title: Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae).
abstract: We examine rate heterogeneity among evolutionary lineages of the grass family at two plasmid loci, ndhF and rbcL, and we introduce a method to determine whether patterns of rate heterogeneity are correlated between loci. We show both that rates of synonymous evolution are heterogeneous among grass lineages and that are heterogeneity is correlated between loci at synonymous sites. At nonsynonymous sites, the pattern of rate heterogeneity is not correlated between loci, primarily due to an aberrant pattern of rate heterogeneity at nonsynonymous sites of rbcL. We compare patterns of synonymous rate heterogeneity to predictors based on the generation time effect and the speciation rate hypotheses. Although there is some evidence for generation time effects, neither generation time effects nor speciation rates appear to be sufficient to explain patterns of rate heterogeneity in the grass plastid sequences.
authors.affiliation: Department of Plant Sciences, Rutgers University, New Brunswick, New Jersey 08903, USA. gaut@ahab.rutgers.edu
authors.forename: B S
authors.initials: BS
authors.lastname: Gaut
authors.forename: L G
authors.initials: LG
authors.lastname: Clark
authors.forename: J F
authors.initials: JF
authors.lastname: Wendel
authors.forename: S V
authors.initials: SV
authors.lastname: Muse
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D001483:Base Sequence; D005075:Biological Evolution; D018742:DNA, Chloroplast / Q000235:genetics*; D017343:Genes, Plant; D008969:Molecular Sequence Data; D009245:NADH Dehydrogenase; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D006109:Poaceae / Q000235:genetics*; D012273:Ribulose-Bisphosphate Carboxylase
chemical_list: D001426:Bacterial Proteins; D018742:DNA, Chloroplast; D010940:Plant Proteins; C489904:NdhF protein, plant; D009245:NADH Dehydrogenase; C101625:RbcL protein, plastid; D012273:Ribulose-Bisphosphate Carboxylase