Data from: Long-term balancing selection on chromosomal variants associated with crypsis in a stick insect

How polymorphisms are maintained within populations over long periods of time remains debated, because genetic drift and various forms of selection are expected to reduce variation. Here, we study the genetic architecture and maintenance of phenotypic morphs that confer crypsis in Timema cristinae stick insects, combining phenotypic information and genotyping-by-sequencing data from 1360 samples across 21 populations. We find two highly divergent chromosomal variants that span megabases of sequence and are associated with color polymorphism. We show that these variants exhibit strongly reduced effective recombination, are geographically widespread, and probably diverged millions of generations ago. We detect heterokaryotype excess and signs of balancing selection acting on these variants through the species’ history. A third chromosomal variant in the same genomic region likely evolved more recently from one of the two color variants and is associated with dorsal pattern polymorphism. Our results suggest that large-scale genetic variation associated with crypsis has been maintained for long periods of time by potentially complex processes of balancing selection.

长期以来，种群内部多态性（polymorphisms）如何在漫长时间尺度下得以维持始终是学界争议的议题，因为遗传漂变（genetic drift）与多种形式的选择理论上均会降低种群的遗传变异水平。本研究以克里斯蒂娜蒂姆竹节虫（Timema cristinae stick insects）为研究对象，结合表型信息与来自21个种群共1360份样本的测序分型（genotyping-by-sequencing）数据，探究其赋予拟态（crypsis）能力的表型形态的遗传结构与维持机制。研究发现两类高度分化的染色体变异（chromosomal variants），其序列覆盖兆碱基级别的基因组区域，且与体色多态性显著相关。我们证实，这类变异的有效重组（effective recombination）水平显著降低，地理分布广泛，且大概率在数百万世代前就已发生分化。本研究检测到异核型过剩（heterokaryotype excess）现象，以及该物种种群演化历史中平衡选择（balancing selection）作用于这类变异的分子信号。同一基因组区域内的第三种染色体变异，大概率由前述两类体色相关变异中的一种近期演化而来，且与背部图案多态性相关。本研究结果表明，与拟态相关的大规模遗传变异，可通过复杂的平衡选择过程在种群中长期维持。