Data from: Population genomics of natural and experimental populations of guppies (Poecilia reticulata)

Convergent evolution represents one of the best lines of evidence for adaptation, but few cases of phenotypic convergence are understood at the genetic level. Guppies inhabiting the Northern Mountain Range of Trinidad provide a classic example of phenotypic convergent evolution, where adaptation to low or high predation environments has been found for a variety of traits. A major advantage of this system is the possibility of long-term experimental studies in nature, including transplantation from high to low predation sites. We used genome scans of guppies from three natural high and low predation populations and from two experimentally established populations and their sources to examine whether phenotypic convergent evolution leaves footprints at the genome level. We used population genetic modeling approaches to reconstruct the demographic history and migration among sampled populations. Naturally colonized low predation populations had signatures of increased effective population size since colonization, while introduction populations had signatures of decreased effective population size. Only a small number of regions across the genome had signatures of selection in all natural populations. However, the two experimental populations shared many genomic regions under apparent selection, more than expected by chance. This overlap coupled with a population decrease since introduction provides evidence for convergent selection occurring in the two introduction populations. The lack of genetic convergence in the natural populations suggests that convergent evolution is lacking in these populations or that the effects of selection become difficult to detect after a long time period.

趋同演化（Convergent evolution）是适应性进化的最佳证据之一，但目前在遗传层面得到阐明的表型趋同案例仍寥寥无几。栖息于特立尼达北部山脉的孔雀鱼是表型趋同演化的经典研究体系：该体系中，多种性状均已被证实存在对低捕食压力或高捕食压力环境的适应性分化。该研究体系的一大显著优势在于可开展长期野外实验研究，包括将孔雀鱼从高捕食压力栖息地移植至低捕食压力栖息地的操控实验。本研究对来自3组天然高/低捕食压力种群、2组人工建立种群及其源种群的孔雀鱼开展全基因组扫描，以探究表型趋同演化是否会在基因组层面留下特征性印记。研究采用种群遗传学建模方法，重构了采样种群的种群历史动态与基因流模式。天然定植的低捕食压力种群自定植以来呈现有效种群规模扩大的遗传特征，而人工引入种群则表现出有效种群规模缩减的信号。仅在少数基因组区域检测到所有天然种群共有的选择印记。但两个人工实验种群共享了大量处于选择作用下的基因组区域，这一重叠程度远超随机预期。这一基因组区域的重叠，结合人工引入后种群规模的缩减现象，为两个引入种群存在趋同选择作用提供了实证依据。天然种群未表现出遗传趋同的现象，这提示两类种群间要么不存在趋同演化，要么经历长期演化后选择作用的信号已难以被检测到。