Allozyme and Microsatellite DNA Analyses of Lingcod from Puget Sound, Washington, and Adjoining Waters

Abstract

In all, 472 lingcod Ophiodon elongatus from six areas of Puget Sound, the Strait of Juan de Fuca, and the outer coast of Washington were assayed for 44 allozyme and 9 microsatellite DNA loci to investigate possible population subdivision. Levels of genetic variation at many of the allozyme loci and all of the microsatellite DNA loci were reasonably high, and there was no evidence of significant Hardy-Weinberg or linkage disequilibrium. Pairwise genotypic tests of population differentiation showed no evidence of genetic structuring among the 23 variable allozyme loci, the 9 microsatellite loci, or all 32 variable loci combined. The results of this investigation are consistent with the existence of a single genetic stock of lingcod throughout the greater Puget Sound region, including the Strait of Juan de Fuca and San Juan Islands. Despite the fact that most of the collections we analyzed did not consist of spawning fish from the spawning grounds, we believe that the combined absence of significant outcomes in the population differentiation tests and the absence of significant heterozygote deficits at any of the 32 variable loci make it highly unlikely that there is significant genetic divergence among the greater Puget Sound populations analyzed in this study. Allozyme data obtained from inland populations in this study were compared with previously published allozyme data from the outer coast. No difference was detected when summed over all variable loci.

Strong population differentiation in lingcod (Ophiodon elongatus) is driven by a small portion of the genome

“…In this study, we identify two distinct genetic clusters of lingcod showing a latitudinal cline in the Eastern Pacific, with a genetic break centered off Northern California between Stewarts Point and Point Reyes. This novel delineation of population boundaries differs from previous lingcod population genetic studies, which have generally suggested coastwide panmixia (Jagielo et al., 1996; LeClair et al., 2006; Marko et al., 2007). Compared to the single mitochondrial sequence or 19–32 nuclear markers used in these prior studies, the sampling of more sites across the genome with >16,000 SNPs empowered the ability to detect this signal of population structure.…”

“…(1996) and LeClair et al. (2006) used allozyme or allozyme and microsatellite markers, respectively, which sample less than a few dozen sites in the nuclear genome, while Marko et al. (2007) specifically evaluated population structure using cytochrome oxidase I in the mitochondrial genome.…”

“…Although Jagielo et al (1996) and Marko et al (2007) did not detect strong structure, both suggested weak genetic differentiation between the inside waters of the Salish Sea and the outer coast. However, LeClair et al (2006) failed to find the same genetic signal with additional individuals from the Salish Sea and the increased power of microsatellite markers in conjunction with allozyme data from Jagielo et al (1996).…”

“…For example, Jagielo et al (1996) and LeClair et al (2006) used allozyme or allozyme and microsatellite markers, respectively, which sample less than a few dozen sites in the nuclear genome, while Marko et al 2007F I G U R E 5 Manhattan plots aligning RADseq contigs with locus-specific F ST values based on 42 sampling sites to the draft lingcod genome assembly scaffolded into chromosomal-scale pseudomolecules (CSPs) using the genomes of (a) Sebastes schlegelii, Korean rockfish; specifically evaluated population structure using cytochrome oxidase I in the mitochondrial genome. Sampling thousands of markers distributed widely throughout the genome allowed us to detect a very strong signal of divergence driven by a small number of outlier loci likely colocalized to a single region in the genome.…”

Advancing the use of local ecological knowledge for assessing data‐poor species in coastal ecosystems

“…We therefore used two sources of information on population status from a Washington-Oregon coastal stock assessment for lingcod: (1) estimated spawning stock biomass, 1950-2009, and (2) catch per unit effort indices from commercial trawl fishery logbook and fish ticket data, 1976-1997(Hamel et al 2009). These indices may be a reasonable proxy for patterns in Puget Sound populations given limited genetic differentiation between lingcod in the inland waters and those on the outer coast of Washington (LeClair et al 2006). In contrast, rockfish populations in Puget Sound are genetically, demographically, and ecologically distinct from coastal stocks (Drake et al 2010); stock assessments or survey time series were not available for Puget Sound rockfishes.…”