• Characterizing the diet and population structure of lampreys Lethenteron spp. using molecular techniques

      Shink, Katie G.; López, Andrés; Murphy, James M. (2017-08)
      Lampreys contribute to the health of aquatic ecosystems and are targeted in both subsistence and commercial fisheries. Despite their ecological and commercial importance, the management and conservation of native lampreys have been largely overlooked. The goal of this study was to close current knowledge gaps of lamprey biology through the examination of Lethenteron spp. in Alaska. This study applied two molecular techniques, DNA metabarcoding and microsatellite genotyping, to (1) characterize the diet of marine-phase Arctic lamprey Lethenteron camtschaticum (N = 250) in the eastern Bering Sea and (2) investigate the population structure of larval lampreys Lethenteron spp. (N = 120) within and among three Yukon River tributaries. A combination of visual observations and DNA metabarcoding revealed the presence of diagnostic structures/tissues (i.e., eggs, fin[s], internal organs, otoliths, and vertebrae) and detected DNA sequences of ten ray-finned fishes in the diets of L. camtschaticum. The most frequent prey taxa were Pacific sand lance Ammodytes hexapterus, Pacific herring Clupea pallasii, gadids, and capelin Mallotus villosus. Five of the ten taxa identified in this study were reported for the first time as prey for L. camtschaticum. To investigate the genetic diversity of larval lampreys, a recognized knowledge gap for populations in Alaska, a total of 81 larval lampreys were successfully genotyped at all loci. Global FST of larvae was 0.074 (95% CI: 0.042 - 0.110), while pairwise FST values among the three localities examined ranged from 0.066 - 0.081. Hierarchical model-based Bayesian clustering analyses detected three genetic clusters (K = 3) among all larval lampreys and two genetic clusters (K = 2) among Chena River larvae; no further genetic clustering was identified within the remaining two tributaries. Estimates of contemporary gene flow indicated reciprocal migration among sites. The diet analyses indicated anadromous L. camtschaticum function as flesh-feeding predators that prey upon pelagic fishes in the eastern Bering Sea, while genetic analyses suggested that larval lamprey aggregations within three Yukon River tributaries exhibited higher levels of genetic diversity than are typically found among broad-ranging populations of anadromous lamprey species. Ultimately, this study highlighted the value of molecular techniques to improve our understanding of the biology of a poorly studied fish species in Alaska.
    • Genetic And Environmental Effects On Developmental Timing, Otolith Formation, And Gill Raker Development In Pink Salmon From Auke Creek, Alaska

      Oxman, Dion; Gharrett, Anthony; Milo, Adkison,; Cailliet, Gregor; Hagen, Peter; Smoker, William (2012)
      To determine how inheritance, environment, and hybridization influenced developmental timing, otolith formation, and gill raker development in pink salmon (Oncorhynchus gorbuscha), full and half-sibling families from Auke Creek, Alaska and third generation outbred hybrids between Auke Creek females and Pillar Creek males from Kodiak Island, Alaska (1,000 km distant) were incubated in ambient, chilled, and warmed water. Variation in development time of embryos from the odd-year broodline was primarily influenced by additive genetic factors, whereas no genetic effect was detected in the even-year run. No genotype-by environment (GxE) effects were associated with sires or families in either broodline, indicating that the observed variation in development time was likely the result of phenotypic plasticity. Hybridization (outbreeding) significantly prolonged development time in both broodlines, indicating that the phenotypic effects of outbreeding can last at least three generations. Early otolith development was genetically conserved and canalized, but the phenotypic expression of these genes is plastic and strongly influenced by environmental factors. There was no evidence that local adaptation or outbreeding influenced otolith morphology or shape. Otoliths from fish exposed to thermal stress were bilaterally asymmetrical, whereas the bilateral symmetry of otoliths from outbred fish exhibited evidence of heterosis because they were more symmetrical than their native counterparts. Unlike development time and otoliths, gill raker development was linear and consistently stable in the face of both hybridization and environmental stress. These results make it clear that different biological attributes respond to genetic control and stress in different ways.
    • Genetic linkage mapping of allozyme loci in even- and odd-year pink salmon (Oncorhynchus gorbuscha)

      Matsuoka, Makoto P.; Smoker, W. W. (1998)
      Genetic linkage maps of allozyme loci were constructed in even- and odd-year pink salmon (Oncorhynchus gorbuscha). The loci were mapped based on the results of gene-centromere (G-C) mapping and joint segregation analysis. For G-C mapping, 160 gynogenetic progeny families were produced, and 8,080 progeny from 74 families were analyzed using starch gel electrophoresis and histochemical stain techniques. G-C distances of 37 loci ranged from 0.5 cM at sMDH-A1* to 50 cM at sMDH-B2*. Eleven loci showed high G-C distances (>45 cM), indicating that one crossover on one chromosome arm is usual in pink salmon. Variation observed at sMDH-B1,2* in even-year families suggests that both of this loci is polymorphic and that there is possible inter-broodline chromosomal variation. Large variation was observed among families in G-C distance at several loci. Whether the variation was a reflection of difference in physical position, recombination rate, or some other factors needs clarification using a technique such as physical mapping with FISH, because this variation affects results of gene mapping based on recombination frequency. For joint segregation analysis, 320 biparental families were produced, and 13,068 progeny from 164 families were electrophoretically analyzed. Joint segregation was analyzed at over 200 locus pairs. Combined this with data from G-C mapping, 14 linkage groups involving 26 loci were constructed. The linkage maps contain eight classical linkage groups and four pseudolinkage groups. Two linkage groups found in pink salmon were conserved in widely divergent vertebrate species. Recombination frequency between linked loci were different between sexes, and it tends to be reduced in males in pink salmon. The order of loci, which probably duplicated in the recent tetraploidization event, in linkage groups I (sAAT-3 * → mAH-4*) and III (mAH-3* → sAAT-4*) was reversed. This is evidence of paracentric inversion during salmonid evolution after the duplication. Development of additional markers that are common (homologous) to many species will be necessary to examine syntenic stability and rearrangement over the evolutionary period.
    • Interannual and spatial variation in the population genetic composition of young-of-the-year Pacific Ocean Perch (Sebastes alutus) in Alaskan waters

      Kamin, Lisa M.; Gharrett, Anthony J.; Heifetz, Jonathan; Tallmon, David (2010-05)
      We know little about the population structure of Gulf of Alaska (GOA) and Bering Sea rockfish, including Pacific ocean perch (POP, Sebastes alutus), and early life history information is sparse for many rockfish species. Young-of-the-year (YOY) POP were collected with surface trawls during surveys of juvenile salmon in the GOA and Bering Sea. These samples presented a unique opportunity to study POP genetics and life history. Fourteen microsatellite loci were used to characterize the genetic variation in POP collected in a total of 45 hauls over five years. The coincidence in timing and location of several collections between years allowed examination of both fine- and broad-scale geographic variation (within cohorts) as well as interannual (between cohorts) genetic variation. The geographic genetic structure of these collections was also compared to geographic structure of adult POP described in a previous study (Palof, 2008). As in the adult study, significant broad-scale geographic divergence was observed in YOY POP in the GOA. Fine-scale geographic divergence was also observed and may be the result of variable current regimes and oceanographic features at several locations. The limited amount of temporal variation observed seems to be the result of variable oceanography and fine-scale population structure rather than the influence of a sweepstakes effect. The relationship between genetic divergence and geographic separation is virtually identical in YOY and adult POP, which confirms that dispersal of POP is limited in all life stages and also demonstrates that most YOY are produced by adults that are located nearby.
    • Population genetic structure of Alaskan Pacific ocean perch (Sebastes alutus)

      Palof, Katie J.; Gharrett, Anthony J.; Heifetz, Jonathan; Hillgruber, Nicola (2008-05)
      Knowledge of the population structure of a species is essential for its effective management and sustained production. Although Pacific ocean perch (Sebastes alutus, POP) is an important species both economically and ecologically, little is known about its population structure and life history in Alaskan waters. The objectives of this study were to describe the population structure of POP in terms of the numbers and geographic scale oflocal populations, their connectivity, and the compatibility of that structure with current management. Fourteen micro satellite loci were used to characterize the population structure genetically in eleven geographically distinct collections from sites along the continental shelf from the Queen Charlotte Islands to the Bering Sea. In spite of the many opportunities for most life stages to disperse, there was strong geographically related genetic structure (Fst =0.0123, p <10⁻⁵). Adults appear to belong to neighborhoods that exchange genetic information at relatively small spatial scales (14 to 90 km). Although this suggests limited movement, connectivity is evidenced by the isolation-by-distance relationship, the apparent northwestward movement of gene flow in the Gulf of Alaska (GOA), and the break in geneflow in the central GOA. The observed population structure has a finer geographic scale than management areas, which suggests that current fisheries management should be revisited.
    • Population Genetics And Mixed Stock Analysis Of Chum Salmon (Oncorhynchus Keta) With Molecular Genetics

      Garvin, Michael R.; Gharrett, A. J.; Kruse, Gordon; Pella, Jerome; Tallman, David (2012)
      Chum salmon (Oncorhynchus keta) are important for subsistence and commercial harvest in Alaska. Variability of returns to western Alaskan drainages that caused economic hardship for stakeholders has led to speculation about reasons, which may include both anthropogenic and environmental causes in the marine environment. Mixed stock analysis (MSA) compares genetic information from an individual caught at sea to a reference baseline of genotypes to assign it to its population of origin. Application of genetic baselines requires several complex steps that can introduce bias. The bias may reduce the accuracy of MSA and result in overly-optimistic evaluations of baselines. Moreover, some applications that minimize bias cannot use informative haploid mitochondrial variation. Costs of baseline development are species-specific and difficult to predict. Finally, because populations of western Alaskan chum salmon demonstrate weak genetic divergence, samples from mixtures cannot be accurately assigned to a population of origin. The chapters of this thesis address three challenges. The first chapter describes technical aspects of genetic marker development. The second chapter describes a method to evaluate the precision and accuracy of a genetic baseline that accepts any type of data and reduces bias that may have been introduced during baseline development. This chapter also includes a method that places a cost on baseline development by predicting the number of markers needed to achieve a given accuracy. The final chapter explores the reasons for the weak genetic structure of western Alaskan chum salmon populations. The results of those analyses and both geological and archaeological data suggest that recent environmental and geological processes may be involved. The methods and analyses in this thesis can be applied to any species and may be particularly useful for other western Alaskan species.
    • Sponges Dominant In The Alaska Intertidal: Biology, Ecology, And Genetic Diversity

      Knowlton, Ann Lynette; Highsmith, Raymond C. (2002)
      The role of the sponge, Halichondria panicea, in a Kachemak Bay, Alaska, intertidal community was investigated through field and laboratory experiments. The relationship between H. panicea and co-occurring macroalgae was studied and results indicate that removing macroalgae had no effect on sponge abundance. A laboratory feeding trial investigating H. panicea and its primary predator Archidoris montereyensis showed that nudibranchs consuming symbiotic sponge had higher feeding and egg production rates than individuals eating aposymbiotic sponge. In a simulated predation event, initial sponge growth rates into experimental feeding scars were high, indicating a response mechanism to tissue damage. A naturally occurring high nudibranch recruitment into a sponge population resulted in the local decline and extinction of both sponge and predator. Genetic studies revealed that at least two sponge species likely comprise the intertidal populations investigated, Halichondria panicea and H. bowerbanki. The reproductive cycle of H. panicea at exposed, hard-substrate habitats, and H. bowerbanki at sheltered, soft-sediment sites, exhibited seasonal peaks in oocyte production and maturation. H. panicea produced embryos 3--4 months earlier than H. bowerbanki. Six genomic DNA microsatellite loci were isolated and utilized in the characterization of two Halichondria panicea populations. The two populations were differentiated from one another with no significant inbreeding or bottleneck effect detected. All individuals were genetically unique, indicating little or no cloning. Sexual reproduction appears to be the dominant mode of reproduction maintaining the populations. DNA sequence analyses suggest that at least two species are likely present in Kachemak Bay. Distributions of ITS and CO1 haplotypes corresponded to habitat type. Analyses of the data grouped Alaska haplotypes separately from European samples of Halichondria panicea and H. bowerbanki , suggesting separate species may occur in Alaska. A re-examination of sponge systematics in southcentral Alaska is needed.
    • The Colonization Mechanism Of Pink Salmon Populations In Glacier Bay, Alaska, Based On Genetic Data

      Kondzela, Christine M.; Gharrett, A. J.; Wilmot, Richard; Pella, Jerry; Smoker, William; Finney, Bruce (2010)
      Following 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.
    • Variability Of Pink Salmon Family Size Has Implications For Conservation And Management Models

      Geiger, Harold Joseph, Iii; Gharrett, A. J. (2002)
      In several populations of pink salmon, the short-term dynamics population size was related to both the mean and variance of individual family sizes, because not all families were equally productive. In the marine lifestage, population increases came disproportionately from the most productive families, especially in populations with the highest average marine survival. Moreover, the trait of marine survival itself had a statistically detectable genetic component. This implies that the most favored phenotypes change from generation to generation, and that the marine environment is unpredictable and changing. These results, together with laboratory studies of freshwater survival and measurements of wild pink salmon in Prince William Sound, Alaska, seemed to indicate that family-specific variation in marine survival and variation in egg retention within the redd were the most important potential influences on variation of pink salmon family size in the studied populations, when density was controlled to intermediate levels. These results provide more justification for maintaining stock sizes at intermediate or high levels, and for protecting metapopulation structure. These results also show the importance of variation and instability in the recruitment process of Pacific salmon, and highlight the inadequacy of current models of salmon recruitment, which emphasize stability and long-term averages.