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，多态性如何在种群中得以维持始终存在学术争议，因为遗传漂变与多种形式的选择均会降低种群的遗传变异水平。本研究以克里斯蒂娜竹节虫（Timema cristinae）为研究对象，探究其赋予隐蔽适应性的表型形态的遗传结构与维持机制，整合了21个种群共1360份样本的表型信息与测序分型（genotyping-by-sequencing，GBS）数据。研究发现两类高度分化的染色体变异体，其覆盖百万碱基级别的序列区段，并与体色多态性显著相关。结果表明，这些变异体的有效重组水平大幅降低，地理分布广泛，且大概率在数百万个世代前就已发生分化。本研究检测到异核型个体过剩的现象，以及该物种演化历史中平衡选择作用于这些变异体的分子信号。同一基因组区域内的第三类染色体变异体，大概率由上述两类体色相关变异体之一新近演化而来，与背侧斑纹多态性相关。本研究结果表明，与隐蔽适应性相关的大规模遗传变异，可通过潜在机制复杂的平衡选择过程在种群中长期维持。