Slatkin M, Maddison W P
Department of Zoology, University of California, Berkeley 94720.
Genetics. 1990 Sep;126(1):249-60. doi: 10.1093/genetics/126.1.249.
We introduce a method for analyzing phylogenies of genes sampled from a geographically structured population. A parsimony method can be used to compute s, the minimum number of migration events between pairs of populations sampled, and the value of s can be used to estimate the effective migration rate M, the value of Nm in an island model with local populations of size N and a migration rate m that would yield the same value of s. Extensive simulations show that there is a simple relationship between M and the geographic distance between pairs of samples in one- and two-dimensional models of isolation by distance. Both stepping-stone and lattice models were simulated. If two demes k steps apart are sampled, then, s, the average value of s, is a function only of k/(Nm) in a one-dimensional model and is a function only of k/(Nm)2 in a two-dimensional model. Furthermore, log(M) is approximately a linear function of log(k). In a one-dimensional model, the regression coefficient is approximately -1 and in a two-dimensional model the regression coefficient is approximately -0.5. Using data from several locations, the regression of log(M) on log(distance) may indicate whether there is isolation by distance in a population at equilibrium and may allow an estimate of the effective migration rate between adjacent sampling locations. Alternative methods for analyzing DNA sequence data from a geographically structured population are discussed. An application of our method to the data of R. L. Cann, M. Stoneking and A. C. Wilson on human mitochondrial DNA is presented.
我们介绍了一种分析从地理结构种群中采样的基因系统发育的方法。可以使用简约法来计算s，即采样的种群对之间迁移事件的最小数量，并且s的值可用于估计有效迁移率M，即在具有大小为N的本地种群和迁移率m的岛屿模型中的Nm值，该模型会产生相同的s值。广泛的模拟表明，在一维和二维距离隔离模型中，M与样本对之间的地理距离之间存在简单关系。对踏脚石模型和晶格模型都进行了模拟。如果对相隔k步的两个deme进行采样，那么在一维模型中，s的平均值仅为k/(Nm)的函数，在二维模型中仅为k/(Nm)²的函数。此外，log(M)近似为log(k)的线性函数。在一维模型中，回归系数约为-1，在二维模型中回归系数约为-0.5。使用来自多个位置的数据，log(M)对log(距离)的回归可能表明处于平衡状态的种群中是否存在距离隔离，并可能允许估计相邻采样位置之间的有效迁移率。还讨论了分析来自地理结构种群的DNA序列数据的替代方法。展示了我们的方法对R.L.坎恩、M.斯通金和A.C.威尔逊关于人类线粒体DNA数据的应用。
