John K. Wenburg

U.S. Fish and Wildlife Service · Alaska Region Conservation Genetics Laboratory

The genetic population structure of coastal cutthroat trout (Oncorhynchus clarki clarki) in Washington state was investigated by analysis of variation in allele frequencies at six highly polymorphic microsatellite loci for 13 anadromous populations, along with one outgroup population from the Yellowstone subspecies (O. clarki bouvieri) (mean hetero...

We examined the assumption that landscape heterogeneity similarly influences the spatial distribution of genetic diversity in closely related and geographically overlapping species. Accordingly, we evaluated the influence of watershed affiliation and nine habitat variables from four categories (spatial isolation, habitat size, climate, and ecology)...

We examine sympatric anadromous (steelhead) and nonanadromous (resident) rainbow trout (Oncorhynchus mykiss) from neighboring locations to test three hypotheses: (1) the sympatric life history types are not genetically different; (2) fine-scale dispersal is the same for both sexes, and (3) fine-scale dispersal is the same for steelhead and resident...

Rates of hybridization and introgression are increasing dramatically worldwide because of translocations of organisms and habitat modifications by humans. Hybridization has contributed to the extinction of many species through direct and indirect means. However, recent studies have found that natural hybridization has played an important role in th...

Colonization of new environments should promote rapid speciation as a by-product of adaptation to divergent selective regimes. Although this process of ecological speciation is known to have occurred over millennia or centuries, nothing is known about how quickly reproductive isolation actually evolves when new environments are first colonized. Usi...

Arctic marine ecosystems are undergoing rapid physical and biological change associated with climate warming and loss of sea ice. Sea ice loss will impact many species through altered spatial and temporal availability of resources. In the Bering and Chukchi Seas, the Pacific walrus Odobenus rosmarus divergens is one species that could be impacted b...

For the sea otter (Enhydra lutris), genetic population structure is an area of research that has not received significant attention, especially in Southwest Alaska where that distinct population segment has been listed as threatened since 2005 pursuant to the U.S. Endangered Species Act. In this study, 501 samples from 14 locations from Prince Will...

Rainbow Trout Oncorhynchus mykiss in southwestern Alaska occupy coastal watersheds near the northern boundary of the species native range and support a world class wild trout sport fishery. Although low freshwater temperatures and a short growing season in this region may favor anadromy, these populations appear to exhibit a freshwater resident lif...

Knowledge of population structure facilitates the effective management of species that are harvested in mixed‐stock fisheries. In this study, we analyzed genetic variation at 19 microsatellite loci for 14 populations of Coho Salmon Oncorhynchus kisutch in the Yukon River. We then used this data to estimate the stock composition of adults that were...

We developed single nucleotide polymorphism (SNP) markers to support a genetics-based capture-mark-recapture (CMR) project implemented for the management of Pacific walrus (Odobenus rosmarus divergens). Using a combination of Restriction-site Associated DNA sequencing (RADSeq) and genome resequencing, 57,504 single nucleotide variants were identifi...

The kin structure of a species at relatively fine spatial scales impacts broad-scale patterns in genetic structure at the population level. However, kin structure rarely has been elucidated for migratory marine mammals. The Pacific walrus (Odobenus rosmarus divergens) exhibits migratory behavior linked to seasonal patterns in sea ice dynamics. Cons...

Thirteen microsatellite loci were used to address three hypotheses regarding genetic diversity in the humpback whitefish Coregonus clupeaformis complex in Alaska. The test results provided further insight into the factors influencing C. clupeaformis complex population structure and level of genetic variation. First, the microsatellite data did not...

We examined the time of origin and genetic diversity of native Kokanee, the nonanadromous ecotype of Sockeye Salmon Oncorhynchus nerka, from three isolated lakes in the Katmai National Park and Preserve in southwest Alaska. These Kokanee evolved independently from Sockeye Salmon when migration barriers arose, blocking ocean access. We used informat...

[This corrects the article DOI: 10.1371/journal.pone.0162277.].

Error-tolerant likelihood-based match calling presents a promising technique to accurately identify recapture events in genetic mark–recapture studies by combining probabilities of latent genotypes and probabilities of observed genotypes, which may contain genotyping errors. Combined with clustering algorithms to group samples into sets of recaptur...

Supplementary Materials are combined into a single .pdf document, with the following contents: Supplement 1: Detail of the error-tolerant likelihood-based match calling and sample clustering approach Supplement 2: R script to implement the error-tolerant likelihood-based match calling model and sample clustering algorithms: MSATs Supplement 3: R sc...

The endangered fountain darter Etheostoma fonticola is found only in the Comal and San Marcos rivers in the Guadalupe River basin in central Texas, USA. Comal River fountain darters were believed to be extirpated following a severe drought in the 1950s and were reintroduced in the early 1970s using 457 darters from the San Marcos River. In this stu...

Determining the success of invasive species eradication efforts is challenging because populations at very low abundance are difficult to detect. Environmental DNA (eDNA) sampling has recently emerged as a powerful tool for detecting rare aquatic animals; however, detectable fragments of DNA can persist over time despite absence of the targeted tax...

Table A. Water quality data of lakes used in the caged and carcass experiments. Table B. eDNA detection and PCR results for the caged, carcass and rotenone experiments. Table C. Gillnetting data from the pre and post-rotenone treated lakes. (DOCX)

U.S. Fish and Wildlife Service;Endangered Species Act

Appendix A. Peer‐reviewed publications produced by U.S. Fish and Wildlife genetics staff between 2005 and 2015.

We agree with Shafer et al. [1] that there is a need for well-documented case studies of the application of genomics in conservation and management as well as increased communication between academics and natural resource managers. However, we challenge Shafer et al.’s [1] relatively pessimistic assertion that ‘conservation genomics is far from see...

We developed and evaluated three qPCR assays for detecting environmental DNA from northern pike (Esox lucius). The assays target the cytochrome oxidase 1 (EluCOI), control region (EluCR), and cytochrome b (EluCytB) genes of the mitochondrial DNA. Target specificity, assessed using the fluorescence signal (at 45 cycles) to noise (at 1 cycle) ratio (...

We investigate adaptive resource polymorphism in kokanee (Oncorhynchus nerka) from Jo-Jo Lake, Alaska, by determin- ing whether previously observed niche expansion occurs at the population or individual level. Utilizing morphological, genetic, and stable isotope techniques, we found no evidence of discrete trophic morphotypes as previously describe...

Sex is determined genetically in most fishes, but the gene responsible for sex determination is not known for the vast majority of fish species, including Chinook Salmon Oncorhynchus tshawytscha. The purpose of this study was to characterize a putative sex-determining gene (“sexually dimorphic on the Y-chromosome” [sdY] gene) in Chinook Salmon and...

Lake trout Salvelinus namaycush is a slow-growing, late-maturing, cold-water-adapted species whose native distribution is described by the glaciated regions of North America. Southwestern Alaska, the western limit of the species range, has undergone repeated episodes of glacial advance and retreat. In this study, lake trout were sampled from 15 lak...

One of the challenges of monitoring and controlling invasive fish species is that of identifying their presence. The use of genetic assays to evaluate environmental DNA (eDNA) from water samples is emerging as a highly sensitive alternative with low environmental impact compared to traditional monitoring methods that depend on live capture. In this...

Molecular markers with inadequate power to discriminate among individuals can lead to false recaptures (shadows), and inaccurate genotyping can lead to missed recaptures (ghosts), potentially biasing genetic mark–recapture estimates. We used simulations to examine the impact of microsatellite (MSAT) and single nucleotide polymorphism (SNP) marker-s...

Kokanee, the non-anadromous and less common form of sockeye salmon, Oncorhynchus nerka, reside in lakes and in their native range generally occur near populations of sockeye salmon. Studies examining the genetic relationship of kokanee and sockeye indicate that geographically proximate populations of the two forms are genetically distinct but are m...

Estimation of genetic population structure, diversity, and effective population size (Ne) is important for defining meaningful conservation units and assessing genetic health. Recent conservation concerns in Alaska have highlighted the need for research on Eulachon Thaleichthys pacificus, a species about which relatively little is known. Therefore,...

Chinook salmon Oncorhynchus tshawytscha support important subsistence and commercial fisheries throughout the Yukon River. Low returns and diverse user groups have made management of these fisheries contentious and have necessitated information on the origin of the spawning migration and harvest. Here we compare estimates of individual assignment a...

This article documents the addition of 299 microsatellite marker loci and nine pairs of single-nucleotide polymorphism (SNP) EPIC primers to the Molecular Ecology Resources (MER) Database. Loci were developed for the following species: Alosa pseudoharengus, Alosa aestivalis, Aphis spiraecola, Argopecten purpuratus, Coreoleuciscus splendidus, Garra...

Following glacial recession in southeast Alaska, waterfalls created by isostatic rebound have isolated numerous replicate populations of coastal cutthroat trout (Oncorhynchus clarkii clarkii) in short coastal streams. These replicate isolated populations offer an unusual opportunity to examine factors associated with the maintenance of genetic dive...

Yukon River chum salmon Oncorhynchus keta are managed under the Pacific Salmon Treaty (PST), which requires conservation and equitable sharing of this fishery resource by the USA and Canada. Fall chum salmon are of special concern because they spawn in both the United States and Canada, and the focus of the PST is on Canadian-origin salmon. Yukon R...

Adult Chinook salmon Oncorhynchus tshawytscha navigate in river systems using olfactory cues that may be influenced by hydrologic factors such as flow and the number, size and spatial distribution of tributaries. Thus, river hydrology may influence both homing success and the level of straying (gene flow), which in turn influences population struct...

We demonstrate an efficient model for standardizing microsatellite DNA data among laboratories studying Oncorhynchus mykiss. Eight laboratories standardized 13 microsatellite loci following allele nomenclature of a central laboratory (average inter-laboratory genotyping concordance >98%). Following this central model, we have currently standardized...

Herein we describe the development of eight microsatellite markers for the northern sea otter, Enhydralutriskenyoni. A total of 45 primer pairs were developed and screened from enriched AAAT, CATC, TACA, and TAGA libraries derived from genomic DNA of E.lutriskenyoni. Of these, eight amplified successfully. The average observed heterozygosity, expec...

Coregonine fishes have a circumpolar distribution in the Arctic and sub-Arctic Northern Hemisphere. This subfamily of Salmonidae consists of three genera: Prosopium, Stenodus and Coregonus, including over 30 species. Many species overlap spatially and are difficult to distinguish based on morphological characteristics, especially as larvae or juven...

We used 20 microsatellite loci to compare genetic diversity and patterns of isolation-by-distance among three groups of chum salmon (Oncorhynchus keta) from two physically distinct watersheds in western Alaska, USA. The results were consistent with the hypothesis that gene flow decreases as the complexity of the hydrographic system increases. Speci...

In a cooperative project among three agencies, variation at 30 microsatellite loci was surveyed for 19 populations of Chinook salmon Oncorhynchus tshawytscha from the Yukon River. The observed number of alleles per locus ranged from 2 to 63. Loci with a greater number of alleles displayed lower genetic differentiation index (FST) values, but loci w...

An international multi-laboratory project was conducted to develop a standardized DNA database for Chinook salmon (Oncorhynchus tshawytscha). This project was in response to the needs of the Chinook Technical Committee of the Pacific Salmon Commission to identify stock composition of Chinook salmon caught in fisheries during their oceanic migration...

The population structure of fall-run Yukon River chum salmon Oncorhynchus keta has been studied previously using allozyme, microsatellite, and mitochondrial markers. However, genetically similar populations from tributaries near the U.S.-Canadian border render mixed-stock analyses (MSAs) difficult in the fisheries from lower portions of the Yukon R...

We surveyed seven regions of the mitochondrial DNA (mtDNA) genome for restriction site variation to investigate the evolution of genetic variability in chum salmon Oncorhynchus keta from the Yukon River. Chum salmon from other Alaska regions were also analyzed to provide context for mtDNA variation. No divergence was observed in mtDNA haplotype fre...

Abstract The management,of Yukon River chum salmon fisheries is difficult because of the need to address a variety of complex issues, such as meeting escapements, while still providing harvest opportunities in a mixed-stock and mixed-spe- cies fishery . Yukon River chum,salmon were assayed for genetic variation at

A sex-specific genetic marker (growth hormone pseudogene) and age-at-maturation data were used to infer the cause of male-biased phenotypic sex ratios in adult chinook salmon Oncorhynchus tshawytscha from the Kwethluk and Tuluksak Rivers, south-west Alaska. The results showed that: (1) adult genetic and phenotypic sex ratios were similar and were m...

Genetic differentiation of Dolly Varden char Salvelinus malma Walbaum from the Asian and North American Pacific coasts was studied. We examined restriction fragment length polymorphism of three mitochondrial DNA (mtDNA) fragments amplified in polymerase chain reaction, which encoded four NADH dehydrogenase subunits, the cytochrome b gene, and a D-l...

We describe the genetic stock structure of Dolly Varden, Salvelinus malma, in Norton and Kotzebue Sounds to develop a method to quantify contributions of Dolly Varden stocks harvested in subsistence fi sheries in the Wulik River. We surveyed genetic variation at seven microsatellite loci in 12 population sam- ples from Norton and Kotzebue Sounds an...

We used microsatellite and mitochondri-al DNA–restriction fragment length polymorphism (mtDNA–RFLP) analyses to test the hypothesis that chum salmon Oncorhynchus keta and coho salmon O. kisutch in the Yukon River, Alaska, exhibit population structure at differing spatial scales. If the hypothesis is true, then the risk of losing genetic diversity b...

The antagonistic pleiotropy theory of senescence postulates genes or traits that have opposite effects on early-life and late-life performances. Because selection is generally weaker late in life, genes or traits that improve early-life performance but impair late-life performance should come to predominate. Variation in the strength of age-specifi...