Novel RAD sequence data reveal a lack of genomic divergence between dietary ecotypes in a landlocked salmonid population
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TECHNICAL NOTE
Novel RAD sequence data reveal a lack of genomic divergence between dietary ecotypes in a landlocked salmonid population Morten T. Limborg1,2 · Wesley A. Larson1,3 · Kyle Shedd4 · Lisa W. Seeb1 · James E. Seeb1
Received: 3 February 2017 / Accepted: 19 June 2017 © Springer Science+Business Media B.V. 2017
Abstract Preservation of heritable ecological diversity within species and populations is a key challenge for managing natural resources and wild populations. Salmonid fish are iconic and socio-economically important species for commercial, aquaculture, and recreational fisheries across the globe. Many salmonids are known to exhibit ecological divergence within species, including distinct feeding ecotypes within the same lakes. Here we used 5559 SNPs, derived from RAD sequencing, to perform population genetic comparisons between two dietary ecotypes of sockeye salmon (Oncorhynchus nerka) in Jo-Jo Lake, Alaska (USA). We tested the standing hypothesis that these two ecotypes are currently diverging as a result
Data archiving RAD sequence data is archived in SRA at NCBI with project accession number SRP099220. Electronic supplementary material The online version of this article (doi:10.1007/s12686-017-0791-4) contains supplementary material, which is available to authorized users. * Morten T. Limborg [email protected] 1
School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA 98195‑5020, USA
2
Present Address: Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5‑7, 1350 Copenhagen, Denmark
3
Present Address: U.S. Geological Survey, Wisconsin Cooperative Fishery Research Unit, University of Wisconsin-Stevens Point, 800 Reserve St., Stevens Point, WI 54481, USA
4
Gene Conservation Laboratory, Division of Commercial Fisheries, Alaska Department of Fish and Game, 333 Raspberry Road, Anchorage, AK 99518, USA
of adaptation to distinct dietary niches; results support earlier conclusions of a single panmictic population. The RAD sequence data revealed 40 new SNPs not previously detected in the species, and our sequence data can be used in future studies of ecotypic diversity in salmonid species. Keywords Ecological speciation · Kokanee salmon · SNPs · RAD sequencing Ecological divergence and speciation, where a single ancestral population diverges through local adaptation to distinct environmental niches, is a fundamental topic in evolutionary biology (Schluter 2000). With the advent of next generation sequencing, genome scans have revealed evidence of ecological speciation among ecotypes for different animal taxa including birds (Ellegren et al. 2012), fish (Jones et al. 2012), and insects (Soria-Carrasco et al. 2014). Identification of such adaptive genetic variation can greatly improve conservation schemes for endangered species (Funk et al. 2012). Salmonid species represent an ideal system for studying ecological speciation because of their importance for conservation and their remarkable lif
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