Encoding and Constructing 1-Nested Phylogenetic Networks with Trinets
Encoding and Constructing 1-Nested Phylogenetic Networks with Trinets
复制标题
DOI：
10.1007/s00453-012-9659-x
复制
发表时间：
2013-07-01
期刊：
影响因子：
1.1
通讯作者：
Moulton, V.
中科院分区：
文献类型：
--
作者：
Huber, K. T.;Moulton, V.
系统发生网络是系统发生树的一种概括，在生物学中用于表示网状或非树状进化。最近，已经开发了几种算法，其目的是使用三元组，即在给定的一组物种的3个元素子集上的二元系统发育树，从生物数据构建系统发育网络。然而，这种方法的一个基本问题是，由系统发育网络显示的三联体不一定唯一地确定或编码网络。在这里，我们提出了一种替代方法来编码和构建系统发育网络，它使用系统发育网络的3元素子集的一组，或tradition，而不是三胞胎。更具体地说，我们表明，对于一个特殊的，研究良好的类型的系统发育网络称为1-嵌套网络，由1-嵌套网络显示的tradition总是编码的网络。我们还提出了一个有效的算法来决定是否密集集的trinitial（即一个包含一个trinet的每一个3元素子集的集合）可以显示1嵌套网络或没有，如果是这样，构造网络。此外，我们讨论了一些潜在的新方向，这种新的方法开辟了构建和比较系统发育网络。
Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from biological data using triplets, i.e. binary phylogenetic trees on 3-element subsets of a given set of species. However, a fundamental problem with this approach is that the triplets displayed by a phylogenetic network do not necessarily uniquely determine or encode the network. Here we propose an alternative approach to encoding and constructing phylogenetic networks, which uses phylogenetic networks on 3-element subsets of a set, or trinets, rather than triplets. More specifically, we show that for a special, well-studied type of phylogenetic network called a 1-nested network, the trinets displayed by a 1-nested network always encode the network. We also present an efficient algorithm for deciding whether a dense set of trinets (i.e. one that contains a trinet on every 3-element subset of a set) can be displayed by a 1-nested network or not and, if so, constructs that network. In addition, we discuss some potential new directions that this new approach opens up for constructing and comparing phylogenetic networks.