title: Indels in protein-coding sequences of Euarchontoglires constrain the rooting of the eutherian tree.
abstract: Despite the availability of large molecular data sets, the position of the root of the eutherian tree remains a controversial issue. Depending on source data, taxon sampling and analytical approach, the root can be placed at either Afrotheria, Xenarthra, Afrotheria+Xenarthra, or murid rodents. We explored the phylogenetic potential of indels in four nuclear protein-coding genes (SCA1, PRNP, TNFalpha, and HspB3) with regard to a possible rooting at the murid branch. According to parsimony principles, five indels were interpreted to contradict such a rooting, and one indel to support it. The results illustrate that indels, despite the occurrence of homoplasy, can be convincing sources of independent molecular evidence to distinguish between alternative phylogenetic hypotheses.
authors.affiliation: Department of Biochemistry, 161 NCMLS, University of Nijmegen, The Netherlands. w.dejong@ncmls.kun.nl
authors.forename: Wilfried W
authors.initials: WW
authors.lastname: de Jong
authors.forename: Marjon A M
authors.initials: MA
authors.lastname: van Dijk
authors.forename: Céline
authors.initials: C
authors.lastname: Poux
authors.forename: Guido
authors.initials: G
authors.lastname: Kappé
authors.forename: Teun
authors.initials: T
authors.lastname: van Rheede
authors.forename: Ole
authors.initials: O
authors.lastname: Madsen
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000067528:Ataxins; D001426:Bacterial Proteins; D001499:Bayes Theorem; D017931:DNA Primers; D006360:Heat-Shock Proteins / Q000235:genetics; D016013:Likelihood Functions; D008322:Mammals / Q000145:classification* / Q000235:genetics*; D008969:Molecular Sequence Data; D009419:Nerve Tissue Proteins / Q000235:genetics; D009687:Nuclear Proteins / Q000235:genetics; D010802:Phylogeny; D017354:Point Mutation / Q000235:genetics*; D014409:Tumor Necrosis Factor-alpha / Q000235:genetics
chemical_list: D000067528:Ataxins; D001426:Bacterial Proteins; D017931:DNA Primers; D006360:Heat-Shock Proteins; C112564:HspB protein, Helicobacter pylori; D009419:Nerve Tissue Proteins; D009687:Nuclear Proteins; D014409:Tumor Necrosis Factor-alpha