Using Novel Phylogenetic Methods to Evaluate Mammalian mtDNA, Including Amino Acid-Invariant Sites-LogDet plus Site Stripping, to Detect Internal Conicts in the Data, with Special Reference to the Positions of Hedgehog, Armadillo, and Elephant

Abstract.—We look at the higher-order phylogeny of mammals, analyzing in detail the complete mtDNAsequences ofmore than 40 species.We test the support for several proposed superordinal re-lationships. To this end, we apply a number of recently programmed methods and approaches, plus better-established methods. New pairwise tests show highly signicant evidence that amino acid frequencies are changing among nearly all the genomes studied when unvaried sites are ignored. LogDet amino acid distances, with modications to take into account invariant sites, are combined with bootstrapping and the Neighbor Joining algorithm to account for these violations of standard models. To weight the more slowly evolving sites, we exclude the more rapidly evolving sites from the data by using “site stripping”. This leads to changing optimal trees with nearly all methods. The bootstrap support for many hypotheses varies widely between methods, and few hypotheses can claim unanimous support from these data. Rather, we uncover good evidence thatmany of the earlier branching patterns in the placental subtree could be incorrect, including the placement of the root. The tRNAgenes, for example, favor a split between thegrouphedgehog, rodents, and primates versus all other sequenced placentals. Such a grouping is not ruled out by the amino acid sequence data. A grouping of all rodents plus rabbit, the old Glires hypothesis, is also feasible with strippe