National Oceanic and Atmospheric Administration, Northwest Fisheries Science Center, Seattle, Washington 98112, USA.
Genetics. 2011 Oct;189(2):633-44. doi: 10.1534/genetics.111.132233. Epub 2011 Aug 11.
Effective population size (Ne) is an important genetic parameter because of its relationship to loss of genetic variation, increases in inbreeding, accumulation of mutations, and effectiveness of selection. Like most other genetic approaches that estimate contemporary Ne, the method based on linkage disequilibrium (LD) assumes a closed population and (in the most common applications) randomly recombining loci. We used analytical and numerical methods to evaluate the absolute and relative consequences of two potential violations of the closed-population assumption: (1) mixture LD caused by occurrence of more than one gene pool, which would downwardly bias Ne and (2) reductions in drift LD (and hence upward bias in Ne) caused by an increase in the number of parents responsible for local samples. The LD method is surprisingly robust to equilibrium migration. Effects of mixture LD are small for all values of migration rate (m), and effects of additional parents are also small unless m is high in genetic terms. LD estimates of Ne therefore accurately reflect local (subpopulation) Ne unless m>∼5-10%. With higher m, Ne converges on the global (metapopulation) Ne. Two general exceptions were observed. First, equilibrium migration that is rare and hence episodic can occasionally lead to substantial mixture LD, especially when sample size is small. Second, nonequilibrium, pulse migration of strongly divergent individuals can also create strong mixture LD and depress estimates of local Ne. In both cases, assignment tests, Bayesian clustering, and other methods often will allow identification of recent immigrants that strongly influence results. In simulations involving equilibrium migration, the standard LD method performed better than a method designed to jointly estimate Ne and m. The above results assume loci are not physically linked; for tightly linked loci, the LD signal from past migration events can persist for many generations, with consequences for Ne estimates that remain to be evaluated.
有效种群大小 (Ne) 是一个重要的遗传参数，因为它与遗传变异的丧失、近交的增加、突变的积累以及选择的有效性有关。与估计当代 Ne 的大多数其他遗传方法一样，基于连锁不平衡 (LD) 的方法假设为封闭群体，并且（在最常见的应用中）随机重组基因座。我们使用分析和数值方法来评估两种潜在违反封闭群体假设的绝对和相对后果：(1) 由多个基因库引起的混合 LD，这会向下偏置 Ne；(2) 由于负责局部样本的父母数量增加而导致的漂移 LD 减少（从而向上偏置 Ne）。LD 方法对平衡迁移具有惊人的鲁棒性。对于所有迁移率 (m) 值，混合 LD 的影响都很小，除非 m 在遗传上很高，否则额外父母的影响也很小。因此，LD 方法估计的 Ne 准确反映了局部（亚种群）Ne，除非 m>∼5-10%。随着 m 的增加，Ne 收敛于全局（复合种群）Ne。观察到两个一般例外。首先，罕见且因此偶发性的平衡迁移偶尔会导致大量混合 LD，尤其是当样本量较小时。其次，强烈分歧个体的非平衡脉冲迁移也会产生强烈的混合 LD，并降低局部 Ne 的估计值。在这两种情况下，分配测试、贝叶斯聚类和其他方法通常可以识别强烈影响结果的近期移民。在涉及平衡迁移的模拟中，标准 LD 方法的表现优于旨在联合估计 Ne 和 m 的方法。上述结果假设基因座没有物理连接；对于紧密连锁的基因座，过去迁移事件的 LD 信号可以持续许多代，对 Ne 估计的影响仍有待评估。
