Department of Plant Sciences, University of Oxford, Oxford, United Kingdom.
PLoS One. 2013 Nov 27;8(11):e80538. doi: 10.1371/journal.pone.0080538. eCollection 2013.
One crucial feature of zygotic linkage disequilibrium (LD) analysis is its direct use of diploid genotyping data, irrespective of the type of mating system. Previous theories from an evolutionary perspective mainly focus on gametic LD, but the equivalent development for zygotic LD is not available. Here I study the evolution of zygotic LD and the covariances between gametic and zygotic LDs or between distinct zygotic LDs in a finite local population under constant immigration from a continent population. I derive the analytical theory under genetic hitchhiking effects or in a neutral process. Results indicate that zygotic LDs (diploid level) are more informative than gametic LD (haploid level) in indicating the effects of different evolutionary forces. Zygotic LDs may be greater than or comparable to gametic LD under the epistatic selection process, but smaller than gametic LD under the non epistatic selection process. The covariances between gametic and zygotic LDs are strongly affected by the mating system, linkage distance, and genetic drift effects, but weakly affected by seed and pollen flow and natural selection. The covariances between different zygotic LDs are generally robust to the effects of gene flow, selection, and linkage distance, but sensitive to the effects of genetic drift and mating system. Consistent patterns exist for the covariances between the zygotic LDs for the two-locus genotypes with one common genotype at one locus or without any common genotype at each locus. The results highlight that zygotic LDs can be applied to detecting natural population history.
合子连锁不平衡（LD）分析的一个关键特征是其直接使用二倍体基因型数据，而与交配系统的类型无关。来自进化角度的先前理论主要集中在配子 LD 上，但合子 LD 的等效发展尚不可用。在这里，我研究了有限局部群体中恒定外来移民条件下合子 LD 的进化以及配子 LD 或不同合子 LD 之间的协方差。我在遗传 hitchhiking 效应或中性过程下推导出了分析理论。结果表明，在指示不同进化力的影响方面，合子 LD（二倍体水平）比配子 LD（单倍体水平）更具信息量。在上位性选择过程中，合子 LD 可能大于或等于配子 LD，但在非上位性选择过程中，合子 LD 小于配子 LD。配子 LD 与合子 LD 之间的协方差强烈受到交配系统、连锁距离和遗传漂变效应的影响，但受到种子和花粉流以及自然选择的影响较弱。不同合子 LD 之间的协方差对基因流、选择和连锁距离的影响一般较为稳健，但对遗传漂变和交配系统的影响较为敏感。对于一个位点上具有一个共同基因型或每个位点上都没有共同基因型的两个基因座基因型的合子 LD 之间的协方差存在一致的模式。结果强调了合子 LD 可用于检测自然群体历史。
