Orientation of Fitch Graphs and Reconciliation-Free Inference of Horizontal Gene Transfer in Gene Trees

Schaller, David; Hellmuth, Marc; Stadler, Peter F.

doi:10.1137/22m150736x

Cited by 2 publications

(1 citation statement)

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“…To this end, we simulated gene family histories (GFHs) using the library AsymmeTree [18]. A GFH is represented as a gene tree T with n leaves embedded into a species tree S, see [19,Figure 2]. The tree S is simulated using a Yule model (constant speciation rate and null extinction rate) on n/2 species.…”

Section: Computational Resultsmentioning

confidence: 99%

Partial Fitch Graphs: Characterization, Satisfiability and Complexity∗

Hellmuth,

Korchmaros,

Ramírez-Rafael

et al. 2024

Preprint

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Horizontal gene transfer is an important contributor to evolution. Following Walter M. Fitch, two genes are xenologs if at least one HGT separates them. More formally, the directed Fitch graph has a set of genes as its vertices, and directed edges (x,y) for all pairs of genes x and y for which y has been horizontally transferred at least once since it diverged from the last common ancestor of x and y. Subgraphs of Fitch graphs can be inferred by comparative sequence analysis. In many cases, however, only partial knowledge about the "full" Fitch graph can be obtained. Here, we characterize Fitch-satisfiable graphs that can be extended to a biologically feasible "full" Fitch graph and derive a simple polynomial-time recognition algorithm. We then proceed to show that several versions of finding the Fitch graph with total maximum (confidence) edge-weights are NP-hard. In addition, we provide a greedy-heuristic for "optimally" recovering Fitch graphs from partial ones. Somewhat surprisingly, even if ~ 80% of information of the underlying input Fitch-graph G is lost (i.e., the partial Fitch graph contains only ~ 20% of the edges of G), it is possible to recover ~ 90% of the original edges of G on average.

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Section: Computational Resultsmentioning

confidence: 99%