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.

用于选择检测的基因组扫描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。我们针对莫瑞慈鲷（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，以评估现存的异域分布色斑分化是否可由遗传漂变解释，并筛选出可能与色斑形成相关的基因组区域内的标记位点。受试的三个色型栖息于坦噶尼喀湖南部相邻的沿岸水域，彼此间被主要的生境屏障所分隔。基因组扫描结果显示，不同色型间存在显著的遗传结构，但仅存在极低比例的在不同色型中固定为不同AFLP等位基因的位点。色型内部较高的多态性水平表明，色斑分化并非仅由中性进化过程所导致。离群位点检测方法在蓝体色型与黄斑点色型的比较中，筛选出6个表现为过度分化的位点；而在这两种色型分别与红色色型的比较中，各筛选出5个不同的离群位点。鉴于拟丽鱼属（Tropheus）的种群扩张与遗传结构易使离群位点检测方法产生假阳性的选择信号，我们针对两种色型之间的遗传与表型梯度，分析了离群位点的等位基因与色斑表型之间的相关性。其中一个离群位点的等位基因频率分布，确实与色斑位点的连锁效应相符。尽管种群结构与种群动态带来了诸多研究挑战，本研究结果仍支持谨慎将基因组扫描方法应用于亚分化种群及近期扩张种群的歧化选择研究。