Major Lineages and Metapopulations in Columbia River Oncorhynchus mykiss Are Structured by Dynamic Landscape Features and Environments

Abstract

It is widely recognized that genetic diversity within species is shaped by dynamic habitats. The quantitative and molecular genetic patterns observed are the result of demographics, mutation, migration, and adaptation. The populations of rainbow trout Oncorhynchus mykiss in the Columbia River basin (including both resident and anadromous forms and various subspecies) present a special challenge to understanding the relative roles of those factors. Standardized microsatellite data were compiled for 226 collections (15,658 individuals) from throughout the Columbia and Snake River basins to evaluate the genetic patterns of structure and adaptation. The data were primarily from fish of the anadromous life history form, and we used a population grouping procedure based on principal components and hierarchical k‐means clustering to cluster populations into eight aggregates or groups with similar allele frequencies. These aggregates approximated geographic regions, and the two largest principal components corresponded to ancestral lineages of Sacramento redband trout O. m. stonei, coastal rainbow trout O. m. irideus, and interior Columbia River redband trout O. m. gairdneri. Genetic data were partitioned among primary aggregates (lower Columbia, middle–upper Columbia, and Snake rivers), and the magnitude of genetic divergence relative to genetic diversity was analyzed (per locus) to test for evidence of selection and subsequent signals of adaptation. Two loci showed higher divergence than expected by chance (i.e., positive selection); however, both of these loci were on the fringe of the 99% confidence level and are potential false positives. Genetic patterns were also significantly correlated with certain environmental and habitat parameters (e.g., precipitation), but the extent to which those correlations are causal as opposed to effectual remains unclear. Despite the remaining questions, these data provide a foundation for more detailed investigations of harvest, admixture, and introgression between hatchery‐ and natural‐origin fish and differences in reproductive success among individuals as well as monitoring trends in productivity.

Relative contributions of neutral and non‐neutral genetic differentiation to inform conservation of steelhead trout across highly variable landscapes

“…; Blankenship et al. ). However, direct evaluations of non‐neutral population differentiation (i.e., putatively adaptive divergence) are likely to reveal stronger, more correlative relationships (Limborg et al.…”

“…; Blankenship et al. ). Some populations of O. m. irideus also have a summer‐run life history, though not necessarily genetically differentiated from sympatric winter‐run populations (Busby et al.…”

“…; Blankenship et al. ). In this study, we investigate patterns of neutral genetic variation in contrast to non‐neutral (putatively adaptive) genetic variation.…”

Introduction to a Special Section: Genetic Adaptation of Natural Salmonid Populations

“…This information accentuates the long-known coastal and inland divisions, genetic intermediacy of transitional populations, and minimal effects of out-of-basin translocations on native populations. The study by Blankenship et al (2011) also presents landscape genetics results that document significant relationships between genetic structure and environmental variables, primarily precipitation. In a study of reproductive success (Berntson et al 2011, this issue), pedigrees for an interior population identify reduced fitness in the wild of fish from hatchery parents as opposed to wild parents.…”

“…Blankenship et al (2011) present a broad, standardized microsatellite baseline (226 populations genotyped at 13 microsatellite loci) of the variation among anadromous (steelhead) and resident rainbow trout O. mykiss within the Columbia River basin that augments previous data (Winans et al 2004) used for within-basin GSI estimates. This information accentuates the long-known coastal and inland divisions, genetic intermediacy of transitional populations, and minimal effects of out-of-basin translocations on native populations.…”