21 Works

North Pacific harbor porpoise SNP and microhaplotype genotypes, mitochondrial control region haplotype sequences

Phillip Morin, Brenna Forester, Karin Forney, Carla Crossman, Brittany Hancock-Hanser, Kelly Robertson, Lance Barrett-Lennard, Robin Baird, John Calambokidis, Pat Gearin, Bradley Hanson, Cassie Schumacher, Timothy Harkins, Michael Fontaine, Barbara Taylor & Kim Parsons
Harbor porpoises in the North Pacific are found in coastal waters from southern California to Japan, but population structure is poorly known outside of a few local areas. We used multiplexed amplicon sequencing of 292 loci and genotyped clusters of SNPs as microhaplotypes (N=271 samples) in addition to mtDNA sequence data (N=413 samples), to examine the genetic structure from samples collected along the Pacific coast and inland waterways from California to southern British Columbia. We...

Data from: Nuclear and mitochondrial patterns of population structure in North Pacific false killer whales (Pseudorca crassidens)

Karen K. Martien, Susan J. Chivers, Robin W. Baird, Frederick I. Archer, Antoinette M. Gorgone, Brittany L. Hancock-Hanser, David Mattila, Daniel J. McSweeney, Erin M. Oleson, Carol Palmer, Victoria L. Pease, Kelly M. Robertson, Gregory S. Schorr, Mark B. Schultz, Daniel L. Webster & Barbara L. Taylor
False killer whales (Pseudorca crassidens) are large Delphinids typically found in deep water far offshore. However, in the Hawaiian Archipelago there are two resident island-associated populations of false killer whales, one in the waters around the main Hawaiian Islands (MHI) and one in the waters around the Northwestern Hawaiian Islands (NWHI). We use mitochondrial DNA (mtDNA) control region sequences and genotypes from 16 nuclear (nucDNA) microsatellite loci from 206 individuals to examine levels of differentiation...

Data from: Familial social structure and socially-driven genetic differentiation in Hawaiian short-finned pilot whales

Amy M. Van Cise, Karen. K. Martien, Sabre D. Mahaffy, Robin W. Baird, Daniel L. Webster, James H. Fowler, Erin M. Oleson & Phillip A. Morin
Social structure can have a significant impact on divergence and evolution within species, especially in the marine environment, which has few environmental boundaries to dispersal. On the other hand, genetic structure can affect social structure in many species, through an individual preference toward associating with relatives. One social species, the short-finned pilot whale (Globicephala macrorhynchus), has been shown to live in stable social groups for periods of at least a decade. Using mitochondrial control sequences...

Data from: Automated peak detection method for behavioral event identification: detecting Balaenoptera musculus and Grampus griseus feeding attempts

David A. Sweeney, Stacy L. DeRuiter, Ye Joo McNamara-Oh, Tiago A. Marques, Patricia Arranz & John Calambokidis
The desire of animal behaviorists for more flexible methods of conducting inter-study and inter-specific comparisons and meta-analysis of various animal behaviors compelled us to design an automated, animal behavior peak detection method that is potentially generalizable to a wide variety of data types, animals, and behaviors. We detected the times of feeding attempts by 12 Risso’s dolphins (Grampus griseus) and 36 blue whales (Balaenoptera musculus) using the norm-jerk (rate of change of acceleration) time series....

Data from: Estimation of a killer whale (Orcinus orca) population’s diet using sequencing analysis of DNA from feces

Michael J. Ford, Jennifer Hempelmann, M. Bradley Hanson, Katherine L. Ayres, Robin W. Baird, Candice K. Emmons, Jessica I. Lundin, Gregory S. Schorr, Samuel K. Wasser & Linda K. Park
Estimating diet composition is important for understanding interactions between predators and prey and thus illuminating ecosystem function. The diet of many species, however, is difficult to observe directly. Genetic analysis of fecal material collected in the field is therefore a useful tool for gaining insight into wild animal diets. In this study, we used high-throughput DNA sequencing to quantitatively estimate the diet composition of an endangered population of wild killer whales (Orcinus orca) in their...

Data from: Mandible allometry in extant and fossil Balaenopteridae (Cetacea: Mammalia): the largest vertebrate skeletal element and its role in rorqual lunge-feeding

Nicholas D. Pyenson, Jeremy A. Goldbogen & Robert E. Shadwick
Rorqual whales (crown Balaenopteridae) are unique among aquatic vertebrates in their ability to lunge-feed. During a single lunge, rorquals rapidly engulf a large volume of prey-laden water at high speed, which they then filter to capture suspended prey. Engulfment biomechanics are mostly governed by the coordinated opening and closing of the mandibles at large gape angles, which differentially exposes the floor of the oral cavity to oncoming flow. Mouth area in rorquals is delimited by...

Discrete-space continuous-time models of marine mammal exposure to Navy sonar

Charlotte Jones-Todd, Enrico Pirotta, John Durban, Diane Claridge, Robin Baird, Erin Falcone, Greg Schorr, Stephanie Watwood & Len Thomas
Assessing the patterns of wildlife attendance to specific areas is relevant across many fundamental and applied ecological studies, particularly when animals are at risk of being exposed to stressors within or outside the boundaries of those areas. Marine mammals are increasingly being exposed to human activities that may cause behavioural and physiological changes, including military exercises using active sonars. Assessment of the population-level consequences of anthropogenic disturbance requires robust and efficient tools to quantify the...

Data from: Sperm whale population structure in the eastern and central North Pacific inferred by the use of single nucleotide polymorphisms (SNPs), microsatellites and mitochondrial DNA

Sarah L. Mesnick, Barbara L. Taylor, Frederick I Archer, Karen K Martien, Sergio Escorza Treviño, Brittany L. Hancock-Hanser, Sandra Carolina Moreno Medina, Victoria L Pease, Kelly M Robertson, Janice M Straley, Robin W Baird, John Calambokidis, Gregory S. Schorr, Paul Wade, Vladimir Burkanov, Chris R. Lunsford, Luke Rendell & Phillip A Morin
We use mitochondrial DNA (400bp), six microsatellites and 36 single nucleotide polymorphisms (SNPs), 20 of which were linked, to investigate population structure of sperm whales (Physeter macrocephalus) in the eastern and central North Pacific. SNP markers, reproducible across technologies and laboratories, are ideal for long-term studies of globally distributed species such as sperm whales, a species of conservation concern due to both historical and contemporary impacts. We estimate genetic differentiation among three strata in the...

Data from: Host‐derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin

Rebecca Hooper, Jaelle C. Brealey, Tom Van Der Valk, Antton Alberdi, John W. Durban, Holly Fearnbach, Kelly M. Robertson, Robin W. Baird, M. Bradley Hanson, Paul Wade, M. Thomas P. Gilbert, Philip A. Morin, Jochen B. W. Wolf, Andrew D. Foote, Katerina Guschanski & Phillip A. Morin
Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro‐organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies...

Data from: Behavioral responses of individual blue whales (Balaenoptera musculus) to mid-frequency military sonar

Brandon L. Southall, Stacy L. DeRuiter, Ari Friedlaender, Alison K. Stimpert, Jeremy A. Goldbogen, Elliott Hazen, Caroline Casey, Selene Fregosi, David E. Cade, Ann N. Allen, Catriona M. Harris, Greg Schorr, David Moretti, Shane Guan & John Calambokidis
This study measured the degree of behavioral responses in blue whales (Balaenoptera musculus) to controlled noise exposure off the southern California coast. High-resolution movement and passive acoustic data were obtained from non-invasive archival tags (n=42) while surface positions were obtained with visual focal follows. Controlled exposure experiments (CEEs) were used to obtain direct behavioral measurements before, during, and after simulated and operational military mid-frequency active sonar (MFAS), pseudorandom noise (PRN), and controls (no noise exposure)....

Data from: Risso' s dolphins plan foraging dives

Patricia Arranz, Kelly J. Benoit-Bird, Brandon L. Southall, John Calambokidis, Ari S. Friedlaender & Peter L. Tyack
Humans remember the past and use that information to plan future actions. Lab experiments that test memory for the location of food show that animals have a similar capability to act in anticipation of future needs, but less work has been done on animals foraging in the wild. We hypothesized that planning abilities are critical and common in breath-hold divers who adjust each dive to forage on prey varying in quality, location, and predictability within...

Data from: First direct measurements of behavioural responses by Cuvier’s beaked whales to mid-frequency active sonar

Stacy L. DeRuiter, Brandon L. Southall, John Calambokidis, Walter M. X. Zimmer, Dinara Sadykova, Erin A. Falcone, Ari S. Friedlaender, John E. Joseph, David Moretti, Gregory S. Schorr, Len Thomas & Peter L. Tyack
Most marine mammal strandings coincident with naval sonar exercises have involved Cuvier’s beaked whales (Ziphius cavirostris). We recorded acoustic and animal movement data on two tagged Ziphius and obtained the first direct measurements of behavioural responses of this species to mid-frequency active (MFA) sonar signals. Each recording included a 30-minute playback (one 1.6-s simulated MFA sonar signal repeated every 25 s); one whale was also incidentally exposed to MFA sonar from distant naval exercises. Whales...

Data from: Strong maternal fidelity and natal philopatry shape genetic structure in North Pacfic humpback whales

C. Scott Baker, Debbie Steel, John Calambokidis, Erin A. Falcone, Ursula Gozález-Peral, Jay Barlow, Alexander M. Burdin, Phillip J. Clapham, John K. B. Ford, Christine M. Gabriele, David Mattila, Janice M. Straley, Barbara L. Taylor, Jorge Urbán, Paul R. Wade, David Weller, Briana H. Witteveen, Manami Yamaguchi, CS Baker, BH Witteveen, E Falcone, BL Taylor, JKB Ford, AM Burdin, PJ Clapham … & JM Straley
We quantified the relative influence of maternal fidelity to feeding grounds and natal fidelity to breeding grounds in humpback whales based on an ocean-wide survey of mitochondrial (mt) DNA diversity in the North Pacific. For 2,193 biopsy samples collected from whales in 10 feeding regions and 8 breeding regions during the winter and summer of 2004 to 2006, we first used microsatellite genotyping (average, 9.5 loci) to identify replicate samples. From sequences of the mtDNA...

Data from: Diving behavior of Cuvier's beaked whales (Ziphius cavirostris) off Cape Hatteras, North Carolina

Jeanne M. Shearer, Nicola J. Quick, William R. Cioffi, Robin W. Baird, Daniel L. Webster, Heather J. Foley, Zachary T. Swaim, Danielle M. Waples, Joel T. Bell & Andrew J. Read
Cuvier’s beaked whales exhibit exceptionally long and deep foraging dives. The species is relatively little studied due to their deep-water, offshore distribution and limited time spent at the surface. We used LIMPET satellite tags to study the diving behavior of Cuvier's beaked whales off Cape Hatteras, North Carolina from 2014 to 2016. We deployed 11 tags, recording 3,242 hours of behavior data, encompassing 5,926 dives. Dive types were highly bimodal; deep dives (>800m, n=1,408) had...

Data from: Discrimination of fast click series produced by tagged Risso’s dolphins (Grampus griseus) for echolocation or communication

Patricia Arranz, Stacy L. DeRuiter, Alison K. Stimpert, Silvana Neves, Ari S. Friedlaender, Jeremy A. Goldbogen, Fleur Visser, John Calambokidis, Brandon L. Southall & Peter L. Tyack
Early studies that categorized odontocete pulsed sounds had few means of discriminating signals used for biosonar-based foraging from those used for communication. This capability to identify the function of sounds is important for understanding and interpreting behavior; it is also essential for monitoring and mitigating potential disturbance from human activities. Archival tags were placed on free-ranging Grampus griseus to quantify and discriminate between pulsed sounds used for echolocation-based foraging and those used for communication. Two...

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: 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: 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...

Endangered predators and endangered prey: seasonal diet of Southern Resident killer whales

Michael Ford, M. Bradley Hanson, Candice Emmons, Meredith Everett, Kim Parsons, Linda Park, Jennifer Hempelmann, Donald Van Doornik, Gregory Schorr, Jeffrey Jacobsen, Mark Sears, Maya Sears, John Sneva, Robin Baird & Lynne Barre
Understanding diet is critical for conservation of endangered predators. The Southern Resident killer whales (SRKW) (Orcinus orca) are an endangered population occurring primarily in the west coast and inland waters of Washington and British Columbia. Insufficient prey has been identified as a factor limiting their recovery, so a clear understanding of the whales’ seasonal diet is a high conservation priority. Previous studies have shown that their summer diet in inland waters consists primarily of Chinook...

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: Sperm whale population structure in the eastern and central North Pacific inferred by the use of single nucleotide polymorphisms (SNPs), microsatellites and mitochondrial DNA

Sarah L. Mesnick, Barbara L. Taylor, Frederick I Archer, Karen K Martien, Sergio Escorza Treviño, Brittany L. Hancock-Hanser, Sandra Carolina Moreno Medina, Victoria L Pease, Kelly M Robertson, Janice M Straley, Robin W Baird, John Calambokidis, Gregory S. Schorr, Paul Wade, Vladimir Burkanov, Chris R. Lunsford, Luke Rendell & Phillip A Morin
We use mitochondrial DNA (400bp), six microsatellites and 36 single nucleotide polymorphisms (SNPs), 20 of which were linked, to investigate population structure of sperm whales (Physeter macrocephalus) in the eastern and central North Pacific. SNP markers, reproducible across technologies and laboratories, are ideal for long-term studies of globally distributed species such as sperm whales, a species of conservation concern due to both historical and contemporary impacts. We estimate genetic differentiation among three strata in the...

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