Radhakrishnan Srihari, Valenzuela Nicole
Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011.
Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011.
J Hered. 2017 Oct 30;108(7):720-730. doi: 10.1093/jhered/esx082.
Sex chromosomes evolve differently from autosomes because natural selection acts distinctly on them given their reduced recombination and smaller population size. Various studies of sex-linked genes compared with different autosomal genes within species support these predictions. Here, we take a novel alternative approach by comparing the rate of evolution between subsets of genes that are sex-linked in selected reptiles/vertebrates and the same genes located in autosomes in other amniotes. We report for the first time the faster evolution of Z-linked genes in a turtle (the Chinese softshell turtle Pelodiscus sinensis) relative to autosomal orthologs in other taxa, including turtles with temperature-dependent sex determination (TSD). This faster rate was absent in its close relative, the spiny softshell turtle (Apalone spinifera), thus revealing important lineage effects, and was only surpassed by mammalian-X linked genes. In contrast, we found slower evolution of X-linked genes in the musk turtle Staurotypus triporcatus (XX/XY) and homologous Z-linked chicken genes. TSD lineages displayed overall faster sequence evolution than taxa with genotypic sex determination (GSD), ruling out global effects of GSD on molecular evolution beyond those by sex-linkage. Notably, results revealed a putative selective sweep around two turtle genes involved in vertebrate gonadogenesis (Pelodiscus-Z-linked Nf2 and Chrysemys-autosomal Tspan7). Our observations reveal important evolutionary changes at the gene level mediated by chromosomal context in turtles despite their low overall evolutionary rate and illuminate sex chromosome evolution by empirically testing expectations from theoretical models. Genome-wide analyses are warranted to test the generality and prevalence of the observed patterns.
性染色体的进化方式与常染色体不同，因为自然选择对它们的作用明显不同，这是由于它们的重组率降低和种群规模较小。对物种内性连锁基因与不同常染色体基因的各种研究支持了这些预测。在这里，我们采用了一种新颖的替代方法，即比较选定爬行动物/脊椎动物中性连锁基因子集与其他羊膜动物常染色体上相同基因的进化速率。我们首次报告了乌龟（中华鳖）中Z连锁基因相对于其他类群（包括具有温度依赖型性别决定（TSD）的乌龟）的常染色体直系同源基因进化得更快。在其近亲刺鳖中没有这种更快的进化速率，从而揭示了重要的谱系效应，并且只有哺乳动物的X连锁基因进化速率超过了它。相比之下，我们发现麝香龟（XX/XY）中的X连锁基因和同源的鸡Z连锁基因进化较慢。TSD谱系显示出总体上比具有基因型性别决定（GSD）的类群更快的序列进化，排除了GSD对分子进化的全局影响，超出了性连锁的影响。值得注意的是，结果揭示了在涉及脊椎动物性腺发生的两个乌龟基因（中华鳖Z连锁的Nf2和锦龟常染色体的Tspan7）周围存在一个假定的选择性清除。我们的观察结果揭示了尽管乌龟总体进化速率较低，但在基因水平上由染色体背景介导的重要进化变化，并通过实证检验理论模型的预期来阐明性染色体的进化。有必要进行全基因组分析来检验所观察到模式的普遍性和普遍性。
