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Galled Perfect Transfer Networks

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Comparative Genomics (RECOMB-CG 2024)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 14616))

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Abstract

Predicting horizontal gene transfers often requires comparative sequence data, but recent work has shown that character-based approaches could also be useful for this task. Notably, perfect transfer networks (PTN) explain the character diversity of a set of taxa for traits that are gained once, rarely lost, but that can be transferred laterally. Characterizing the structure of such characters is an important step towards understanding more complex characters. Although efficient algorithms can infer such networks from character data, they can sometimes predict overly complicated transfer histories.

With the goal of recovering the simplest possible scenarios in this model, we introduce galled perfect transfer networks, which are PTNs that are galled trees. Such networks are useful for characters that are incompatible in terms of tree-like evolution, but that do fit in an almost-tree scenario. We provide polynomial-time algorithms for two problems: deciding whether one can add transfer edges to a tree to transform it into a galled PTN, and deciding whether a set of characters are galled-compatible, that is, they can be explained by some galled PTN.

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Notes

  1. 1.

    Note that we are not aware of complexity results for binary characters on PPNs without the no-loss condition.

  2. 2.

    Suppressing a subdivision node u with parent p and child v consists of removing u and adding an edge from p to v.

  3. 3.

    Note that we adapted this characterization, since in the original definition of PTNs, the taxa were treated as sets of characters instead of the other way around.

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Authors and Affiliations

  1. Department of Computer Science, Université de Sherbrooke, 2500 boul de l’Université, Quebec, J1K2R1, Canada

    Alitzel López Sánchez & Manuel Lafond

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  1. Alitzel López Sánchez
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  2. Manuel Lafond
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Correspondence to Alitzel López Sánchez .

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Editors and Affiliations

  1. CNRS, University of Montpellier, Montpellier, France

    Celine Scornavacca

  2. Center for Research and Advanced Studies, Irapuato, Mexico

    Maribel Hernández-Rosales

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López Sánchez, A., Lafond, M. (2024). Galled Perfect Transfer Networks. In: Scornavacca, C., Hernández-Rosales, M. (eds) Comparative Genomics. RECOMB-CG 2024. Lecture Notes in Computer Science(), vol 14616. Springer, Cham. https://doi.org/10.1007/978-3-031-58072-7_2

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