The least cost path from landscape genetics to landscape genomics: challenges and opportunities to explore NGS data in a spatially explicit context

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An illustration of clines. X-axes correspond to position along geographic transects (ecological gradient) or hybrid indexes (genomic gradient) in the case of genomic cline analyses. (A) Illustration of the three parameters typically estimated in the use of geographic of genomic cline analysis. Cline slope is the estimate of the rate of allele frequency turnover at the steepest point in the cline. In genomic cline analysis this corresponds to the rate of introgression. Cline center corresponds to the point along the geographic transect or hybrid index at which allele frequency turnover is greatest. Cline width corresponds to the region along the gradient at which it's influence on allele frequency is greatest. (B) Three examples of clines. (i) A transect along which no selection appears to be acting, or the effects of gene flow are such that changes in allele frequency are purely a function of distance. In the case of genomic cline analyses, the loci under consideration appears to be favored equally in both parental taxa. (ii) A modest cline in which the allele favored by selection changes along the gradient. Given its shallower slope, selection may either be weaker, gene flow stronger (in the case of geographic transects) or the ecotone separating ends of the transect greater. (iii) A steep cline, often called a step cline. In the case of geographic clines, these are formed either by strong selection acting in favor of one allele along a sudden ecotone, or extremely limited gene flow along said ecotone. In the case of genomic clines, this may be due to heterozygote disadvantage, as in the case of reinforcement.
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