Data from: Patterns of genome-wide nucleotide diversity in the gynodioecious plant Thymus vulgaris are compatible with recent sweeps of cytoplasmic genes

Gynodioecy is a sexual dimorphism where females coexist with hermaphrodite individuals. In most cases, this dimorphism involves the interaction of cytoplasmic male sterility (CMS) genes and nuclear restorer genes. Two scenarios can account for how these interactions maintain gynodioecy. Either CMS genes recurrently enter populations at low frequency via mutation or migration and go to fixation unimpeded (successive sweeps), or CMS genes maintain polymorphism over evolutionary time through interactions with a nuclear restorer allele (balanced polymorphism). To distinguish between these scenarios, we used transcriptome sequencing in gynodioecious Thymus vulgaris and surveyed genome-wide diversity in 18 naturally occurring individuals sampled from populations at a local geographic scale. We contrast the amount and patterns of nucleotide diversity in the nuclear and cytoplasmic genome, and find ample diversity at the nuclear level (π = 0.019 at synonymous sites) but reduced genetic diversity and an excess of rare polymorphisms in the cytoplasmic genome relative to the nuclear genome. Our finding is incompatible with the maintenance of gynodioecy via scenarios invoking long-term balancing selection, and instead suggests the recent fixation of CMS lineages in the populations studied.

雌全异株（gynodioecy）是一类性二态性，表现为雌性个体与雌雄同体个体在种群中共存。多数情况下，该性二态性依赖于细胞质雄性不育（cytoplasmic male sterility, CMS）基因与核恢复基因之间的互作。目前有两种演化情景可解释此类互作如何维持雌全异株：其一，CMS基因通过突变或迁移以低频率反复侵入种群，并不受阻碍地达到固定状态，即连续选择性清除（successive sweeps）；其二，CMS基因通过与核恢复等位基因的互作，在长期进化时间尺度上维持多态性，即平衡多态性（balanced polymorphism）。为区分这两种情景，本研究对雌全异株物种普通百里香（Thymus vulgaris）开展转录组测序，并对局部地理尺度下多个自然种群的18个野生个体进行全基因组多样性分析。我们对比了核基因组与细胞质基因组的核苷酸多样性水平与分布模式，结果显示核基因组存在丰富的遗传多样性（同义位点的核苷酸多样性π值为0.019）；而相较于核基因组，细胞质基因组的遗传多样性更低，且存在过量的稀有多态性位点。本研究结果与"通过长期平衡选择维持雌全异株"的演化情景不符，反而表明所研究种群中的CMS谱系近期发生了固定。