TreeBASE Search-Trees for study 994

@ARTICLE{TreeBASE2Ref15748, author = {John Harshman and Christopher J. Huddleston and Jonathan P. Bollback and Thomas J. Parsons and Michael J. Braun}, title = {True and False Gavials: A Nuclear Gene Phylogeny of Crocodylia.}, year = {2003}, keywords = {c-myc; crocodylia; data conflict; data partitions; partitioned likelihood analysis; phylogeny; rooting}, doi = {10.1080/10635150390197028}, url = {}, pmid = {}, journal = {Systematic Biology}, volume = {52}, number = {3}, pages = {386--402}, abstract = {The phylogeny of Crocodylia offers an unusual twist on the usual ?molecules vs. morphology? story. The true gharial (Gavialis gangeticus) and the false gharial (Tomistoma schlegelii), as their common names imply, are found in all cladistic morphological analyses to be distantly related species, convergent upon a similar morphology. In contrast, all previous molecular studies have found them to be sister taxa. We present the first phylogenetic study of Crocodylia using a nuclear gene. We cloned and sequenced the c-myc proto-oncogene from Alligator mississippiensis to facilitate primer design. Then we sequenced an 1100bp fragment that includes both coding and non-coding regions, as well as informative indels, for one species in each extant crocodylian genus and six avian outgroups. Phylogenetic analyses using parsimony, maximum likelihood, and Bayesian inference all strongly agree on the same tree, which is identical to the tree found in previous molecular analyses: Gavialis and Tomistoma are sister taxa, and together are the sister group of Crocodylidae. Kishino-Hasegawa tests reject the morphological tree in favor of the molecular tree. We exclude long branch attraction and variation in base composition among taxa as explanations for this topology. To explore the causes of discrepancy between molecular and morphological estimates of crocodylian phylogeny, we examined puzzling features of the morphological data using a priori partitions of the data based on anatomical regions, and investigated the effects of different codings of two obvious morphological similarities of the two gharials.} }