Indirect identification of horizontal gene transfer

Abstract

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.

A complete theoretical framework for inferring horizontal gene transfers using partial order sets

“…In addition to the above, there are a number of theoretical approaches to problems related to HGT transfer: [28][29][30][31]. These are typically about mathematically-oriented methodologies for reconstructing a species tree or reconciling gene and species trees.…”

Relative Timing Information and Orthology inEvolutionary Scenarios

“…David Schaller 1 , Tom Hartmann 1 , Manuel Lafond 3 , Peter F. Stadler 1,5,6,7,8,9 , Nicolas Wieseke 4 and Marc Hellmuth 2*…”

“…In [4], we derived an algorithmic approach that recognizes LDT graphs and constructs a relaxed scenario S for (G < , σ ) in the positive case. Here, we adapt the algorithmic idea to the case that, instead of (G < , σ ), the graph 3-partition G = (G < , G = , G > , σ ) is given, see Algorithm 1.…”

“…In particular, every x ∈ L(T (u)) satisfies x ∈ L ′ . Algorithm 1 is a generalization of the algorithm presented in [4] for the construction of a relaxed scenario S for a given LDT graph (G, σ ). A key property of the algorithm is that the restriction of S to S(u S ), i.e., the incomplete scenarios obtained for given u S satisfies the time consistency constraints (S2) and (S3).…”

“…The conceptual relevance of scenarios in evolutionary biology derives from the fact that they define key relationships between genes, in particular orthology, paralogy, and xenology [1]. On the practical side, scenarios also imply relations on the set of genes that can be inferred directly from sequence similarity data, such as the best match relation [2,3] or the later divergence time (LDT) relation [4], which is closely related to the inference of horizontal gene transfer events.…”