Evaluation of the linkage-disequilibrium method for the estimation of effective population size when generations overlap: an empirical case.
Evaluation of the linkage-disequilibrium method for the estimation of effective population size when generations overlap: an empirical case.
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DOI：
10.1186/s12864-015-2167-z
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发表时间：
2015-11-11
期刊：
影响因子：
4.4
通讯作者：
Villanueva B
中科院分区：
文献类型：
--
作者：
Saura M;Tenesa A;Woolliams JA;Fernández A;Villanueva B
在估计有效群体大小（Ne）的遗传学方法中，基于连锁不平衡（LD）的方法比其他方法具有优势，尽管其在应用于具有重叠世代的群体时的准确性是有争议的。目前还不清楚在实施这种方法时，解释突变和样本大小的最佳方法。在这里，我们已经解决了这种方法的适用性，使用全基因组信息时，世代重叠，从伊比利亚猪的实验种群中获得完整和准确的系谱。Ne的精确的基于谱系的估计值被认为是比较基于LD的估计值的基线。我们假设了六种不同的统计模型，这些模型在对突变和样本量进行调整时有所不同。该方法使我们能够确定最合适的统计模型的调整时，LD方法用于物种重叠世代。这里使用的一种新方法是将不同世代视为同一种群的重复，以评估基于LD的Ne估计值的误差。LD为基础的Ne估计获得的突变参数的数据，并通过使用1/2n项校正样本量是最接近的基于谱系的估计。牛群建立时（26代前）的Ne为20.8 ± 3.7（重复间的平均值和SD），而基于系谱的估计值为21。从那时起，这一趋势与基于系谱的Ne。我们的研究结果表明，当使用全基因组信息时，LD方法是准确的，广泛适用于小群体，即使世代重叠。这支持使用的方法来估计Ne时，系谱信息是不可用的，以有效地监测和管理人口，并及早发现人口下降。据我们所知，这是第一个研究使用重复的经验数据来评估LD方法的适用性，通过比较结果与准确的基于谱系的估计。本文的在线版本（doi：10.1186/s12864-015-2167-z）包含补充材料，可供授权用户使用。
Within the genetic methods for estimating effective population size (Ne), the method based on linkage disequilibrium (LD) has advantages over other methods, although its accuracy when applied to populations with overlapping generations is a matter of controversy. It is also unclear the best way to account for mutation and sample size when this method is implemented. Here we have addressed the applicability of this method using genome-wide information when generations overlap by profiting from having available a complete and accurate pedigree from an experimental population of Iberian pigs. Precise pedigree-based estimates of Ne were considered as a baseline against which to compare LD-based estimates. We assumed six different statistical models that varied in the adjustments made for mutation and sample size. The approach allowed us to determine the most suitable statistical model of adjustment when the LD method is used for species with overlapping generations. A novel approach used here was to treat different generations as replicates of the same population in order to assess the error of the LD-based Ne estimates. LD-based Ne estimates obtained by estimating the mutation parameter from the data and by correcting sample size using the 1/2n term were the closest to pedigree-based estimates. The Ne at the time of the foundation of the herd (26 generations ago) was 20.8 ± 3.7 (average and SD across replicates), while the pedigree-based estimate was 21. From that time on, this trend was in good agreement with that followed by pedigree-based Ne. Our results showed that when using genome-wide information, the LD method is accurate and broadly applicable to small populations even when generations overlap. This supports the use of the method for estimating Ne when pedigree information is unavailable in order to effectively monitor and manage populations and to early detect population declines. To our knowledge this is the first study using replicates of empirical data to evaluate the applicability of the LD method by comparing results with accurate pedigree-based estimates. The online version of this article (doi:10.1186/s12864-015-2167-z) contains supplementary material, which is available to authorized users.