Mitogenomic relationships of placental mammals and molecular estimates of their divergences

• Published in: Gene Vol. 421; no. 1; pp. 37 - 51
• Main Authors: Arnason, Ulfur, Adegoke, Joseph A., Gullberg, Anette, Harley, Eric H., Janke, Axel, Kullberg, Morgan
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 15-09-2008
• Subjects: Animals; Artiodactyla; Biogeography; Biologi; Biological Sciences; Carnivora; Cetacea; Chiroptera; Dermoptera; Genome, Mitochondrial; Geography; Hominidae - classification; Hominidae - genetics; Humans; Hyracoidea; Lagomorpha; Lipotyphla; Macroscelidea; Mammalia; Mammals - classification; Mammals - genetics; Mammuthus; Mitochondrial Eve; Mitochondrial Proteins - genetics; Natural Sciences; Naturvetenskap; Perissodactyla; Pholidota; Phylogeny; Placentalia; Primates; Proboscidea; Rodentia; Sequence Analysis, Protein; Sirenia; Suillus; Temporal estimates of eutherian divergences; Tubulidentata; Xenarthra; aa; K/T boundary; Placentalia; Mammalia; MYA; nt; mt; Mitochondrial Eve; Primates; Biogeography; Temporal estimates of eutherian divergences; Phylogeny
• ISSN: 0378-1119; 1879-0038; 1879-0038
• DOI: 10.1016/j.gene.2008.05.024

Molecular analyses of the relationships of placental mammals have shown a progressive congruence between mitogenomic and nuclear phylogenies. Some inconsistencies have nevertheless persisted, notably with respect to basal divergences. The current study has aimed to extend the representation of groups, whose position in the placental tree has been difficult to establish in mitogenomic studies. Both ML (maximum likelihood) and Bayesian analyses identified four basal monophyletic groups, Afroplacentalia (=
Afrotheria: Hyracoidea, Proboscidea, Sirenia, Tenrecidea, Tubulidentata, Macroscelidea, Chrysochloridea), Xenarthra, Archontoglires (Primates, Dermoptera, Scandentia, Lagomorpha, Rodentia) and Laurasiaplacentalia (Lipotyphla, Chiroptera, Pholidota, Carnivora, Perissodactyla, Artiodactyla, Cetacea). All analyses joined Archontoglires and Laurasiaplacentalia on a common branch (Boreoplacentalia), but the relationship between Afroplacentalia, Xenarthra and Boreoplacentalia was not conclusively resolved. The phylogenomic hypothesis with a sister group relationship between Notoplacentalia (Afroplacentalia/Xenarthra) and Boreoplacentalia served as the basis for estimating the times of placental divergences using paleontologically well-supported mammalian calibration points. These estimates placed the basal placental divergence between Boreoplacentalia and Notoplacentalia at ≈
102 MYA (million years ago). The current estimates of ordinal placental divergences are congruent with recent estimates based on nuclear data, but inconsistent with paleontological notions that have placed the origin of essentially all placental orders within an interval of 5–10 MY in the early Tertiary. Among less deep divergences the estimates placed the split between
Gorilla and
Pan/
Homo at ≈
11.5 MYA and that between
Pan and
Homo at ≈
8 MYA. As a consequence of these estimates, which are in accord with recent progress in primate paleontology, the earliest divergences among recent humans become placed ≈
270,000 years ago, i.e. ≈
100,000 years earlier than the traditional age of “Mitochondrial Eve”. Comparison between the two new mt genomes of
Hylomys suillus (short-tailed gymnure) patently demonstrates the inconsistency that may exist between taxonomic designations and molecular difference, as the distance between these two supposedly conspecific genomes exceeds that of the three elephantid genera
Elephas,
Mammuthus and
Loxodonta. In accordance with the progressive use of the term Placentalia for extant orders and extinct taxa falling within this group we forward new proposals for the names of some superordinal clades of placental mammals.