Population Structure of Steelhead in Coastal California

Abstract

Steelhead Oncorhynchus mykiss are the most widespread of the Pacific salmonids Oncorhynchus spp. and are found in nearly all basins within their native range around the northern Pacific Rim. Here, we elucidate genetic population structure of steelhead in coastal basins from most of their coastal‐California range using variation at 15 microsatellite loci. Juvenile fish from 60 streams in 40 river basins were sampled in a single year from a single cohort. As samples of juvenile salmonids often contain sibling groups, a method was implemented to identify and eliminate all but one member of larger sibships. This, in conjunction with a rigorous sampling protocol and hierarchical sampling design, provided substantially improved resolution for understanding patterns of migration and demography. A pattern of isolation by distance was evident, as indicated by both phylograms that were largely concordant with geography and a significant regression of genetic distance on geographic distance, indicating that population structure is largely determined by migration that is dependent upon geographic distance. Within‐basin genetic distances tended to be smaller than those between basins, although there was substantial overlap between them. Using a Bayesian clustering method to evaluate signals of population structure above the level of a river basin, four geographic sites were identified where genetic composition shifted abruptly. These areas largely correspond to major geographic features of the coastline: San Francisco and Humboldt bays and two extended sections of coast (the so‐called Lost Coast and Russian Gulch areas) with no streams reaching inland more than several kilometers. Only one of these boundaries is concordant with the current delineation of steelhead Distinct Population Segments designated under the U.S. Endangered Species Act. Finally, there was a strong correlation between latitude and genetic variation, with fewer alleles present in the south, a pattern consistent with generally smaller population sizes in the south.

Parallel evolution of the summer steelhead ecotype in multiple populations from Oregon and Northern California

“…IBD analysis found that almost 50% of the variation in genetic differentiation among populations from all sampling sites was explained by geographic distance (Figure 3). This pattern is consistent with previous studies of coastal steelhead, which found similar signals of IBD Garza et al 2014). A similar pattern of structuring by geography and not phenotype has also been observed in other anadromous and resident O.mykiss populations (Docker et al 2003;Olsen et al 2006;Pearse et al 2007;Clemento et al 2009).…”

“…States, steelhead populations are administratively designated and managed as distinct population segments (DPSs), which are delineated on the basis of geographical, ecological, and genetic variation (Busby et al 1996;Garza et al 2014 Table 1. Summary statistics for all populations included in the present study.…”

“…In California and Oregon, steelhead populations are categorized into distinct population segments (DPSs) for management and conservation purposes. The DPS boundaries are based on many factors, including geography, migratory behavior, spawn timing, and genetic structure (Busby et al 1996;Garza et al 2014). Because of spatial differences in temperature, water flow, sediment type, sedimentation rate, and other characteristics among rivers, divergent selection may drive the adaptation of steelhead to their local environment (Taylor 1991;Narum et al 2008b;Narum et al 2013;Matala et al 2014).…”

“…Microsatellite markers are highly polymorphic and informative, have a long history of use in population genetics (Sunnucks 2000), and have been used extensively to study O. mykiss populations (e.g Heath et al 2002;Hauser et al 2006;Pearse et al 2007Pearse et al , 2009Clemento et al 2009;Martínez et al 2011;Garza et al 2014). However, because of the ease of genotyping and portability of the resulting data, single nucleotide polymorphism (SNP) markers are increasingly used in population genetic investigations (Morin et al 2004), including to assess population demography, estimate phylogenetic relationships and for parentage analysis (e.g.…”

Effective number of breeders in relation to census size as management tools for Atlantic salmon conservation in a context of stocked populations

“…Each river was sampled each year for a targeted 100 parr. Sampling took place for each river in five distinct sections of 10-100 m, for approximately 14-25 parr per section in order to control for potential within-river genetic structure (Garant et al 2000;Vaha et al 2007) and to limit potential upward bias in relatedness due to spatial grouping of juveniles from similar parents (Garza et al 2014). Sampling such a relatively large number of individuals per river was justified by the recommendations of previous studies Whiteley et al 2012;Frankham et al 2014).…”