Escaping the matrix: a new algorithm for phylogenetic comparative studies of co-evolution

An algorithm for generating host cladograms from parasite‐host cladograms derived from parasite phylogenies, Phylogenetic Analysis for Comparing Trees (PACT), is described. PACT satisfies Assumption 0, that all the information in each parasite‐host cladogram must be used in a co‐evolutionary analysis, and that the host relationships depicted in the final host cladogram must be logically consistent with the phylogenetic relationships depicted in every part of every parasite‐host cladogram used to construct the host cladogram. It accounts for cases of speciation by host switching and expansion of host range, and reticulated host relationships, in addition to co‐speciation, sympatric speciation, and extinction in all input parasite‐host cladograms, and does so without a priori weighting schemes and without a posteriori manipulation of the data.