Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, UK.
Mol Ecol. 2022 Nov;31(21):5524-5537. doi: 10.1111/mec.16674. Epub 2022 Sep 10.
The guppy Y chromosome has been considered a model system for the evolution of suppressed recombination between sex chromosomes, and it has been proposed that complete sex-linkage has evolved across about 3 Mb surrounding this fish's sex-determining locus, followed by recombination suppression across a further 7 Mb of the 23 Mb XY pair, forming younger "evolutionary strata". Sequences of the guppy genome show that Y is very similar to the X chromosome. Knowing which parts of the Y are completely nonrecombining, and whether there is indeed a large completely nonrecombining region, are important for understanding its evolution. Here, we describe analyses of PoolSeq data in samples from within multiple natural populations from Trinidad, yielding new results that support previous evidence for occasional recombination between the guppy Y and X. We detected recent demographic changes, notably that downstream populations have higher synonymous site diversity than upstream ones and other expected signals of bottlenecks. We detected evidence of associations between sequence variants and the sex-determining locus, rather than divergence under a complete lack of recombination. Although recombination is infrequent, it is frequent enough that associations with SNPs can suggest the region in which the sex-determining locus must be located. Diversity is elevated across a physically large region of the sex chromosome, conforming to predictions for a genome region with infrequent recombination that carries one or more sexually antagonistic polymorphisms. However, no consistently male-specific variants were found, supporting the suggestion that any completely sex-linked region may be very small.
孔雀鱼的 Y 染色体一直被认为是研究性染色体之间抑制重组进化的模式系统，有人提出，在这种鱼类的性别决定基因座周围约 3Mb 的区域内，完全性连锁已经进化，随后在 23Mb 的 XY 对中进一步抑制重组，形成较年轻的“进化层”。孔雀鱼基因组的序列表明，Y 染色体与 X 染色体非常相似。了解 Y 染色体的哪些部分完全不发生重组，以及是否确实存在一个大的完全不重组区域，对于理解其进化过程非常重要。在这里，我们描述了在来自特立尼达多个自然种群的样本中进行 PoolSeq 数据的分析，这些新结果支持了之前关于孔雀鱼 Y 和 X 染色体之间偶尔发生重组的证据。我们检测到了最近的种群动态变化，特别是下游种群的同义位点多样性高于上游种群，以及其他预期的瓶颈信号。我们检测到了序列变异与性别决定基因座之间的关联，而不是在完全缺乏重组的情况下的分歧。尽管重组很少见，但它足够频繁，以至于与 SNPs 的关联可以提示性别决定基因座所在的区域。整个性染色体的物理区域都存在较高的多样性，这符合在携带一个或多个性拮抗多态性的区域中，重组频率较低的预测。然而，没有发现一致的雄性特异性变体，这支持了任何完全性连锁区域可能非常小的观点。
