Data from: Patterns of cyto-nuclear linkage disequilibrium in Silene latifolia: genomic heterogeneity and temporal stability

Non-random association of alleles in the nucleus and cytoplasmic organelles, or cyto-nuclear linkage disequilibrium (LD), is both an important component of a number of evolutionary processes and a statistical indicator of others. The evolutionary significance of cyto-nuclear LD will depend on both its magnitude and how stable those associations are through time. Here, we use a longitudinal population genetic data set to explore the magnitude and temporal dynamics of cyto-nuclear disequilibria through time. We genotyped 135 and 170 individuals from 16 and 17 patches of the plant species Silene latifolia in Southwestern VA, sampled in 1993 and 2008, respectively. Individuals were genotyped at 14 highly polymorphic microsatellite markers and a single-nucleotide polymorphism (SNP) in the mitochondrial gene, atp1. Normalized LD (D′) between nuclear and cytoplasmic loci varied considerably depending on which nuclear locus was considered (ranging from 0.005–0.632). Four of the 14 cyto-nuclear associations showed a statistically significant shift over approximately seven generations. However, the overall magnitude of this disequilibrium was largely stable over time. The observed origin and stability of cyto-nuclear LD is most likely caused by the slow admixture between anciently diverged lineages within the species’ newly invaded range, and the local spatial structure and metapopulation dynamics that are known to structure genetic variation in this system.

细胞核与细胞质细胞器内的等位基因非随机关联，即核质连锁不平衡（cyto-nuclear linkage disequilibrium, LD），既是诸多进化过程的重要组成部分，也是反映其他进化现象的统计学指标。核质连锁不平衡的进化意义，取决于其强度大小以及这些关联随时间推移的稳定性。本研究利用纵向群体遗传数据集，探究核质连锁不平衡的强度及其随时间变化的动态特征。我们分别于1993年和2008年，在弗吉尼亚州西南部的16个和17个斑块样地中，对植物物种Silene latifolia的135株和170株个体进行了基因分型。所有个体均通过14个高度多态性微卫星标记（microsatellite markers）以及线粒体基因atp1中的单核苷酸多态性（single-nucleotide polymorphism, SNP）完成基因分型。细胞核与细胞质基因座间的标准化连锁不平衡值（Normalized LD, D′）差异显著，其取值范围为0.005至0.632，具体数值取决于所考量的核基因座。14组核质关联中，有4组在约7个世代间呈现出统计学上显著的变化。但总体而言，该不平衡现象的强度在时间维度上基本保持稳定。本研究观测到的核质连锁不平衡的起源与稳定性，最可能源于该物种新近入侵范围内古代分化支系间的缓慢基因渐渗，以及此前已被证实可塑造该系统遗传变异的局域空间结构与集合种群动态。