Population genetic structure and phylogeography of common eiders (Somateria mollissima)

Thesis (Ph.D.) University of Alaska Fairbanks, 2006Population genetic structure of Common Eiders (Somateria mollissima) was assessed at increasing spatial scales (microgeographic [<1 km] to throughout their circumpolar distribution), using molecular markers with varying modes of inheritance and rates of evolution. Population genetic subdivision was observed at all spatial scales; however, the degree of structure differed among marker types. Relatively lower levels of spatial genetic structuring were observed at bi-parentally inherited markers, and high levels of structuring were observed at a maternally inherited locus. Differences in the degree of subdivision between marker types may be attributable to the breeding biology of eiders. Pair formation occurs on the wintering grounds; where several populations of eiders interact. Female eiders exhibit high natal and breeding philopatry; whereas, males accompany females back to breeding sites and may disperse long distances between breeding seasons. Significant structuring observed at microgeographic scales indicates that eiders may nest in kin groups. Though the underlying mechanism enabling female eiders to discriminate kin is unknown, waterfowl may achieve kin recognition indirectly through association during brood rearing. Genetic signatures of philopatry among Common Eider populations do vary among Alaskan populations. No genetic structuring at mitochondrial DNA (mtDNA) was observed among islands in the Beaufort Sea in close geographic proximity (1-49 km apart). However, high structuring was observed among island groups, suggesting females are philopatric to island groups rather than individual islands. In contrast, moderate levels of genetic partitioning for mtDNA were observed among Yukon-Kuskokwim Delta (YKD) colonies (9-63 km apart); therefore, female eiders may be philopatric to individual colonies. MtDNA haplotypes representing Aleutian and YKD populations are more genetically similar to Canadian and Scandinavian populations than northern Alaska populations, indicating that southern Alaskan populations were colonized from central Canadian refugia. Data indicate that the North Slope may have been a refugium for eiders but contributed little to the post-glacial colonization of North America and Scandinavia. Finally, philopatry and winter site fidelity observed in waterfowl have predictable effects on population genetic structure. Researchers characterizing populations using molecular techniques could under- or over-estimate the degree of population genetic differentiation if estimates are based on a single marker type.1. Do waterfowl nest in kin groups? Evidence from the common eider (Somateria mollissima) breeding in the Beaufort Sea, Alaska -- 2. Population genetic structure of common eiders (Somateria mollissima) breeding in the Beaufort Sea, Alaska -- 3. Genetic characterization of common eiders (Somateria mollissima) breeding on the Yukon-Kuskokwim Delta, Alaska -- 4. Multilocus phylogeography and population structure of common eiders breeding in North America and Scandinavia -- 5. Detection of sex-linkage in "autosomal" microsatellite locus and its implication on an estimator of population differentiation -- Conclusions -- Literature cited

Species-specific responses to landscape features shaped genomic structure within Alaska galliformes

Aim: Connectivity is vital to the resiliency of populations to environmental change and stochastic events, especially for cold-adapted species as Arctic and alpine tundra habitats retract as the climate warms. We examined the influence of past and current landscapes on genomic connectivity in cold-adapted galliformes as a critical first step to assess the vulnerability of Alaska ptarmigan and grouse to environmental change. We hypothesize that the mosaic of physical features and habitat within Alaska promoted the formation of genetic structure across species. Location: Alaska, United States of America. Taxa: Ptarmigan and Grouse (Galliformes: Tetraoninae). Methods: We collected double digest restriction-site- associated DNA sequence data from six ptarmigan and grouse species (N = 13–145/ species) sampled across multiple ecosystems up to ~10 degrees of latitude. Spatial genomic structure was analysed using methods that reflect different temporal scales: (1) principal components analysis to identify major trends in the distribution of genomic variation; (2) maximum likelihood clustering analyses to test for the presence of multiple genomic groupings; (3) shared co-ancestry analyses to assess contemporary relationships and (4) effective migration surfaces to identify regions that deviate from a null model of isolation by distance. Results: Levels of genomic structure varied across species (ΦST =0.009–0.042). Three general patterns of structure emerged: (1) east-west partition located near the Yukon-Tanana uplands; (2) north-south split coinciding with the Alaska Range and (3) northern group near the Brooks Range. Species-specific patterns were observed; not all landscape features were barriers to gene flow for all ptarmigan and grouse and temporal contrasts were detected at the Brooks Range. Main conclusions: Within Alaska galliformes, patterns of genomic structure coincide with physiographic features and highlight the importance of physical and ecological barriers in shaping how genomic diversity is arrayed across the landscape. Lack of concordance in spatial patterns indicates that species behaviour and habitat affinities play key roles in driving the contrasting patterns of genomic structure

Record fledging count from a seven-egg clutch in the Cooper’s Hawk (\u3ci\u3eAccipiter cooperii\u3c/i\u3e)

Cooper’s Hawks (Accipiter cooperii) typically lay 3–5 eggs per clutch, rarely 6 eggs, and there are 2 accounts of 7-egg clutches and 1 record of a maximum 8-egg clutch for the species. Brood sizes of 3–5 young are common and the previous maximum brood count is 6 young. However, in 2019, we found an urban nest in Stevens Point, Wisconsin, with 7 eggs that resulted in a record high of 7 fledglings. We genetically confirmed that the attending male sired all the offspring and the attending female laid all 7 eggs. Larger body size of the tending adults may have been a factor in the exceptional reproduction reported here. El gavila´n Accipiter cooperii t´ıpicamente pone 3–5 huevos por puesta, rara vez 6. Hay 2 reportes de puestas de 7 huevos y 1 registro ma´ximo de una puesta de 8 huevos para esta especie. Los tama˜nos de nidada de 3–5 polluelos son comunes y la nidada ma´xima es de 6 polluelos. Sin embargo, en 2019 encontramos un nido urbano en Stevens Point, Wisconsin, con 7 huevos que result ´o en un r´ecord ma´ximo de 7 polluelos emancipados. Confirmamos gen´eticamente que el macho que los cuidaba era el padre de todos los polluelos y que la hembra que los cuidaba puso los 7 huevos. El tama˜no corporal de los adultos a cargo podr´ıa ser un factor en el evento de reproducci´on extraordinario que reportamos aqu´ı

Phylogenomics reveals ancient and contemporary gene flow contributing to the evolutionary history of sea ducks (Tribe Mergini)

Insight into complex evolutionary histories continues to build through broad comparative phylogenomic and population genomic studies. In particular, there is a need to understand the extent and scale that gene flow contributes to standing genomic diversity and the role introgression has played in evolutionary processes such as hybrid speciation. Here, we investigate the evolutionary history of the Mergini tribe (sea ducks) by coupling multi-species comparisons with phylogenomic analyses of thousands of nuclear ddRAD-seq loci, including Z-sex chromosome and autosomal linked loci, and the mitogenome assayed across all extant sea duck species in North America. All sea duck species are strongly structured across all sampled marker types (pair-wise species ΦST \u3e 0.2), with clear genetic assignments of individuals to their respective species, and phylogenetic relationships recapitulate known relationships. Despite strong species integrity, we identify at least 18 putative hybrids; with all but one being late generational backcrosses. Most interesting, we provide the first evidence that an ancestral gene flow event between long-tailed ducks (Clangula hyemalis) and true Eiders (Somateria spp.) not only moved genetic material into the former species, but likely generated a novel species — the Steller’s eider (Polysticta stelleri) — via hybrid speciation. Despite generally low contemporary levels of gene flow, we conclude that hybridization has and continues to be an important process that shifts novel genetic variation between species within the tribe Mergini. Finally, we outline methods that permit researchers to contrast genomic patterns of contemporary versus ancestral gene flow when attempting to reconstruct potentially complex evolutionary histories

Development of On-Shore Behavior Among Polar Bears (\u3ci\u3eUrsus maritimus\u3c/i\u3e) in the Southern Beaufort Sea: Inherited or Learned?

Polar bears (Ursus maritimus) are experiencing rapid and substantial changes to their environment due to global climate change. Polar bears of the southern Beaufort Sea (SB) have historically spent most of the year on the sea ice. However, recent reports from Alaska indicate that the proportion of the SB subpopulation observed on‐shore during late summer and early fall has increased. Our objective was to investigate whether this on‐shore behavior has developed through genetic inheritance, asocial learning, or through social learning. From 2010 to 2013, genetic data were collected from SB polar bears in the fall via hair snags and remote biopsy darting on‐shore and in the spring from captures and remote biopsy darting on the sea ice. Bears were categorized as either on‐shore or off‐shore individuals based on their presence on‐shore during the fall. Levels of genetic relatedness, first‐order relatives, mother–offspring pairs, and father–offspring pairs were determined and compared within and between the two categories: on‐shore versus off‐shore. Results suggested transmission of on‐shore behavior through either genetic inheritance or social learning as there was a higher than expected number of first‐order relatives exhibiting on‐shore behavior. Genetic relatedness and parentage data analyses were in concurrence with this finding, but further revealed mother–offspring social learning as the primary mechanism responsible for the development of on‐shore behavior. Recognizing that on‐shore behavior among polar bears was predominantly transmitted via social learning from mothers to their offspring has implications for future management and conservation as sea ice continues to decline

Gull plumages are, and are not, what they appear to human vision

Clear correlations between human and bird visual assessments of color have been documented, and are often assumed, despite fundamental differences in human and avian visual physiology and morphology. Analyses of plumage colors with avian perceptual models have shown widespread hidden inter-sexual and inter-specific color variation among passerines perceived as monochromatic to humans, highlighting the uncertainty of human vision to predict potentially relevant variation in color. Herein, we use reflectance data from 13 Larus gull species as an exemplar data set to study concordance between human vision and avian visual modeling of feather colors near, or below, the human threshold for discrimination. We found little evidence among gulls for sexual dichromatism hidden from human vision, but did find inter-specific color variation among gulls that is not seen by humans. Neither of these results were predictable a priori, and we reassert that reflectance measurements of actual feather colors, analyzed with avian relevant visual models, represent best practice when studying bird coloration

Implications of historical and contemporary processes on genetic differentiation of a declining boreal songbird: the rusty blackbird

The arrangement of habitat features via historical or contemporary events can strongly influence genomic and demographic connectivity, and in turn affect levels of genetic diversity and resilience of populations to environmental perturbation. The rusty blackbird (Euphagus carolinus) is a forested wetland habitat specialist whose population size has declined sharply (78%) over recent decades. The species breeds across the expansive North American boreal forest region, which contains a mosaic of habitat conditions resulting from active natural disturbance regimes and glacial history. We used landscape genomics to evaluate how past and present landscape features have shaped patterns of genetic diversity and connectivity across the species’ breeding range. Based on reduced-representation genomic and mitochondrial DNA, genetic structure followed four broad patterns influenced by both historical and contemporary forces: (1) an east–west partition consistent with vicariance during the last glacial maximum; (2) a potential secondary contact zone between eastern and western lineages at James Bay, Ontario; (3) insular differentiation of birds on Newfoundland; and (4) restricted regional gene flow among locales within western and eastern North America. The presence of genomic structure and therefore restricted dispersal among populations may limit the species’ capacity to respond to rapid environmental change

Ancient bears provide insights into Pleistocene ice age refugia in Southeast Alaska

During the Late Pleistocene, major parts of North America were periodically covered by ice sheets. However, there are still questions about whether ice-free refugia were present in the Alexander Archipelago along the Southeast (SE) Alaska coast during the last glacial maximum (LGM). Numerous subfossils have been recovered from caves in SE Alaska, including American black (Ursus americanus) and brown (U. arctos) bears, which today are found in the Alexander Archipelago but are genetically distinct from mainland bear populations. Hence, these bear species offer an ideal system to investigate long-term occupation, potential refugial survival and lineage turnover. Here, we present genetic analyses based on 99 new complete mitochondrial genomes from ancient and modern brown and black bears spanning the last ~45,000 years. Black bears form two SE Alaskan subclades, one preglacial and another postglacial, that diverged \u3e100,000 years ago. All postglacial ancient brown bears are closely related to modern brown bears in the archipelago, while a single preglacial brown bear is found in a distantly related clade. A hiatus in the bear subfossil record around the LGM and the deep split of their pre-and postglacial subclades fail to support a hypothesis of continuous occupancy in SE Alaska throughout the LGM for either species. Our results are consistent with an absence of refugia along the SE Alaska coast, but indicate that vegetation quickly expanded after deglaciation, allowing bears to recolonize the area after a short-lived LGM peak

Hybridization among Arctic white-headed gulls (\u3ci\u3eLarus\u3c/i\u3e spp.) obscures the genetic legacy of the Pleistocene

We studied the influence of glacial oscillations on the genetic structure of seven species of white-headed gull that breed at high latitudes (Larus argentatus, L. canus, L. glaucescens, L. glaucoides, L. hyperboreus, L. schistisagus, and L. thayeri). We evaluated localities hypothesized as ice-free areas or glacial refugia in other Arctic vertebrates using molecular data from 11 microsatellite loci, mitochondrial DNA (mtDNA) control region, and six nuclear introns for 32 populations across the Holarctic. Moderate levels of genetic structure were observed for microsatellites (FST = 0.129), introns (ΦST = 0.185), and mtDNA control region (ΦST = 0.461), with among-group variation maximized when populations were grouped based on subspecific classification. Two haplotype and at least two allele groups were observed across all loci. However, no haplotype/allele group was composed solely of individuals of a single species, a pattern consistent with recent divergence. Furthermore, northernmost populations were not well differentiated and among-group variation was maximized when L. argentatus and L. hyberboreus populations were grouped by locality rather than species, indicating recent hybridization. Four populations are located in putative Pleistocene glacial refugia and had larger τ estimates than the other 28 populations. However, we were unable to substantiate these putative refugia using coalescent theory, as all populations had genetic signatures of stability based on mtDNA. The extent of haplotype and allele sharing among Arctic white-headed gull species is noteworthy. Studies of other Arctic taxa have generally revealed species-specific clusters as well as genetic structure within species, usually correlated with geography. Aspects of white-headed gull behavioral biology, such as colonization ability and propensity to hybridize, as well as their recent evolutionary history, have likely played a large role in the limited genetic structure observed