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            Abstract Rooted binarygalledtrees generalize rooted binary trees to allow a restricted class of cycles, known asgalls. We build upon the Wedderburn-Etherington enumeration of rooted binary unlabeled trees withnleaves to enumerate rooted binary unlabeled galled trees withnleaves, also enumerating rooted binary unlabeled galled trees withnleaves andggalls,$$0 \leqslant g \leqslant \lfloor \frac{n-1}{2} \rfloor $$ . The enumerations rely on a recursive decomposition that considers subtrees descended from the nodes of a gall, adopting a restriction on galls that amounts to considering only the rooted binarynormalunlabeled galled trees in our enumeration. We write an implicit expression for the generating function encoding the numbers of trees for alln. We show that the number of rooted binary unlabeled galled trees grows with$$0.0779(4.8230^n)n^{-\frac{3}{2}}$$ , exceeding the growth$$0.3188(2.4833^n)n^{-\frac{3}{2}}$$ of the number of rooted binary unlabeled trees without galls. However, the growth of the number of galled trees with only one gall has the same exponential order 2.4833 as the number with no galls, exceeding it only in the subexponential term,$$0.3910n^{\frac{1}{2}}$$ compared to$$0.3188n^{-\frac{3}{2}}$$ . For a fixed number of leavesn, the number of gallsgthat produces the largest number of rooted binary unlabeled galled trees lies intermediate between the minimum of$$g=0$$ and the maximum of$$g=\lfloor \frac{n-1}{2} \rfloor $$ . We discuss implications in mathematical phylogenetics.more » « less
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            Mathur, Shaili; Rosenberg, Noah A. (, Algorithms for Molecular Biology)Abstract Objective In mathematical phylogenetics, a labeled rooted binary tree topology can possess any of a number of labeled histories, each of which represents a possible temporal ordering of its coalescences. Labeled histories appear frequently in calculations that describe the combinatorics of phylogenetic trees. Here, we generalize the concept of labeled histories from rooted phylogenetic trees to rooted phylogenetic networks, specifically for the class of rooted phylogenetic networks known as rooted galled trees . Results Extending a recursive algorithm for enumerating the labeled histories of a labeled tree topology, we present a method to enumerate the labeled histories associated with a labeled rooted galled tree. The method relies on a recursive decomposition by which each gall in a galled tree possesses three or more descendant subtrees. We exhaustively provide the numbers of labeled histories for all small galled trees, finding that each gall reduces the number of labeled histories relative to a specified galled tree that does not contain it. Conclusion The results expand the set of structures for which labeled histories can be enumerated, extending a well-known calculation for phylogenetic trees to a class of phylogenetic networks.more » « less
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