Genetic integrity of European grayling (Thymallus thymallus L. 1758) within the Vienne River drainage basin after five decades of stockings

European grayling of the upper Vienne River drainage basin represent the westernmost populations inside the natural distribution of the species. Since the 19th century, their extension across this sub-basin has been dramatically reduced by the harnessing of the river network for dams, initially serving mills but then hydroelectric power generation. Since the 1960s, local fishing authorities have attempted to compensate for these declines with stocking programs, but the efficiency of these efforts have never been accurately monitored. We aim to evaluate the genetic imprints of these stocking programs and thus provide an indirect measure of the long-term survival of stocked fish. Three target populations were analyzed at both mtDNA (Control Region) and nDNA levels (12 µSats), and compared to populations representative of surrounding drainage basins or fish farm facilities. Among 37 "wild" fish sequenced, only three control region haplotypes were identified, all belonging to the highly divergent Loire basin lineage. Two were specific to the Upper Vienne area, and one was observed in some individuals of the most downstream location, but previously described from the upper Allier sub-drainage. Microsatellite analysis of 87 "wild" fish also demonstrated a rather low diversity within each population (but typical for the Loire drainage) with all Upper Vienne individuals belonging to a single diagnosable unit. This genetic cluster was clearly distinct from all other samples including hatchery strains, which strongly supports its native origin. The only piece of evidence of a possible stocking contribution was the occurrence of the Allier haplotype, but it cannot be excluded that this haplotype was also native to this reach of river. The total lack of genetic impact of five decades of stocking deeply questions the efficacy of this management approach, at least in a regional context

Data from: AFLP genome scans suggest divergent selection on colour patterning in allopatric colour morphs of a cichlid fish

Genome scan-based tests for selection are directly applicable to natural populations to study the genetic and evolutionary mechanisms behind phenotypic differentiation. We conducted AFLP genome scans in three distinct geographic colour morphs of the cichlid fish Tropheus moorii to assess whether the extant, allopatric colour pattern differentiation can be explained by drift and to identify markers mapping to genomic regions possibly involved in colour patterning. The tested morphs occupy adjacent shore sections in southern Lake Tanganyika and are separated from each other by major habitat barriers. The genome scans revealed significant genetic structure between morphs, but a very low proportion of loci fixed for alternative AFLP alleles in different morphs. This high level of polymorphism within morphs suggested that colour pattern differentiation did not result exclusively from neutral processes. Outlier detection methods identified six loci with excess differentiation in the comparison between a bluish and a yellow-blotch morph and five different outlier loci in comparisons of each of these morphs with a red morph. As population expansions and the genetic structure of Tropheus make the outlier approach prone to false-positive signals of selection, we examined the correlation between outlier locus alleles and colour phenotypes in a genetic and phenotypic cline between two morphs. Distributions of allele frequencies at one outlier locus were indeed consistent with linkage to a colour locus. Despite the challenges posed by population structure and demography, our results encourage the cautious application of genome scans to studies of divergent selection in subdivided and recently expanded populations

Genetic integrity of European grayling (Thymallus thymallus L. 1758) population within the Vienne River drainage basin after five decades of stockings

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AFLP data

AFLP data for 269 individuals of Tropheus moorii (Cichlidae) from 12 populations. Sample IDs are composed of population name and sample number

Data from: Shifting barriers and phenotypic diversification by hybridisation

The establishment of hybrid taxa relies on reproductive isolation from the parental forms, typically achieved by ecological differentiation. Here, we present an alternative mechanism, in which shifts in the strength and location of dispersal barriers facilitate diversification by hybridisation. Our case study concerns the highly diverse, stenotopic rock-dwelling cichlids of the African Great Lakes, many of which display geographic colour pattern variation. The littoral habitat of these fish has repeatedly been restructured in the course of ancient lake level fluctuations. Genetic data and an experimental cross support the hybrid origin of a distinct yellow-coloured variant of Tropheus moorii from ancient admixture between two allopatric, red and bluish variants. Deficient assortative mating preferences imply that reproductive isolation continues to be contingent on geographic separation. Linking paleolimnological data with the establishment of the hybrid variant, we sketch a selectively neutral diversification process governed solely by rearrangements of dispersal barriers