Now showing items 1-20 of 185

  • Microsatellite and allozyme analyses reveal few genetic differences among spatially distinct aggregations of geoduck clams (Panopea abrupta, Conrad 1849) 

    Vadopalas, B., LL Leclair, and P. Bentzen. 2004. "Microsatellite and allozyme analyses reveal few genetic differences among spatially distinct aggregations of geoduck clams (Panopea abrupta, Conrad 1849)." Journal of Shellfish Research 23(3): 693-706.
    The genetic population structure of geoduck clams (Panopea abrupta) in inland waters of Washington may affect fishery management and aquacultural practices involving this species. To investigate genetic differentiation ...
  • Contemporary nuclear and mitochondrial genetic clines in a north temperate estuarine fish reflect Pleistocene vicariance 

    Bradbury, I. R., M. W. Coulson, S. E. Campana, I. G. Paterson, et al. 2011. "Contemporary nuclear and mitochondrial genetic clines in a north temperate estuarine fish reflect Pleistocene vicariance." Marine Ecology Progress Series 438: 207-U235. doi:10.3354/meps09286
    Contemporary genetic spatial structure in north temperate marine species is likely the culmination of multiple vicariant and dispersive cycles. Here we evaluate spatial genetic structure in an estuarine fish, rainbow ...
  • Otolith elemental composition and adult tagging reveal spawning site fidelity and estuarine dependency in rainbow smelt 

    Bradbury, I. R., S. E. Campana, and P. Bentzen. 2008. "Otolith elemental composition and adult tagging reveal spawning site fidelity and estuarine dependency in rainbow smelt." Marine Ecology Progress Series 368: 255-268. doi:10.3354/meps07583
    Observations of homing and straying in marine organisms based on traditional Eulerian approaches may fail to resolve dispersal kernels or be unable to differentiate homing from invariant local residency, The roles of ...
  • Non-linear genetic isolation by distance: implications for dispersal estimation in anadromous and marine fish populations 

    Bradbury, Ian R., and Paul Bentzen. 2007. "Non-linear genetic isolation by distance: implications for dispersal estimation in anadromous and marine fish populations." Marine Ecology Progress Series 340: 245-257. doi:10.3354/meps340245
    Indirect genetic approaches such as those based on the association between genetic and geographic distance (isolation by distance, IBD) may provide one of the best means of estimating dispersal in marine systems. We ...
  • Genomic islands of divergence and their consequences for the resolution of spatial structure in an exploited marine fish 

    Bradbury, Ian R., Sophie Hubert, Brent Higgins, Sharen Bowman, et al. 2013. "Genomic islands of divergence and their consequences for the resolution of spatial structure in an exploited marine fish." Evolutionary Applications 6(3): 450-461.
    As populations diverge, genomic regions associated with adaptation display elevated differentiation. These genomic islands of adaptive divergence can inform conservation efforts in exploited species, by refining the ...
  • Synchronized hatch and its ecological significance in rainbow smelt Osmerus mordax in St. Mary's Bay, Newfoundland 

    Bradbury, IR, SE Campana, P. Bentzen, and PVR Snelgrove. 2004. "Synchronized hatch and its ecological significance in rainbow smelt Osmerus mordax in St. Mary's Bay, Newfoundland." Limnology and Oceanography 49(6): 2310-2315. DOI:10.4319/lo.2004.49.6.2310
    Early life history stages in most marine animals are subject to high mortality through predation, starvation, and dispersal. Accordingly, the potential exists for the selection of behavioral mechanisms that reduce ...
  • Mixed evidence for reduced local adaptation in wild salmon resulting from interbreeding with escaped farmed salmon: complexities in hybrid fitness 

    Fraser, Dylan J., Adam M. Cook, James D. Eddington, Paul Bentzen, et al. 2008. "Mixed evidence for reduced local adaptation in wild salmon resulting from interbreeding with escaped farmed salmon: complexities in hybrid fitness." Evolutionary Applications 1(3): 501-512.
    Interbreeding between artificially-selected and wild organisms can have negative fitness consequences for the latter. In the Northwest Atlantic, farmed Atlantic salmon recurrently escape into the wild and enter rivers where ...
  • Population Structure as Revealed by mtDNA and Microsatellites in Northern Fur Seals, Callorhinus ursinus, throughout Their Range 

    Dickerson, Bobette R., Rolf R. Ream, Sacha N. Vignieri, and Paul Bentzen. 2010. "Population Structure as Revealed by mtDNA and Microsatellites in Northern Fur Seals, Callorhinus ursinus, throughout Their Range." Plos One 5(5): 10671-e10671. doi:10.1371/journal.pone.0010671
    Background: The northern fur seal (Callorhinus ursinus; NFS) is a widely distributed pinniped that has been shown to exhibit a high degree of philopatry to islands, breeding areas on an island, and even to specific ...
  • Identifying Canadian Freshwater Fishes through DNA Barcodes 

    Hubert, Nicolas, Robert Hanner, Erling Holm, Nicholas E. Mandrak, et al. 2008. "Identifying Canadian Freshwater Fishes through DNA Barcodes." Plos One 3(6): 2490-e2490. doi:10.1371/journal.pone.0002490
    Background: DNA barcoding aims to provide an efficient method for species-level identifications using an array of species specific molecular tags derived from the 59 region of the mitochondrial cytochrome c oxidase I ...
  • Both Geography and Ecology Contribute to Mating Isolation in Guppies 

    Schwartz, Amy K., Dylan J. Weese, Paul Bentzen, Michael T. Kinnison, et al. 2010. "Both Geography and Ecology Contribute to Mating Isolation in Guppies." Plos One 5(12): 15659-e15659. doi:10.1371/journal.pone.0015659
    Local adaptation to different environments can promote mating isolation - either as an incidental by-product of trait divergence, or as a result of selection to avoid maladaptive mating. Numerous recent empirical examples ...
  • Improving Evolutionary Models for Mitochondrial Protein Data with Site-Class Specific Amino Acid Exchangeability Matrices 

    Dunn, Katherine A., Wenyi Jiang, Christopher Field, and Joseph P. Bielawski. 2013. "Improving Evolutionary Models for Mitochondrial Protein Data with Site-Class Specific Amino Acid Exchangeability Matrices." Plos One 8(1): 55816-e55816.
    Adequate modeling of mitochondrial sequence evolution is an essential component of mitochondrial phylogenomics (comparative mitogenomics). There is wide recognition within the field that lineage-specific aspects of ...
  • Positive Darwinian Selection in the Piston That Powers Proton Pumps in Complex I of the Mitochondria of Pacific Salmon 

    Garvin, Michael R., Joseph P. Bielawski, and Anthony J. Gharrett. 2011. "Positive Darwinian Selection in the Piston That Powers Proton Pumps in Complex I of the Mitochondria of Pacific Salmon." Plos One 6(9): 24127-e24127.
    The mechanism of oxidative phosphorylation is well understood, but evolution of the proteins involved is not. We combined phylogenetic, genomic, and structural biology analyses to examine the evolution of twelve mitochondrial ...
  • Methods for selecting fixed-effect models for heterogeneous codon evolution, with comments on their application to gene and genome data 

    Bao, Le, Hong Gu, Katherine A. Dunn, and Joseph P. Bielawski. 2007. "Methods for selecting fixed-effect models for heterogeneous codon evolution, with comments on their application to gene and genome data." Bmc Evolutionary Biology 7: 5-S5.
    Background: Models of codon evolution have proven useful for investigating the strength and direction of natural selection. In some cases, a priori biological knowledge has been used successfully to model heterogeneous ...
  • Multilocus Genotyping Assays for Single Nucleotide Polymorphism-Based Subtyping of Listeria monocytogenes Isolates 

    Ward, Todd J., Thomas F. Ducey, Thomas Usgaard, Katherine A. Dunn, et al. 2008. "Multilocus Genotyping Assays for Single Nucleotide Polymorphism-Based Subtyping of Listeria monocytogenes Isolates." Applied and Environmental Microbiology 74(24): 7629-7642.
    Listeria monocytogenes is responsible for serious invasive illness associated with consumption of contaminated food and places a significant burden on public health and the agricultural economy. We recently developed a ...
  • Phylogenomic analysis of natural selection pressure in Streptococcus genomes 

    Anisimova, Maria, Joseph Bielawski, Katherine Dunn, and Ziheng Yang. 2007. "Phylogenomic analysis of natural selection pressure in Streptococcus genomes." Bmc Evolutionary Biology 7: 154-154.
    Background: In comparative analyses of bacterial pathogens, it has been common practice to discriminate between two types of genes: (i) those shared by pathogens and their non-pathogenic relatives (core genes), and (ii) ...
  • Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts 

    Sullivan, Matthew B., Debbie Lindell, Jessica A. Lee, Luke R. Thompson, et al. 2006. "Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts." Plos Biology 4(8): 1344-1357.
    Cyanophages ( cyanobacterial viruses) are important agents of horizontal gene transfer among marine cyanobacteria, the numerically dominant photosynthetic organisms in the oceans. Some cyanophage genomes carry and express ...
  • Reduced Retinal Function in the Absence of Na(v)1.6 

    Smith, Benjamin J., and Patrice D. Cote. 2012. "Reduced Retinal Function in the Absence of Na(v)1.6." Plos One 7(2): 31476-e31476.
    Background: Mice with a function-blocking mutation in the Scn8a gene that encodes Na(v)1.6, a voltage-gated sodium channel (VGSC) isoform normally found in several types of retinal neurons, have previously been found to ...
  • The dystroglycan complex is necessary for stabilization of acetylcholine receptor clusters at neuromuscular junctions and formation of the synaptic basement membrane 

    Jacobson, C., PD Cote, SG Rossi, RL Rotundo, et al. 2001. "The dystroglycan complex is necessary for stabilization of acetylcholine receptor clusters at neuromuscular junctions and formation of the synaptic basement membrane." Journal of Cell Biology 152(3): 435-450.
    The dystrophin-associated protein (DAP) complex spans the sarcolemmal membrane linking the cytoskeleton to the basement membrane surrounding each myofiber. Defects in the DAP complex have been linked previously to a ...
  • Mechanisms Influencing the Timing and Success of Reproductive Migration in a Capital Breeding Semelparous Fish Species, the Sockeye Salmon 

    Crossin, Glenn T., Scott G. Hinch, Steven J. Cooke, Michael S. Cooperman, et al. 2009. "Mechanisms Influencing the Timing and Success of Reproductive Migration in a Capital Breeding Semelparous Fish Species, the Sockeye Salmon." Physiological and Biochemical Zoology 82(6): 635-652. doi:10.1086/605878
    Two populations of homing sockeye salmon (Oncorhynchus nerka; Adams and Chilko) were intercepted in the marine approaches around the northern and southern ends of Vancouver Island (British Columbia, Canada) en route to ...
  • Pacific Salmon in Hot Water: Applying Aerobic Scope Models and Biotelemetry to Predict the Success of Spawning Migrations 

    Farrell, A. P., S. G. Hinch, S. J. Cooke, DA Patterson, et al. 2008. "Pacific Salmon in Hot Water: Applying Aerobic Scope Models and Biotelemetry to Predict the Success of Spawning Migrations." Physiological and Biochemical Zoology 81(6): 697-708. doi:10.1086/592057
    Concern over global climate change is widespread, but quantifying relationships between temperature change and animal fitness has been a challenge for scientists. Our approach to this challenge was to study migratory ...