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测（Genome scan-based tests for selection）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。我们对慈鲷（cichlid fish）莫氏丽体鱼（Tropheus moorii）的三种不同地理色彩形态开展了扩增片段长度多态性（Amplified Fragment Length Polymorphism, AFLP）基因组扫描，旨在评估现存的异域色彩模式分化（allopatric colour pattern differentiation）能否通过遗传漂变（genetic drift）得以解释，并定位可能参与色彩模式形成的基因组区域相关标记。所测试的色彩形态种群栖息于坦噶尼喀湖（Lake Tanganyika）南部相邻的湖岸区域，彼此间被主要的生境屏障分隔。基因组扫描结果显示，不同形态种群间存在显著的遗传结构，但在不同形态中被固定为不同AFLP等位基因的位点比例极低。种群内部极高的多态性水平表明，色彩模式分化并非仅由中性进化过程（neutral processes）导致。异常值检测（outlier detection）方法在蓝体色与黄斑体色形态的对比分析中，鉴定出6个分化程度过量的位点；而在这两种形态分别与红色形态的对比中，各鉴定出5个不同的异常值位点。鉴于莫氏丽体鱼的种群扩张与遗传结构易使异常值检测方法出现假阳性的选择信号，我们在两种形态间的遗传与表型渐变群（phenotypic cline）中，分析了异常值位点等位基因与色彩表型的相关性。某一异常值位点的等位基因频率分布确实与色彩位点存在连锁关联。尽管种群结构与种群动态带来了诸多研究挑战，但本研究结果仍支持：在结构化种群（subdivided population）且近期经历种群扩张的种群中，可谨慎应用基因组扫描开展歧化选择（divergent selection）相关研究。