Estimating Contemporary Effective Population Size on the Basis of Linkage Disequilibrium in the Face of Migration
Estimating Contemporary Effective Population Size on the Basis of Linkage Disequilibrium in the Face of Migration
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DOI：
10.1534/genetics.111.132233
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发表时间：
2011-10-01
期刊：
影响因子：
3.3
通讯作者：
England, Phillip R.
中科院分区：
文献类型：
--
作者：
Waples, Robin S.;England, Phillip R.
有效群体大小（N-e）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、突变的积累和选择的有效性有关。像大多数其他遗传方法估计当代N-e，连锁不平衡（LD）的基础上的方法假设一个封闭的群体和（在最常见的应用）随机重组基因座。我们使用分析和数值方法来评估封闭总体假设的两个潜在违反的绝对和相对后果：（1）由多于一个基因库的出现引起的混合LD，其将使（N）向下偏向于cap（e），和（2）由负责本地样本的亲本数量增加引起的漂移LD的减少（以及因此（N）相对于cap（e）的向上偏差）。LD方法对平衡迁移具有令人惊讶的鲁棒性。混合LD的影响是小的迁移率（m）的所有值，和额外的父母的影响也很小，除非m是高的遗传条件。因此，N-e的LD估计值准确地反映了局部（亚群）N-e，除非m >相似于5- 10%。当m较大时，（N）在cap（e）上收敛于全局（集合种群）N-e。观察到两个一般性例外。首先，平衡迁移是罕见的，因此偶尔会导致大量的混合物LD，特别是当样本量很小。第二，非平衡，脉冲迁移的强烈发散的个人也可以创建强大的混合LD和压低估计的本地N-e。在这两种情况下，分配测试，贝叶斯聚类和其他方法通常会允许识别对结果产生强烈影响的最近移民。在涉及平衡迁移的模拟中，标准LD方法的性能优于设计用于联合估计N-e和m的方法。上述结果假设基因座不是物理连锁的;对于紧密连锁的基因座，来自过去迁移事件的LD信号可以持续许多代，N-e估计的结果仍有待评估。
Effective population size (N-e) 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 N-e, 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 (N) over cap (e), and (2) reductions in drift LD (and hence upward bias in (N) over cap (e)) 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 N-e therefore accurately reflect local (subpopulation) N-e unless m > similar to 5-10%. With higher m, (N) over cap (e) converges on the global (metapopulation) N-e. 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 N-e. 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 N-e 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 N-e estimates that remain to be evaluated.