• 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.
    • Cytogenetics and sex determination in collared lemmings

      Jarrell, Gordon Hamilton; Shields, Gerald F. (1989)
      Collared lemmings (Dicrostonyx groenlandicus rubricatus) from northeastern Alaska were found to have sex chromosomes that differ from those of their Siberian congeners, because of fusion to a particular pair of autosomes. But, as in Siberian lemmings, breeding experiments showed that sex determination involves an X-linked "male-repressor," which causes carriers to develop as fertile females, despite the presence of a Y chromosome. Genotypic frequencies in offspring are consistent with Mendelian expectations of such a system, hence natal sex ratios normally favor females. X-linkage of the male-repressor in Siberia and in Alaska indicates that the gene is probably located on the "original" arms of the X chromosome rather than on the fused autosomal arms, which differ on the two continents. One consequence of the autosomal fusion to the sex chromosomes is that deleterious recessive alleles on the autosome fused to the X chromosome are more resistant to selection than at truly autosomal loci. Another consequence is that, because males are heterozygous for loci fused to the sex chromosomes, they are more resistant to inbreeding depression than XX females. One inbred line produced a natal sex ratio of 67% males. The male-bias probably resulted from loss of the male-repressor and from a lethal carried on the formerly autosomal arm of the X chromosome. As inbreeding coefficients approached 0.3, the lethal would have been homozygous in half of the homogametic (female) zygotes. This phenomenon may explain the excess of males and XY females observed in earlier work. Also, if under the natural mating system, inbreeding depression limits fitness, then fusions of autosomal chromatin to the heterochromosomes could be an adaptation to reduce inbreeding depression in heterogametic individuals. Some other genetic features of collared lemmings do suggest endogamy. Female-biased sex ratios can evolve when mating occurs between neighboring individuals who are more related than if mating occurred randomly. Two proposed sources of such "viscous" gene flow in lemmings are cyclical changes in population density and mosaic habitat. Alternatively, could climate may favor winter aggregation and inhibit the dispersal of winter-born offspring, which would mature and mate with close relatives; dispersal and outbreeding would occur in summer. Thus, inbreeding would be seasonal rather than density-dependent and it is unnecessary to suppose discontinuous habitat.
    • Divergence, gene flow, and the speciation continuum in trans-Beringian birds

      McLaughlin, Jessica F.; Winker, Kevin; Takebayashi, Naoki; Hundertmark, Chris (2017-08)
      Understanding the processes of divergence and speciation, particularly in the presence of gene flow, is key to understanding the generation of biodiversity. I investigated divergence and gene flow in nine lineages of birds with a trans-Beringian distribution, including pairs of populations, subspecies, and species, using loci containing ultraconserved elements (UCEs). I found that although these lineages spanned conditions from panmixia to fully biologically isolated species, they were not smoothly distributed across this continuum, but formed two discontinuous groups: relatively shallow splits with gene flow between Asian and North American populations, no fixed SNPs, and lower divergence; and relatively deeply split lineages with multiple fixed SNPs, higher divergence, and relatively low rates of gene flow. All eight lineages in which two populations were distinguishable shared the same divergence model, one with gene flow without a prolonged period of isolation. This was despite the diversity of lineages included that might not have responded in the same ways to the glacial-interglacial cycles of connection and isolation in Beringia. Together, these results highlight the role of gene flow in influencing divergence in these Beringian lineages. Sample size is a critical aspect of study design in population genomics research, yet few empirical studies have examined the impacts of small sample sizes. Using split-migration models optimized with full datasets, I subsampled the datasets from Chapter 1 at sequentially smaller sample sizes from full datasets of 6 - 8 diploid individuals per population and then compared parameter estimates and their variances. Effective population size parameters (ν) tended to be underestimated at low sample sizes (fewer than 3 diploid individuals per population), migration (m) was fairly reliably estimated until under 2 individuals per population, and no trend of over- or underestimation was found in either time since divergence (T) or Θ (4Nrefμ) . Lineages that were split above the population level (subspecies and species pairs) tended to have lower variance at smaller sample sizes than population-level splits, with many parameters reliably estimated at levels as low as 3 diploid individuals per population, whereas shallower splits (i.e., populations) often required at least 5 individuals per population for reliable demographic inferences. Although divergence levels may be unknown at the outset of study design, my results provide a framework for planning appropriate sampling, and for interpreting results if smaller sample sizes must be used.
    • Ecogeographic, Adaptive, And Phylogenetic Variations In The Crested Duck (Lophonetta Specularioides) And Their Hemoglobins In The Andes

      Bulgarella, Mariana; McCracken, Kevin; Takebayashi, Naoki; Tubaro, Pablo L.; Winker, Kevin S. (2010)
      Tolerance to high-altitude hypoxia in animals varies widely and is a key factor in determining survival at high elevation. The Andean Cordillera of South America, which spans large elevational and latitudinal gradients, enables the study of native highland populations and the characteristics of hemoglobin proteins that are locally adapted for high-altitude respiration. The waterfowl populations of South America are understudied, little data on demographics and behavior are currently available, and only recently have they been investigated using molecular tools. We studied population genetics, phylogeography, and ecogeographic variation in the crested duck ( Lophonetta specularioides). The crested duck is a dabbling duck, and it comprises two subspecies endemic to highland and lowland regions of South America. The primary objective of this study was to investigate the genetic differentiation between highland and lowlands populations of crested ducks using molecular markers with varying modes of inheritance and rates of substitution. The second objective was to evaluate morphological differences between the subspecies to better understand the forces shaping morphology in the two different environments. A third objective was to provide additional information on the taxonomic relationships and natural history of the crested duck. First, we examined the population genetics of the three adult hemoglobins (alphaD, alphaA, betaA), six autosomal introns, and mtDNA. This multi-locus analysis revealed a significant pattern of differentiation between highland and lowland populations. Four hemoglobin amino acid replacements were found in crested duck that may play a role in influencing high-altitude respiration. The lack of evidence for gene flow for hemoglobin alleles between highland and lowland populations and the biochemical properties of the amino acid substitutions themselves are consistent with the effects of selection acting on these loci. Overall body size was larger for the highland subspecies, body size was intermediate in mid-elevation environments, and smaller individuals were found in the lowlands of Patagonia. We also performed a multi-locus phylogenetic analysis to determine the relationships of Lophonetta within the South American duck clade. Finally, we determined the proportion of genes expressed in bone marow of adult crested duck finding mostly genes related to hemopoietic and immune function.
    • From Forest To Tundra: Historical Biogeography, Floristic Diversity And Nucleotide Variation In Balsam Poplar

      Breen, Amy L.; Olson, Matthew; Murray, David F.; Taylor, D. Lee; Walker, Donald A.; Wolf, Diana E. (2010)
      The North America boreal forest extends across more than 10� of latitude from central Labrador to interior Alaska. Periods of major climate fluctuations, including glacial and interglacial cycles, drove major migrations in the Quaternary history of the boreal forest. Beringia, the unglaciated region between the Lena and Mackenzie rivers, is recognized as an important refugium for arctic plants during the last ice age, but its role for boreal trees remains controversial. The paleobotanical record indicates Populus balsamifera (balsam poplar) survived within Beringia during the last glacial. My research employed an interdisciplinary approach, combining techniques in the fields of ecology, evolution and population genetics, to reconstruct the late Quaternary migration history of balsam poplar and to describe and classify balsam poplar plant communities in the Alaskan Arctic. Chapter 1 describes the motivation for the research. Chapter 2 addresses whether a demographically-detectable population of balsam poplar was present within Beringia during the most recent ice age. I found that patterns of variation in chloroplast DNA are most consistent with the presence of a single population of balsam poplar south of the continental ice sheets through the Late Quaternary. Chapter 3 is an analysis of floristic diversity in balsam poplar communities across the Arctic Slope, Interior Alaska and the Yukon Territory and asks whether one balsam poplar-associated plant community spans the arctic and boreal regions, or if these communities differ. I found that arctic communities are dominated by arctic-alpine taxa, whereas boreal communities are dominated by boreal taxa. A strong linkage between climate and the occurrence of balsam poplar also was observed on the Arctic Slope. Chapter 4 is a study of nucleotide diversity in three nuclear loci across the range of balsam poplar. This was the first study to document geographic structure in genetic variation within the species. It also showed that diversity in three North American poplars (P. balsamifera, P. deltoides and P. trichocarpa) was substantially less than that of three Eurasian poplars (P. alba, P. nigra and P. tremula). Chapter 5 summarizes the research and points toward future research directions.
    • Gene-By-Diet Interactions And Obesity Among Yup'ik People Living In Southwest Alaska

      Lemas, Dominick; Boyer, Bert B.; O'Brien, Diane M.; Schulte, Marvin K.; Tiwari, Hemant K. (2012)
      BACKGROUND: Molecular approaches have expedited the discovery of human obesity genes, however the heritability explained by these loci remains low (<2%). Gene-by-environment interactions may partially account for the "missing heritability" attributed to variation in obesity phenotypes. OBJECTIVE: The specific aims of this dissertation were to (i) identify genetic polymorphisms associated with obesity-related phenotypes in Yup'ik people and (ii) evaluate how n-3 polyunsaturated fatty acid (n-3 PUFA) intake modifies associations between genetic polymorphisms and obesity-related phenotypes in a population with widely varying intake of n-3 PUFAs. APPROACH: We genotyped genetic polymorphisms in (1) candidate genes with a strong physiological role in obesity pathophysiology; (2) candidate genes identified in obesity whole-genome linkage studies that were regulated by n-3 PUFAs; and (3) candidate genes reproducibly implicated in obesity genome-wide association studies (GWAS). DATA & ANALYSES: We used Center for Alaska Native Health Research (CANHR) data collected between 2001 and 2008. We estimated dietary intake of n-3 PUFA using nitrogen stable isotope ratios (delta15N) of red blood cells (RBC) and obesity-related phenotypes were obtained by trained staff. Genotype-phenotype analyses used generalized linear models that accounted for familial correlations. RESULTS: Our analyses of candidate genes based on physiology revealed a polymorphism called P479L in carnitine palmitoyltransferase 1A (CPT1A) that was associated with elevated fasting HDL-cholesterol and all obesity phenotypes. Our investigation of candidate genes that are regulated by n-3 PUFAs and implicated in obesity whole-genome linkage studies demonstrate that polymorphisms in stearoyl CoA desaturase (SCD) and steroyl regulatory element binding protein (SLC2A4) were associated with obesity-related phenotypes; however n-3 PUFA intake did not modify associations between SCD and SLC2A4 polymorphisms and obesity phenotypes. Finally, our investigation of candidate genes reproducibly implicated in obesity GWAS demonstrated that genetic predisposition to obesity is associated with adiposity and that interactions with n-3 PUFA intake accounted for more than twice the phenotypic variation in adiposity. CONCLUSION: Taken together, results from this dissertation suggest that selecting candidate genes based on large-scale genomic analyses, such as linkage analyses and GWAS, has the potential to identify gene-by-environment interactions that partially account for the "missing heritability" attributed to obesity.
    • Genetic Ancestry Modeling And Performance Association In The Alaskan Sled Dog

      Huson, Heather Jay; Runstadler, Jonathan; Hundertmark, Kris; Ostrander, Elaine; Bailey-Wilson, Joan (2011)
      Alaskan sled dogs present us with the unique opportunity to study the development of a population of dogs produced from the selective breeding of high performance athletes. I establish that sled dogs are a genetically distinct population of dogs that segregate into two sub-groups based on their racing style of "sprint" or short distance and "distance" or long distance. The practice of interbreeding Alaskan sled dogs with various purebred dogs over the past century has allowed us to investigate the impact of these domestic breeds on the sled dog genome and their potential contribution to athletic performance. Here, I establish genetic profiles of both the sprint and the distance racing dogs using microsatellite-based markers, single-nucleotide polymorphism (SNP) arrays, and ancestry modeling. Population structure is assessed using clustering and principle component analyses. Inbreeding patterns are examined through population structure, inbreeding statistics, estimations of linkage disequilibrium, and autozygosity. Purebred breed components and their potential role in influencing performance attributes of Alaskan sled dogs were determined through genetic breed identification. Ancestry modeling was used to localize genomic regions of specific breed selection. These breeds were then analyzed for their genetic contribution to regions experiencing selection within the sprint or distance racing dogs. I determined regions of selective sweep and genome-wide association to the sprint or distance racing dogs. A genome-wide association analysis of heat tolerance performance in sprint dogs identified SNPs potentially regulating the MYH9 gene. This was the first genetic assessment of ancestry, inbreeding, and performance genes attributed to racing Alaskan sled dogs.
    • 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 * &rarr; mAH-4*) and III (mAH-3* &rarr; 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.
    • Molecular phylogenetics of arvicoline rodents

      Conroy, Christopher John; Cook, Joseph A. (1998)
      The impetus for this dissertation was an interest in geographic variation in Microtus longicaudus with a particular focus on populations in the Alexander Archipelago of southeastern Alaska. To establish a framework for interpreting intraspecific variation in M. longicaudus, I examined the phylogenetics of 28 species of the genus Microtus, including all North American species (Chapters 2 and 4). That study, which corroborates a rapid pulse of diversification noted in the fossil record, necessitated a deeper phylogenetic perspective. Thus, a third objective of the dissertation was to investigate relationships among genera of arvicolines within the framework of other murid rodents. I examined variation in the mitochondrial cytochrome b and ND4 genes using maximum parsimony, distance, and maximum likelihood phylogenetic analyses. Relationships at several taxonomic levels appear intractable due to rapid accumulation and survival of genetic lineages. These rapid radiations were found among species, genera, and possibly subfamilies; however, strong support at these levels for other taxa (e.g., the monophyly of Microtus) suggests these genes have strong phylogenetic signal. Many of the well-supported sister species pairs within Microtus (Chapters 2 and 4) had been previously identified based on morphologic or allozyme work (e.g., M. pennsylvanicus and M. montanus, M. pinetorum and M. quasiater). The sequence data supported a clade of taiga dwelling species in North America and a clade of eastern and central Asian species. The southernmost arvicoline species of Mexico and Guatemala, though previously suggested to be derived from a single ancient invasion, did not appear to be either ancient or monophyletic. Within M. longicaudus, a large east-west phylogeographic break was detected that is equivalent in genetic distance to other sister species pairs in the genus. This break may indicate mid to late-Pleistocene differentiation (Chapter 3) within the genus. At higher latitudes, populations of M. longicaudus exhibited evidence of recent range expansion including absence of correlation between geographic and genetic structure; and pairwise mismatches among DNA sequences with a single peak and few differences.
    • Molecular Population Genetics And Systematics Of Alaska Brown Bear (Ursus Arctos L.)

      Talbot, Sandra Looman; Follmann, Erich (2006)
      Complete nucleotide sequences of the mitochondrial cytochrome b, tRNAproline and tRNA threonine genes of the eight extant species of ursids, as well as 166 brown bears (Ursus arctos L.) from 10 geographic regions of Alaska and elsewhere, are used to generate hypotheses about phylogenetic relationships among ursids and phylogeographic relationships among brown bears. Additional data were obtained from mitochondrial DNA control region from over 200 brown bears among 14 populations in Alaska, to assess structuring among brown bears. Phylogenetic analyses indicate the giant panda (Ailuropoda melanoleuca) and spectacled bear (Tremarctos ornata) represent basal extant taxa. Ursines, including the sun bear (Helarctos malayanus), sloth bear (Melursus ursinus), Asiatic and American black bears (Ursus thibetanus and U. americanus), brown bear, and polar bear (U. maritimus) apparently experienced rapid radiation during the mid-Pliocene to early Pleistocene. The two black bears appear to be sister taxa; brown and polar bear are the most recently derived of the ursines. Polar bears apparently arose during the Pleistocene from within a clade of brown bears ancestral to populations currently inhabiting islands of the Alexander Archipelago of southeastern Alaska. Thus, brown bears are paraphyletic with respect to polar bears. Parsimony and distance analyses suggest two distinct clades of mtDNA: one (Clade I) composed only of Alexander Archipelago bears, and the other clade comprised of bears inhabiting all other regions of Alaska (Clade II). This latter clade represents bears inhabiting eastern (Clade IIa) and western (Clade IIb) Alaska. Mismatch analysis uncovered a pattern suggestive of recent expansion among some populations comprising Clade IIb. Over 90% of populations in Alaska were significantly differentiated as measured by variance in haplotype frequencies, suggesting limited contemporary female-mediated gene flow and/or shifts in gene frequency through genetic drift. The degree of population genetic differentiation revealed using mtDNA, as well as limited information from comparisons of multilocus microsatellite genotypes from bears representing four Alaska populations, suggests many Alaskan populations are evolving independently. Analyses of molecular variance gave little support for currently accepted subspecies hypotheses. This research has provided new perspectives on processes that drive population structure of brown bears of Alaska and worldwide.
    • Molecular systematics and biogeography of long-tailed shrews (Insectivora: Sorex) and northern flying squirrels (Rodentia: Glaucomys)

      Demboski, John Richard; Cook, Joseph A. (1999)
      Insight into phylogenetic and biogeographic relationships among several mammalian taxa in western North America was provided with DNA sequences of two mitochondrial genes (cytochrome b and ND4). Members of two species complexes of long-tailed shrews (genus Sorex ) and northern flying squirrels (genus Glaucomys) were examined, and a common theme of responses to past climate change and glacial cycles was evident. Diversification events indicated by the DNA sequences provide new perspectives regarding the deep and shallow history of these taxa. Analysis of seven species of the Sorex cinereus complex (and related species) revealed two major clades within the complex, Northern and Southern. These generally corroborate proposed morphological relationships and correspond to broadly defined habitat affiliations (xeric and mesic), respectively. Within the Northern clade, amphiberingian species represented a monophyletic group suggesting Beringia was a center of endemism. Next, five species of the S. vagrans complex and related species were assessed. Significant molecular variation was revealed that does not correspond to morphological differences within the complex. Two major clades within S. monticolus were observed, a widespread Continental clade (Arizona to Alaska, including S. neomexicanus) and a restricted Coastal clade (Oregon to southeast Alaska, including S. bairdi and S. pacificus). A regional examination of genetic variation in the northern flying squirrel in southeast Alaska was also performed. Results suggested that southern islands in the Alexander Archipelago were the result of recent colonization (founder event). Finally, a comparative phylogeographic analysis of a reduced data set (S. monticolus), a molecular data set for the American Pine Marten, Martes americana, and other published molecular studies were used to reexamine the role of glacial refugia in the biogeography of the north Pacific coast. Previous ideas regarding purported refugia may be overstated and may be the result of limited geographic sampling. This thesis provides new perspectives on processes (e.g., post-glacial colonization) driving mammalian phylogenetic and biogeographic structuring in western North America.
    • The phylogenetics and evolutionary history of the northern latitude plant genus Therorhodion (Maxim.) small (Ericaceae)

      Oliver, Margaret G.; Ickert-Bond, Stefanie M.; Wolf, Diana E.; Stensvold, Mary C. (2017-08)
      Taxonomic uncertainty in the Arctic-alpine flowering plant genus Therorhodion (Maxim.) Small (Ericaceae) can be attributed to two distinctly different viewpoints representing the taxonomic diversity. Russian taxonomists recognize two species, one with two subspecies, whereas three distinct species are recognized in North America following a broader species concept. Therorhodion redowskianum Hutch. is restricted to Asia, and is unambiguously recognized by both viewpoints. Therorhodion camtschaticum Small and T. glandulosum Standl. ex Small have an amphiberingian distribution in eastern Asia and Alaska with T. glandulosum sometimes recognized as a subspecies of T. camtschaticum. Investigating this taxonomic disagreement creates an opportunity to learn more about the diversification of Beringian taxa and how past glacial events have influenced speciation and the exchange of biota between the continents. I set out to unravel the taxonomic relationships within Therorhodion and the likely dispersal route/s of these amphiberingian taxa through the measurement of macromorphological characteristics from voucher specimens, phylogenetic analyses using plastid and nuclear DNA markers, and divergence time analyses. A comparison of age estimates was also performed based on secondary constraints versus fossil constraints. Although leaf length and width measurements were not reliable delimiting characters, there is strong molecular support for Therorhodion as the sister clade to Rhododendron, and within Therorhodion three strongly supported monophyletic clades representing three species were recovered. The use of secondary constraints in the divergence time analyses resulted in younger age estimates than when fossil constraints were applied, corroborating previous studies. Using fossil constraints I inferred a divergence of Therorhodion from Rhododendron in the late Paleocene with the Asian-restricted species diverging first from the T. camtschaticum/ T. glandulosum clade during the middle Miocene, supporting an Asian origin for the genus. Subsequently, the remaining two species are inferred to have diverged in the middle to late Miocene and further dispersed throughout the Pliocene and Pleistocene as suitable habitat became available through a cooling climate.
    • Phylogeography and molecular phylogenetics of the hoary marmot (Marmota caligata)

      Kerhoulas, Nicholas John; Olson, Link; Sikes, Derek; Takebayashi, Naoki (2017-12)
      In this dissertation I documented the phylogeographic history of the Hoary Marmot (Marmota caligata) and its phylogenetic relationships with the Vancouver Island (M. vancouverensis) and Olympic (M. olympus) marmots. The Hoary Marmot is an iconic alpine mammal that is broadly distributed throughout the Pacific Northwest (PNW) from Washington and central Idaho in the south to Alaska in the north. Vancouver Island and Olympic marmots have much more restricted geographic distributions, occurring only on Vancouver Island (British Columbia, Canada) and the Olympic Peninsula (Washington, USA), respectively. In my first chapter I used mitochondrial DNA (mtDNA) sequence data to document the existence of 2 mtDNA clades in Hoary Marmots. I also used mtDNA and nuclear sequence data to infer historic gene flow from Hoary into Vancouver Island marmots, which resulted in the latter "capturing" the mitochondrial genome of the former. Analyses of nuclear sequence data also suggested the potential for historic gene flow between Hoary Marmots and Olympic Marmots in Washington. In my second chapter I investigated the origins of Hoary Marmots on Sud Island, Alaska, part of the Maritime National Wildlife Refuge. This island population of marmots was purported to have been introduced by humans and detrimental to nesting seabirds. As a result, the United States Fish and Wildlife Service undertook efforts to eradicate the Hoary Marmot population on Sud Island between 2009-2011. I conducted a literature review of marmot introductions in Alaska and used molecular data to determine the geographic origin of marmots on Sud Island. Through my literature review I found no direct evidence that marmots were introduced to Sud Island or any documentation that they were detrimental to nesting seabirds on this island. Molecular analysis identified the Hoary Marmot population on Sud Island as a distinct genetic cluster, with divergence time estimates similar to those of a naturally occurring island population, suggesting a natural colonization of Sud Island by Hoary Marmots. In my third chapter I investigated potential refugia used by Hoary Marmots during the Last Glacial Maximum (LGM) and the potential effects of climate change on the future distribution of suitable habitat. To address these questions I used species distribution models (SDMs) based on all available museum specimens and population genetic summary statistics calculated from mtDNA sequence data. I found the most likely areas of LGM refugia were located south of the glacial margins of the Pleistocene and along the PNW coast. Habitat in the southernmost portion of the Hoary Marmot current geographic distribution was predicted to be the most negatively impacted by future climate change. Additionally, populations from this region were the most genetically diverse, indicating that these populations may be important for conservation of the species as a whole. In my final chapter I used microsatellite and sequence (mtDNA and nuclear) data to revisit the findings of my first chapter and to test for gene flow between Hoary, Vancouver Island, and Olympic marmots, as well as between the 2 Hoary Marmot mtDNA clades. I also improved the known distribution of the Hoary Marmot mtDNA clades by determining clade membership of 98 museum specimens for which no fresh tissues exist. Analysis of the combined sequence and microsatellite data confirmed previous findings that introgression led to Vancouver Island Marmots capturing the mitochondrial genome of Hoary Marmots. The addition of microsatellite data did not resolve the origin of nuclear alleles shared between Hoary Marmots from Washington and Olympic Marmots. Regarding the 2 Hoary Marmot mtDNA clades, molecular results suggested unidirectional gene flow between the clades and that male-biased dispersal is likely occurring in the species. The additional mtDNA clade membership data from the 98 museum specimens revealed that British Columbia is predominantly occupied by a single mtDNA clade. Overall, my research has shown that populations in the southern portion of the Hoary Marmot's geographic distribution are likely to be the most important for conservation and that additional research in this region is needed. I also documented the existence of introgression between Hoary and Vancouver Island marmots, highlighting the importance of using multiple unlinked loci for phylogenetic and phylogeographic analysis. Lastly, my findings call attention tothe importance of rigorously verifying primary sources of information before undertaking species eradications.
    • Phylogeography And Population Genetic Structure Of Beringian Landbirds

      Pruett, Christin Leigh; Winker, Kevin (2002)
      Molecular genetic approaches can be used to evaluate the historic and current relationships among populations. Mitochondrial DNA sequences and nuclear microsatellite loci were used to examine questions in avian community ecology, biogeography, and population genetics, including: (1) how have simple, high latitude bird communities been historically assembled; (2) how have past climate changes affected a species that has its entire distribution in an area that has experienced many glacial cycles; and (3) what are the genetic effects of sequential peripheral isolation in a natural vertebrate system? Landbird communities in the Aleutian Islands are simple and replicated, having only eight members. Traditional community assembly theory would describe this co-distribution as being due to nonrandom, likely contemporary ecological factors. However, I found that many species had unique colonization and persistence patterns. Results suggest that these communities were assembled randomly, and that simple ecological assembly rules could not adequately describe this complex process. Species endemic to Beringia, such as the rock sandpiper (Calidris ptilocnemis), would likely have been strongly affected by Pleistocene glacial cycles. MtDNA data suggest that these past climate changes have shaped current distribution and geographic variation in this species. Multiple instances of isolation and differentiation in glacial refugia and subsequent post-glacial population expansions are apparent. This study shows the complex biological responses of endemic Beringian species to climate change and isolation in glacial refugia. Populations that are increasingly isolated from a species' main distribution should provide a useful model for examining the genetic effects of sequential peripheral isolation. Song sparrows (Melospiza melodia) in Alaska have such a distribution, and the most distant populations have morphological and behavioral differences concordant with trends in peripheral or island populations in other species. I examined mtDNA sequences and nuclear microsatellite loci that evolve at different rates, and found that the combined processes of genetic drift, isolation, and divergent selection likely caused rapid morphological and behavioral changes in the most peripheral populations. Results of this study suggest that the examination of molecular markers that evolve at different rates can provide insight into the processes that lead to subspecies differentiation or the first steps in speciation.
    • Phylogeography Of Moose (Alces Alces): Genetic Signatures Of Population History

      Hundertmark, Kris Joseph; Bowyer, R. Terry; Shields, Gerald F. (2002)
      Through analysis of mitochondrial DNA (mtDNA) sequences, I examined phylogeographic relationships among moose (Alces alces) from Europe, Asia, and North America and inferred historic population trends explaining present-day structure of genetic variance. Diversity of nucleotide composition in cytochrome b was low worldwide, with no variation detected among North American moose. The North American lineage was more closely related to European than to Asian lineages, indicating a recent colonization of North America and refuting the theory of eastern and western races of moose. An analysis of the control region provided greater resolution, which revealed similar yet more detailed patterns, including detectable variation within North America subspecies. Patterns of genetic variation among regional populations identified central Asia as the source of extant lineages of moose. Moreover, a recent coalescence was indicated, with the most recent common ancestor dating to the last ice age. Two historic expansions of moose populations were detected: an initial expansion in Eurasia coincident with an interstade of the last ice age, and a second expansion in eastern Asia; and North America following the end of the last ice age. Data indicate a low effective population size in Eurasia during the peak of the last ice age followed by population and range expansion, likely facilitated by climate change. Haplotypes within North America formed a star phylogeny, indicative of recent expansion. Nucleotide and haplotype diversity were greatest in central North America and least in peripheral populations (Alaska, Colorado, and eastern North America). My data indicate a pattern of colonization consistent with a large central population providing founders for peripheral populations, perhaps resulting from leptokurtic dispersal. Low diversity in Alaska indicated a bottleneck subsequent to colonization and recent population expansion. Establishment of regional populations through small numbers of founders combined with selection pressure for smaller body size likely led to morphological differentiation among regional populations and likely was adequate for rapid development of subspecies. Nucleotide and haplotype diversity were low in southeastern Alaska, but were high in neighboring areas of British Columbia; there was little sharing of haplotypes occurred despite close proximity, indicating recent admixture of separate colonizing populations.
    • Phylogeography, Ecogeographic Variation, And Evolutionary History Of The Collared Pika (Ochotona Collaris)

      Lanier, Hayley Christine Stover; Olson, Link (2010)
      In this dissertation I address the evolutionary history, ecogeographic variation, and phylogeography (single species and comparative) of collared pikas (Ochotona collaris). Pikas are small (ca. 150 g) lagomorphs (order Lagomorpha: rabbits, hares, and pikas) found in alpine habitats throughout much of the Holarctic. Only two of the 30 extant pika species occur in the New World. The northern of the two species, O. collaris is separated 800 km north of the American pika (O. princeps). In the first chapter, I employ recently developed molecular analytical techniques to examine when the two North American species diverged. This chapter sets the evolutionary context for the subsequent diversification within O. collaris. In the second chapter, I take a finer-scale view of morphological and ecogeographic variation in the collared pika. I examined morphological variation along a latitudinal gradient and over the past half century. While the length of the growing season appears to best explain latitudinal trends, temporal changes in body size are better explained by interrelated pressures resulting from heat stress and loss of snow cover. In the third chapter, I assess the major phylogeographic patterns within O. collaris and compare the observed levels of diversity within O. collaris to those in other alpine-adapted small mammal species. There are two main phylogroups in O. collaris, which appear to be in contact in Wrangell-St. Elias National Park and Preserve. The within-phylogroup and within-species genetic diversity in O. collaris is lower than that observed in other pikas. In the fourth chapter, I contrast the two O. collaris phylogroups with similar patterns in four co-distributed arctic-alpine small mammals in a comparative phylogeographic context. Although there are differences in the amount of diversity and extent of each phylogroup, simultaneous divergence into similarly distributed intraspecific phylogroups in all five species is supported. Four of the species, including O. collaris, show evidence of Pleistocene population expansion followed by recent demographic decline. Throughout the dissertation, I focus on the role of location (latitude) and time frame in geographically structuring genetic and morphological variation.
    • 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.