists with studies typically relying on experimental approaches. Pink salmon, a highly-abundant and widely-ranging salmonid, provide a naturally-occurring opportunity to study the effects of similar environments on divergent genetic backgrounds due to a strict two-year semelparous life-history. The species is composed of two reproductively-isolated lineages with overlapping ranges that share the same spawning and rearing environments in alternate years. We used restriction site-associated DNA (RAD) sequencing to discover and genotype approximately 8,000 SNP loci in three population pairs of even- and odd-year pink salmon along a latitudinal gradient in North America. We found greater differentiation within the odd-year than the even-year lineage and greater differentiation in the southern pair from Puget Sound than in the northern Alaskan population pairs. We identified 15 SNPs reflecting signatures of parallel selection using both a differentiation-based method (BAYESCAN) and an environmental correlation method (BAYENV). These SNPs represent genomic regions that may be particularly informative in understanding adaptive evolution in pink salmon and exploring how differing genetic backgrounds within a species respond to selection from the same natural environment. This article is protected by copyright. All rights reserved.

PMID: 24762204 [PubMed – as supplied by publisher]

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Rank and order: evaluating the performance of SNPs for individual assignment in a non-model organism.

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Rank and order: evaluating the performance of SNPs for individual assignment in a non-model organism.

PLoS One. 2012;7(11):e49018

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Abstract
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PMID: 23185290 [PubMed – indexed for MEDLINE]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/pubmed/23185290?dopt=Abstract

Rank and Order: Evaluating the Performance of SNPs for Individual Assignment in a Non-Model Organism.

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Rank and Order: Evaluating the Performance of SNPs for Individual Assignment in a Non-Model Organism.

PLoS One. 2012;7(11):e49018

Authors: Storer CG, Pascal CE, Roberts SB, Templin WD, Seeb LW, Seeb JE

Abstract
Single nucleotide polymorphisms (SNPs) are valuable tools for ecological and evolutionary studies. In non-model species, the use of SNPs has been limited by the number of markers available. However, new technologies and decreasing technology costs have facilitated the discovery of a constantly increasing number of SNPs. With hundreds or thousands of SNPs potentially available, there is interest in comparing and developing methods for evaluating SNPs to create panels of high-throughput assays that are customized for performance, research questions, and resources. Here we use five different methods to rank 43 new SNPs and 71 previously published SNPs for sockeye salmon: F(ST), informativeness (I(n)), average contribution to principal components (LC), and the locus-ranking programs BELS and WHICHLOCI. We then tested the performance of these different ranking methods by creating 48- and 96-SNP panels of the top-ranked loci for each method and used empirical and simulated data to obtain the probability of assigning individuals to the correct population using each panel. All 96-SNP panels performed similarly and better than the 48-SNP panels except for the 96-SNP BELS panel. Among the 48-SNP panels, panels created from F(ST), I(n), and LC ranks performed better than panels formed using the top-ranked loci from the programs BELS and WHICHLOCI. The application of ranking methods to optimize panel performance will become more important as more high-throughput assays become available.

PMID: 23185290 [PubMed – in process]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/PubMed/23185290?dopt=Abstract