Genomics, biogeography, and the diversification of placental mammals

doi:10.1073/pnas.0704342104

Genomics, biogeography, and the diversification of placental mammals

^†Perinatology Research Branch, National Institute of Child Health and Human Development/National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892;
^‡Center For Molecular Medicine and Genetics, and
Departments of ^§Obstetrics and Gynecology and
^‡‡Anatomy and Cell Biology, Wayne State University, Detroit, MI 48201;
^‖School of Biological Sciences, University of Nebraska, Lincoln, NE 68588; and
^††Laboratory of Computer Science, Robotics, and Microelectronics, Centre National de la Recherche Scientifique, Université Montpellier II, 161 Rue Ada, 34392 Montpellier, France

Contributed by Morris Goodman, May 9, 2007 (received for review May 4, 2007)

Abstract

Previous molecular analyses of mammalian evolutionary relationships involving a wide range of placental mammalian taxa have been restricted in size from one to two dozen gene loci and have not decisively resolved the basal branching order within Placentalia. Here, on extracting from thousands of gene loci both their coding nucleotide sequences and translated amino acid sequences, we attempt to resolve key uncertainties about the ancient branching pattern of crown placental mammals. Focusing on ≈1,700 conserved gene loci, those that have the more slowly evolving coding sequences, and using maximum-likelihood, Bayesian inference, maximum parsimony, and neighbor-joining (NJ) phylogenetic tree reconstruction methods, we find from almost all results that a clade (the southern Atlantogenata) composed of Afrotheria and Xenarthra is the sister group of all other (the northern Boreoeutheria) crown placental mammals, among boreoeutherians Rodentia groups with Lagomorpha, and the resultant Glires is close to Primates. Only the NJ tree for nucleotide sequences separates Rodentia (murids) first and then Lagomorpha (rabbit) from the other placental mammals. However, this nucleotide NJ tree still depicts Atlantogenata and Boreoeutheria but minus Rodentia and Lagomorpha. Moreover, the NJ tree for amino acid sequences does depict the basal separation to be between Atlantogenata and a Boreoeutheria that includes Rodentia and Lagomorpha. Crown placental mammalian diversification appears to be largely the result of ancient plate tectonic events that allowed time for convergent phenotypes to evolve in the descendant clades.

Footnotes

^¶To whom correspondence may be addressed. E-mail: prbchiefstaff{at}med.wayne.edu, dwildman{at}med.wayne.edu, or mgoodwayne{at}aol.com
Author contributions: D.E.W., J.C.O., R.R., and M.G. designed research; D.E.W., M.U., J.C.O., and G.L., performed research; D.E.W., M.U., J.C.O., G.L., V.L., S.G., O.G., and M.G. analyzed data; and D.E.W., M.U., J.C.O., L.I.G., R.R., and M.G. wrote the paper.
The authors declare no conflict of interest.
This article contains supporting information online at www.pnas.org/cgi/content/full/0704342104/DC1.
Abbreviations:

MP,

maximum parsimony;

ML,

maximum likelihood;

NJ,

neighbor-joining.
Freely available online through the PNAS open access option.