Integration of morphological data sets for phylogenetic analysis of amniota: The importance of integumentary characters and increased taxonomic sampling

The amniote integument (skin and its associated structures) represents a highly diversified anatomical system that has repeatedly undergone modification into structurally and functionally unique forms. Because it consists primarily of soft tissues, the integument is frequently disregarded in studies of vertebrate morphology that incorporate fossils. Osteoderms ("skin bones"), however, present an exceptional opportunity to study the integument in extinct animals due to their high fossilization potential. Here, the anatomy and histological microstructure of the soft and osseous components of the integument are described for all major clades of amniotes that possess osteoderms. The integumentary data gathered are added to existing morphological data sets to examine the effects on phylogeny of increasing both taxonomic and character sampling. In this context, I address the historically confounding issue of the evolutionary relationships of turtles. Evaluation of character data compiled from prior studies of ammote phylogeny supports the hypothesis that, despite their solidly constructed and seemingly plesiomorphic skulls, turtles are phylogenetically nested among diapsids, reptiles with a doubly fenestrated skull roof. Doubling the number of ingroup taxa leads to a decrease in overall phylogenetic resolution, indicating that existing characters used for amniote phylogeny are insufficient to explain the evolution of more highly nested taxa. Incorporation of new data from the soft and osseous components of the integument, however, helps resolve relationships among both basal and highly nested amniote taxa. Analysis of the largest morphological data set compiled to date for amniotes (80 taxa and 368 characters, 71 original to this study) supports monophyly of Amniota, Synapsida, Reptilia, Parareptilia, Eureptilia, Eosuchia, Diapsida, Neodiapsida, Sauria, Lepidosauria, and Archosauriformes, as well as several more highly nested divisions within the latter two clades. Turtles are here resolved as the sister taxon to a monophyletic Lepidosauria (squamates + Sphenodon ), a novel phylogenetic position that nevertheless is consistent with recent molecular and morphological studies that have hypothesized diapsid affinities for this clade.