Davison D, Pritchard J K, Coop G
Committee on Evolutionary Biology, University of Chicago, USA.
Theor Popul Biol. 2009 Jun;75(4):331-45. doi: 10.1016/j.tpb.2009.04.001. Epub 2009 Apr 9.
We describe a new approximate likelihood for population genetic data under a model in which a single ancestral population has split into two daughter populations. The approximate likelihood is based on the 'Product of Approximate Conditionals' likelihood and 'copying model' of Li and Stephens [Li, N., Stephens, M., 2003. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165 (4), 2213-2233]. The approach developed here may be used for efficient approximate likelihood-based analyses of unlinked data. However our copying model also considers the effects of recombination. Hence, a more important application is to loosely-linked haplotype data, for which efficient statistical models explicitly featuring non-equilibrium population structure have so far been unavailable. Thus, in addition to the information in allele frequency differences about the timing of the population split, the method can also extract information from the lengths of haplotypes shared between the populations. There are a number of challenges posed by extracting such information, which makes parameter estimation difficult. We discuss how the approach could be extended to identify haplotypes introduced by migrants.
我们描述了一种在单一祖先群体分裂为两个子群体的模型下，用于群体遗传数据的新近似似然方法。该近似似然基于Li和Stephens [Li, N., Stephens, M., 2003. 使用单核苷酸多态性数据建模连锁不平衡并识别重组热点。遗传学165 (4), 2213 - 2233] 的“近似条件乘积”似然和“复制模型”。这里开发的方法可用于对不连锁数据进行基于近似似然的高效分析。然而，我们的复制模型也考虑了重组的影响。因此，一个更重要的应用是针对松散连锁的单倍型数据，到目前为止，尚未有明确以非平衡群体结构为特征的高效统计模型。所以，除了等位基因频率差异中关于群体分裂时间的信息外，该方法还可以从群体间共享单倍型的长度中提取信息。提取此类信息存在诸多挑战，这使得参数估计变得困难。我们讨论了该方法如何扩展以识别由移民引入的单倍型。
