Reconstruction of time-consistent species trees

Lafond, Manuel; Hellmuth, Marc

doi:10.1186/s13015-020-00175-0

Cited by 9 publications

(3 citation statements)

References 52 publications

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“…The main remaining unresolved question is whether the resulting HGT-free subtrees can be combined into a complete scenario using only relational information such as best match data. One way to attack this is to employ the techniques used by Lafond and Hellmuth ( 2020 ) to characterize the conditions under which a fully event-labled gene tree can be reconciled with unknown species trees. These not only resulted in an polynomial-time algorithm but also establishes additional constraints on the HGT-free subtrees.…”

Section: Discussion and Future Directionsmentioning

confidence: 99%

Indirect identification of horizontal gene transfer

et al. 2021

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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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Section: Discussion and Future Directionsmentioning

confidence: 99%

Indirect identification of horizontal gene transfer

et al. 2021

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“…Lemma 7 defines the "informative species triples" [15][16][17] that play a key role for the characterization of feasible reconciliation maps in a slightly different setting.…”

Section: Informative Triplesmentioning

confidence: 99%

Relative Timing Information and Orthology inEvolutionary Scenarios

Schaller

Hartmann

Lafond

et al. 2023

Preprint

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Background: Evolutionary scenarios describing the evolution of a family of genes within a collection of species comprise the mapping of the vertices of a gene tree T to vertices and edges of a species tree S. The relative timing of the last common ancestors of two extant genes (leaves of T) and the last common ancestors of the two species (leaves of S) in which they reside is indicative of horizontal gene transfers (HGT) and ancient duplications. Orthologous gene pairs, on the other hand, require that their last common ancestors coincides with a corresponding speciation event. The relative timing information of gene and species divergences is captured by three colored graphs that have the extant genes as vertices and the species in which the genes are found as vertex colors: the equal-divergence-time (EDT) graph, the later-divergence-time (LDT) graph and the prior-divergence-time (PDT) graph, which together form an edge partition of the complete graph. Results: Here we give a complete characterization in terms of informative and forbidden triples that can be read off the three graphs and provide a polynomial time algorithm for constructing an evolutionary scenario that explains the graphs, provided such a scenario exists. While both LDT and PDT graphs are cographs, this is not true for the EDT graph in general. We show that every EDT graph is perfect. While the information about LDT and PDT graphs is necessary to recognize EDT graphs in polynomial-time for general scenarios, this extra information can be dropped in the HGT-free case. However, recognition of EDT graphs without knowledge of putative LDT and PDT graphs is NP-complete for general scenarios. In contrast, PDT graphs can be recognized in polynomial-time. We finally connect the EDT graph to the alternative definitions of orthology that have been proposed for scenarios with horizontal gene transfer. With one exception, the corresponding graphs are shown to be colored cographs.

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“…In related work, we recently characterized under which conditions an orthology graph, i.e., a symbolic ultrametric, and a Fitch graph are consistent in the sense that they can be explained by a common vertex-and edge-annotated gene tree T . Using this information, a GFH, i.e., a species tree S together with a time-consistent reconciliation map between the annotated gene tree T and S, can then be determined in polynomial time, provided it exists (Hellmuth, 2017;Nøjgaard et al, 2018;Lafond and Hellmuth, 2020). From a practical point of view, however, this result is of limited use since so far there is no efficient means of inferring the directed Fitch graph directly from data, while its symmetrized counterpart is accessible from empirical data .…”

Section: Introductionmentioning

confidence: 99%

Orientation of Fitch Graphs and Detection of Horizontal Gene Transfer in Gene Trees

Schaller¹,

Hellmuth²,

Stadler³

2021

Preprint

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Horizontal gene transfer events partition a gene tree T and thus, its leaf set into subsets of genes whose evolutionary history is described by speciation and duplication events alone. Indirect phylogenetic methods can be used to infer such partitions P from sequence similarity or evolutionary distances without any a priory knowledge about the underlying tree T . In this contribution, we assume that such a partition P of a set of genes X is given and that, independently, an estimate T of the original gene tree on X has been derived. We then ask to what extent T and the xenology information, i.e., P can be combined to determine the horizontal transfer edges in T . We show that for each pair of genes x and y with x, y being in different parts of P, it can be decided whether there always exists or never exists a horizontal gene transfer in T along the path connecting y and the most recent common ancestor of x and y. This problem is equivalent to determining the presence or absence of the directed edge (x, y) in so-called Fitch graphs; a more finegrained version of graphs that represent the dependencies between the sets in P. We then consider the generalization to insufficiently resolved gene trees and show that analogous results can be obtained. We show that the classification of (x, y) can be computed in constant time after linear-time preprocessing. Using simulated gene family histories, we observe empirically that the vast majority of horizontal transfer edges in the gene tree T can be recovered unambiguously.

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Reconstruction of time-consistent species trees

Cited by 9 publications

References 52 publications

Indirect identification of horizontal gene transfer

Indirect identification of horizontal gene transfer

Relative Timing Information and Orthology inEvolutionary Scenarios

Orientation of Fitch Graphs and Detection of Horizontal Gene Transfer in Gene Trees

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