论文标题

根源系统发育网络的显示集的超管和汉密尔顿周期

Hypercubes and Hamilton cycles of display sets of rooted phylogenetic networks

论文作者

Döcker, Janosch, Linz, Simone, Semple, Charles

论文摘要

在从系统发育树中重建系统发育网络的背景下,已经建立了几种特征和随后的算法来重建一个系统发育网络,该网络以某种最低限度的方式将所有树共同嵌入所有树木。但是,对于许多情况,所得网络还嵌入了不属于输入的其他系统发育树。但是,这些推断的树知之甚少。在本文中,我们探讨了嵌入给定系统发育网络中的所有系统发育树之间的关系。 First, we investigate some combinatorial properties of the collection P of all rooted binary phylogenetic trees that are embedded in a rooted binary phylogenetic network N. To this end, we associated a particular graph G, which we call rSPR graph, with the elements in P and show that, if |P|=2^k, where k is the number of vertices with in-degree two in N, then G has a Hamiltonian cycle.其次,通过利用超线的RSPR图和性能,我们转向研究良好的二进制二进制级别1网络,并为一组生根的二进制系统发育树嵌入一组级别-1网络中,而无需推断任何其他树木。最后,我们展示了这些条件如何转化为多项式时间算法,以重建该网络(如果存在)。

In the context of reconstructing phylogenetic networks from a collection of phylogenetic trees, several characterisations and subsequently algorithms have been established to reconstruct a phylogenetic network that collectively embeds all trees in the input in some minimum way. For many instances however, the resulting network also embeds additional phylogenetic trees that are not part of the input. However, little is known about these inferred trees. In this paper, we explore the relationships among all phylogenetic trees that are embedded in a given phylogenetic network. First, we investigate some combinatorial properties of the collection P of all rooted binary phylogenetic trees that are embedded in a rooted binary phylogenetic network N. To this end, we associated a particular graph G, which we call rSPR graph, with the elements in P and show that, if |P|=2^k, where k is the number of vertices with in-degree two in N, then G has a Hamiltonian cycle. Second, by exploiting rSPR graphs and properties of hypercubes, we turn to the well-studied class of rooted binary level-1 networks and give necessary and sufficient conditions for when a set of rooted binary phylogenetic trees can be embedded in a level-1 network without inferring any additional trees. Lastly, we show how these conditions translate into a polynomial-time algorithm to reconstruct such a network if it exists.

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