Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing

Rapid and inexpensive methods for genomewide single nucleotide polymorphism (SNP) discovery and genotyping are urgently needed for population management and conservation. In hybridized populations, genomic techniques that can identify and genotype thousands of species‐diagnostic markers would allow...

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Published in:Molecular ecology Vol. 22; no. 11; pp. 3002 - 3013
Main Authors: Hohenlohe, Paul A., Day, Mitch D., Amish, Stephen J., Miller, Michael R., Kamps-Hughes, Nick, Boyer, Matthew C., Muhlfeld, Clint C., Allendorf, Fred W., Johnson, Eric A., Luikart, Gordon
Format: Journal Article
Language:English
Published: England Blackwell Publishing Ltd 01-06-2013
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Summary:Rapid and inexpensive methods for genomewide single nucleotide polymorphism (SNP) discovery and genotyping are urgently needed for population management and conservation. In hybridized populations, genomic techniques that can identify and genotype thousands of species‐diagnostic markers would allow precise estimates of population‐ and individual‐level admixture as well as identification of ‘super invasive’ alleles, which show elevated rates of introgression above the genomewide background (likely due to natural selection). Techniques like restriction‐site‐associated DNA (RAD) sequencing can discover and genotype large numbers of SNPs, but they have been limited by the length of continuous sequence data they produce with Illumina short‐read sequencing. We present a novel approach, overlapping paired‐end RAD sequencing, to generate RAD contigs of >300–400 bp. These contigs provide sufficient flanking sequence for design of high‐throughput SNP genotyping arrays and strict filtering to identify duplicate paralogous loci. We applied this approach in five populations of native westslope cutthroat trout that previously showed varying (low) levels of admixture from introduced rainbow trout (RBT). We produced 77 141 RAD contigs and used these data to filter and genotype 3180 previously identified species‐diagnostic SNP loci. Our population‐level and individual‐level estimates of admixture were generally consistent with previous microsatellite‐based estimates from the same individuals. However, we observed slightly lower admixture estimates from genomewide markers, which might result from natural selection against certain genome regions, different genomic locations for microsatellites vs. RAD‐derived SNPs and/or sampling error from the small number of microsatellite loci (n = 7). We also identified candidate adaptive super invasive alleles from RBT that had excessively high admixture proportions in hybridized cutthroat trout populations.
Bibliography:ark:/67375/WNG-FSF4C132-L
BPA - No. #199101993
Montana Fish Wildlife and Parks and NSF - No. DEB-1067613
Fig. S1 Frequency histograms of contig length across all loci assembled from overlapping paired-end restriction-site-associated DNA sequencing, using velvet.Fig. S2 A representative example of discrimination of duplicate sequence with longer reads and paired-end restriction-site-associated DNA sequencing.
U.S. National Institutes of Health/NCRR - No. P20RR16448
istex:5BFEB52CE46B0CD33EECDE047E53A6DAF65EBE0D
ArticleID:MEC12239
U.S. National Science Foundation - No. DEB-0742181
ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:0962-1083
1365-294X
DOI:10.1111/mec.12239