Previous analyses of relations, divergence times, and diversification patterns among extant mammalian families have relied on supertree methods and local molecular clocks. We constructed a molecular supermatrix for mammalian families and analyzed these data with likelihood-based methods and relaxed molecular clocks. Phylogenetic analyses resulted in a robust phylogeny with better resolution than phylogenies from supertree methods. Relaxed clock analyses support the long-fuse model of diversification and highlight the importance of including multiple fossil calibrations that are spread across the tree. Molecular time trees and diversification analyses suggest important roles for the Cretaceous Terrestrial Revolution and Cretaceous-Paleogene (KPg) mass extinction in opening up ecospace that promoted interordinal and intraordinal diversification, respectively. By contrast, diversification analyses provide no support for the hypothesis concerning the delayed rise of present-day mammals during the Eocene Period.

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Kangaroos and kin (Macropodiformes) are the most conspicuous elements of the Australasian marsupial fauna. The approximately 70 living species can be divided into three families: (1) Hypsiprymnodontidae (the musky rat kangaroo); (2) Potoroidae (potoroos and bettongs); and (3) Macropodidae (larger kangaroos, wallabies, banded hare wallaby and pademelons). Here we examine macropodiform relationships using protein-coding portions of the ApoB, BRCA1, IRBP, Rag1 and vWF genes via maximum parsimony, maximum likelihood and Bayesian methods. We estimate times of divergence using two different relaxed molecular clock methods to present a timescale for macropodiform evolution and reconstruct ancestral states for grades of dental organisation. We find robust support for a basal split between Hypsiprymnodontidae and the other macropodiforms, potoroid monophyly and macropodid monophyly, with Lagostrophus as the sister-taxon to all other macropodids. Our divergence estimates suggest that kangaroos diverged from Phalangeroidea in the early Eocene, that crown-group Macropodiformes originated in the late Eocene or early Oligocene and that the potoroid–macropodid split occurred in the late Oligocene or early Miocene followed by rapid cladogenesis within these families 5 to 15 million years ago. These divergence estimates coincide with major geological and ecological changes in Australia. Ancestral state reconstructions for grades of dental organisation suggest that the grazer grade evolved independently on two different occasions within Macropodidae.

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The phylogenetic relationship among primates, ferungulates (artiodactyls + cetaceans + perissodactyls + carnivores), and rodents was examined using proteins encoded by the H strand of mtDNA, with marsupials and monotremes as the outgroup. Trees estimated from individual proteins were compared in detail with the tree estimated from all 12 proteins (either concatenated or summing up log-likelihood scores for each gene). Although the overall evidence strongly suggests ((primates, ferungulates), rodents), the ND1 data clearly support another tree, ((primates, rodents), ferungulates). To clarify whether this contradiction is due to (1) a stochastic (sampling) error; (2) minor model-based errors (e.g., ignoring site rate variability), or (3) convergent and parallel evolution (specifically between either primates and rodents or ferungulates and the outgroup), the ND1 genes from many additional species of primates, rodents, other eutherian orders, and the outgroup (marsupials + monotremes) were sequenced. The phylogenetic analyses were extensive and aimed to eliminate the following artifacts as possible causes of the aberrant result: base composition biases, unequal site substitution rates, or the cumulative effects of both. Neither more sophisticated evolutionary analyses nor the addition of species changed the previous conclusion. That is, the statistical support for grouping rodents and primates to the exclusion of all other taxa fluctuates upward or downward in quite a tight range centered near 95% confidence. These results and a site-by-site examination of the sequences clearly suggest that convergent or parallel evolution has occurred in ND1 between primates and rodents and/or between ferungulates and the outgroup. While the primate/rodent grouping is strange, ND1 also throws some interesting light on the relationships of some eutherian orders, marsupials, and montremes. In these parts of the tree, ND1 shows no apparent tendency for unexplained convergences.