In Search of Homoplastic Tendencies: Statistical Inference of Topological Patterns in Homoplasy

Abstract

The "tendency" for homoplasy to appear in closely related taxa has been widely discussed but rarely quantified. This paper proposes statistical tests that examine the topological distribution of homoplasy within characters in phylogenies. They test whether character changes are localized (confined to some subtree), or clustered (occur in proximity to each other), relative to two null models of character evolution. Null Model I assumes that the observed number of character changes are dispersed randomly among the internodes of the tree, whereas Model II weights the probability that an internode contains a change by the length of that internodeestimated by the total number of character changes along that internode. Localization is measured by the largest furthest-neighbor distance between changes, clustering by the mean nearest neighbor distance. Distances are measured either by the number of intervening branches or the number of intervening character changes. Analyses of four cladistic data sets from the literature reveal very few characters that exhibit significant levels of clustering or localization-no more than would be expected by chance. In every data set a majority of characters exhibited at least weak tendencies, but in only one data set was there a significant excess of such characters. The present findings do not provide compelling evidence for the existence of "tendencies" in homoplasy, at least among characters used to reconstruct phylogenies. They should be sought elsewhere, in cladistic analyses oflarger scope, probably among a class of characters defined a priori on a structural or functional basis.

A Phylogenetic Hot Spot for Evolutionary Novelty in Middle American Treefrogs

“…The idea that the same feature may repeatedly evolve among closely related species has a long history in evolutionary biology (reviewed by Sanderson 1991). Some of this history is related to the idea of “orthogenesis,” which suggests that species are predisposed to evolve certain traits, although orthogenesis itself has been largely discredited (Sanderson 1991; Futuyma 2005). Sanderson (1991) developed statistical phylogenetic methods for testing for such “homoplastic tendencies,” but did not focus on novelties per se as we have done.…”

“…Some of this history is related to the idea of “orthogenesis,” which suggests that species are predisposed to evolve certain traits, although orthogenesis itself has been largely discredited (Sanderson 1991; Futuyma 2005). Sanderson (1991) developed statistical phylogenetic methods for testing for such “homoplastic tendencies,” but did not focus on novelties per se as we have done. His tests address whether changes in a given character: (1) occur near other changes in the same character on the tree, and (2) occur in only one localized subclade of the tree.…”

Why Does a Trait Evolve Multiple Times Within a Clade? Repeated Evolution of Snakeline Body Form in Squamate Reptiles

“…Dates were estimated using penalized likelihood (Sanderson 2002), a modified molecular clock method that does not assume rate homogeneity among lineages. Eleven fossil calibration points were utilized.…”

“…Yet these factors are largely neglected in the current literature, including an edited volume devoted exclusively to homoplasy (Sanderson and Hufford 1996). Previous studies have also discussed general trends in character evolution (e.g., Mc-Namara 1990;McShea 1994;Wagner 1996), and biased patterns of homoplasy (e.g., more changes in some clades than others or more losses than gains ;Sanderson 1991;, but with little discussion of the roles of biogeography and competition. Nevertheless, some phylogenetic studies have described cases where competition and/or biogeography may drive patterns of homoplasy.…”

Power of the Concentrated Changes Test for Correlated Evolution

“…The CCT could be modi ed to allow different probabilities of change on different branches by changing the null model from one of random distribution of changes to one where the probability of change on a branch depends on its length (Sanderson, 1991). Pagel (1994a) developed a maximum likelihood approach that gives a measure of the correlated evolution of two traits while taking branch lengths into account.…”