60 Works

Data from: Phylogeographic structure and deep lineage diversification of the red alga Chondrus ocellatus Holmes in the Northwest Pacific

Zi-Min Hu, Jing-Jing Li, Zhong-Min Sun, Jung-Hyun Oak, Jie Zhang, Pablo Fresia, W. Stewart Grant & De-Lin Duan
A major goal of phylogeographic analysis using molecular markers is to understand the ecological and historical variables that influence genetic diversity within a species. Here, we used sequences of the mitochondrial Cox1 gene and nuclear internal transcribed spacer to reconstruct its phylogeography and demographic history of the intertidal red seaweed Chondrus ocellatus over most of its geographical range in the Northwest Pacific. We found three deeply separated lineages A, B and C, which diverged from...

Data from: Natal and breeding philopatry of female Steller sea lions in southeastern Alaska

Kelly K. Hastings, Lauri A. Jemison, Grey W. Pendleton, Kimberly L. Raum-Suryan & Kenneth W. Pitcher
Information on drivers of dispersal is critical for wildlife conservation but is rare for long-lived marine mammal species with large geographic ranges. We fit multi-state mark-recapture models to resighting data of 369 known-aged Steller sea lion (Eumetopias jubatus) females marked as pups on their natal rookeries in southeastern Alaska from 1994-2005 and monitored from 2001-15. We estimated probabilities of females being first observed parous at their natal site (natal philopatry), and of not moving breeding...

Data from: Population genetics reveal Myotis keenii (Keen’s myotis) and Myotis evotis (long-eared myotis) to be a single species

Cori Lausen, Michael F. Proctor, David Nagorsen, Doug Burles, David Paetkau, Erin Harmston, Karen Blejwas, Purnima Govindarajulu & Laura Friis
Abstract: Recognizing delineations of gene flow among groups of animals can be challenging, but necessary for conservation and management. Of particular importance is the identification of species boundaries. Several physical and genetic traits have been used with mixed success to distinguish Myotis keenii (Merriam, 1895) (Keen’s myotis) and Myotis evotis (H. Allen, 1864) (long-eared myotis), but it is unclear whether species distinction is biologically warranted. We generated 12-14 microsatellite loci genotypes for 275 long-eared Myotis...

Ultraconserved elements data for Amarsipus and Pelagiaria

Richard Harrington, Matt Friedman, Masaki Miya, Thomas Near & Matthew Campbell
Amarsipus carlsbergi is a rare mesopelagic fish distributed in the Indian and Pacific Oceans, and is the only species classified in the family Amarsipidae. Since its description in 1969, phylogenetic hypotheses have varied regarding its relationship with other percomorph lineages, but most have indicated a close relationship with the traditional suborder Stromateoidei. Molecular phylogenies place families previously classified in Stromateoidei within a diverse clade– Pelagiaria– that includes fishes such as tunas, cutlassfishes, and pomfrets. A...

Anadromous cataloging and fish inventory in select drainages of the Upper Tanana and Yukon Rivers 2019

Charles Cathcart
During the summer of 2019, Alaska Department of Fish and Game Division of Sport Fish staff conducted a rapid systematic inventory of anadromous fish distribution and associated aquatic and riparian habitat in select drainages of the upper Yukon River and Tanana River. Target streams will be selected to fill gaps in coverage of the State of Alaska's Catalog of Waters Important for the Spawning, Rearing or Migration of Anadromous Fishes (AWC) for freshwater habitats expected...

Trawl Data from the NOAA Bell M. Shimada during the 2022 International Year of the Salmon Pan-Pacific Winter High Seas Expedition

Laurie Weitkamp, Ed Farley, Katherine Howard, Sabrina Garcia, Jim Murphy & Jamal Moss
This dataset contains the trawl and specimen data collected aboard the R/V Bell M. Shimada for the IYS survey in 2022 in the North Pacific Ocean. This package contains three components; event, catch, and specimen data. The event data contains all of the sampling event information, including time, location, and duration. All dates and times are in UTC. The catch data contains all of the catch records, as counts, weights, and lengths, for each species/taxa...

Data from: Landscape heterogeneity and local adaptation define the spatial genetic structure of Pacific salmon in a pristine environment

Michael W. Ackerman, William D. Templin, James E. Seeb & Lisa W. Seeb
Identifying the spatial distribution of genetic variation across the landscape is an essential step in informing species conservation. Comparison of closely related and geographically overlapping species can be particularly useful in cases where landscape may similarly influence genetic structure. Congruent patterns among species highlight the importance that landscape heterogeneity plays in determining genetic structure whereas contrasting patterns emphasize differences in species-specific ecology and life-history or the importance of species-specific adaptation to local environments. We examined...

Data from: Fine-scale sampling reveals distinct isolation by distance patterns in chum salmon (Oncorhynchus keta) populations occupying a glacially dynamic environment

Eleni L. Petrou, James E. Seeb, Lorenz Hauser, Mark J. Witteveen, William D. Templin & Lisa W. Seeb
Populations with spatially restricted gene flow are characterized by genetic differentiation that may be positively correlated with the geographic distance separating populations, a pattern known as isolation by distance (IBD). Here we examined the fine-scale genetic structure of 66 chum salmon (Oncorhynchus keta) populations spawning in Alaska waterways and explored patterns of IBD using 90 nuclear and 3 mitochondrial single nucleotide polymorphisms. Estimating population structure of chum salmon in Alaska is of increasing concern because...

Data from: Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha)

Wesley A. Larson, Lisa W. Seeb, Meredith V. Everett, Ryan K. Waples, William D. Templin & James E. Seeb
Recent advances in population genomics have made it possible to detect previously unidentified structure, obtain more accurate estimates of demographic parameters, and explore adaptive divergence, potentially revolutionizing the way genetic data are used to manage wild populations. Here, we identified 10 944 single-nucleotide polymorphisms using restriction-site-associated DNA (RAD) sequencing to explore population structure, demography, and adaptive divergence in five populations of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. Patterns of population structure were similar to...

Data from: Signals of heterogeneous selection at an MHC locus in geographically proximate ecotypes of sockeye salmon

Wesley A. Larson, James E. Seeb, Tyler H. Dann, Daniel E. Schindler & Lisa W. Seeb
The genes of the major histocompatibility complex (MHC) are an important component of the vertebrate immune system and can provide insights into the role of pathogen-mediated selection in wild populations. Here we examined variation at the MHC class II peptide binding region in 27 populations of sockeye salmon (Oncorhynchus nerka), distributed among three distinct spawning ecotypes, from a complex of interconnected rivers and lakes in southwestern Alaska. We also obtained genotypes from 90 putatively neutral...

Data from: Becoming pure: identifying generational classes of admixed individuals within lesser and greater scaup populations

Philip Lavretsky, Jeffrey Peters, Kevin Winker, Volker Bahn, Irina Kulikova, Yuri Zhuravlev, Robert Wilson, Christopher Barger, Kirsty Gurney, Kevin McCracken, Jeffrey L. Peters, Chris Barger & Kevin G. McCracken
Estimating the frequency of hybridization is important to understand its evolutionary consequences and its effects on conservation efforts. In this study, we examined the extent of hybridization in two sister species of ducks that hybridize. We used mitochondrial control region sequences and 3,589 double-digest restriction-associated DNA sequences (ddRADseq) to identify admixture between wild lesser scaup (Aythya affinis) and greater scaup (A. marila). Among 111 individuals, we found one introgressed mitochondrial DNA haplotype in lesser scaup...

Data from: Apex predators and the facilitation of resource partitioning among mesopredators

Kelly J. Sivy, Casey B. Pozzanghera, Kassidy E. Colson, Matthew A. Mumma & Laura R. Prugh
Apex predators may influence carnivore communities through the suppression of competitively dominant mesopredators, however they also provide carrion subsidies that could influence foraging and competition among sympatric mesopredators when small prey is scarce. We assessed coyote Canis latrans and red fox Vulpes vulpes winter diet overlap and composition from scats collected in two study areas with >3-fold difference in grey wolf Canis lupus density due to a wolf control program. We hypothesized that differences in...

Data from: Female American black bears do not alter space use or movements to reduce infanticide risk

D. Cody Norton, Jerrold L. Belant, John G. Bruggink, Dean E. Beyer, Nathan J. Svoboda & Tyler R. Petroelje
Infanticide occurs in a variety of animal species and infanticide risk has large implications for the evolution of behavior. Further, the sex hypothesis of sexual segregation predicts that for species in which infanticide occurs, females with dependent young will avoid males to reduce risk of sexually-selected infanticide. Infanticide risk-avoidance behavior has been studied primarily in social species, but also occurs in some solitary species. We used generalized linear mixed models to determine if space use...

Data from: Spatial distribution, movements, and geographic range of Steller sea lions (Eumetopias jubatus) in Alaska

Lauri A. Jemison, Grey W. Pendleton, Kelly K. Hastings, John M. Maniscalco & Lowell W. Fritz
The two stocks of Steller sea lions (Eumetopias jubatus) in Alaska include an endangered western stock, recently recovering in parts of its range following decades of decline, and an eastern stock which was removed from the U.S. Endangered Species List in 2013 following increasing numbers since the 1970s. Information on overlapping distributions of eastern and western sea lions is needed for management considerations. We analyzed >30,000 sightings collected from 2000-2014 of 2,385 sea lions that...

Sonar estimation of summer chum and pink salmon in the Anvik River, Alaska, 2019

Naomi Brodersen
Dual-frequency identification sonar (DIDSON) was used to estimate adult summer chum salmon Oncorhynchus keta and pink salmon O. gorbuscha passage in the Anvik River from June 16 to July 26, 2019. Apportionment to species was determined from data collected from tower counts. A total of 249,014 (SE 2,034) summer chum and 241 (SE 81) pink salmon were estimated to have passed the sonar site. A beach seine sample fishery was conducted to collect age, sex,...

Lesser Yellowlegs location data describing the occurrence of birds within harvest zones in the Caribbean and South America

Laura A. McDuffie, Katherine S. Christie, Autumn-Lynn Harrison, Audrey R. Taylor, Brad A. Andres, Benoit Laliberte & James A. Johnson
Shorebirds have experienced a precipitous reduction in abundance over the past four decades. While some threats to shorebirds are widespread (e.g. habitat alteration), others are regional and may affect specific populations. Lesser Yellowlegs (Tringa flavipes) are long-distance migrants that breed across the North American boreal biome and have declined in abundance by 60-80% since the 1970s. The documented harvest of Lesser Yellowlegs in the Caribbean and northeastern South America during southward migration is a possible...

Results of survey for selected parasites in Alaska brown bears (Ursus arctos)

Ellen Haynes, Sarah Coker, Michael Yabsley, Kevin Niedrighaus, Andrew Ramey, Guilherme Verocai, Grant Hilderbrand, Kyle Joly, David Gustine, Buck Mangipane, William Leacock, Anthony Crupi & Christopher Cleveland
To assess the prevalence of endo- and ectoparasites in Alaska brown bears (Ursus arctos), blood and fecal samples were collected during 2013 – 2016 from five locations: Gates of the Arctic National Park and Preserve (GAAR), Katmai National Park (KATM), Lake Clark National Park and Preserve (LACL), Yakutat Forelands (YAK), and Kodiak Island (KOD). Standard fecal centrifugal-flotation was used to screen for gastrointestinal parasites, molecular techniques were used to test blood for the presence of...

Data from: Crossing to safety: Dispersal, colonization and mate choice in evolutionarily distinct populations of Steller sea lions, Eumetopias jubatus.

Gregory O’Corry-Crowe, Tom Gelatt, Lorrie Rea, Carolina Bonin, Michael Rehberg & Greg O'Corry-Crowe
Population growth typically involves range expansion and establishment of new breeding sites, while the opposite occurs during declines. Although density-dependence is widely invoked in theoretical studies of emigration and colonization in expanding populations, few empirical studies have documented the mechanisms. Still fewer have documented the direction and mechanisms of individual transfer in declining populations. Here we screen large numbers of pups sampled on their natal rookeries for variation in mtDNA (n=1,106) and 16 microsatellite loci...

Data from: Number of alleles as a predictor of the relative assignment accuracy of STR and SNP baselines for chum salmon

Christian T. Smith & Lisa W. Seeb
Short tandem repeat (STR) markers, which exhibit many alleles per locus, are commonly used to assign fish to their populations of origin. Single nucleotide polymorphisms (SNPs), which have many technical advantages over STRs, typically exhibit only two alleles per locus. Simulation studies have indicated that number of independent alleles is a good predictor of accuracy of genetic markers for fishery applications. Extant STR baselines for salmon contain hundreds of alleles, and it has been extrapolated...

Data from: Single nucleotide polymorphisms across a species' range: implications for conservation studies of Pacific salmon

Lisa W Seeb, William D Templin, Shunpei Sato, Syuiti Abe, Kenneth Warheit, Jung Youn Park & James E Seeb
Studies of the oceanic and near-shore distributions of Pacific salmon, whose migrations typically span thousands of kilometers, have become increasingly valuable in the presence of climate change, increasing hatchery production, and potentially high rates of bycatch in offshore fisheries. Genetics data offer considerable insights into both the migratory routes as well as the evolutionary histories of the species. However, these types of studies require extensive datasets from spawning populations originating from across the species? range....

Data from: Potential of environmental DNA to evaluate Northern pike (Esox lucius) eradication efforts: an experimental test and case study

Kristine J. Dunker, Adam J. Sepulveda, Robert L. Massengill, Jeffrey B. Olsen, Ora L. Russ, John K. Wenburg & Anton Antonovich
Determining the success of invasive species eradication efforts is challenging because populations at very low abundance are difficult to detect. Environmental DNA (eDNA) sampling has recently emerged as a powerful tool for detecting rare aquatic animals; however, detectable fragments of DNA can persist over time despite absence of the targeted taxa and can therefore complicate eDNA sampling after an eradication event. This complication is a large concern for fish eradication efforts in lakes since killed...

Data from: Migratory culture, population structure and stock identity in North Pacific beluga whales (Delphinapterus leucas)

Greg O'Corry-Crowe, Robert Suydam, Lori Quakenbush, Brooke Potgieter, Lois Harwood, Dennis Litovka, Tatiana Ferrer, John Citta, Vladimir Burkanov, Kathy Frost, Barbara Mahoney & Greg O’Corry-Crowe
The annual return of beluga whales, Delphinapterus leucas, to traditional seasonal locations across the Arctic may involve migratory culture, while the convergence of discrete summering aggregations on common wintering grounds may facilitate outbreeding. Natal philopatry and cultural inheritance, however, has been difficult to assess as earlier studies were of too short a duration, while genetic analyses of breeding patterns, especially across the beluga's Pacific range, have been hampered by inadequate sampling and sparse information on...

Data from: Evidence for interannual variation in genetic structure of Dungeness crab (Cancer magister) along the California Current System

Tyler M. Jackson, G. Curtis Roegner & Kathleen G. O'Malley
Using a combination of population- and individual-based analytical approaches, we provide a comprehensive examination of genetic connectivity of Dungeness crab (Cancer magister) along ~1,200 km of the California Current System (CCS). We sampled individuals at 33 sites in 2012 to establish a baseline of genetic diversity and hierarchal population genetic structure, and then assessed inter-annual variability in our estimates by sampling again in 2014. Genetic diversity showed little variation among sites or across years. In...

Data from: Interactions between demography, genetics, and landscape connectivity increase extinction probability for a small population of large carnivores in a major metropolitan area

John F. Benson, Peter J. Mahoney, Jeff A. Sikich, Laurel E.K. Serieys, John P. Pollinger, Holly B. Ernest, Seth P.D. Riley, Laurel E. K. Serieys & Seth P. D. Riley
The extinction vortex is a theoretical model describing the process by which extinction risk is elevated in small, isolated populations owing to interactions between environmental, demographic, and genetic factors. However, empirical demonstrations of these interactions have been elusive. We modelled the dynamics of a small mountain lion population isolated by anthropogenic barriers in greater Los Angeles, California, to evaluate the influence of demographic, genetic, and landscape factors on extinction probability. The population exhibited strong survival...

Data from: Using citizen-science observations to understand long-term trends in common and Pacific loon populations in urbanized Southcentral Alaska

Laura A. McDuffie, Julie C. Hagelin, Marian L. Snively, Grey W. Pendleton & Audrey R. Taylor
For over 30 years, the Alaska Loon Watch (1985−1999) and the Alaska Loon and Grebe Watch (2000−2015) engaged citizen scientist participants to record over 10,000 observations of common Gavia immer and Pacific loons Gavia pacifia at 346 lakes in five sub-regions of Southcentral Alaska. We used generalized linear mixed models to estimate long-term trends in adult loon counts and chick survival and examined environmental variables associated with loon abundance. Adult common loon counts increased in...

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Affiliations

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