83 Works

Data from: Genetic and individual assignment of tetraploid green sturgeon with SNP assay data

Eric C. Anderson, Thomas C. Ng, Eric D. Crandall & John Carlos Garza
Polyploid organisms pose substantial obstacles to genetic analysis, as molecular assay data are usually difficult to evaluate in a Mendelian framework. Green sturgeon (Acipenser medirostris) is a tetraploid species and is facing significant conservation challenges, including bycatch in ocean fisheries. We present here novel molecular genetic assays and analytical methodology for green sturgeon that allow discrimination of fish from the two visually indistinguishable distinct population segments (DPSs), and also provide individual-specific genetic tags. We show...

Data from: Post-glacial habitat release and incipient speciation in the genus Delphinus

Iris Segura-García, Juan Pablo Gallo, Susan Chivers, Raúl Díaz-Gamboa & A. Rus Hoelzel
The role of ecological and changing environmental factors in the radiation of species diversity is a fundamental question in evolutionary biology. Of particular interest is the potential for these factors to determine the boundary between what we would consider differentiation among populations and incipient speciation. Dolphins in the genus Delphinus provide a useful test case, exhibiting morphological variation in beak length, coloration and body size across their wide geographic distribution, and in particular among coastal...

Data from: Phylogenomic resolution of the cetacean tree of life using target sequence capture

Michael McGowen, Georgia Tsagkogeorga, Sandra Álvarez-Carretero, Mario Dos Reis, Monika Struebig, Rob Deaville, Paul Jepson, Simon Jarman, Andrea Polanowski, Phillip Morin & Stephen Rossiter
The evolution of the cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, while the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using...

Data from: Mitogenomic phylogenetics of fin whales (Balaenoptera physalus spp.): genetic evidence for revision of subspecies

Frederick I. Archer, Phillip A. Morin, Brittany L. Hancock-Hanser, Kelly M. Robertson, Matthew S. Leslie, Martine Bérubé, Simone Panigada & Barbara L. Taylor
There are three described subspecies of fin whales (Balaenoptera physalus): B. p. physalus Linnaeus, 1758 in the Northern Hemisphere, B. p. quoyi Fischer, 1829 in the Southern Hemisphere, and a recently described pygmy form, B. p. patachonica Burmeister, 1865. The discrete distribution in the North Pacific and North Atlantic raises the question of whether a single Northern Hemisphere subspecies is valid. We assess phylogenetic patterns using ~16 K base pairs of the complete mitogenome for...

Data from: Demography or selection on linked cultural traits or genes? Investigating the driver of low mtDNA diversity in the sperm whale using complementary mitochondrial and nuclear genome analyses

Phillip A. Morin, Andrew D. Foote, Charles Scott Baker, Brittany L. Hancock-Hanser, Kristin Kaschner, Bruce R. Mate, Sarah L. Mesnick, Victoria L. Pease, Patricia E. Rosel & Alana Alexander
Mitochondrial DNA has been heavily utilized in phylogeography studies for several decades. However, underlying patterns of demography and phylogeography may be misrepresented due to coalescence stochasticity, selection, variation in mutation rates, and cultural hitchhiking (linkage of genetic variation to culturally transmitted traits affecting fitness). Cultural hitchhiking has been suggested as an explanation for low genetic diversity in species with strong social structures, counteracting even high mobility, abundance and limited barriers to dispersal. One such species...

Data from: Mapping migration in a songbird using high-resolution genetic markers

Kristen Ruegg, Eric C. Anderson, Kristina L. Paxton, Vanessa Apkenas, Sirena Lao, Rodney B. Siegel, David F. DeSante, Frank Moore, Thomas B. Smith & Kristen C. Ruegg
Neotropical migratory birds are declining across the Western Hemisphere, but conservation efforts have been hampered by the inability to assess where migrants are most limited – the breeding grounds, migratory stopover sites, or wintering areas. A major challenge has been the lack of an efficient, reliable, and broadly applicable method for measuring the strength of migratory connections between populations across the annual cycle. Here we show how high-resolution genetic markers can be used to identify...

Data from: Circumpolar diversity and geographic differentiation of mtDNA in the critically endangered Antarctic blue whale (Balaenoptera musculus intermedia)

Angela L. Sremba, Brittany Hancock-Hanser, Trevor A. Branch, Rick L. LeDuc & C. Scott Baker
The Antarctic blue whale (Balaenoptera musculus intermedia) was hunted to near extinction between 1904 and 1972, declining from an estimated initial abundance of more than 250,000 to fewer than 400. Here, we describe mtDNA control region diversity and geographic differentiation in the surviving population of the Antarctic blue whale, using 218 biopsy samples collected under the auspices of the International Whaling Commission (IWC) during research cruises from 1990–2009. Microsatellite genotypes and mtDNA sequences identified 166...

Data from: Blue whale population structure along the eastern South Pacific Ocean: evidence of more than one population

Juan P. Torres-Florez, Rodrigo Hucke-Gaete, Rick LeDuc, Aimee Lang, Barbara Taylor, Lida E. Pimper, Luis Bedriñana-Romano, Howard C. Rosenbaum & Christian C. Figueroa
Blue whales (Balaenoptera musculus) were among the most intensively exploited species of whales in the world. As a consequence of this intense exploitation, blue whale sightings off the coast of Chile were uncommon by the end of the 20th century. In 2004, a feeding and nursing ground was reported in southern Chile (SCh). With the aim to investigate the genetic identity and relationship of these Chilean blue whales to those in other Southern Hemisphere areas,...

Data from: Small founding number and low genetic diversity in an introduced species exhibiting limited invasion success (speckled dace, Rhinichthys osculus)

Andrew P. Kinziger, Rodney J. Nakamoto, Eric C. Anderson & Bret C. Harvey
Molecular evaluations of successful invaders are common, however studies of introduced species that have had limited invasion success, or have died out completely, are rare. We studied an introduced population of speckled dace (Rhinichthys osculus) from northern California, USA that has rapidly increased in abundance but remained restricted to a 25-km stretch of river since its introduction in the mid-1980s. Field and laboratory analyses indicate that invasion success of speckled dace is constrained by the...

Data from: Genetic variation in blue whales in the eastern Pacific: implication for taxonomy and use of common wintering grounds

Richard G. LeDuc, F.I. Archer, Aimee R. Lang, Karen K. Martien, Brittany Hancock-Hanser, Juan P. Torres-Florez, Rodrigo Hucke-Gaete, Howard C. Rosenbaum, Koen Van Waerebeek, Robert L. Brownell, Barbara L. Taylor & F. I. Archer
Many aspects of blue whale biology are poorly understood. Some of the gaps in our knowledge, such as those regarding their basic taxonomy and seasonal movements, directly affect our ability to monitor and manage blue whale populations. As a step towards filling in some of these gaps, microsatellite and mtDNA sequence analyses were conducted on blue whale samples from the Southern Hemisphere, the eastern tropical Pacific (ETP), and the northeast Pacific. The results indicate that...

Data from: Comparative population genetic analysis of bocaccio rockfish Sebastes paucispinis using anonymous and gene-associated simple sequence repeat loci

Vincent P. Buonaccorsi, Carol A. Kimbrell, Eric A. Lynn & John R. Hyde
Comparative population genetic analyses of traditional and emergent molecular markers aid in determining appropriate use of new technologies. The bocaccio rockfish Sebastes paucispinis is a high-gene-flow marine species off the west coast of North America that experienced strong population decline over the past three decades. We used 18 anonymous and 13 gene associated simple sequence repeat loci (EST-SSRs) to characterize range-wide population structure with temporal replicates. No FST-outliers were detected using the LOSITAN program, suggesting...

Data from: Genetic diversity and population structure of the Pelagic Thresher Shark (Alopias pelagicus) in the Pacific Ocean: evidence for two evolutionarily significant units

Diego Cardeñosa, John Hyde & Susana Caballero
There has been an increasing concern about shark overexploitation in the last decade, especially for open ocean shark species, where there is a paucity of data about their life histories and population dynamics. Little is known regarding the population structure of the pelagic thresher shark, Alopias pelagicus. Though an earlier study using mtDNA control region data, showed evidence for differences between eastern and western Pacific populations, the study was hampered by low sample size and...

Data from: Phylogenomic species delimitation dramatically reduces species diversity in an Antarctic adaptive radiation

Elyse Parker, Alex Dornburg, Carl Struthers, Christopher Jones & Thomas Near
Application of genetic data to species delimitation often builds confidence in delimitations previously hypothesized using morphological, ecological, and geographic data and frequently yields recognition of previously-undescribed cryptic diversity. However, a recent critique of genomic data-based species delimitation approaches is that they have the potential to conflate population structure with species diversity, resulting in taxonomic oversplitting. The need for an integrative approach to species delimitation, in which molecular, morphological, ecological, and geographic lines of evidence are...

Physical and biological constraints on the capacity for life-history expression of anadromous salmonids: an Eel River, California, case study

Alyssa FitzGerald, David Boughton, Joshua Fuller, Sara John, Benjamin Martin, Lee Harrison & Nathan Mantua
Recovery of anadromous salmonid populations is complicated by the fact that these fish have complex life-histories. Habitat valuation and capacity methods need to account for spatiotemporal variability in temperature, geomorphic features, and a species’ thermal sensitivity mediated by biological interactions. We examined this interplay in a case study of steelhead trout (Oncorhynchus mykiss) and Chinook Salmon (O. tshawytscha) in California’s Eel River watershed. We estimated habitat suitability and fish capacity for each salmonid run and...

Data from: Genetic assignment with isotopes and habitat suitability (GAIAH), a migratory bird case study

Kristen C. Ruegg, Eric C. Anderson, Ryan J. Harrigan, Kristina L. Paxton, Jeffrey F. Kelly, Frank Moore & Thomas B. Smith
1. Identifying migratory connections across the annual cycle is important for studies of migrant ecology, evolution, and conservation. While recent studies have demonstrated the utility of high-resolution SNP-based genetic markers for identifying population-specific migratory patterns, the accuracy of this approach relative to other intrinsic tagging techniques has not yet been assessed. 2. Here, using a straightforward application of Bayes' Rule, we develop a method for combining inferences from high-resolution genetic markers, stable isotopes, and habitat...

Data from: Crossing the line: tunas actively exploit submesoscale fronts to enhance foraging success

Stephanie Snyder, Peter J. S. Franks, Lynne D. Talley, Yi Xu & Suzanne Kohin
Fronts – i.e., the boundaries between water masses – are ubiquitous in the world oceans and have been shown to significantly influence pelagic ecosystems with enhanced local productivity and increased abundances of forage fish and top predators. Here we use data from archival tags to document how four juvenile albacore tunas foraged at and exploited a thermal front. Of the 3,098 observed trips, the albacore mainly swam across the front between the warm side above...

Data from: Influences of past climatic changes on historical population structure and demography of a cosmopolitan marine predator, the common dolphin (genus Delphinus)

Ana Amaral, Luciano Beheregaray, Kerstin Bilgmann, Luís Freitas, Kelly Robertson, Marina Sequeira, Karen Stockin, M. M. Coelho & Luciana Möller
Climatic oscillations during the Pleistocene have greatly influenced the distribution and connectivity of many organisms, leading to extinctions but also generating biodiversity. While the effects of such changes have been extensively studied in the terrestrial environment, studies focusing on the marine realm are still scarce. Here we used sequence data from one mitochondrial and five nuclear loci to assess the potential influence of Pleistocene climatic changes on the phylogeography and demographic history of a cosmopolitan...

Data from: A worldwide perspective on the population structure and genetic diversity of bottlenose dolphins (Tursiops truncatus) in New Zealand

Gabriela Tezanos-Pinto, Charles S Baker, Kirsty Russell, Karen Martien, Robin Baird, Alistair Hutt, Gregory Stone, Antonio A Mignucci-Giannoni, Susana Caballero, Tetsuya Endo, Shane Lavery, Marc Oremus, Carlos Olavarria & Claire Garrigue
Bottlenose dolphins (Tursiops truncatus) occupy a wide range of coastal and pelagic habitats throughout tropical and temperate waters worldwide. In some regions, "inshore" and "offshore" forms or ecotypes differ genetically and morphologically, despite no obvious boundaries to interchange. Around New Zealand, bottlenose dolphins inhabit 3 coastal regions: Northland, Marlborough Sounds, and Fiordland. Previous demographic studies showed no interchange of individuals among these populations. Here, we describe the genetic structure and diversity of these populations using...

Data from: Quantifying physiological influences on otolith microchemistry

Anna M. Sturrock, Ewan Hunter, J. Andrew Milton, Edinburgh Ion Microprobe Facility, Rachel C. Johnson, Colin P. Waring & Clive N. Trueman
1. Trace element concentrations in fish earstones (“otoliths”) are widely used to discriminate spatially discrete populations or individuals of marine fish, based on a commonly held assumption that physiological influences on otolith composition are minor, and thus variations in otolith elemental chemistry primarily reflect changes in ambient water chemistry. 2. We carried out a long-term (1-yr) experiment, serially sampling seawater, blood plasma and otoliths of mature and immature European plaice (Pleuronectes platessa L.) to test...

Data from: What influences the worldwide genetic structure of sperm whales (Physeter macrocephalus)?

Alana Alexander, Debbie Steel, Kendra Hoekzema, Sarah L. Mesnick, Daniel Engelhaupt, Iain Kerr, Roger Payne & Charles Scott Baker
The interplay of natural selection and genetic drift, influenced by geographic isolation, mating systems and population size, determines patterns of genetic diversity within species. The sperm whale provides an interesting example of a long-lived species with few geographic barriers to dispersal. Worldwide mtDNA diversity is relatively low, but highly structured among geographic regions and social groups, attributed to female philopatry. However, it is unclear whether this female philopatry is due to geographic regions or social...

Data from: Resource partitioning facilitates coexistence in sympatric cetaceans in the California Current

Sabrina Fossette, Briana Abrahms, Elliott L. Hazen, Steven J. Bograd, Kelly M. Newton, John Calambokidis, Julia A. Burrows, Jeremy A. Goldbogen, James T. Harvey, Baldo Marinovic, Bernie Tershy, Donald A. Croll & Kelly M. Zilliacus
1. Resource partitioning is an important process driving habitat use and foraging strategies in sympatric species that potentially compete. Differences in foraging behavior are hypothesized to contribute to species coexistence by facilitating resource partitioning, but little is known on the multiple mechanisms for partitioning that may occur simultaneously. Studies are further limited in the marine environment, where the spatial and temporal distribution of resources is highly dynamic and subsequently difficult to quantify. 2. We investigated...

Data from: Rethinking ‘normal’: the role of stochasticity in the phenology of a synchronously breeding seabird

Casey Youngflesh, Stephanie Jenouvrier, Jefferson T. Hinke, Lauren DuBois, Judy St. Leger, Wayne Z. Trivelpiece, Susan G. Trivelpiece & Heather J. Lynch
1. Phenological changes have been observed in a variety of systems over the past century. There is concern that, as a consequence, ecological interactions are becoming increasingly mismatched in time, with negative consequences for ecological function. 2. Significant spatial heterogeneity (inter-site) and temporal variability (inter-annual) can make it difficult to separate intrinsic, extrinsic, and stochastic drivers of phenological variability. The goal of this study was to understand the timing and variability of breeding phenology of...

Data from: Staying close to home? Genetic differentiation of rough-toothed dolphins near oceanic islands in the central Pacific Ocean

G. Renee Albertson, Robin W. Baird, Marc Oremus, M. Michael Poole, Karen K. Martien & C. Scott Baker
Rough-toothed dolphins have a worldwide tropical and subtropical distribution, yet little is known about the population structure and social organization of this typically open-ocean species. Although it has been assumed that pelagic dolphins range widely due to the lack of apparent barriers and unpredictable prey distribution, recent evidence suggests rough-toothed dolphins exhibit fidelity to some oceanic islands. Using the most comprehensively extensive dataset for this species to date, we assess the isolation and interchange of...

Data from: Microhaplotypes provide increased power from short-read DNA sequences for relationship inference

Diana S. Baetscher, Anthony J. Clemento, Thomas C. Ng, Eric C. Anderson & John C. Garza
The accelerating rate at which DNA sequence data is now generated by high-throughput sequencing instruments provides both opportunities and challenges for population genetic and ecological investigations of animals and plants. We show here how the common practice of calling genotypes from a single SNP per sequenced region ignores substantial additional information in the phased short-read sequences that are provided by high-throughput sequencing instruments. We target sequenced regions with multiple SNPs in kelp rockfish (Sebastes atrovirens)...

Data from: Colonizing the wild west: low diversity of complete mitochondrial genomes in western North Pacific killer whales suggests a founder effect

Olga A. Filatova, Ekaterina A. Borisova, Ilya G. Meshchersky, Maria D. Logacheva, Nataliia V. Kuzkina, Olga V. Shpak, Phillip A. Morin, Erich Hoyt & Ilya G Meschersky
In the North Pacific, fish-eating R-type “resident” and mammal-eating T-type “transient” killer whales do not interbreed and differ in ecology and behavior. Full-length mitochondrial genomes (about 16.4 kbp) were sequenced and assembled for 12 R-type and 14 T-type killer whale samples from different areas of the western North Pacific. All R-type individuals had the same haplotype, previously described for R-type killer whales from both eastern and western North Pacific. However, haplotype diversity of R-type killer...

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  • Southwest Fisheries Science Center
  • University of California, Santa Cruz
  • National Marine Fisheries Service
  • University of California System
  • Alaska Fisheries Science Center
  • Oregon State University
  • University of California, San Diego
  • Cascadia Research
  • Pacific Islands Fisheries Science Center
  • National Oceanic and Atmospheric Administration