Continuous Track Analysis: A New Phylogenetic and Biogeographic Method

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Abstract
—Continuous track analysis (CTA) can depict reticulate evolutionary patterns in phylogenetics and biogeography. A reticulate connection implies convergence, hybridization, or introgression in an evolutionary graph of taxa and implies dispersal in an evolutionary graph of biogeographic areas. CTA finds graphs that (1) have a minimal number of connections and (2) imply that most character states or taxa have distributions or tracks across taxa or areas (objects) that are continuous, i.e., can be traced across the connections among the objects including that state without traveling through any other objects. Continuous tracks imply either that character states in phylogenies have unique evolutionary origins or that taxa in biogeographic analyses are monophyletic. Relatively simple graphs usually cannot imply completely continuous tracks. Therefore, CTA graphs seek to minimize the number of track fragments, which are locally continuous parts of a track; tracks with more than one fragment are discontinuous. Minimizing fragments is the same as minimizing character-state transitions only if there are no reticulations. Because hypothetical ancestors do little to reduce the number of fragments, CTA tends to place known taxa or areas at internal nodes. A heuristic algorithm analogous to tree bisection-reconnection is used to find highly parsimonious CTA graphs. In phylogenetic analyses, CTA employs a special complementary binary coding convention that serendipitously solves the missing characters/missing data problem. Although the problem of ancestors “inheriting” states from hybrid descendants is irrelevant if reticulations merely represent convergence patterns, CTA includes an optional algorithm that avoids such instances by explicitly identifying ancestors and descendants. CTA was compared with standard parsimony analysis using a data set of 17 Neogene species of North American fossil hipparionine horses. CTA separates the three major clades and illustrates their. convergent features with reticulations, whereas standard parsimony analysis groups the three in an unresolved polytomy. CTA also minimizes the number of hypothetical, unsampled ancestors and lineages.

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