• Defining genetic population structure and historical connectivity of snow crab (Chionoecetes opilio)

      Albrecht, Gregory T.; Hardy, Sarah M.; Lopez, J. Andres; Hundertmark, Kris J. (2011-08)
      The snow crab (Chionoecetes opilio) is a valuable commercial resource within the Bering Sea, as well as other areas in the North Pacific and Atlantic Oceans. Large populations are known to exist within the Chukchi and Beaufort Seas, including recently discovered commercial sized individuals (Beaufort). However, genetic connectivity throughout these regions has not been examined until now. Based on seven polymorphic microsatellite loci, relatively low population genetic structuring occurs throughout the Alaskan region (Gst = 0.001). This homogeneity is likely due to long-distance larval dispersal, adult migrations, and a possible recent population expansion following the last glacial maximum. Furthermore, meta-population analysis was conducted for Alaskan and Northwest Atlantic stocks. Although significant genetic divergence characterizes the West Greenland stock in relation to all other populations, low divergence (Gst = 0.005) was found between Atlantic Canada crabs and those from the Alaska region. Larval dispersal between regions is highly unlikely due to the transit distance. Therefore, low divergence is likely the result of a recent population expansion into the Northwest Atlantic <5000 years ago.
    • Examination of saffron cod (Eleginus gracilis) population genetic structure

      Smé, Noël A.; Gharrett, Anthony; Mueter, Franz; Heifetz, Jonathan (2019-05)
      The Saffron Cod (Eleginus gracilis) is an abundant forage fish that inhabits the coastlines of the north Pacific and Arctic oceans. We examined Saffron Cod population genetic structure to provide a reference baseline in anticipation of human and climate-change alterations of the Arctic environment. Nine microsatellites were designed to describe the genetic compositions of and variation among 40 collections of Saffron Cod from four regions (northwestern Alaska, Gulf of Alaska, Sea of Okhotsk, and Gulf of Anadyr). The northwestern Alaska collections (Bering Sea, Norton Sound, and Chukchi Sea) exhibited little genetic divergence. The Gulf of Anadyr collection differed from other regions but was most similar to those of the northwestern Alaska region. The two collections within the Sea of Okhotsk (Sakhalin Island and Hokkaido Island) differed genetically, but not to the extent they did from other regions. The collections from the Gulf of Alaska (Kodiak Island and Prince William Sound) comprised a lineage that was distinct from all of the other collections, including the geographically adjacent northwestern Alaska collections. The absence of genetic structure among northwestern Alaska collections probably reflects their recent expansion into previously unavailable habitat that became available after the Last Glacial Maximum (~16,000 years ago). The divergence of the Gulf of Alaska lineage may have resulted from recurrent episodes of isolation from previous glaciations.
    • Genetic diversity and population genetic structure of tanner crab Chionoecetes bairdi in Alaskan waters

      Johnson, Genevieve M.; López, J. Andrés; Eckert, Ginny L.; Hardy, Sarah M. (2019-05)
      Tanner crab (Chionoecetes bairdi) is a large-bodied species of crab harvested in commercial, personal use, and subsistence fisheries across Alaska. The commercial fisheries were highly productive until the 1980s, when most stocks faced major declines and were closed to harvest. The recovery success of stocks throughout the state has been variable throughout the subsequent decades, leading managers to question whether there are aspects of the population dynamics that are not accounted for. There is limited information on the genetic population structure of C. bairdi in Alaskan waters, which has caused uncertainty about whether established management areas align well with distribution and migration patterns for this species. I applied novel high throughput sequencing methods to measure genetic diversity and investigate the genetic population structure of C. bairdi in Alaskan waters. Genomic DNA was isolated from samples collected from Southeast Alaska, Prince William Sound, and the Eastern Bering Sea, both east and west of 166°W longitude, and processed according to a Double-Digest Restriction-Associated DNA Sequencing protocol. The final genotype assembly included 89 individuals that were genotyped at 2,740 independent, neutral single-nucleotide polymorphism (SNP) sites, and contained 3.06% missing data. The average observed heterozygosity across SNP sites within regions was significantly lower than the average heterozygosity expected for populations in Hardy-Weinberg equilibrium. An analysis of molecular variance indicated that genetic variability was mostly found within individuals (90%), 10% of variability was observed between individuals within sampling regions, and no significant amount of variation was detected between sampling regions. Furthermore, pairwise FST estimates between sampling regions were low, and thus the null model of panmixia could not be rejected. Principal components analysis was also congruent with a model of no differentiation among regions. Bayesian analysis implemented in the program STRUCTURE did not support any population partitioning above K = 1 clusters, again indicating that there is not substantial genetic differentiation among the regions sampled from across the state of Alaska. These results indicate high gene flow throughout the distribution of Tanner crab across the Alaska continental shelf. Recognized stocks are genetically indistinguishable from each other. This may indicate that stocks exchange a substantial number of migrants, and may not operate independently. This new information can provide insights as management plans are evaluated and refined.
    • Harmothoe imbricata: species complex or complex species?

      Gastaldi, Angela; Lopez, J. Andres; Hardy, Sarah; Kelley, Amanda; Sikes, Derek (2019-05)
      Accurate estimates of species diversity are constrained by cryptic species complexes, in which multiple closely related species are grouped under a single species name due to the absence of clear morphological differences. Cryptic diversity is known to be prevalent in polychaete worms, a mostly marine group commonly known as bristle worms. A recent survey of polychaete diversity discovered that the widespread scale-worm Harmothoe imbricata comprises multiple distinct mitochondrial lineages based on analysis of the Cytochrome c oxidase I (COI) gene, which is often referred to as the 'barcoding' gene. Analyses based solely on DNA sequences from COI may overestimate the number of lineages comprising a cryptic species complex, so it has been recommended that cryptic species investigations incorporate nuclear gene sequences. The goal of this study was to determine whether the incorporation of DNA sequences from the nuclear genome corroborates the designation of H. imbricata as a cryptic species complex. I sequenced segments of COI and five nuclear genes: ITS1, ITS2, H3, and portions of the 18S and 28S genes of H. imbricata and analyzed them using distance measures, maximum likelihood, and Bayesian inference. I compared phylogenetic trees produced from mitochondrial and nuclear DNA sequences, as well as from a combined mitochondrial/nuclear dataset. Harmothoe imbricata was found to include five mitochondrial lineages, whereas the nuclear sequences only supported four well-defined lineages. These results corroborate previous reports showing COIbased cryptic species investigations find more lineages than nuclear DNA based investigations. These results provide additional lines of evidence that H. imbricata is a cryptic species complex. These divergent lineages likely arose after being separated during the last glacial maximum but they are now found in sympatry. A thorough morphological study of H. imbricata populations may reveal phenotypic differences correlated with the genetic lineages identified here.
    • Impacts of a top predator (Esox lucius) on salmonids in Southcentral Alaska: genetics, connectivity, and vulnerability

      Jalbert, Chase S.; Falke, Jeffrey; Westley, Peter; López, J. Andrés; Dunker, Kristine (2018-12)
      Worldwide invasion and range expansion of northern pike (pike; Esox lucius) have been linked to the decline of native fishes and new techniques are needed to assess the effects of invasion over broad geographic scales. In Alaska, pike are native north and west of the Alaska Mountain Range but were introduced into Southcentral Alaska in the 1950s and again in the 1970s. To investigate the history of the invasion into Southcentral Alaska, I identified 7,889 single nucleotide polymorphisms (SNPs) from three native and seven introduced populations in Alaska and examined genetic diversity, structure, and affinities of native and invasive pike. Pike exhibited low genetic variability in native populations (mean heterozygosity = 0.0360 and mean π = 0.000241) and further reductions in introduced populations (mean heterozygosity = 0.0227 and mean π = 0.000131), which suggests a bottleneck following introduction. Population differentiation was high among some populations (global FST = 0.424; max FST = 0.668) when compared to other freshwater fishes. I identified five genetically distinct clusters of populations, consisting of three native groups, a single Susitna River basin invasive group, and a Kenai Peninsula group, with little evidence of admixture among groups. The extremely reduced genetic diversity observed in invasive northern pike populations does not appear to affect their invasion success as the species range Southcentral Alaska continues to expand. To assess the vulnerability of five species of Pacific salmon (Oncorhynchus spp.) to the invasion, I combined intrinsic potential habitat modeling, connectivity estimates, and Bayesian networks across 22,875km of stream reaches in the Matanuska-Susitna basin, Alaska, USA. Pink salmon were the most vulnerable species, with 15.2% (2,458 km) of their range identified as "highly" vulnerable. They were followed closely by chum salmon (14.8%) and coho salmon (14.7%). Finally, analysis of the intersection of vulnerable salmon habitats revealed 1,001 km of streams that were highly vulnerable for all five Pacific salmon. This framework is easy to implement, adaptable to any species or region, and cost effective. With increasing threats of species introductions, fishery managers need new tools like those described here to efficiently identify critical areas shared by multiple species, where management actions can have the greatest impact.
    • Novel fungal taxa in an Alaskan boreal forest: phylogenetic affinities, ecologies, and ribosomal RNA secondary structures

      Glass, Daniel; Taylor, D. Lee; Olson, Link E.; Takebayashi, Naoki; Duffy, Lawrence (2011-12)
      Phylogenetic analyses suggest that a novel DNA sequence (NS1) found in a boreal forest soil-clone library belongs to the fungal kingdom but does not fall unambiguously within any known class. In order to determine if NS1 codes for an authentic ribosomal RNA (rRNA) gene-copy, I modeled ribosomal RNA secondary structure for four gene regions. Such analyses have never been used on environmental ribosomal sequences before. It appears that NS1 does code for an authentic gene-copy and is not a biological or lab artifact. I also elucidated the habitat preferences, horizon preferences, and fine-scale spatial structure of NS1 using molecular methods. I determined that NS1 was associated with spruce and was found in both the organic and mineral soil horizons. It appears to have a clumped distribution on the scale of a few meters and its spatial distribution shows little inter-annual variability. Together these findings suggest that NS1 does represent an authentic gene-copy and also shed light on the ecology of this putative taxon. I hope future efforts will expand our understanding of both its identity and function.
    • Phylogeography and population genetics of a Beringian endemic: Dallia (Esociformes: Teleostei)

      Campbell, Matthew A.; López, J. Andrés; Takebayashi, Naoki; Olson, Matthew (2011-08)
      In this thesis I examine the population genetics of an endemic Beringian freshwater fish genus, Dallia (blackfish). The current distribution of blackfish was heavily influenced by paleoclimatic instability during the Pleistocene. Beringian paleoclimatic changes during the Pleistocene included the fluctuating growth and decline of glaciers and an overall decrease in temperature and increased aridity in areas not adjacent to the Bering Sea. Pleistocene glacial advances resulted in the cyclical emergence of the Bering land bridge. The effects of paleoclimatic instability on blackfish distribution and abundance can be inferred through the distribution of genetic variation across the Beringian landscape. I address three basic questions: 1: Are separate populations of blackfish taxonomically distinct entities? I found that while there is clear genetic structuring and isolation, there is insufficient information to make a strong statement in this regard. 2: Did blackfish survive Pleistocene glaciations within multiple Beringian refugia? My results indicate that blackfish persisted in at least four broad geographic areas. 3: How did the Bering land bridge influence intercontinental aquatic interchange? My evidence points to close genetic relationships and potentially high exchange of blackfish across the Bering land bridge, which supports the Bering land bridge as conduit for freshwater aquatic migration.
    • Seedling recruitment, genetic diversity, and secondary growth of deciduous shrubs in Arctic tundra disturbed by retrogressive thaw slump thermokarst on Alaska's North Slope

      Huebner, Diane C.; Bret-Harte, M. Syndonia; Wagner, Diane; Wolf, Diana E.; Douhovnikoff, Vladimir (2020-05)
      Since the 1970s, Arctic temperatures have risen by 2.7 °C, more than twice that of lower latitudes. Productivity of tundra vegetation is historically nutrient-limited, largely due to low rates of decomposition in soils underlain by permafrost, where cold temperatures limit nutrient uptake by plants. However, climate warming is implicated in the recent expansion of tall (≥ 0.5 m) deciduous woody shrubs across the Arctic. Among the largest tundra plants, deciduous shrubs exert strong controls on hydrology, heat balance, nutrient cycling, and food webs. These shrubs may be key players in carbon storage and re-stabilization of thaw-deformed permafrost landscapes (thermokarst), however, shrub-climate feedbacks are complex and their magnitude remains uncertain. Warming associated with recent thermokarst activity includes large (≥ 1 ha) de-vegetated depressions on hillslopes caused by mass soil thaw, known as retrogressive thaw slumps (RTS). RTS have increased on Alaska's North Slope by two-thirds since the 1980s. Within a few decades, some RTS near Toolik Lake support tall willow (Salix spp.) and dwarf birch (Betula nana) colonies. This study quantified three aspects of plant response in RTS of different ages (chronosequences) at two North Slope lakes: 1) recruitment (seedlings m⁻² and percent germination of soil seedbanks), 2) clonal (asexual) growth of dominant vegetation (willow), and 3) secondary growth (annual rings) of dwarf birch and willow. I hypothesized that conditions in RTS support greater recruitment, genetic diversity, and growth than conditions in undisturbed moist acidic tussock tundra, and that the climate signal (June mean temperature) is amplified in RTS shrub ring widths. The study found higher seedling density and seedbank viability associated with warm, nutrient-rich bare soil in recent RTS. Willow species richness was higher in RTS than in undisturbed tundra, but all willows showed high heterozygosity and low clonal spread regardless of disturbance. Ramets (branches) within clones were more widely spaced in RTS, suggesting that RTS can fragment and disperse asexual propagules. Shrub rings in RTS were wider than in undisturbed tundra, but climate sensitivity to warmer temperatures was not amplified in the growth rings of most RTS shrubs. Most RTS shrubs had wider rings associated with greater September precipitation in the previous year, while shrubs growing outside of RTS did not, which suggests protective effects of early snow accumulations in RTS depressions. These results demonstrate that some North Slope RTS support greater seedling recruitment and shrub growth than undisturbed tundra and may enhance tundra shrub growth.
    • Shining light on hibernator genomes: using radiation to reveal DNA damage and repair dynamics in Arctic ground squirrels

      Yancey, Krysta L.; Podlutsky, Andrej; Drew, Kelly; Harris, Michael (2018-12)
      Mammalian hibernation is characterized by dynamic changes in metabolism and body temperature; it may be sustained for up to nine months in some species. The majority of hibernation is spent in torpor, a dormant state, which is regularly interrupted by brief periods of activity referred to as interbout arousal. Upon arousal thermogenesis begins in vascularized fat and ends with whole-body shivering until the animal reaches a body temperature around 36-37 °C. Interbout arousal is usually less than a day long and is commonly thought to be necessary for maintenance and repair of tissues, in addition to the cycling and replenishment of metabolites. While physiologically extreme, torpor-arousal cycles do not drastically impact the health of hibernators. Rather, hibernators are recognized for their longevity and resistance to a variety of stresses, such as ischemia/reperfusion and the brain damage that typically follows. It remains unknown how the process of hibernation challenges genome stability and the basic molecular mechanisms of DNA repair. Therefore, this thesis begins with a review on current knowledge of genome maintenance in the context of mammalian hibernation, distinguishing it from other similar and often correlated conditions like hypothermia. Then, we present the first cellular and molecular study to be conducted on DNA damage and repair dynamics in a hibernator using the Alaskan arctic ground squirrel. Our results indicate that hibernators can avoid genome instability during torpor-arousal cycles through status-specific combinations of strategies for preventing DNA damage and efficient DNA repair, paired with anti-apoptotic environments. The unique suite of adaptations necessary to endure torpor-arousal cycles may help explain the longevity and radio-resistance that are often observed in hibernating species.