Gambette Philippe, Huber Katharina T
IML, CNRS, Université Marseille 2, Marseille, France.
J Math Biol. 2012 Jul;65(1):157-80. doi: 10.1007/s00285-011-0456-y. Epub 2011 Jul 14.
Phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees, such networks canonically induce collections of phylogenetic trees, clusters, and triplets, respectively. Thus it is not surprising that many network approaches aim to reconstruct a phylogenetic network from such collections. Related to the well-studied perfect phylogeny problem, the following question is of fundamental importance in this context: When does one of the above collections encode (i.e. uniquely describe) the network that induces it? For the large class of level-1 (phylogenetic) networks we characterize those level-1 networks for which an encoding in terms of one (or equivalently all) of the above collections exists. In addition, we show that three known distance measures for comparing phylogenetic networks are in fact metrics on the resulting subclass and give the diameter for two of them. Finally, we investigate the related concept of indistinguishability and also show that many properties enjoyed by level-1 networks are not satisfied by networks of higher level.
系统发育网络如今已与系统发育树一同成为系统发育学研究的核心内容。与系统发育树一样，此类网络通常分别诱导出系统发育树、聚类和三元组的集合。因此，许多网络方法旨在从这些集合中重建系统发育网络也就不足为奇了。与研究充分的完美系统发育问题相关，在这种情况下，以下问题至关重要：上述集合之一何时能编码（即唯一描述）诱导它的网络？对于一大类1级（系统发育）网络，我们刻画了那些可以用上述集合之一（或等效地用所有集合）进行编码的1级网络。此外，我们表明，用于比较系统发育网络的三种已知距离度量实际上是所得子类上的度量，并给出了其中两种度量的直径。最后，我们研究了不可区分性的相关概念，并表明1级网络所具有的许多属性并不为更高级别的网络所满足。
