Limitations to the Use of Tissue-specific Gene Expression Characters in the Phylogenetic Analyses of Non-avian Reptiles
Ecology, Evolution, and Organismal Biology
Tissue-specific gene expression characters have only limited value for ascertaining phylogenetic relationships when tested using the known phylogeny of non-avian reptiles. Two different coding methods were employed to test the utility of this data set. In the first coding method, the tissue is treated as the character and the presence/absence of the enzyme activity of a particular locus is the character state. The second method employed the locus as the character and the tissue array as the state.
When rooted with a tortoise (Gopherus) as the outgroup, no trees produced the expected result showing the two squamates (Crotalus and Cnemidophorus) as a monophyletic taxon with Sphenodon their sister and with Alligator. sister group to the lepidosaur clade. Testing for skewness in the frequency distribution of tree lengths yielded values for the g(1) statistic indicating that there was little phylogenetic information to be found in these data. When the tissue distribution characters were plotted on the expected tree, the majority of them proved to be phylogenetically uninformative. Forty-two of them (72%) were interpreted as being autapomorphies or homoplasies. Only 16 of the 58 characters were synapomorphies and, of these, 9 represented the loss of expression in a tissue. With only seven of the characters acting as reliable synapomorphies, tissue-specific gene expression data were of limited value in trying to resolve higher level relationships among non-avian reptiles.
Biochemical Systematics and Ecology
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