Genetic diversity and population structure of domestic brown trout (Salmo trutta) in France

Animals in captivity are subject to similar evolutionary forces that act on natural populations, which can facilitate the generation of population genetic structure. Understanding the extent of genetic differentiation among captive populations provides insights into industry practices and the domestication process. We investigated the genetic structure of domestic brown trout (Salmo trutta) in France by surveying fish collected from 20 fish farms. Using microsatellite markers, we calculated basic measures of genetic diversity and differentiation among these various farms. We also evaluated population structure using tree-based approaches, model-based clustering methods, and ordination techniques. Differences in genetic diversity reflected founding histories and source stocks among the fish farms. Fish farms that raise trout originating from Mediterranean watersheds had lower levels of genetic diversity and much higher divergence than populations of Atlantic origin. Stocks believed to originate fromthe common Atlantic-based trout strain demonstrated low-levels of population structure. We observed fish of mixed ancestry in some fish farms and the presence of multiple genetic stocks within the same facility. Our findings reveal patterns of genetic structure that reflect differences in founding practices and movement of individuals and strains between fish farms. Such findings have consequences for fisheriesmanagers stocking natural ecosystems with captive-reared fish, biologists attempting to understand the interactions between wild and domestic brown trout, and fish farmers involved in stocking or restoration activities

Data from: Population and genetic outcomes 20 years after reintroducing bobcats (Lynx rufus) to Cumberland Island, Georgia USA

In 1988–1989, 32 bobcats Lynx rufus were reintroduced to Cumberland Island (CUIS), Georgia, USA, from which they had previously been extirpated. They were monitored intensively for 3 years immediately post-reintroduction, but no estimation of the size or genetic diversity of the population had been conducted in over 20 years since reintroduction. We returned to CUIS in 2012 to estimate abundance and effective population size of the present-day population, as well as to quantify genetic diversity and inbreeding. We amplified 12 nuclear microsatellite loci from DNA isolated from scats to establish genetic profiles to identify individuals. We used spatially explicit capture–recapture population estimation to estimate abundance. From nine unique genetic profiles, we estimate a population size of 14.4 (SE = 3.052) bobcats, with an effective population size (Ne) of 5–8 breeding individuals. This is consistent with predictions of a population viability analysis conducted at the time of reintroduction, which estimated the population would average 12–13 bobcats after 10 years. We identified several pairs of related bobcats (parent-offspring and full siblings), but ~75% of the pairwise comparisons were typical of unrelated individuals, and only one individual appeared inbred. Despite the small population size and other indications that it has likely experienced a genetic bottleneck, levels of genetic diversity in the CUIS bobcat population remain high compared to other mammalian carnivores. The reintroduction of bobcats to CUIS provides an opportunity to study changes in genetic diversity in an insular population without risk to this common species. Opportunities for natural immigration to the island are limited; therefore, continued monitoring and supplemental bobcat reintroductions could be used to evaluate the effect of different management strategies to maintain genetic diversity and population viability. The successful reintroduction and maintenance of a bobcat population on CUIS illustrates the suitability of translocation as a management tool for re-establishing felid populations

Cumberland Island Genotypes

Microsatellite genotypes of all bobcat scats collected on Cumberland Island (1st spreadsheet tab), and summary of genotypes of 9 bobcats that could be individually identified (2nd spreadsheet tab). Amplification conditions are described in primary manuscript (Diefenbach et al.) and in associated supplementary information

BAPS_input_files

These files are GenePop files that were used for the BAPS analyses. Each file reflects whether it contains 'Known' or 'Unknown' individuals incorporated in the BAPS analysis, along with the year and training set. Those with just a year in the file name are for the 'Update' training set, whereas those ending with '12years' were part of the '12 years' training set

STRUCTURE_input_files

This contains all the input files used for the STRUCTURE analyses. Each file represents a separate year and training set. See our publication for more details. The ReadMe file contains the details of the parameter settings and input files

Data from: Evaluating the ability of Bayesian clustering methods to detect hybridization and introgression using an empirical red wolf dataset

Bayesian clustering methods have emerged as a popular tool for assessing hybridization using genetic markers. Simulation studies have shown these methods perform well under certain conditions; however, these methods have not been evaluated using empirical datasets with individuals of known ancestry. We evaluated the performance of two Bayesian clustering programs, BAPS and STRUCTURE, with genetic data from a reintroduced red wolf (Canis rufus) population in North Carolina, USA. Red wolves hybridize with coyotes (C. latrans), and a single hybridization event resulted in introgression of coyote genes into the red wolf population. A detailed pedigree has been reconstructed for the wild red wolf population that includes individuals of 50–100% red wolf ancestry, providing an ideal case study for evaluating the ability of these methods to estimate admixture. Using 17 microsatellite loci, we tested the programs using different training set compositions and varying numbers of loci. STRUCTURE was more likely than BAPS to detect an admixed genotype and correctly estimate an individual’s true ancestry composition. However, STRUCTURE was more likely to misclassify a pure individual as a hybrid. Both programs were outperformed by a maximum-likelihood-based test designed specifically for this system, which never misclassified a hybrid (50-75% red wolf) as a red wolf or vice versa. Both training set composition and the number of loci had an impact on accuracy but their relative importance varied depending on the program. Our findings demonstrate the importance of evaluating methods used for evaluating hybridization in the context of endangered species management

Canid_genotypes_Dryad

This file contains microsatellite genotypes of all individuals used in the simulation study. The first column contains the identification number for each individual. Column two indicates which group the individual was assigned to as part of our study (note: this matches the 'Founders' training set in our publication). The third column indicates whether the individual was included as a 'known' individual in the STRUCTURE analysis. A '1' indicates that an individual's genotype was included in estimating the allele frequencies, a '0' means is was not. All the remaining columns contain genotypic information, with each column containing genotyped alleles. There are two columns per microsatellite locus

Data and R code to estimate abundance

This zip folder contains: (1) file containing the locations of ID'd individuals on Cumberland Island; (2) the locations of transects (x-y of center of each 200-m segment); (3) shapefiles of island boundary (multiple files); (4) R code for spatially explicit capture-recapture population estimation (SECR) for abundanc

Individual_scat_locations

Tab-delimited text file containing individual canids detected via non-invasive genetic sampling and their geographic coordinates. The first column contains the identification code for each individual. The second column contains the identification code for the individual fecal (scat) sample from which those individuals were genotyped. The third column contains the year the sample was collected. The remaining columns contain information for the geographic coordinates, which are in UTM. Note that for UTM coordinates are for the northern hemisphere

Red_wolf_coyote_original_genotypes

GenePop file containing original genotypes used to simulate hybridization scenarios. The first population contains genotypes for coyotes captured in North Carolina and Virginia. The second population contains genotypes for the red wolves used to found the captive red wolf population