Abstract
DNA-based species assignment and delimitation are two important problems in systematic biology. In a recent work of O'Meara, species delimitation is investigated through coupling it with species tree inference in the framework of gene tree and species tree reconciliation. We present a polynomial time algorithm for splitting individuals into species to minimize the deep coalescence cost of the gene tree and species tree reconciliation, a species assignment problem arises from species delimitation via gene tree and species tree reconciliation. How to incorporate this proposed algorithm into the heuristic search strategy of O'Meara for species delimitation is also discussed. The proposed algorithm is implemented in C++.
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