Protected Species Research Publications - Taxonomy and Genetics

2015-2016

• Ackerman et al. 2016. Effective number of breeders from sibship reconstruction: empirical evaluations using hatchery steelhead.  Evolutionary Applications
• Alexander et al. 2016. What influences the worldwide genetic structure of sperm whales (Physeter macrocephalus)? Molecular Ecology
• Bradbury et al. 2016. Genetic mixed stock analysis disentangles spatial and temporal variation in composition of the West Greenland Atlantic Salmon fishery. ICES Journal of Marine Science  
• Caldarone et al. 2016. Evaluation of nucleic acids and plasma IGF1 levels for estimating short-term responses of post-smolt Atlantic salmon (Salmo salar) to food availability. Fishery Bulletin
• Cise et al. 2016. Redrawing the map: mtDNA provides new insights into the distribution and diversity of short-finned pilot whales in the Pacific Ocean. Marine Mammal Science
• Costa et al. 2016. Offshore and coastal common bottlenose dolphins of the western South Atlantic face-to-face: What the skull and the spine can tell us.  Marine Mammal Science
• Devlin-Durante et al. 2016. How old are you? Genet age estimates in a clonal animal. Molecular Ecology
• Foote and Morin. 2016. Genome-wide SNP data suggests complex ancestry of sympatric North Pacific killer whale ecotypes. Heredity
• Ford et al. 2016. Estimation of a killer whale (Orcinus orca) population's diet using sequencing analysis of DNA from feces. PLos One
• Ford et al. 2016. Broodstock history strongly influences natural spawning success in hatchery steelhead (Oncorhynchus mykiss). PLoS One
• Gilbert-Horvath et al. 2016. Hierarchical phylogeographic structure of Coho Salmon, Oncorhynchus kisutch, in California.  Transactions of the American Fisheries Society
• Hale et al. 2016. RNA-seq reveals differential gene expression in the brains of juvenile resident and migratory smolt rainbow trout (Oncorhynchus mykiss).  Comparative Biochemistry and Physiology Part D: Genomics and Proteomics
• Leitwein et al. 2016. Ancestry and adaptive evolution of anadromous, resident, and adfluvial rainbow trout (Oncorhynchus mykiss) in the San Francisco Bay Area: application of adaptive genomic variation to conservation in a highly impacted landscape. Evolutionary Applications
• Leslie and Morin. 2016. Using genome-wide SNPs to detect structure in high-diversity and low-divergence populations of severely impacted eastern tropical Pacific spinner (Stenella longirostris) and pantropical spotted dolphins (S. attenuata). Frontiers in Marine Science
• Matsuzawa et al. 2016. Fine scale genetic population structure of loggerhead turtles in the Northwest Pacific. Endangered Species Research
• Morin et al. 2016. Genetic structure of the beaked whale genus Berardius in the North Pacific, with genetic evidence for a new species. Marine Mammal Science
• Moser et al. 2016. Biology and life history of green sturgeon (Acipenser medirostris): state of the science. Journal of Applied Ichthyology
• Morley et al. 2016. Seasonal variation exceeds effects of salmon carcass additions on benthic food webs in the Elwha River. Ecosphere
• Pearse. 2016. Saving the spandrels? Adaptive genomic variation in conservation and fisheries management. FIsh Biology
• Roegner et al. 2016. Comparative use by Pacific salmon of shallow and deepwater habitats in the Columbia River estuary prior to ocean entry. Journal of Marine and Coastal Fisheries: Dynamics, Management, and Ecosystem Science
• Sather et al. 2016. Shallow tidal freshwater habitats of the Columbia River: spatial and temporal variability of fish communities and density, size, and genetic stock composition of juvenile Chinook Salmon. Transactions of the American Fisheries Society
• Segura-Garcia et al. 2016. Post-glacial habitat release and incipient speciation in the genus Delphinus. Heredity
• Springer et al. 2016. Inactivation of cone-specific phototransduction genes in rod monochromatic cetaceans.  Frontiers in Ecology and Evolution
• Yamamoto et al. 2016. Alterations in gene expression during fasting-induced atresia of early secondary growth ovarian follicles of coho salmon, Oncorhynchus kisutch. Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology 
   

2017

• Abadia-Cardoso et al. 2017. Molecular population genetics of the northern elephant seal Mirounga angustirostris. Journal of Heredity
• Anderson et al. 2017. Genetic and individual assignment of tetraploid green sturgeon with SNP assay data. Conservation Genetics
• Apprill et al. 2017. Extensive core microbiome in drone-captured whale blow supports a framework for health monitoring. Host-Microbe Biology
• Archer et al. 2017. Diagnosability of mtDNA with Random Forests: Using sequence data to delimit subspecies. Marine Mammal Science
• Davis et al. 2017. Identification of multiple genetically distinct populations of Chinook salmon (Oncorhynchus tshawytscha) in a small coastal watershed. Environmental Biology of Fishes
• Gaos et al. 2017. Natal foraging philopatry of hawksbill turtles in the eastern Pacific Ocean.  The Royal Society Open Science
• Jost et al. 2017. Differentiation measures for conservation genetics. Evolutionary Applications
• Kodama et al. 2017. Mapping of quantitative trait loci for temporal growth and age at maturity in coho salmon: evidence for genotype-by-sex interactions. Marine Genomics
• Komoroske et al. 2017. Advances in the application of genetics in marine turtle biology & conservation. Frontiers in Marine Science
• Lin et al. 2017. Modeling local adaptation and gene flow in sockeye salmon. Ecosphere
• Macqueen et al. 2017. Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation, and aquaculture. BMC Genomics
• Martien et al. 2017. Analytical approaches to subspecies delimitation with genetic data. Marine Mammal Science
• Martien et al. 2017. Unexpected patterns of global population structure in melon-headed whales (Peponocephala electra). Marine Ecology Progress Series
• Neely et al. 2017. Skin transcriptomes of common bottlenose dolphins (Tursiops truncatus) from the northern Gulf of Mexico and southeastern U.S. Atlantic coasts. Marine Genomics
• Robertson et al. 2017. Genetic sexing of pinnipeds: a real-time, single step qPCR technique. Conservation Genetics Resources
• Roden et al. 2017. Genetic fingerprinting reveals natal origins of male leatherback turtles encountered in the Atlantic Ocean and Mediterranean Sea. Marine Biology
• Rosel et al. 2017. Examining metrics and magnitudes of molecular genetic differentiation used to delimit cetacean subspecies based on mitochondrial DNA control region sequences. Marine Mammal Science
• Rosel et al. 2017. A review of molecular genetic markers and analytical approaches that have been used for delimiting marine mammal subspecies and species. Marine Mammal Science
• Stacy et al. 2017. Evidence of diversity, site and host specificity of sea turtle blood flukes (Digenea: Schistosomatoidea: "Spirorchiidae"): a molecular prospecting study. The Journal of Parasitology
• Taylor et al. 2017. Why we should develop guidelines and quantitative standards for using genetic data to delimit subspecies for data-poor organisms like cetaceans. Marine Mammal Science
• Taylor et al. 2017. Guidelines and quantitative standards to improve consistency in cetacean subspecies and species delimitation relying on molecular genetic data. Marine Mammal Science
• Van Cise et al. 2017. Familial social structure and socially-driven genetic differentiation in Hawaiian short-finned pilot whales. Molecular Ecology
• Van Cise et al. 2017. Acoustic differentiation of Shiho- and Naisa-type short-finned murilot whales in the Pacific Ocean. Journal of the Acoustical Society of America
• Vollmer et al. 2017. Fine-scale population structure of common bottlenose dolphins (Tursiops truncatus) in offshore and coastal waters of the U.S. Gulf of Mexico. Marine Biology
• Waples and Anderson. 2017. Purging putative siblings from population genetic datasets: a cautionary view. Molecular Ecology
• Wu et al. 2017. Identification of three Brucella ceti genotypes in bottlenose dolphins (Tursiops truncatus) using a multiplex SYBR green real-time PCR. Aquatic Mammals
• Yeh et al. 2017. Effect of contaminants of emerging concern on liver mitochondrial function in Chinook salmon. Aquatic Toxicology
   

2018

• Andrews et al. 2018. Cooperative research sheds light on the listing status of threatened and endangered rockfish species. Conservation Genetics
• Archer et al. 2018. Taxonomic status of a “finner whale” (Balaenoptera swinhoei Gray, 1865) from southern Taiwan. Marine Mammal Science 
• Cammen et al. 2018. Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds. Ecology and Evolution
• Conrad et al. 2018. Ancient DNA analysis of sea turtles (Cheloniidae) from the Gold Rush-era (1850s) eastern Pacific Ocean. Open Quaternary
• Ford et al. 2018. Inbreeding in an endangered killer whale population. Animal Conservation
• Gaos et al. 2018. Prevalence of polygyny in a critically endangered marine turtle population. Journal of Experimental Marine Biology and Ecology
• Gao et al. 2018. A new single nucleotide polymorphism database for rainbow trout generated through whole genome resequencing. Frontiers in Genetics
• Hill et al. 2018. Short-finned pilot whales (Globicephala macrorhynchus) of the Mariana Archipelago: individual affiliations, movements, and spatial use. Marine Mammal Science
• Hoffman et al. 2018.  A global cline in a color polymorphism suggests a limited contribution of gene flow towards the recovery of a heavily exploited marine mammal. Royal Society Open Access
• Jensen et al. 2018. Environmental warming and feminisation of one of the largest sea turtle populations in the world. Current Biology
• Leslie and Morin 2018. Structure and phylogeography of two tropical predators, spinner (Stenella longirostris) and pantropical spotted (S. attenuata) dolphins, from SNP data. Royal Society Open Science
• Pearse et al. 2019. Sex-dependent dominance maintains migration supergene in rainbow trout. Nature Ecology & Evolution
• Shamblin et al. 2018. Mixed stock analyses indicate population-scale connectivity effects of active dispersal by surface-pelagic green turtles. Marine Ecology Progress Series
• Stewart et al. 2018.  Using mixed stock analysis to assess source populations for at‐sea bycaught juvenile and adult loggerhead turtles (Caretta caretta) in the north‐west Atlantic. Fish and Fisheries
• Stoffel et al. 2018. Demographic histories and genetic diversity across pinnipeds are shaped by human exploitation, ecology and life-history. Nature Communications
• Waples et al. 2018. Guidelines for genetic data analysis. Journal of Cetacean Research and Management
• Waples and Lindley 2018. Genomics and conservation units: the genetic basis of adult migration timing in Pacific salmonids. Evolutionary Applications
• Waters et al. 2018. Genomewide association analyses of fitness traits in captive‐reared Chinook salmon: applications in evaluating conservation strategies. Evolutionary Applications
• Wringe et al. 2018. Development and evaluation of SNP panels for the detection of hybridization between wild and escaped Atlantic salmon (Salmo salar) in the western Atlantic. Canadian Journal of Fisheries and Aquatic Sciences
   

2019

• Banerjee et al. 2019. Single nucleotide polymorphism markers for genotyping hawksbill turtles (Eretmochelys imbricata). Conservation Genetics Resources
• Costa et al. 2019. Ecological divergence and speciation in common bottlenose dolphins in the western South Atlantic. Journal of Evolutionary Biology
• Foote et al. 2019. Killer whale genomes reveal a complex history of recurrent admixture and vicariance summary. Molecular Ecology 
• Jensen et al. 2019. The evolutionary history and global phylogeography of the green turtle (Chelonia mydas). Journal of Biogeography
• Pearse et al. 2019. Sex-dependent dominance maintains migration supergene in rainbow trout. Nature Ecology & Evolution
• Piovano et al. 2019. Mixed stock analysis of juvenile green turtles aggregating at two foraging grounds in Fiji reveals major contribution from the American Samoa Management Unit. Scientific Reports
• Van Cise et al. 2019. Oceanographic barriers, divergence, and admixture: phylogeography and taxonomy of two putative subspecies of short-finned pilot whale. Molecular Ecology
• Vollmer et al. 2019. Taxonomic revision of the dolphin genus Lagenorhynchus. Marine Mammal Science 
• Vos et al. 2019. Age and growth analyses for the endangered belugas in Cook Inlet, Alaska. Marine Mammal Science