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Gene Tree Parsimony in the Presence of Gene Duplication, Loss, and Incomplete Lineage Sorting

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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

Inferring species trees from multi-locus data needs to account for gene tree discordance due to various biological processes, including incomplete lineage sorting (ILS) and gene duplication and loss (GDL). Gene tree parsimony (GTP) is a popular approach for estimating species trees that seeks to minimize the number of evolutionary events required to reconcile the species tree with gene trees. Minimizing gene duplication and loss (MGD and MGDL) are GTP approaches that typically make the simplifying assumption that population-related effects such as incomplete lineage sorting (ILS) are negligible. However, this assumption is problematic for denser phylogenies, where ILS is more prominent. Here, we extend the existing GTP methods to account for both GDL and ILS by minimizing a weighted sum of the GDL and “deep” coalescence events required for a given collection of gene trees. We provide a graph-theoretic characterization and present a dynamic programming algorithm for this problem. Through an extensive evaluation study on a collection of simulated and empirical datasets, we compared our proposed GTP approaches with the leading methods in the field.

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Data Availability Statement

DynaDup-DLX is freely available in open source form at https://github.com/prottoy99/DynaDup. All the datasets analyzed in this paper are from previously published studies and are publicly available.

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Authors and Affiliations

  1. Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, 1205, Bangladesh

    Prottoy Saha, Md. Shamiul Islam, Tasnim Rahman, Adiba Shaira, Kazi Noshin, Rezwana Reaz & Md. Shamsuzzoha Bayzid

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  1. Prottoy Saha
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  2. Md. Shamiul Islam
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  4. Adiba Shaira
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  5. Kazi Noshin
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  7. Md. Shamsuzzoha Bayzid
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Correspondence to Md. Shamsuzzoha Bayzid .

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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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Saha, P. et al. (2024). Gene Tree Parsimony in the Presence of Gene Duplication, Loss, and Incomplete Lineage Sorting. 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_6

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