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ASSESSMENT OF POPULATION GENOMICS AS A TOOL FOR DISCRIMINATING AMONG POPULATIONS OF GREAT LAKES SEA LAMPREY
T. J. Krabbenhoft¹ and T. E. Dowling¹
1 Department of Biology, Wayne State University, Detroit
We present the results from a one-year pilot project to assess the efficacy of using population genomics as a tool for discriminating among populations of Great Lakes sea lamprey. We used novel population genomics tools (single nucleotide polymorphisms, “SNPs”) to test the following hypotheses: (1) larval sea lampreys are genetically homogeneous among streams within lakes and among lakes; (2) a few SNPs distributed throughout the genome exhibit signatures of adaptation to local stream conditions as evidenced by outlier fixation index (Fst) values; (3) these high Fst SNPs (i.e., those presumed to be under natural selection) can be used to diagnose the stream or region of origin of parasitic-phase lamprey collected in open lake habitats. We genotyped 25,603 SNP markers in 96 sea lamprey individuals, representing five streams in the Great Lakes. Genetic differentiation among localities was generally low for most SNPs (Fst < 0.05); however, twelve outlier SNPs exhibited patterns of significant differentiation among streams consistent with local adaptation through diversifying selection. Principal component analysis, neighbor-joining trees, and STRUCTURE analysis on the twelve outlier SNPs revealed largely consistent patterns of variation across loci. Specifically, two of the streams appear to be genetically distinct from the others: Goodings Creek (a tributary of the Saginaw River in Lake Huron) and, to a lesser extent, the Manistique River (Lake Michigan basin). While it is not surprising that the sample from Lake Michigan was distinct from Lake Huron samples, the degree of genetic distinctiveness in Goodings Creek from the other Huron samples was unexpected. Two of the outlier loci were located in the protein coding genes, with physiological functions that may be relevant to lamprey biology and/or TFM lampricide treatment history differences among streams. One locus corresponded to the gene “glucosidase, beta, acid”, which encodes a protein involved in brain metabolism and may be an important locus in light of TFM lampricide treatment, which affects energy availability in sea lamprey brains. Genotypes for the glucosidase, beta, acid locus differed mainly between the St. Clair River and the remaining streams, where individuals were collected with lampricide and electrofishing, respectively. The other locus corresponded to the gene “XK, Kell blood group complex subunit-related family, member 8,” which controls apoptosis (programmed cell death) and may also be relevant to TFM treatment history. While conclusions presented in this pilot study are tentative, these data show that this approach can yield additional characters for finer discrimination among samples, information that is critical for the Great Lakes sea lamprey control program.