Data Set Incongruence and the Phylogeny of Crocodilians

Abstract

Published sets of systematic data on crocodilians (18S and 28S nuclear ribosomal DNA [rDNA] restriction fragments, mitochondrial rDNA restriction fragments, 12S mitochondrial rDNA sequences, osteology, external morphology, dentition, nest type, albumin, parasites) were used to test hypotheses of data set incongruence and phylogeny. Comparing incongruence indices between molecular versus molecular data set comparisons and molecular versus morphological data set comparisons showed the morphological/molecular comparisons to be significantly more incongruent, and experiments removing taxa suggested that morphological incongruence can be localized to the separation of Gavialis from Tomistotna. Significance tests of incongruence between the five larger crocodilian data sets relative to each other and to combined data sets supported these hypotheses and demonstrated that only 1 (12S sequences vs. morphology) of the 10 pairwise comparisons of data sets show significant incongruence. Three hypotheses of crocodilian phylogeny were evaluated using combined parsimony analysis, separate parsimony analyses, and evaluation of uncombinable data. The (alligatorids(crocodylids(Gavialis, Tomistoma))) hypothesis of crocodilian relationships was best supported. Although this hypothesis is not supported by one of the molecular data sets and requires additional morphological homoplasy beyond that required in most-parsimonious trees based on morphology, other hypotheses require even more homoplasy, and any particular hypothesis of crocodilian evolution requires additional homoplasy in more than one data set. Alligatorid relationships were robustly supported in both combined and separate analyses. Crocodylus relationships were not well resolved in most-parsimonious trees from any individual data set but were completely resolved in the combined analysis.