Genetic variation and effective population size in isolated populations of coastal cutthroat

Abstract 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 diversity. We used eight microsatellites to examine genetic variation within and differentiation among 12 population pairs sampled from above and below these natural migration barriers. Geological evidence indicated that the above-barrier populations have been isolated for 8,000-12,500 years. Genetic differentiation among below-barrier populations (F ST = 0.10, 95% C.I. 0.08-0.12) was similar to a previous study of more southern populations of this species. Above-barrier populations were highly differentiated from adjacent below-barrier populations (mean pairwise F ST = 0.28; SD 0.18) and multiple lines of evidence were consistent with asymmetric downstream gene flow that varied among streams. Each above-barrier population had reduced within-population genetic variation when compared to the adjacent belowbarrier population. Within-population genetic diversity was significantly correlated with the amount of available habitat in above-barrier sites. Increased genetic differentiation of above-barrier populations with lower genetic diversity suggests that genetic drift has been the primary cause of genetic divergence. Long-term estimates of N e based on loss of heterozygosity over the time since isolation were large (3,170; range 1,077-7,606) and established an upper limit for N e if drift were the only evolutionary process responsible for loss of genetic diversity. However, it is likely that a combination of mutation, selection, and gene flow have also contributed to the genetic diversity of above-barrier populations. Contemporary above-barrier N e estimates were much smaller than long-term N e estimates, not correlated with withinpopulation genetic diversity, and not consistent with the amount of genetic variation retained, given the approximate 10,000-year period of isolation. The populations isolated by waterfalls in this study that occur in larger stream networks have retained substantial genetic variation, which suggests that the amount of habitat in headwater streams is an important consideration for maintaining the evolutionary potential of isolated populations

Development of a Standardized DNA Database for Chinook Salmon

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 migrations. Nine genetics laboratories identified 13 microsatellite loci that could be reproducibly assayed in each of the laboratories. To test that the loci were reproducible among laboratories, blind tests were conducted to verify scoring consistency for the nearly 500 total alleles. Once standardized, a dataset of over 16,000 Chinook salmon representing 110 putative populations was constructed ranging throughout the area of interest of the Pacific Salmon Commission from Southeast Alaska to the Sacramento River in California. The dataset differentiates the major known genetic lineages of Chinook salmon and provides a tool for genetic stock identification of samples collected from mixed fisheries. A diverse group of scientists representing the disciplines of fishery management, genetics, fishery administration, population dynamics, and sampling theory are now developing recommendations for the integration of these genetic data into ocean salmon management.Original Abstract: Se realizo un proyecto internacional con la participation de diversos laboratorios con la finalidad de desarrollar una base de datos estandarizada de DNA para el salmon rey (Oncorhynchus tshawytscha). Dicho proyecto surgi6 como respuesta a las necesidades del Comite Tecnico Chinook de la Comision del Salmon del Pacifico para identificar la composition poblacional del salmon rey que es capturado por la pesqueria durante su migration. Un total de nueve laboratorios de analisis geneticos identificaron y reprodujeron cada uno 13 loci microsatelites. Con el objeto de probar que dichos loci fueran reproducibles entre laboratorios, se condujeron pruebas anonimas para verificar la consistencia de casi 500 alelos. Una vez estandarizada, se construyo una base de datos construida con information proveniente de mas de 16,000 salmones que representan 110 poblaciones putativas distribuidas a lo largo del area de interes de la Comision del Salm6n del Pacifico, del sureste de Alaska hasta el Rio Sacramento, California. La base de datos sirve tanto para identificar gene'ticamente los distintos stocks de salmon rey a partir de muestras combinadas provenientes de la pesqueria como para diferenciar el linaje genetico conocido mas importante de esta especie. En la actualidad, un importante grupo de cientificos especializados en disciplinas como el manejo y administracion de pesquerias, genetica, dinamica poblacional y teoria del muestreo estan desarrollando recomendaciones para que esta base de datos geneticos se incorpore en el manejo del salmon

Alaskan coho salmon genotypes

Genotype data from nine microsatellite loci for 2584 coho salmon in 32 locations in Alaska. This data file is formatted for use in the computer program GenePop v4.0. The genotypes in this file have NOT been standardized with other laboratories -- see readme file for further information

Data from: Contemporary factors influencing genetic diversity in the Alaska humpback whitefish Coregonus clupeaformis complex

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, themicrosatellite data did not provide evidence of two spatially distinct Beringian and Eurasian refugial groups as revealed in previous phylogeographic analyses ofmitochondrialDNAvari- ation. Rather, the population structure inferred from the microsatellite variation appears to reveal the influence of factors on amore recent time scale, including gene flowamong the refugial groups and iso- lation of some anadromous and freshwater resident populations. Second, anadromous C. clupeaformis complex collections exhibited higher intra-population genetic diversity than freshwater resident col- lections. This outcome is consistent with previous meta analyses suggesting that freshwater resident populations probably have smaller historical effective population sizes and less conspecific gene flow because the habitat tends to be smaller and supports fewer and smaller populations. Finally, the analy- sis of contemporary immigration rates was consistent with, but did not provide statistical support for, the hypothesis that gene flow among anadromous C. clupeaformis complex populations along coastal Alaska is influenced by the Alaska Coastal Current. Further studies are needed to evaluate gene flow among coastal Alaska C. clupeaformis complex populations. Publishe

Data from: Patterns of intra- and inter-population genetic diversity in Alaskan coho salmon: implications for conservation

Little is known about the genetic diversity of coho salmon in Alaska, although this area represents half of the species’ North American range. In this study, nine microsatellite loci were used to genotype 32 putative coho salmon populations from seven regions of Alaska. The primary objectives were to estimate and evaluate the degree and spatial distribution of neutral genetic diversity within and among populations of Alaskan coho salmon. Genetic analysis yielded four results that provide insight into forces influencing genetic diversity in Alaskan coho salmon and have important conservation implications: 1) significant population differentiation was found within each region; 2) the degree of differentiation (FST = 0.099) among populations was as large or larger than that reported for other Pacific salmon species in Alaska; 3) phenetic clustering of populations showed weak geographic concordance; 4) strong genetic isolation by distance was only apparent at the finest geographic scale (within a drainage). These results suggest that coho salmon populations are small relative to populations of other Pacific salmon, and the genetic diversity within and among coho salmon populations is influenced primarily by genetic drift, and not gene flow. Resource management and conservation actions affecting coho salmon in Alaska must recognize that the populations are generally small, isolated, and probably exhibit local adaptation to different spawning and freshwater rearing habitats. These factors justify managing and conserving Alaskan coho salmon at a fine geographic scale

Potential of Environmental DNA to Evaluate Northern Pike (Esox lucius) Eradication Efforts: An Experimental Test and Case Study.

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 taxa and can therefore complicate eDNA sampling after an eradication event. This complication is a large concern for fish eradication efforts in lakes since killed fish can sink to the bottom and slowly decay. DNA released from these carcasses may remain detectable for long periods. Here, we evaluated the efficacy of eDNA sampling to detect invasive Northern pike (Esox lucius) following piscicide eradication efforts in southcentral Alaskan lakes. We used field observations and experiments to test the sensitivity of our Northern pike eDNA assay and to evaluate the persistence of detectable DNA emitted from Northern pike carcasses. We then used eDNA sampling and traditional sampling (i.e., gillnets) to test for presence of Northern pike in four lakes subjected to a piscicide-treatment designed to eradicate this species. We found that our assay could detect an abundant, free-roaming population of Northern pike and could also detect low-densities of Northern pike held in cages. For these caged Northern pike, probability of detection decreased with distance from the cage. We then stocked three lakes with Northern pike carcasses and collected eDNA samples 7, 35 and 70 days post-stocking. We detected DNA at 7 and 35 days, but not at 70 days. Finally, we collected eDNA samples ~ 230 days after four lakes were subjected to piscicide-treatments and detected Northern pike DNA in 3 of 179 samples, with a single detection at each of three lakes, though we did not catch any Northern pike in gillnets. Taken together, we found that eDNA can help to inform eradication efforts if used in conjunction with multiple lines of inquiry and sampling is delayed long enough to allow full degradation of DNA in the water

Table 1

Location, site abbreviation (Abbr), sample year, sample size (n), and life stage (A = adult, J = juvenile) of fish sampled from 32 putative coho salmon populations in seven regions of Alaska

Alaskan coho salmon genotypes

Genotype data from nine microsatellite loci for 2584 coho salmon in 32 locations in Alaska. This data file is formatted for use in the computer program GenePop v4.0. The genotypes in this file have NOT been standardized with other laboratories -- see readme file for further information

Correction: Potential of Environmental DNA to Evaluate Northern Pike (Esox lucius) Eradication Efforts: An Experimental Test and Case Study.

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

Microsatellite genotypes for fountain darters

Genotype data from 23 microsatellite loci used to evaluate genetic diversity in 327 fountain darters (E. fonticola) from 16 sample locations in the Comal (CR) and San Marcos (SMR) rivers, Guadalupe River Basin, Texas, USA. The genotype data is formatted for use in the computer program FSTAT