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Genomics and introgression： Discovery and mapping of thousands of species-diagnostic SNPs using RAD sequencing

Current Zoology 2015年第1期61卷 146-154页

作者： Brian K. HAND Tyler D. HETHER Ryan P. KOVACH Clint C. MUHLFELD Stephen J. AMISH Matthew C. BOYER Sean M. O'ROURKE Michael R. MILLER Winsor H. LOWE Paul A. HOHENLOHE gordon luikart Flathead Lake Biological Station Fish and Wildlife Genomics Group University of Montana Poison MT 59860 USA Institute for Bioinformatics and Evolutionary Studies Department of Biological Sciences University of Idaho Moscow ID 83844 USA U. S. Geological Survey Northem Rocky Mountain Science Center Glacier National Park West Glacier Montana 59936 USA Fish and Wildlife Genomics Group Division of Biological Sciences The University of Montana Missoula Montana 59812USA Montana Fish Wildlife and Parks Kalispell Montana 59901 USA Department of Animal Science University of California Davis One Shields Avenue Davis CA 95616 USA University of Montana Division of Biological Sciences Missoula Montana 59812 USA

Invasive hybridization and introgression pose a serious threat to the persistence of many native species. Understand- ing the effects of hybridization on native populations （e.g., fitness consequences） requires numerous species-diagnostic loci dis- tributed genome-wide. Here we used RAD sequencing to discover thousands of single-nucleotide polymorphisms （SNPs） that are diagnostic between rainbow trout （RBT, Oncorhynchus mykiss）, the world＇s most widely introduced fish, and native westslope cutthroat trout （WCT, （9. clarkii lewisi） in the northern Rocky Mountains, USA. We advanced previous work that identified 4,914 species-diagnostic loci by using longer sequence reads （100 bp vs. 60 bp） and a larger set of individuals （n = 84）. We sequenced RAD libraries for individuals from diverse sampling sources, including native populations of WCT and hatchery broodstocks of WCT and RBT. We also took advantage of a newly released reference genome assembly for RBT to align our RAD loci. In total, we discovered 16,788 putatively diagnostic SNPs, 10,267 of which we mapped to anchored chromosome locations on the RBT genome. A small portion of previously discovered putative diagnostic loci （325 of 4,914） were no longer diagnostic （i.e., fixed between species） based on our wider survey of non-hybridized RBT and WCT individuals. Our study suggests that RAD loci mapped to a draft genome assembly could provide the marker density required to identify genes and chromosomal regions in- fluencing selection in admixed populations of conservation concern and evolutionary interest [Current Zoology 61 （1）： 146-154, 2015].

关键词： Conservation genetics Hybridization Invasive species Next generation sequencing Salmonid fish SNP discovery

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