The Colonization Mechanism Of Pink Salmon Populations In Glacier Bay, Alaska, Based On Genetic Data

Thesis (Ph.D.) University of Alaska Fairbanks, 2010Following retreat of the last glacial advance in the early 1700s, pink salmon Oncorhynchus gorbuscha colonized many watersheds in Glacier Bay, Alaska. Streams in the lower Bay were populated first, and colonization proceeded up the Bay during the last 200 years. The objective of this study was to use analyses of genetic data---microsatellite and allozyme loci, and mitochondrial DNA haplotypes---to elucidate the colonization mechanism. The even- and odd-year broodlines served as replicate experiments; the mechanisms of colonization for the two broodlines were similar in most respects. The population genetic structure, based on allele/haplotype frequencies and genetic diversity (FST), suggested that in general, deglaciated streams were populated by colonists from nearby locations. The populations in lower Glacier Bay were likely established by colonists from populations outside Glacier Bay. In turn, the lower Bay populations contributed colonists to populations farther up the Bay, which subsequently provided colonists to the most recently deglaciated locations in the upper Bay, although in the even-year there appeared to be some contribution to the youngest populations from older populations, outside of or in lower Glacier Bay. Few genetically divergent donor sources contributed colonists based on the limited linkage disequilibrium, higher relatedness, and lower allelic diversity within Glacier Bay populations. The number of fish involved in initial colonization was not large, based on slightly reduced genetic diversity within Glacier Bay, but minimal founder effect signals precluded very small numbers of fish as well. Most of the genetic variation appeared early in the formation of populations and effective population size estimates were >100 fish in every population. Some gene flow after initial colonization is supported by the increased allelic diversity and decline in relatedness with population age, but heterogeneity within Glacier Bay suggested that gene flow must be limited among some populations. Colonization of the youngest streams coincided with the historically high abundance of pink salmon in Southeast Alaska during the 1990s; I speculate that the rapid expansion in the size of these populations subsequent to this study was the result of high survival rather than extensive gene flow

Genetic variation of rougheye rockfish (Sebastes aleutianus) and shortraker rockfish (S. borealis) inferred from allozymes

Rougheye rockfish (Sebastes aleutianus) and shortraker rockfish (Sebastes borealis) were collected from the Washington coast, the Gulf of Alaska, the southern Bering Sea, and the eastern Kamchatka coast of Russia (areas encompassing most of their geographic distribution) for population genetic analyses. Using starch gel electrophoresis, we analyzed 1027 rougheye rockfish and 615 shortraker rockfish for variation at 29 proteincoding loci. No genetic heterogeneity was found among shortraker rockfish throughout the sampled regions, although shortraker in the Aleutian Islands region, captured at deeper depths, were found to be significantly smaller in size than the shortraker caught in shallower waters from Southeast Alaska. Genetic analysis of the rougheye rockfish revealed two evolutionary lineages that exist in sympatry with little or no gene f low between them. When analyzed as two distinct species, neither lineage exhibited heterogeneity among regions. Sebastes aleutianus seems to inhabit waters throughout the Gulf of Alaska and more southern waters, whereas S. sp. cf. aleutianus inhabits waters throughout the Gulf of Alaska, Aleutian Islands, and Asia. The distribution of the two rougheye rockfish lineages may be related to depth where they are sympatric. The paler color morph, S. aleutianus, is found more abundantly in shallower waters and the darker color morph, Sebastes sp. cf. aleutianus, inhabits deeper waters. Sebastes sp. cf. aleutianus, also exhibited a significantly higher prevalence of two parasites, N. robusta and T. trituba, than did Sebastes aleutianus, in the 2001 samples, indicating a possible difference in habitat and (or) resource use between the two lineages

Potentially adaptive mitochondrial haplotypes as a tool to identify divergent nuclear loci

1. Genetic tools are commonly used for conservation and management of at-risk species. Individuals are often sampled from mixtures that are composed of many populations, which creates a need to assign individuals to their source. This can be problematic when the genetic divergence among source populations is weak but can be improved using adaptive genetic loci, which should show stronger levels of divergence. 2. We previously reported a signature of positive selection in the mitochondrial-encoded ND5 subunit of complex I in diverse taxa. The respiratory machinery of the mitochondria in salmonids is composed of more than 80 nuclear genes and there is substantial interaction between nuclear and mitochondrial expressed gene products. Recent studies report adaptive variation in mitochondrial function as well as co-evolution between mitochondrial and nuclear genomes. We used potentially adaptive ND5-based mitochondrial haplotypes to identify nuclear loci that would display increased levels of genetic divergence compared to neutral nuclear loci in chum salmon (Oncorhynchus keta). Populations in a geographic area the size of France have previously demonstrated weak genetic divergence even after substantial discovery efforts by multiple laboratories for allozymes, microsatellites and SNPs over the last two decades. 3. We used RAD-based next-generation sequencing and identified a nuclear-encoded subunit of mitochondrial complex I that was a significant FST outlier and 14 other divergent nuclear markers that improve genetic assignment of individuals to their population of origin relative to assignments based on neutral markers alone. 4. This work demonstrates how a known adaptive marker can be leveraged to increase the probability of identifying divergent markers for applied genetics tools that may be biologically linked to it

Garvin et al. 2016 RAD_Tag_Data

This file contains the 19,098, 200bp RAD-tags that were produced. For each RAD-tag, the variable nucleotide (potential SNP) is listed for each individual and individuals are grouped by collection. The colored boxes at the top identify the mutation that was found in the mitochondrial DNA for that particular individual

Data from: Potentially adaptive mitochondrial haplotypes as a tool to identify divergent nuclear loci

1. Genetic tools are commonly used for conservation and management of at-risk species. Individuals are often sampled from mixtures composed of many populations, which creates a need to assign individuals to their source. This can be problematic when the genetic divergence among source populations is weak but can be improved using adaptive genetic loci, which should show stronger levels of divergence. 2. We previously reported a signature of positive selection in the mitochondrial-encoded ND5 subunit of complex I in diverse taxa. The respiratory machinery of the mitochondria in salmonids is composed of more than 80 nuclear genes and there is substantial interaction between nuclear and mitochondrial expressed gene products. Recent studies report adaptive variation in mitochondrial function as well as co-evolution between mitochondrial and nuclear genomes. We used potentially adaptive ND5-based mitochondrial haplotypes to identify nuclear loci that would display increased levels of genetic divergence compared to neutral nuclear loci in chum salmon (Oncorhynchus keta). Populations in a geographic area the size of France have previously demonstrated weak genetic divergence even after substantial discovery efforts by multiple laboratories for allozymes, microsatellites and SNPs over the last two decades. 3. We used RAD-based Next-Generation Sequencing and identified a nuclear-encoded subunit of mitochondrial complex I that was a significant FST outlier and 14 other divergent markers that improve genetic assignment of individuals to their population of origin relative to assignments based on neutral markers alone. 4. This work demonstrates how a known adaptive marker can be leveraged to increase the probability of identifying divergent markers for applied genetics tools that may be biologically linked to it