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.

基于基因组扫描的选择检验方法可直接应用于自然种群，以研究表型分化背后的遗传与进化机制。我们对莫氏三湖慈鲷（Tropheus moorii）的三种不同地理分布色型开展了扩增片段长度多态性（Amplified Fragment Length Polymorphism，AFLP）基因组扫描，以评估现存的异域色型分化是否可由遗传漂变（Genetic Drift）解释，并定位可能参与色素图案形成的基因组区域标记。受试的三个色型栖息于坦噶尼喀湖南部相邻的湖岸区域，彼此之间被主要的生境屏障分隔开。基因组扫描结果显示，不同色型间存在显著的遗传结构，但固定有不同AFLP等位基因的位点比例极低。色型内高水平的多态性表明，色型分化并非仅由中性演化过程导致。离群位点检测方法（Outlier detection methods）在蓝色型与黄斑型的比较中，共鉴定出6个分化程度显著偏离中性预期的位点；在上述两种色型分别与红色型的比较中，各鉴定出5个不同的离群位点。鉴于莫氏三湖慈鲷的种群扩张及其遗传结构会导致离群位点检测方法易产生假阳性的选择信号，我们在两种色型之间的遗传与表型渐变群（cline）中，检验了离群位点等位基因与颜色表型之间的相关性。一个离群位点的等位基因频率分布确实与颜色位点的连锁关系相符。尽管面临种群结构与种群动态带来的诸多挑战，我们的研究结果仍支持在种群结构分化且近期发生种群扩张的自然种群中，谨慎应用基因组扫描方法开展趋异选择相关研究。