Graphs obtained from a binary leaf labelled ('phylogenetic') tree by adding an edge so as to introduce a cycle provide a useful representation of hybrid evolution in biology. This class of graphs (which we call 'phylogenetic clocks') also has some attractive combinatorial properties, which we present. We characterize when a set of binary phylogenetic trees is displayed by a phylogenetic clock in terms of tree rearrangement operations. This leads to a triple-wise compatibility theorem, and a simple, fast algorithm to determine clock compatibility. We also use generating function techniques to provide closed-form expressions that enumerate phylogenetic clocks with specified or unspecified cycle length.
SubjectsField of Research::01 - Mathematical Sciences::0102 - Applied Mathematics::010202 - Biological Mathematics
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