Solution: network methods

Phylogenetic methods that allow for   persistent ancestral nodes, multifurcations and reticulations are needed to   take these population phenomena into account. The advantage of networks over   strictly bifurcating trees for estimating within-species relationships now   becomes obvious. Networks can account effectively for processes acting at the   species level and they might be able to incorporate predictions from   population genetics theory (Box 2). In addition, networks provide a way of   representing more of the phylogenetic information present in a data set (Fig.   2). For example, the presence of loops in a network might indicate   recombination. In other cases, loops are the product of homoplasies and precisely   indicate the occurrence of reverse or parallel mutations. Most network   methods are distance methods, with the common idea of minimizing (with some   specific restrictions) the distances (number of mutations) among haplotypes.   In other cases, the likelihood function is maximized.

解决方案：网络方法

研究种群想象的系统发育方法需要考虑持续祖先节点、多岐分叉和网状结构。与严格的二岐分叉树相比，网络方法用于估计种内关系的优势现在变得越发明显了。网络可以有效地解释在物种层面上作用的过程，并且它们可能将群体遗传学理论的预测整合进来（框注2）。此外，网络提供了一种表示数据集中存在的更多系统发育信息的方法（图2）。例如，网络中的闭环可能表示重组。在其他情况下，闭环是趋同进化的产物，精确地指示了回复突变或平行突变的发生。大多数网络方法都是距离法，其共同的思想是最小化单倍型之间的距离（突变数）。在其他情况下，似然函数最大化。