Soft anatomy, diffuse homoplasy, and the relationships of lizards and snakes

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Abstract
Most previous phylogenetic analyses of squamates (‘lizards’ and snakes) employing large character sets have focused on osteology. Soft anatomical traits bearing on this problem have usually been considered in small subsets. Here, a comprehensive phylogenetic analysis of squamate soft anatomy is attempted. 126 informative characters are assessed for 23 squamate lineages, representing snakes, amphisbaenians, dibamids, and all the traditionally recognized ‘families’ of lizards. The traditionally recognized groupings Iguania, Scleroglossa, Gekkota, Scincomorpha, Anguimorpha and Varanoidea are corroborated in this analysis. More controversial taxa are resolved as follows. Xantusiids, amphisbaenians and dibamids cluster with gekkotans, and snakes are strongly allied with anguimorphs in general, and varanids in particular. Nearly all these clades are congruent with those found in a recent comprehensive osteological analysis; the strong support for snake‐varanid relationships found in both studies is particularly notable. This congruence is surprising given that previous studies of soft anatomy tended to give differing and often heterodox results. These previous results can be attributed to overrepresentation of misleading characters in small isolated data sets. Such misleading signals are minimized when data sets are combined. For instance, the snake‐varanid clade is contradicted by many characters, and analyses of particular organ systems therefore give differing results. However, characters that are incongruent with the snake‐varanid clade also disagree with each other (diffuse homoplasy), rather than forming coherent support for some particular alternative clade (concerted homoplasy). In a combined analysis these incongruent but diffuse characters cancel each other out to leave a very strong (and orthodox) phylogenetic signal. These results underscore the view that the raw amount of homoplasy — as revealed by consistency and retention indices — is not the only determinant of phylogenetic signal; the distribution of that homoplasy is also important. Thus, questioning a phylogenetic hypothesis (e.g. the snake‐varanid clade) by identifying numerous conflicting characters is insufficient — the structure of the conflicting characters should be assessed in a rigorous phylogenetic analysis.