Data from: Using novel phylogenetic methods to evaluate mammalian mtDNA, including amino acid-invariant sites-LogDet plus site stripping, to detect internal conflicts in the data, with special reference to the positions of hedgehog, armadillo, and elephant

We look at the higher-order phylogeny of mammals, analyzing in detail the complete mtDNA sequences of over 40 species. We test the support for several proposed super-ordinal relationships. To this end, we apply a number of recently programmed methods and approaches, plus better established methods. New pairwise tests show that there is highly significant evidence that amino acid frequencies are changing among nearly all the genomes studied when unvaried sites are ignored. LogDet amino acid distances, with modifications 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 slower evolving sites, we exclude the more rapidly evolving sites from the data 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 that many of the earlier branching patterns in the placental subtree could be incorrect, and this includes the placement of the root. The tRNA genes, for example, favour a split between the group hedgehog, 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 stripped amino acid data, while rodent monophyly is also common. The elephant sequence allows confident rejection of the older taxon Ferungulata (Simpson 1945). In its place, the new taxa Scrotifera and Fereuungulata is defined. A new likelihood ratio test is used to detect differences between the optimal tree for tRNA versus that for amino acids. While not clearly significant as made, there are indications the test is tending towards significance with more general models of evolution. Individual placement tests suggest alternative positions for hedgehog, and the elephant. There are striking congruence arguments to support elephant and armadillo together, suggesting a superordinal group composed of Xenarthra and African endemic mammals, which in turn may be near the root of the placental subtree. Thus, the analyses while casting doubt on some recent conclusions, are also unveiling some interesting new possibilities