title: Protein sequence signatures support the African clade of mammals.
abstract: DNA sequence evidence supports a superordinal clade of mammals that comprises elephants, sea cows, hyraxes, aardvarks, elephant shrews, golden moles, and tenrecs, which all have their origins in Africa, and therefore are dubbed Afrotheria. Morphologically, this appears an unlikely assemblage, which challenges-by including golden moles and tenrecs-the monophyly of the order Lipotyphla (Insectivora). We here identify in three proteins unique combinations of apomorphous amino acid replacements that support this clade. The statistical support for such "sequence signatures" as unambiguous synapomorphic evidence for the naturalness of the Afrotherian clade is reported. Using likelihood, combinatorial, and Bayesian methods we show that the posterior probability of the mammalian tree containing the Afrotherian clade is effectively 1.0, based on conservative assumptions. Presenting sequence data for another African insectivore, the otter shrew Micropotamogale lamottei, we demonstrate that such signatures are diagnostic for including newly investigated species in the Afrotheria. Sequence signatures provide "protein-morphological" synapomorphies that may aid in visualizing monophyletic groupings.
authors: Department of Biochemistry, University of Nijmegen, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands.
authors: M A
authors: MA
authors: van Dijk
authors: O
authors: O
authors: Madsen
authors: F
authors: F
authors: Catzeflis
authors: M J
authors: MJ
authors: Stanhope
authors: W W
authors: WW
authors: de Jong
authors: M
authors: M
authors: Pagel
mesh_terms: D000349:Africa; D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D000818:Animals; D051399:Aquaporin 2; D051403:Aquaporin 6; D020346:Aquaporins / Q000737:chemistry / Q000235:genetics; D001499:Bayes Theorem; D019295:Computational Biology; D003459:Crystallins / Q000737:chemistry / Q000235:genetics; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics; D019992:Databases as Topic; D019143:Evolution, Molecular; D016013:Likelihood Functions; D008322:Mammals / Q000145:classification / Q000235:genetics; D008969:Molecular Sequence Data; D009687:Nuclear Proteins; D010802:Phylogeny; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment; D017421:Sequence Analysis
chemical_list: D051399:Aquaporin 2; D051403:Aquaporin 6; D020346:Aquaporins; D003459:Crystallins; D004268:DNA-Binding Proteins; D009687:Nuclear Proteins; D011506:Proteins