USGS ScienceSearch

Geology topics

Sandra L. Talbot

Publications and source records attributed to Sandra L. Talbot.

At least 19 recordsLinked to original sources

Combined high rates of alternative breeding strategies unexpectedly found among populations of a solitary nesting raptor

Social monogamy is the prevalent mating system in birds, but alternative strategies of extra-pair paternity (EPP) and conspecific brood parasitism (CBP) occur in many species. Raptors are virtually absent in discussions of broad taxonomic reviews regarding EPP and CBP likely because these strategies are mostly absent or at low frequency; CBP is unreported in solitary nesting raptors. In contrast, we found high frequencies of EPP (16%–31%) and CBP (15%–26%) nests among three populations of Cooper's Hawks ( Accipiter cooperii ) across the northern breeding range of this solitary nesting, socially monogamous species. EPP and CBP combined occurred in 42%–46% of all nests among populations and hence unexpectedly were nearly equivalent to proportions of genetically monogamous nests. Select covariates failed to predict presence of EPP and CBP in part because virtually all extra-pair adults were uncaught and likely were floaters. We found no support for the hypothesis that territorial females traded copulations for food to maximize energy intake for increased production. Our unique discoveries enhance knowledge of the extent and diversity of alternative breeding strategies among groups of avian and other animal species.

North Dakota, Wisconsin

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 >100,000 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.

Alaska

As the goose flies: Migration routes and timing influence patterns of genetic diversity in a circumpolar migratory herbivore

Migration schedules and the timing of other annual events (e.g., pair formation and molt) can affect the distribution of genetic diversity as much as where these events occur. The greater white-fronted goose ( Anser albifrons ) is a circumpolar goose species, exhibiting temporal and spatial variation of events among populations during the annual cycle. Previous range-wide genetic assessments of the nuclear genome based on eight microsatellite loci suggest a single, largely panmictic population despite up to five subspecies currently recognized based on phenotypic differences. We used double digest restriction-site associated DNA (ddRAD-seq) and mitochondrial DNA (mtDNA) sequence data to re-evaluate estimates of spatial genomic structure and to characterize how past and present processes have shaped the patterns of genetic diversity and connectivity across the Arctic and subarctic. We uncovered previously undetected inter-population differentiation with genetic clusters corresponding to sampling locales associated with current management groups. We further observed subtle genetic clustering within each management unit that can be at least partially explained by the timing and directionality of migration events along with other behaviors during the annual cycle. The Tule Goose ( A. a. elgasi ) and Greenland subspecies ( A. a. flavirostris ) showed the highest level of divergence among all sampling locales investigated. The recovery of previously undetected broad and fine-scale spatial structure suggests that the strong cultural transmission of migratory behavior restricts gene flow across portions of the species’ range. Our data further highlight the importance of re-evaluating previous assessments conducted based on a small number of highly variable genetic markers in phenotypically diverse species.

Circumpolar Arctic

Low levels of hybridization between sympatric cold-water-adapted Arctic cod and Polar cod in the Beaufort Sea confirm genetic distinctiveness

As marine ecosystems respond to climate change and other stressors, it is necessary to evaluate current and past hybridization events to gain insight on the outcomes and drivers of such events. Ancestral introgression within the gadids has been suggested to allow cod to inhabit a variety of habitats. Little attention has been given to contemporary hybridization, especially within cold-water-adapted cod ( Boreogadus saida Lepechin, 1774 and Arctogadus glacialis Peters, 1872). We used whole-genome, restriction-site associated, and mitochondrial sequence data to explore the degree and direction of hybridization between these species where previous hybridization had not been reported. Although nearly identical morphologically at certain life stages, we detected very distinct nuclear and mitochondrial lineages. We detected one potential hybrid with a Arctogadus mitochondrial haplotype and Boreogadus nuclear genotype, but no early generational hybrids. The presence of a late generation hybrid suggests that at least some hybrids survive to maturity and reproduce. However, a historical introgression event could not be excluded. Contemporary gene flow appears asymmetrical from Arctogadus into Boreogadus , which may be due to overlap in timing of spawning, environmental heterogeneity, or differences in population size. This study provides important baseline information for the degree of potential hybridization between these species within Alaska marine environments.

Beaufort Sea, Chukchi Sea

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 (Φ ST =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.

Alaska

Dynamic landscapes in northwestern North America structured populations of wolverines (Gulo gulo)

Cyclic climatic and glacial fluctuations of the Late Quaternary produced a dynamic biogeographic history for high latitudes. To refine our understanding of this history in northwestern North America, we explored geographic structure in a wide-ranging carnivore, the wolverine ( Gulo gulo ). We examined genetic variation in populations across mainland Alaska, coastal Southeast Alaska, and mainland western Canada using nuclear microsatellite genotypes and sequence data from the mitochondrial DNA (mtDNA) control region and Cytochrome b ( Cytb ) gene. Data from maternally inherited mtDNA reflect stable populations in Northwest Alaska, suggesting the region harbored wolverine populations since at least the Last Glacial Maximum (LGM; 21 Kya), consistent with their persistence in the fossil record of Beringia. Populations in Southeast Alaska are characterized by minimal divergence, with no genetic signature of long-term refugial persistence (consistent with the lack of pre-Holocene fossil records there). The Kenai Peninsula population exhibits mixed signatures depending on marker type: mtDNA data indicate stability (i.e., historical persistence) and include a private haplotype, whereas biparentally inherited microsatellites exhibit relatively low variation and a lack of private alleles consistent with a more recent Holocene colonization of the peninsula. Our genetic work is largely consistent with the early 20 th century taxonomic hypothesis that wolverines on the Kenai Peninsula belong to a distinct subspecies. Our finding of significant genetic differentiation of wolverines inhabiting the Kenai Peninsula, coupled with the peninsula’s burgeoning human population and the wolverine’s known sensitivity to anthropogenic impacts, provides valuable foundational data that can be used to inform conservation and management prescriptions for wolverines inhabiting these landscapes.

Alaska, British Columbia, Northwest Territories, N

Using next generation sequencing of alpine plants to improve fecal metabarcoding diet analysis for Dall’s sheep

Objectives Dall’s sheep ( Ovis dalli dalli ) are important herbivores in the mountainous ecosystems of northwestern North America, and recent declines in some populations have sparked concern. Our aim was to improve capabilities for fecal metabarcoding diet analysis of Dall’s sheep and other herbivores by contributing new sequence data for arctic and alpine plants. This expanded reference library will provide critical reference sequence data that will facilitate metabarcoding diet analysis of Dall’s sheep and thus improve understanding of plant-animal interactions in a region undergoing rapid climate change. Data description We provide sequences for the chloroplast rbcL gene of 16 arctic-alpine vascular plant species that are known to comprise the diet of Dall’s sheep. These sequences contribute to a growing reference library that can be used in diet studies of arctic herbivores.

BMC Research Notes

Metabarcoding of environmental samples suggest wide distribution of eelgrass (Zostera marina) pathogens in the north Pacific

Seagrass meadows provide important ecological services to the marine environment but are declining worldwide. Although eelgrass meadows in the north Pacific are thought to be relatively healthy, few studies have assessed the presence of known disease pathogens in these meadows. In a pilot study to test the efficacy of the methods and to provide foundational disease biodiversity data in the north Pacific, we leveraged metabarcoding of environmental DNA extracted from water, sediment, and eelgrass tissue samples collected from five widely distributed eelgrass meadows in Alaska and one in Japan and uncovered wide prevalence of two classes of pathogenic organisms – Labyrinthula zosterae and other associated strains of Labyrinthula , and the Phytophthora / Halophytophthora blight species complex – known to have caused decline in eelgrass ( Zostera marina ) elsewhere in the species’ global distribution. Although the distribution of these disease organisms is not well understood in the north Pacific, we uncovered the presence of at least one eelgrass pathogen at every locality sampled.

Metabarcoding and Metagenomics

Whole‐genome resequencing reveals persistence of forest‐associated mammals in Late Pleistocene refugia along North America’s North Pacific Coast

Aim Numerous glacial refugia have been hypothesized along North America's North Pacific Coast that may have increased divergence of refugial taxa, leading to elevated endemism and subsequently clustered hybrid zones following deglaciation. The locations and community composition of these ice‐free areas remains controversial, but whole‐genome sequences now enable detailed analysis of the demographic and evolutionary histories of refugial taxa. Here, we use genomic data to test spatial and temporal processes of diversification among martens with respect to the Coastal Refugium Hypothesis, to understand the role of climate cycling in shaping diversity across complex landscapes. Location North America and North Pacific Coast archipelagos. Taxon North American martens ( Martes ). Methods Short‐read whole‐genome resequencing data were generated for 11 martens: four M. americana , four M. caurina , two hybrids, and one outgroup ( Martes zibellina ). Sampling was representative of known genetic clades within New World martens, including sampling within insular and continental hybrid zones and along the North Pacific Coast (five island populations). ADMIXTURE , F‐statistics, and D ‐statistics (ABBA‐BABA) were used to identify introgression and infer directionality. Heterozygosity densities, estimated via PSMC, were used to characterize historical demography at and below the species level to infer refugial and colonization processes. Results Forest‐associated Pacific martens ( M. caurina ) are divided into distinct insular and continental clades consistent with the Coastal Refugium Hypothesis. There was no evidence of introgression on islands that received historical translocations of American pine martens ( M. americana ), but introgression was detected in two active zones of secondary contact: one insular and one continental. Only early‐generational hybrids were identified across multiple hybrid zones, a pattern consistent with potential genetic swamping of M. caurina by M. americana . Main conclusions Despite an incomplete fossil record, genomic evidence supports the persistence of forest‐associated martens, likely the insular Pacific marten lineage, along the western edges of the Alexander Archipelago during the Last Glacial Maximum. This discovery informs our understanding of refugial paleoenvironments, critical to interpreting refugial timing, duration, and community composition. Genomic reevaluations of other taxa along North America's North Pacific Coast may yield new and deeper perspectives on the history of refugial forest communities and the role of dynamic climate shifts in shaping high‐latitude diversity across complex insular landscapes.

Alaska, British Columbia, California, Oregon, Wash

Extrinsically reinforced hybrid speciation within Holarctic ermine (Mustela spp.) produces an insular endemic

Aim Refugial isolation during glaciation is an established driver of speciation; however, the opposing role of interglacial population expansion, secondary contact, and gene flow on the diversification process remains less understood. The consequences of glacial cycling on diversity are complex and especially so for archipelago species, which experience dramatic fluctuations in connectivity in response to both lower sea levels during glacial events and increased fragmentation during glacial recession. We test whether extended refugial isolation has led to the divergence of genetically and morphologically distinct species within Holarctic ermine ( Mustela erminea ), a small cosmopolitan carnivore species that harbours 34 extant subspecies, 14 of which are insular endemics. Location Holarctic. Methods We use genetic sequences (complete mitochondrial genomes, four nuclear genes) from >100 ermine (stoats) and geometric morphometric data for >200 individuals (27 of the 34 extant subspecies) from across their Holarctic range to provide an integrative perspective on diversification and endemism across this complex landscape. Multiple species delimitation methods ( iBPP , bPTP ) assessed congruence between morphometric and genetic data. Results Our results support the recognition of at least three species within the M. erminea complex, coincident with three of four genetic clades, tied to diversification in separate glacial refugia. We found substantial geographic variation within each species, with geometric morphometric results largely consistent with historical infraspecific taxonomy. Main conclusions Phylogeographic structure mirrors patterns of diversification in other Holarctic species, with a major Nearctic‐Palearctic split, but with greater intraspecific morphological diversity. Recognition of insular endemic species M. haidarum is consistent with a deep history of refugial persistence and highlights the urgency of mindful management of island populations along North America's North Pacific Coast. Significant environmental modification (e.g. industrial‐scale logging, mining) has been proposed for a number of these islands, which may elevate the risk of extinction of insular palaeoendemics.

Diversity and Distributions

High site fidelity does not equate to population genetic structure for common goldeneye and Barrow's goldeneye in North America

Delineation of population structure provides valuable information for conservation and management of species, as levels of demographic and genetic connectivity not only affect population dynamics but also have important implications for adaptability and resiliency of populations and species. Here, we measure population genetic structure and connectivity across the ranges of two sister species of sea ducks: Barrow's goldeneye Bucephala islandica and common goldeneye B. clangula . We use two different marker types: 7–8 nuclear microsatellite loci assayed across 229 samples and 3678 double digest restriction‐site associated DNA sequencing (ddRAD‐seq) loci assayed across 61 samples. First, both datasets found no evidence of genetic structure within common or Barrow's goldeneye, including between North American and European samples of common goldeneye. These results are in contrast with previous mitochondrial DNA, band recovery and telemetry data which suggest that goldeneyes are structured across their range. We posit that the discordance between autosomal genetic markers and other data types suggests that males, possibly subadult males, may be maintaining genetic connectivity across each species' respective ranges. Next, although mate choice consequences resulting from inter‐specific brood parasitism was hypothesized to cause some level of gene flow between goldeneye species, we only identified a single F1 hybrid with no further evidence of contemporary or historical gene flow. Despite ddRAD‐seq demographic analyses which recovered an optimum evolutionary model of split‐with‐migration (i.e. secondary contact), estimates of gene flow were <<1 migrant per generation in both directions. Together, we conclude that either strong ecological barriers or assortative mating are likely playing a role in preventing further backcrossing. Finally, demographic analyses estimated a relatively deep divergence time between Barrow's goldeneye and common goldeneye of ~1.6 million years before present and suggests that the genomes of both species have been under similar evolutionary constraints.

Journal of Avian Biology

Isolation and characterization of microsatellite loci in merlins (Falco columbarius) and cross-species amplification in gyrfalcons (F. rusticolus) and peregrine falcons (F. peregrinus)

I. Background: Merlins, Falco columbarius, breed throughout temperate and high latitude habitats in Asia, Europe, and North America. Like peregrine falcons, F. peregrinus, merlins underwent population declines during the mid-to-late 20th century, due to organochlorine-based contamination, and have subsequently recovered, at least in North American populations. II. Methods and Results: To better understand levels of genetic diversity and population structuring in contemporary populations and to assess the impact of the 20th century decline, we used genomic data archived in public databases and constructed genomic libraries to isolate and characterize a suite of 17 microsatellite markers for use in merlins. We also conducted cross-amplification experiments to determine the markers’ utility in peregrine falcons and gyrfalcons, F. rusticolus. III. Conclusions: These markers provide a valuable addition to marker suites that can be used to determine individual identity and conduct genetic analyses on merlins and congeners.

Molecular Biology Reports

Microbiomes from biorepositories? 16S rRNA bacterial amplicon sequencing of archived and contemporary intestinal samples of wild mammals (Eulipotyphla: Soricidae)

Interest in gut microbial community composition has exploded recently as a result of the increasing ability to characterize these organisms and a growing understanding of their role in host fitness. New technologies, such as next generation amplicon (16S rRNA) sequencing, have enabled identification of bacterial communities from samples of diverse origin (e.g., fecal, skin, genital, environmental, etc.). Relatively little work, however, has explored the feasibility of utilizing historical samples (e.g., museum archived samples) of varying age, quality, and preservation type. Because natural history collections span multiple decades, these biorepositories have the potential to provide fundamental historical baselines to measure and better understand biodiversity on a changing planet. Utilizing even a small proportion of museum specimens could provide a means of sampling past microbial communities, allowing for direct comparison to contemporary communities and more complete understanding of dynamic shifts through time. We examined the feasibility of obtaining 16S rRNA amplicon microbiome data from whole gastrointestinal tracts (GIs) of shrews of varying age and preservation method, including 5 freshly collected shrew GIs immediately fixed in liquid nitrogen (LN2), 10 ten-year old shrew GIs frozen at −20°C (whole animal), and 10 shrews of varying ages (4 from 1968, 1 from 1980, 1 from 2001, 1 from 2004, 1 from 2007, 1 from 2011 and 2 from 2013) fixed and stored whole in 70% ethanol. Not surprisingly, results of 16S rDNA amplicon sequencing reveal significantly different bacterial communities between different preservation techniques and age of samples. Ten-year old frozen samples had bacterial communities most similar to freshly collected (LN2) samples, while the bacterial communities of both were significantly different from the 70% ethanol preserved samples of various ages. Amongst those preserved in 70% ethanol, age of samples also influenced bacterial community composition. Additionally, we compare results of OTU based and ASV based analyses. Looking ahead, field collectors and museums should develop and adopt best practices related to frozen preservation to ensure adequate material for future microbiome investigations.

Frontiers in Ecology and Evolution

Identifying reliable indicators of fitness in polar bears

Animal structural body size and condition are often measured to evaluate individual health, identify responses to environmental change and food availability, and relate food availability to effects on reproduction and survival. A variety of condition metrics have been developed but relationships between these metrics and vital rates are rarely validated. Identifying an optimal approach to estimate the body condition of polar bears is needed to improve monitoring of their response to decline in sea ice habitat. Therefore, we examined relationships between several commonly used condition indices (CI), body mass, and size with female reproductive success and cub survival among polar bears ( Ursus maritimus ) measured in two subpopulations over three decades. To improve measurement and application of morphometrics and CIs, we also examined whether CIs are independent of age and structural size–an important assumption for monitoring temporal trends—and factors affecting measurement precision and accuracy. Maternal CIs and mass measured the fall prior to denning were related to cub production. Similarly, maternal CIs, mass, and length were related to the mass of cubs or yearlings that accompanied her. However, maternal body mass, but not CIs, measured in the spring was related to cub production and only maternal mass and length were related to the probability of cub survival. These results suggest that CIs may not be better indicators of fitness than body mass in part because CIs remove variation associated with body size that is important in affecting fitness. Further, CIs exhibited variable relationships with age for growing bears and were lower for longer bears despite body length being related to cub survival and female reproductive success. These results are consistent with findings from other species indicating that body mass is a useful metric to link environmental conditions and population dynamics.

PLoS ONE

DNA metabarcoding of feces to infer summer diet of Pacific walruses

Environmental conditions in the Chukchi Sea are changing rapidly and may alter the abundance and distribution of marine species and their benthic prey. We used a metabarcoding approach to identify potentially important prey taxa from Pacific walrus ( Odobenus rosmarus divergens ) fecal samples ( n = 87). Bivalvia was the most dominant class of prey (66% of all normalized counts) and occurred in 98% of the samples. Polychaeta and Gastropoda occurred in 70% and 62% of the samples, respectively. The remaining nine invertebrate classes comprised <21% of all normalized counts. The common occurrence of these three prey classes is consistent with examinations of walrus stomach contents. Despite these consistencies, biases in the metabarcoding approach to determine diet from feces have been highlighted in other studies and require further study, in addition to biases that may have arisen from our opportunistic sampling. However, this noninvasive approach provides accurate identification of prey taxa from degraded samples and could yield much‐needed information on shifts in walrus diet in a rapidly changing Arctic.

Alaska

Mitochondrial genome diversity and population mitogenomics of Polar cod (Boreogadus saida) and Arctic dwelling gadoids

High-latitude fish typically exhibit a narrow thermal tolerance window, which may pose challenges when coping with temperatures that shift outside of a species’ range of tolerance. Due to its role in aerobic metabolism and energy balance, the mitochondrial genome is likely critical for the acclimation and adaptation to differing temperature regimes in marine ectotherms. As oceans continue to warm, there is growing need to understand the ability of organisms to respond to changing environmental conditions given evidence that some species, in particular cold-water species, may already be experiencing difficulties. To assess how Arctic gadids in Alaska have responded to differential thermal preferences in the past and how regions are interconnected, we sequenced complete mitochondrial genomes for four Arctic gadids to determine the distribution of mitochondrial diversity and population-level structure as well as to detect signatures of selection acting on the mitochondrial genome. We found little population-level structure within all four species with the clear exception of Gulf of Alaska saffron cod ( Eleginus gracilis ). Northern localities exhibited higher levels of genetic diversity and primarily northern lineages were observed within polar cod ( Boreogadus saida ) and saffron cod, likely reflecting asymmetrical dispersal and potentially admixture of distinct lineages via ocean currents. The main evolutionary force shaping the evolution of the mitogenome appears to be purifying selection, but we also identified potential positive selection of candidate amino acid replacements primarily in complex I (ND genes) in polar cod. The high levels of mitochondrial diversity observed in our study and large population size may provide this species with the ability to respond evolutionarily (i.e. long-term) to a changing environment.

Alaska

Are migratory waterfowl vectors of seagrass pathogens?

Migratory waterfowl vector plant seeds and other tissues, but little attention has focused on the potential of avian vectoring of plant pathogens. Extensive meadows of eelgrass (Zostera marina) in southwest Alaska support hundreds of thousands of waterfowl during fall migration and may be susceptible to plant pathogens. We recovered DNA of organisms pathogenic to eelgrass from environmental samples and in the cloacal contents of eight of nine waterfowl species that annually migrate along the Pacific coast of North America and Asia. Coupled with a signal of asymmetrical gene flow of eelgrass running counter to that expected from oceanic and coastal currents between Large Marine Ecosystems, this evidence suggests waterfowl are vectors of eelgrass pathogens.

Alaska

Conservation genomics in a changing arctic

Although logistically challenging to study, the Arctic is a bellwether for global change and is becoming a model for questions pertinent to the persistence of biodiversity. Disruption of Arctic ecosystems is accelerating, with impacts ranging from mixing of biotic communities to individual behavioral responses. Understanding these changes is crucial for conservation and sustainable economic development. Genomic approaches are providing transformative insights into biotic responses to environmental change, but have seen limited application in the Arctic due to a series of limitations. To meet the promise of genome analyses, we urge rigorous development of biorepositories from high latitudes to provide essential libraries to improve the conservation, monitoring, and management of Arctic ecosystems through genomic approaches.

Trends in Ecology and Evolution