Department of Cell and Systems Biology, University of Toronto, Ontario, Canada.
Department of Biology, University of Toronto Mississauga, Ontario, Canada.
Genome Biol Evol. 2020 Apr 1;12(4):370-380. doi: 10.1093/gbe/evaa057.
Recombination confers a major evolutionary advantage by breaking up linkage disequilibrium between harmful and beneficial mutations, thereby facilitating selection. However, in species that are only periodically sexual, such as many microbial eukaryotes, the realized rate of recombination is also affected by the frequency of sex, meaning that infrequent sex can increase the effects of selection at linked sites despite high recombination rates. Despite this, the rate of sex of most facultatively sexual species is unknown. Here, we use genomewide patterns of linkage disequilibrium to infer fine-scale recombination rate variation in the genome of the facultatively sexual green alga Chlamydomonas reinhardtii. We observe recombination rate variation of up to two orders of magnitude and find evidence of recombination hotspots across the genome. Recombination rate is highest flanking genes, consistent with trends observed in other nonmammalian organisms, though intergenic recombination rates vary by intergenic tract length. We also find a positive relationship between nucleotide diversity and physical recombination rate, suggesting a widespread influence of selection at linked sites in the genome. Finally, we use estimates of the effective rate of recombination to calculate the rate of sex that occurs in natural populations, estimating a sexual cycle roughly every 840 generations. We argue that the relatively infrequent rate of sex and large effective population size creates a population genetic environment that increases the influence of selection on linked sites across the genome.
重组通过打破有害和有益突变之间的连锁不平衡，从而促进选择，赋予了主要的进化优势。然而，在那些仅周期性有性繁殖的物种中，如许多微生物真核生物，实际的重组率也受到性别的频率的影响，这意味着尽管重组率高，但不频繁的性别会增加连锁位点的选择效应。尽管如此，大多数兼性有性物种的性别的频率仍然未知。在这里，我们使用全基因组连锁不平衡的模式来推断兼性有性绿藻莱茵衣藻基因组中精细尺度的重组率变化。我们观察到高达两个数量级的重组率变化，并在整个基因组中发现了重组热点的证据。重组率在侧翼基因处最高，与在其他非哺乳动物生物中观察到的趋势一致，尽管基因间重组率随基因间片段长度而异。我们还发现核苷酸多样性与物理重组率之间存在正相关关系，这表明基因组中连锁位点的选择普遍存在影响。最后，我们利用有效重组率的估计值来计算自然种群中发生的性别的频率，估计大约每 840 代发生一次有性循环。我们认为，相对不频繁的性别的频率和大的有效种群大小创造了一个种群遗传环境，增加了选择对基因组中连锁位点的影响。
