Extant ancestral nodes

In natural populations, most haplotypes   in the gene pool exist as sets of multiple, identical copies that originated   by DNA replication. When one of these copies mutates to a new haplotype, it   is extremely unlikely that other copies of the ancestral haplotype also   mutate or that all copies of the ancestral haplotype rapidly become extinct.   Thus, the ancestral haplotypes are expected to persist in the population and   to be sampled together with their descendants. Traditional phylogenetic methods,   based on a bifurcating TREE, can detect and artificially represent persistent   ancestral haplotypes as occupying a branch of zero length at the basal node   of a cluster. However, this approach relies on modifying (e.g. by estimation   of branch lengths) an inappropriate model – a bifurcating   tree with all haplotypes occupying tips or terminal branches.

现存的祖先节点

在自然种群中，基因库中的大多数单倍型以多组拷贝形式存在，这些拷贝由DNA复制而来。当这些拷贝中的一个突变为一个新的单倍型时，祖先单倍型的其他拷贝极不可能也跟着突变，或者祖先单倍型的所有拷贝都很快灭绝。因此，祖先的单倍型将在种群中持续存在，并与后代一起被取样。传统的系统发育方法基于一个分叉树，可以检测并人工表示持续的祖先单倍型，即在一个簇的基部节点上占据一个零长度的分支。然而，这种方法依赖于设置（例如，通过估计分支长度）一个不合适的模型，在这一分叉树模型中，所有单倍型都占据末梢或末端分支。