Spatio-temporal genetic structure, effective population size, and parentage simulations from contemporary genetic samples and historic demographic data of sockeye salmon (Oncorhynchus nerka) in Auke Lake, Alaska

Abstract

Pacific salmon (Oncorhynchus spp.) have great ecological, economic, and cultural importance. Accordingly, understanding the genetic diversity of Pacific salmon populations is critical for their effective management and conservation. Spatial and temporal homing fidelity, a central life-history characteristic of Pacific salmon, generates genetic structure through reproductive isolation. Within and among populations, heterogeneity in the freshwater environment should lead to selection for traits that maximize fitness resulting in local adaptation. This adaptation increases productivity of individual populations while diversity among populations can promote long-term stability. Additionally, the demographic properties (age structure, generation length, size) of a population will affect genetic structure by regulating its response to the evolutionary forces of selection, migration, and genetic drift. The scale and extent to which reproductive isolation can produce genetic structure is incompletely understood. In this dissertation, I investigated spatial and temporal trends in population genetic structure and estimated the effective population size (Ne) of Sockeye Salmon from Auke Lake in Southeast Alaska from contemporary genetic samples (2008, 2009, 2011) and historic demographic data (1980-2017). A simulation library in the R statistical environment was developed to assess the accuracy of parentage and sibship inference from genetic markers. This library proved useful in evaluating the sibship method for estimating Ne from genetic data and evaluating genetic markers for a large-scale parentage project. I detected substantial genetic differentiation between Auke Lake and other Southeast Alaska populations (average FST = 0.1137) and an isolation-by-time pattern within the Auke Lake population. A genetically distinct cluster was identified in the late portion of the 2008 return. This group may represent a spatially segregated spawning aggregation previously described in tagging studies; however, because fish were sampled as they passed through the weir, spatial structure within Auke Lake could not be evaluated. Genetic tests for demographic change within the population indicated that the Auke Lake Sockeye Salmon population underwent a historical bottleneck event but has since increased in size. Demographic estimates of Ne from a long-term dataset from the Auke Creek weir revealed that the effective population size was low in the early 1980s and has since increased. Over the six generations evaluated, the major demographic factors that determined Ne were variance in family size, variable contribution to the next generation by brood years within a generation, and fluctuations in population size. Contemporary estimates of Ne from genetic methods were smaller than those from demographic methods and indicated that Ne may be roughly the size of an individual return year. Genetic estimates of the ratio of the effective population size to the census size (Ne/Nc = 0.21) were consistent with values previously reported for other salmonids. Collectively, these chapters contribute to an improved understanding of Sockeye Salmon population genetics and provide a useful tool to assess the power of genetic markers for parentage and sibship inference.