Identifiability of local and global features of phylogenetic networks from average distances
Identifiability of local and global features of phylogenetic networks from average distances
复制标题
DOI：
10.1007/s00285-022-01847-8
复制
发表时间：
2023-01-01
影响因子：
1.9
通讯作者：
Ane, Cecile
中科院分区：
文献类型：
--
作者：
Xu, Jingcheng;Ane, Cecile
系统发生网络扩展了系统发生树，以模拟非垂直遗传，即一个谱系从多个亲本继承材料。用基于似然的方法从全基因组数据估计系统发育网络的计算复杂性限制了可以处理的网络的大小。基于成对距离的方法可以提供更快的替代方案。我们在这里研究的信息，平均成对距离包含在底层的系统发育网络，通过表征本地和全球的功能，可以或不能被识别。对于一般的网络，我们澄清，根和边长相邻的网状是不可识别的，然后专注于类的拉链半有向网络。我们提供了一个标准，交换子图的本地，如3圈，导致不可区分的网络。我们提出了“距离分裂树”，它可以从成对距离构造，并证明它是网络的斑点树的细化，捕捉网络的树状特征。对于1级网络，这个距离分裂树等于改进的斑点树，以分离多分裂斑点，我们证明了网络的混合表示是可识别的。信息丢失集中在4个周期左右，无法识别网状结构的位置。混合表示结合了4-循环的分裂边缘，半有向网络的规则树和混合边缘，以及对平均成对距离可识别的所有信息进行编码的边缘参数。
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with likelihood-based methods limits the size of networks that can be handled. Methods based on pairwise distances could offer faster alternatives. We study here the information that average pairwise distances contain on the underlying phylogenetic network, by characterizing local and global features that can or cannot be identified. For general networks, we clarify that the root and edge lengths adjacent to reticulations are not identifiable, and then focus on the class of zipped-up semidirected networks. We provide a criterion to swap subgraphs locally, such as 3-cycles, resulting in indistinguishable networks. We propose the "distance split tree ", which can be constructed from pairwise distances, and prove that it is a refinement of the network's tree of blobs, capturing the tree-like features of the network. For level-1 networks, this distance split tree is equal to the tree of blobs refined to separate polytomies from blobs, and we prove that the mixed representation of the network is identifiable. The information loss is localized around 4-cycles, for which the placement of the reticulation is unidentifiable. The mixed representation combines split edges for 4-cycles, regular tree and hybrid edges from the semidirected network, and edge parameters that encode all information identifiable from average pairwise distances.