Data from: Estimation of effective population size in continuously distributed populations: there goes the neighborhood

Use of genetic methods to estimate effective population size (N^e) is rapidly increasing, but all approaches make simplifying assumptions unlikely to be met in real populations. In particular, all assume a single, unstructured population, and none has been evaluated for use with continuously distributed species. We simulated continuous populations with local mating structure, as envisioned by Wright's concept of neighborhood size (NS), and evaluated performance of a single-sample estimator based on linkage disequilibrium (LD), which provides an estimate of the effective number of parents that produced the sample (N^b). Results illustrate the interacting effects of two phenomena, drift and mixture, that contribute to LD. Samples from areas equal to or smaller than a breeding window produced estimates close to the NS. As the sampling window increased in size to encompass multiple genetic neighborhoods, mixture LD from a two-locus Wahlund effect overwhelmed the reduction in drift LD from incorporating offspring from more parents. As a consequence, N^b never approached the global N^e, even when the geographic scale of sampling was large. Results indicate caution is needed in applying standard methods for estimating effective size to continuously distributed populations.利用遗传方法估算有效种群大小（effective population size，N^e）的研究正快速增加，但所有方法均采用了在自然种群中几乎无法满足的简化假设。具体而言，所有方法均假设种群为单一、无结构的群体，且尚无研究对其在连续分布物种中的应用效果进行评估。我们基于莱特（Wright）提出的邻域大小（neighborhood size，NS）概念，模拟了具有局部交配结构的连续种群，并评估了基于连锁不平衡（linkage disequilibrium，LD）的单样本估计量的性能，该估计量可用于估算产生样本的亲本有效数量（N^b）。研究结果揭示了两种对连锁不平衡产生作用的现象——遗传漂变与群体混合——的交互效应。当采样区域等于或小于繁殖窗口时，估计值与邻域大小（NS）较为接近。随着采样窗口扩大至涵盖多个遗传邻域，由双位点沃尔隆德效应（Wahlund effect）引发的群体混合连锁不平衡，会抵消因纳入更多亲本后代所带来的遗传漂变相关连锁不平衡的削弱。因此，即便采样的地理尺度较大，N^b始终无法趋近全局有效种群大小（N^e）。研究结果表明，将标准有效种群大小估算方法应用于连续分布种群时，需保持谨慎。