Efficiency of model‐based Bayesian methods for detecting hybrid individuals under different hybridization scenarios and with different numbers of loci

Vähä, Juha‐Pekka; Primmer, Craig R.

doi:10.1111/j.1365-294x.2005.02773.x

Cited by 801 publications

(805 citation statements)

References 44 publications

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“…Of the JDF12 fish, 14 (87.5%) individuals had similar ancestries as coastal fish, and two JDF12 individuals appeared to cluster with the Salish Sea sample. Only three fish (2.6% of total; one JDF12 and two SS12) may have had mixed ancestries between the coast and Salish Sea ( Q ≥ 0.10; Vähä & Primmer, 2006). …”

Section: Resultsmentioning

confidence: 99%

“…The optimal K ‐value was determined using the method of Evanno, Regnaut, and Goudet (2005) implemented by Structure Harvester (Earl & Vonholdt, 2012). Individuals with a Q < 0.9 of any one population were considered of mixed ancestry (Vähä & Primmer, 2006). Similar analyses in coastal samples only reproduced the isolation‐by‐distance pattern shown by other analyses and are not shown.…”

Section: Methodsmentioning

confidence: 99%

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Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)

Drinan

Gruenthal

Canino

et al. 2018

Evolutionary Applications

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The discernment of populations as management units is a fundamental prerequisite for sustainable exploitation of species. A lack of clear stock boundaries complicates not only the identification of spatial management units, but also the assessment of mixed fisheries by population assignment and mixed stock analysis. Many marine species, such as Pacific cod, are characterized by isolation by distance, showing significant differentiation but no clear stock boundaries. Here, we used restriction‐site‐associated DNA (RAD) sequencing to investigate population structure and assess power to genetically assign Pacific cod to putative populations of origin. Samples were collected across the species range in the eastern Pacific Ocean, from the Salish Sea to the Aleutian Islands. A total of 6,425 putative biallelic single nucleotide polymorphisms were identified from 276 individuals. We found a strong isolation‐by‐distance signal along coastlines that mirrored previous microsatellite results and pronounced genetic differentiation between coastal samples and those from the inland waters of the Salish Sea, with no evidence for hybridization between these two populations. Individual assignment success based on two methods was high overall (≥84%) but decreased from south to north. Assignment to geographic location of origin also was successful, with average distance between capture and assignment location of 220 km. Outlier analyses identified more loci potentially under selection along the coast than between Salish Sea and coastal samples, suggesting more diverse adaptation to latitudinal environmental factors than inshore vs. offshore environments. Our results confirm previous observations of sharp genetic differentiation of the Salish Sea population and isolation by distance along the coast, but also highlight the feasibility of using modern genomic techniques to inform stock boundaries and fisheries management in a low F ST marine species.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)

Drinan

Gruenthal

Canino

et al. 2018

Evolutionary Applications

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“…The causes of strongly variable introgression rates in different parts of Europe are not known, although historical factors (e.g., eradication of local wildcat populations and rapid expansion of free‐ranging domestic cats in Scotland) or landscape features (e.g., patch of forests intermixed with traditional agricultural fields in Hungary) could have had a role locally. Moreover, backcrossed cats are not easily identified by limited panels of microsatellite markers (Vähä and Primmer 2006), and local rates of introgression could have been underestimated. The use of more informative DNA markers (e.g., ancestral informative SNPs; Nussberger et al.…”

Section: Discussionmentioning

confidence: 99%

European wildcat populations are subdivided into five main biogeographic groups: consequences of Pleistocene climate changes or recent anthropogenic fragmentation?

Mattucci

Oliveira

Lyons

et al. 2015

Ecology and Evolution

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Extant populations of the European wildcat are fragmented across the continent, the likely consequence of recent extirpations due to habitat loss and over‐hunting. However, their underlying phylogeographic history has never been reconstructed. For testing the hypothesis that the European wildcat survived the Ice Age fragmented in Mediterranean refuges, we assayed the genetic variation at 31 microsatellites in 668 presumptive European wildcats sampled in 15 European countries. Moreover, to evaluate the extent of subspecies/population divergence and identify eventual wild × domestic cat hybrids, we genotyped 26 African wildcats from Sardinia and North Africa and 294 random‐bred domestic cats. Results of multivariate analyses and Bayesian clustering confirmed that the European wild and the domestic cats (plus the African wildcats) belong to two well‐differentiated clusters (average Ф ST = 0.159, rst = 0.392, P > 0.001; Analysis of molecular variance [AMOVA]). We identified from c. 5% to 10% cryptic hybrids in southern and central European populations. In contrast, wild‐living cats in Hungary and Scotland showed deep signatures of genetic admixture and introgression with domestic cats. The European wildcats are subdivided into five main genetic clusters (average Ф ST = 0.103, rst = 0.143, P > 0.001; AMOVA) corresponding to five biogeographic groups, respectively, distributed in the Iberian Peninsula, central Europe, central Germany, Italian Peninsula and the island of Sicily, and in north‐eastern Italy and northern Balkan regions (Dinaric Alps). Approximate Bayesian Computation simulations supported late Pleistocene–early Holocene population splittings (from c. 60 k to 10 k years ago), contemporary to the last Ice Age climatic changes. These results provide evidences for wildcat Mediterranean refuges in southwestern Europe, but the evolution history of eastern wildcat populations remains to be clarified. Historical genetic subdivisions suggest conservation strategies aimed at enhancing gene flow through the restoration of ecological corridors within each biogeographic units. Concomitantly, the risk of hybridization with free‐ranging domestic cats along corridor edges should be carefully monitored.

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“…'s (2005) statistic Δk as calculated by structure harvester (Earl and vonHoldt 2012). Pure northern individuals were then identified as having a q ≥ 0.90, pure southern as those having q ≤ 0.10, with all remaining individuals being characterized as admixed (0.10 < q < 0.90; Vaha and Primmer 2006). …”

Section: Methodsmentioning

confidence: 99%

Steep, coincident, and concordant clines in mitochondrial and nuclear‐encoded genes in a hybrid zone between subspecies of Atlantic killifish,Fundulus heteroclitus

McKenzie

Dhillon

Schulte

2016

Ecology and Evolution

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Steep genetic clines resulting from recent secondary contact between previously isolated taxa can either gradually erode over time or be stabilized by factors such as ecological selection or selection against hybrids. We used patterns of variation in 30 nuclear and two mitochondrial SNPs to examine the factors that could be involved in stabilizing clines across a hybrid zone between two subspecies of the Atlantic killifish, Fundulus heteroclitus. Increased heterozygote deficit and cytonuclear disequilibrium in populations near the center of the mtDNA cline suggest that some form of reproductive isolation such as assortative mating or selection against hybrids may be acting in this hybrid zone. However, only a small number of loci exhibited these signatures, suggesting locus‐specific, rather than genomewide, factors. Fourteen of the 32 loci surveyed had cline widths inconsistent with neutral expectations, with two SNPs in the mitochondrial genome exhibiting the steepest clines. Seven of the 12 putatively non‐neutral nuclear clines were for SNPs in genes related to oxidative metabolism. Among these putatively non‐neutral nuclear clines, SNPs in two nuclear‐encoded mitochondrial genes (SLC25A3 and HDDC2), as well as SNPs in the myoglobin, 40S ribosomal protein S17, and actin‐binding LIM protein genes, had clines that were coincident and concordant with the mitochondrial clines. When hybrid index was calculated using this subset of loci, the frequency distribution of hybrid indices for a population located at the mtDNA cline center was non‐unimodal, suggesting selection against advanced‐generation hybrids, possibly due to effects on processes involved in oxidative metabolism.

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Efficiency of model‐based Bayesian methods for detecting hybrid individuals under different hybridization scenarios and with different numbers of loci

Cited by 801 publications

References 44 publications

Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)

Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)

European wildcat populations are subdivided into five main biogeographic groups: consequences of Pleistocene climate changes or recent anthropogenic fragmentation?

Steep, coincident, and concordant clines in mitochondrial and nuclear‐encoded genes in a hybrid zone between subspecies of Atlantic killifish,Fundulus heteroclitus

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