论文标题

间接鉴定水平基因转移

Indirect Identification of Horizontal Gene Transfer

论文作者

Schaller, David, Lafond, Manuel, Stadler, Peter F., Wieseke, Nicolas, Hellmuth, Marc

论文摘要

推断水平基因转移(HGT)的几种隐式方法集中于仅在基因驻留的两种物种分歧后才差异的基因对。这种情况定义了图的边缘集,即后期差异时间(LDT)图,其顶点对应于其物种染色的基因。我们在放松的场景的设置中调查了这些图,即涵盖文献中所有常用的重复转移损失情景的变体的进化场景。我们将LDT图描述为正确的顶点色的Cophicts的子类,并提供了多项式识别算法以及一种算法,以构建解释给定LDT的放松场景。 LDT图中的边缘意味着两个相应的基因被至少一个HGT事件分开。但是,相反是不正确的。我们表明,完整的Xenology关系由RS-fitch图(即完整的多方图满足顶点着色的约束)描述。这类顶点色的图在多项式时间也可以识别。我们最终在借助广泛的重复,丢失和HGT事件的进化场景的帮助下,解决了“ LDT图中所有有关HGT事件的信息”的问题。特别是,我们表明一种简单的贪婪图编辑方案可用于有效检测LDT图中隐含包含的HGT事件。

Several implicit methods to infer Horizontal Gene Transfer (HGT) focus on pairs of genes that have diverged only after the divergence of the two species in which the genes reside. This situation defines the edge set of a graph, the later-divergence-time (LDT) graph, whose vertices correspond to genes colored by their species. We investigate these graphs in the setting of relaxed scenarios, i.e., evolutionary scenarios that encompass all commonly used variants of duplication-transfer-loss scenarios in the literature. We characterize LDT graphs as a subclass of properly vertex-colored cographs, and provide a polynomial-time recognition algorithm as well as an algorithm to construct a relaxed scenario that explains a given LDT. An edge in an LDT graph implies that the two corresponding genes are separated by at least one HGT event. The converse is not true, however. We show that the complete xenology relation is described by an rs-Fitch graph, i.e., a complete multipartite graph satisfying constraints on the vertex coloring. This class of vertex-colored graphs is also recognizable in polynomial time. We finally address the question "how much information about all HGT events is contained in LDT graphs" with the help of simulations of evolutionary scenarios with a wide range of duplication, loss, and HGT events. In particular, we show that a simple greedy graph editing scheme can be used to efficiently detect HGT events that are implicitly contained in LDT graphs.

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