Abstract
The gene duplication model, which has been pioneered by Goodman et al. nearly 40 years ago, is widely-used for resolving the discordance between the evolutionary history of a gene family (gene tree), and the species tree through which this family has evolved. This discordance is explained by reconciling the gene tree with postulated gene duplications that have occurred while the gene tree has evolved along the edges of the species tree, such that the reconciled tree can be embedded into the species tree. Today, for many gene families lower bounds on the number of gene duplications that have occurred along each edge in the species tree can be derived, for example, from known genome duplications. Here, we augment the gene duplication model by using a species tree for the reconciliation whose edges are decorated with such lower bounds, called a (duplication) scenario. A scenario is feasible for a gene family under consideration if there exists a reconciled gene tree for this family whose embedding into the species tree satisfies the lower bounds of the scenario. Non-feasibility of a credible scenario for a gene family can provide a strong indication that this family might not be well-resolved, and identifying well-resolved gene families is a challenging task in evolutionary biology. Here, we provide a linear time algorithm that decides whether a scenario is not feasible when provided a gene family.
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Markin, A., Vadali, V.S.K.T., Eulenstein, O. (2018). Solving the Gene Duplication Feasibility Problem in Linear Time. In: Wang, L., Zhu, D. (eds) Computing and Combinatorics. COCOON 2018. Lecture Notes in Computer Science(), vol 10976. Springer, Cham. https://doi.org/10.1007/978-3-319-94776-1_32
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DOI: https://doi.org/10.1007/978-3-319-94776-1_32
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