14 Works

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: Signatures of natural selection among lineages and habitats in Oncorhynchus mykiss

Morten T. Limborg, Scott M. Blankenship, Sewall F. Young, Fred M. Utter, Lisa W. Seeb, Mette H. H. Hansen & James E. Seeb
Recent advances in molecular interrogation techniques now allow unprecedented genomic inference about the role of adaptive genetic divergence in wild populations. We used high-throughput genotyping to screen a genome-wide panel of 276 single nucleotide polymorphisms (SNPs) for the economically and culturally important salmonid Oncorhynchus mykiss. Samples included 805 individuals from 11 anadromous and resident populations from the northwestern United States and British Columbia, and represented two major lineages including paired populations of each life history...

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: Coexistence and origin of trophic ecotypes of pygmy whitefish, Prosopium coulterii, in southwestern Alaskan lake

Tom P. Quinn, Conrad P. Gowell, Eric B. Taylor, T. P. Quinn & E. B. Taylor
Ecologically, morphologically, and genetically distinct populations within single taxa often co-exist in postglacial lakes and have provided important model systems with which to investigate ecological and evolutionary processes such as niche partitioning and ecological speciation. Within the Salmonidae, these species complexes have been well studied, particularly within the Coregonus clupeaformis-C. laveratus (lake and European whitefish, respectively) group, but the phenomenon has been less well documented in the other whitefish genera, Prosopium and Stenodus. Here, we...

Data from: Reproductive success of captively bred and naturally spawned Chinook salmon colonizing newly accessible habitat

Joseph H. Anderson, Paul L. Faulds, William I. Atlas & Thomas P. Quinn
Captively reared animals can provide an immediate demographic boost in reintroduction programs but may also reduce the fitness of colonizing populations. Construction of a fish passage facility at Landsburg Diversion Dam on the Cedar River, WA, USA, provided a unique opportunity to explore this trade-off. We thoroughly sampled adult Chinook salmon (Oncorhynchus tshawytscha) at the onset of colonization (2003 – 2009), constructed a pedigree from genotypes at 10 microsatellite loci, and calculated reproductive success (RS)...

Data from: Positive selection within a diatom species acts on putative protein interactions and transcriptional regulation

Julie A. Koester, Willie J. Swanson & E. Virginia Armbrust
Diatoms are the most species-rich group of micro-algae, and their contribution to marine primary production is important on a global scale. Diatoms can form dense blooms through rapid asexual reproduction; mutations acquired and propagated during blooms likely provide the genetic, and thus phenotypic, variability upon which natural selection may act. Positive selection was tested using genome and transcriptome-wide pair-wise comparisons of homologs in three genera of diatoms, Pseudo-nitzschia, Ditylum, and Thalassiosira that represent decreasing phylogenetic...

Data from: Quantifying past and present connectivity illuminates a rapidly changing landscape for the African elephant

Clinton W. Epps, Samuel K. Wasser, Jonah L. Keim, Benezeth M. Mutayoba & Justin S. Brashares
There is widespread concern about impacts of land-use change on connectivity among animal and plant populations, but those impacts are difficult to quantify. Moreover, lack of knowledge regarding ecosystems before fragmentation may obscure appropriate conservation targets. We use occurrence and population genetic data to contrast connectivity for a long-lived mega-herbivore over historical and contemporary time frames. We test whether (i) historical gene flow is predicted by persistent landscape features rather than human settlement, (ii) contemporary...

Data from: Relationship between effective population size, inbreeding, and adult fitness-related traits in a steelhead (Oncorhynchus mykiss) population released in the wild

Kerry A. Naish, Todd T. Seamons, Michael B. Dauer, Lorenz Hauser, Thomas P. Quinn, K. A. Naish, T. R. Seamons, M. B. Dauer, L. Hauser & T. P. Quinn
Inbreeding is of concern in supportive breeding programmes in Pacific salmonids, Oncorhynchus spp, where the number of breeding adults is limited by rearing space or poor survival to adulthood, and large numbers are released to supplement wild stocks and fisheries. We reconstructed the pedigree of 6602 migratory hatchery steelhead (Oncorhynchus mykiss) over four generations, to determine the incidence and fitness consequences of inbreeding in a northwest USA programme. The hatchery maintained an effective population size,...

Data from: Dragons in our midst: phyloforensics of illegally traded Southeast Asian monitor lizards

Welton J. Luke, Cameron D. Siler, Charles W. Linkem, Arvin C. Diesmos, Mae L. Diesmos, Emerson Sy, Rafe M. Brown & Luke J. Welton
We provide a phylogenetic and population genetic evaluation of the illegal pet and bush meat trade of monitor lizards in the Philippines. We use a molecular dataset assembled from vouchered samples with known localities throughout the country, as a reference for statistical phylogenetic, population genetic, and DNA barcoding analyses of genetic material obtained during a three year survey of the Manila pet trade. Our results provide the first genetic evaluation of a major Southeast Asian...

Data from: Fine-scale local adaptation in an invasive freshwater fish has evolved in contemporary time

Peter A. H. Westley, Eric J. Ward, Ian A. Fleming, P. A. H. Westley, I. A. Fleming & E. J. Ward
Adaptive evolutionary change in only a few generations can increase the ability of non-native invasive species to spread, and yet adaptive divergence is rarely assessed in recently established populations. In this paper, we experimentally test for evidence of fine-scale local adaptation in juvenile survival and growth among three populations of an invasive freshwater fish with reciprocal transplants and common-garden experiments. Despite intrinsic differences in habitat quality, in two out of three populations we detected evidence...

Data from: Estimation of genotyping error rate from repeat genotyping, unintentional recaptures and known parent-offspring comparisons in 16 microsatellite loci for brown rockfish (Sebastes auriculatus)

Maureen A. Hess, James G. Rhydderch, Larry L. LeClair, Raymond M. Buckley, Mitsuhiro Kawase & Lorenz Hauser
Genotyping errors are present in almost all genetic data and can affect biological conclusions of a study, particularly for studies based on individual identification and parentage. Many statistical approaches can incorporate genotyping errors, but usually need accurate estimates of error rates. Here, we used a new microsatellite data set developed for brown rockfish (Sebastes auriculatus) to estimate genotyping error using three approaches: (i) repeat genotyping 5% of samples, (ii) comparing unintentionally recaptured individuals and (iii)...

Data from: Evidence for climate-driven diversification? A caution for interpreting ABC inferences of simultaneous historical events

Jamie R. Oaks, Jeet Sukumaran, Jacob A. Esselstyn, Charles W. Linkem, Cameron David Siler, Mark T. Holder & Rafe M. Brown
Approximate Bayesian computation (ABC) is rapidly gaining popularity in population genetics. One example, msBayes, infers the distribution of divergence times among pairs of taxa, allowing phylogeographers to test hypotheses about historical causes of diversification in co-distributed groups of organisms. Using msBayes, we infer the distribution of divergence times among 22 pairs of populations of vertebrates distributed across the Philippine Archipelago. Our objective was to test whether sea-level oscillations during the Pleistocene caused diversification across the...

Data from: Can interbreeding of wild and artificially propagated animals be prevented by using broodstock selected for a divergent life history?

Todd R. Seamons, Lorenz Hauser, Kerry Ann Naish & Thomas P. Quinn
Two strategies have been proposed to avoid negative genetic effects of artificially propagated individuals on wild populations: (i) integration of wild and captive populations to minimize domestication selection, and (ii) segregation of released individuals from the wild population to minimize interbreeding. We tested the efficacy of the strategy of segregation by divergent life history in a steelhead trout, Oncorhynchus mykiss system, where hatchery fish were selected to spawn months earlier than the indigenous wild population....

Data from: A parapatric propensity for breeding precludes the completion of speciation in common teal (Anas crecca, sensu lato)

Jeffrey L. Peters, Kevin G. McCracken, Christin L. Pruett, Sievert Rohwer, Sergei V. Drovetski, Yuri N. Zhuravlev, Irina Kulikova, Daniel D. Gibson & Kevin Winker
Speciation is a process in which genetic drift and selection cause divergence over tSpeciation is a process in which genetic drift and selection cause divergence over time. However, there is no rule dictating the time required for speciation, and even low levels of gene flow hinder divergence, so that taxa may be poised at the threshold of speciation for long periods of evolutionary time. We sequenced mitochondrial DNA (mtDNA) and eight nuclear introns (nuDNA) to...

Registration Year

  • 2012

Resource Types

  • Dataset


  • University of Washington
  • University of Kansas
  • University of South Dakota
  • Oregon State University
  • Washington Department of Fish and Wildlife
  • National Museum
  • University of Santo Tomas
  • Sokoine University of Agriculture
  • Duke University
  • University of California, Berkeley