Evaluating the ability of Bayesian clustering methods to detect hybridization and introgression using an empirical red wolf data set

Bohling, Justin H.; Adams, Jennifer R.; Waits, Lisette P.

doi:10.1111/mec.12109

Cited by 52 publications

(82 citation statements)

References 50 publications

(70 reference statements)

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“…As observed by Bohling et al . [25], S tructure seems better than BAPS to describe an admixed individual, but it cannot assure that an individual is of pure lineage.…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity and Conservation of the Prespa Trout in the Balkans

Berrebi

Tougard

Dubois

et al. 2013

IJMS

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The Balkans are known to have a high level of biodiversity and endemism. No less than 15 taxa have been recorded in salmonids of the Salmo genus. Among them, the Prespa trout is found in only four river systems flowing into Lake Macro Prespa, three in the Former Yugoslav Republic of Macedonia and one in Greece. This is the first comprehensive survey of all streams located within the Macro Prespa Basin, encompassing the whole taxon range. A large genetic sample of 536 Prespa trout was collected mainly between 2005 and 2007. The sampling included 59 individuals from the Golema river system, 93 from the Kranska, 260 from the Brajcinska, 119 from the Agios Germanos, and five individuals from the lake itself. These specimens were analyzed with six microsatellite markers and by sequencing the mitochondrial control region. Nuclear data were examined through multidimensional analysis and assignment tests. Five clusters were detected by assignment: Golema, Kranska, Brajcinska upstream, Rzanska Brajcinska tributary and Brajcinska downstream. Most of these river systems thus hosted differentiated Prespa trout populations (with past gene flows likely dating before the construction of dams), except Agios Germanos, which was found to be composed of 5% to 32% of each cluster. Among the five trout individuals from the lake, four originated from Kranska River and one was admixed. Supported parsimonious hypotheses are proposed to explain these specificities. Conservation of this endemic taxon should take these results into account. No translocation should be performed between different tributaries of the lake and preservation of the Brajcinska populations should address the upstream-downstream differentiation described.

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“…As observed by Bohling et al . [25], S tructure seems better than BAPS to describe an admixed individual, but it cannot assure that an individual is of pure lineage.…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity and Conservation of the Prespa Trout in the Balkans

Berrebi

Tougard

Dubois

et al. 2013

IJMS

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“…A3). The higher power of Structure to detect genetic pollution compared to BAPS has been previously noted by Bohling et al (2013). We took advantage of detailed background knowledge on the genetic make-up of the two parental species involved.…”

Section: Hybridization On the Veluwementioning

confidence: 99%

Genetic pollution of a threatened native crested newt species through hybridization with an invasive congener in the Netherlands

Meilink

Arntzen

Delft³

et al. 2015

Biological Conservation

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a b s t r a c tGenetic pollution of a native species through hybridization with an invasive species poses an insidious conservation threat. To expose genetic pollution, molecular methods employing multilocus data are required. We present a case study of genetic pollution via hybridization of a native crested newt species, Triturus cristatus, by the invasive Triturus carnifex on the Veluwe in the Netherlands. We sequenced 50 nuclear markers by next generation sequencing and one mitochondrial marker by Sanger sequencing for four populations from the native range of both parent species and eleven ponds on the Veluwe. We use three population genetic approaches (HIest, BAPS and Structure) to determine the genetic composition of the Veluwe newts based on all nuclear markers, a subset of 18 diagnostic markers and the complementary 32 non-diagnostic markers, with and without parental populations. BAPS underestimates genetic pollution, whereas Structure is comparatively accurate compared to HIest, although Structure's relative advantage decreases with the diagnosticity of the markers. Data simulation confirms these findings. Genetic composition of the Veluwe ponds ranges from completely native, via different degrees of genetic admixture, to completely invasive. The observed hybrid zone appears to be bimodal, suggesting negative selection against hybrids. A genetic footprint of the native species is present in invasive populations, evidencing that the invasive locally replaced the native species. Genetic pollution is currently confined to a small area, but the possibility of further expansion cannot be excluded. Removal of genetic pollution will not be easy. We emphasize the need for legal guidance to manage genetic pollution.

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“…v.74, n.6, p.443-449, November/December 2017 hybridization occurs (Boecklen and Howard, 1997;Sanz et al, 2008;Hashimoto et al, 2014). Tests using different numbers of markers have demonstrated that the variation in these numbers is directly related to the differentiation between loci among parental species (Sanz et al, 2006;Bohling et al, 2013); that is, the greater the difference, the smaller the number of markers required in the analysis. This was confirmed in this study, where the markers were 100 % fixed between species and were useful for detecting even introgressive hybridization.…”

Section: Discussionmentioning

confidence: 99%

Imputation of genetic composition for missing pedigree data in Serrasalmidae using morphometric data

Costa

Balestre

Botelho

et al. 2017

Sci. agric. (Piracicaba, Braz.)

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This study aimed to impute the genetic makeup of individual fishes of Serrasalmidae family on the basis of body weight and morphometric measurements. Eighty-three juveniles, belonging to the genetic groups Pacu, Pirapitinga, Tambaqui, Tambacu, Tambatinga, Patinga, Paqui and Piraqui, were separated into 16 water tanks in a recirculation system, with two tanks per genetic group, where they remained until they reached 495 days of age. They were then weighed and analyzed according to the following morphometric parameters: Standard Length (SL), Head Length (HL), Body Height (BH), and Body Width (BW). The identity of each fish was confirmed with two SNPs and two mitochondrial markers. Two analyses were performed: one for the validating the imputation and another for imputing a genetic composition of animals considered to be advanced hybrids (post F1). In both analyses, we used linear mixed models with a mixture of normal distributions to impute the genetic makeup of the fish based on phenotype. We applied the mixed models method, whereby the environmental effects were estimated by the Empirical Best Linear Unbiased Estimator (EBLUE) and genetic effects are considered random, obtaining the Empirical Best Linear Unbiased Predictor (EBLUP) from the general (GCA) and the specific (SCA) combining ability effects. The results showed that validation of the genetic makeup imputation based on body weight can be used because of the strong correlation between the observed and imputed genotype. The fish classified as advanced hybrids had a genetic composition with a high probability of belonging to known genotypes and there was consistency in genotype imputation according to the different characteristics used.

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Evaluating the ability of Bayesian clustering methods to detect hybridization and introgression using an empirical red wolf data set

Cited by 52 publications

References 50 publications

Genetic Diversity and Conservation of the Prespa Trout in the Balkans

Genetic Diversity and Conservation of the Prespa Trout in the Balkans

Genetic pollution of a threatened native crested newt species through hybridization with an invasive congener in the Netherlands

Imputation of genetic composition for missing pedigree data in Serrasalmidae using morphometric data

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