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Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon ( Thaleichthys pacificus , Osmeridae), an anadromous Pacific smelt
Author(s) -
Candy John R.,
Campbell Nathan R.,
Grinnell Matthew H.,
Beacham Terry D.,
Larson Wesley A.,
Narum Shawn R.
Publication year - 2015
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12400
Subject(s) - biology , smelt , fish migration , evolutionary biology , population , genetics , zoology , ecology , fishery , fish <actinopterygii> , demography , habitat , sociology
Abstract Twelve eulachon ( Thaleichthys pacificus , Osmeridae) populations ranging from Cook Inlet, Alaska and along the west coast of North America to the Columbia River were examined by restriction‐site‐associated DNA ( RAD ) sequencing to elucidate patterns of neutral and adaptive variation in this high geneflow species. A total of 4104 single‐nucleotide polymorphisms ( SNP s) were discovered across the genome, with 193 putatively adaptive SNP s as determined by F ST outlier tests. Estimates of population structure in eulachon with the putatively adaptive SNP s were similar, but provided greater resolution of stocks compared with a putatively neutral panel of 3911 SNP s or previous estimates with 14 microsatellites. A cline of increasing measures of genetic diversity from south to north was found in the adaptive panel, but not in the neutral markers ( SNP s or microsatellites). This may indicate divergent selective pressures in differing freshwater and marine environments between regional eulachon populations and that these adaptive diversity patterns not seen with neutral markers could be a consideration when determining genetic boundaries for conservation purposes. Estimates of effective population size ( N e ) were similar with the neutral SNP panel and microsatellites and may be utilized to monitor population status for eulachon where census sizes are difficult to obtain. Greater differentiation with the panel of putatively adaptive SNP s provided higher individual assignment accuracy compared to the neutral panel or microsatellites for stock identification purposes. This study presents the first SNP s that have been developed for eulachon, and analyses with these markers highlighted the importance of integrating genome‐wide neutral and adaptive genetic variation for the applications of conservation and management.