title: Size of the protein-coding genome and rate of molecular evolution.
abstract: In diploid populations of size N, there will be 2 Nmu mutations per nucleotide (nt) site (or per locus) per generation (mu stands for mutation rate). If either the population or the coding genome double in size, one expects 4 Nmu mutations. What is important is not the population size per se but the number of genes (coding sites), the two being often interconverted. Here we compared the total physical length of protein-coding genomes (n) with the corresponding absolute rates of synonymous substitution (K(S)), an empirical neutral reference. In the classical occupancy problem and in the coupons collector (CC) problem, n was expressed as the mean rate of change (K(CC)). Despite inherently very low power of the approaches involving averaging of rates, the mode of molecular evolution of the total size phenotype of the coding genome could be evidenced through differences between the genomic estimates of K(CC) [K(CC)=1/(ln n + 0.57721) n] and rate of molecular evolution, K(S). We found that (1) the estimates of n and K(S) are reciprocally correlated across taxa (r=0.812; p<< 0.001); (2) the gamete-cell division hypothesis (Chang et al. Proc Natl Acad Sci USA 91:827-831, 1994) can be confirmed independently in terms of K(CC)/K(S) ratios; (3) the time scale of molecular evolution changes with change in mutation rate, as previously shown by Takahata (Proc Natl Acad Sci USA 87:2419-2423, 1990), Takahata et al. (Genetics 130:925-938, 1992), and Vekemans and Slatkin (Genetics 137:1157-1165, 1994); (4) the generation time and population size (Lynch and Conery, Science 302:1401-1404, 2003) effects left their "signatures" at the level of the size phenotype of the protein-coding genome.
authors.affiliation: Institute of Hematology, University Clinical Center, University of Belgrade, ul. Dr. Koste Todorovica br. 2, 11000, Belgrade, Serbia.
authors.forename: Zoran A
authors.initials: ZA
authors.lastname: Rajic
authors.affiliation: Institute of Hematology, University Clinical Center, University of Belgrade, ul. Dr. Koste Todorovica br. 2, 11000, Belgrade, Serbia. gradjank@EUnet.yu.
authors.forename: Gradimir M
authors.initials: GM
authors.lastname: Jankovic
authors.affiliation: Institute of Hematology, University Clinical Center, University of Belgrade, ul. Dr. Koste Todorovica br. 2, 11000, Belgrade, Serbia.
authors.forename: Ana
authors.initials: A
authors.lastname: Vidovic
authors.affiliation: Faculty of Medicine, Institute for Medical Statistics and Informatics, Belgrade, Serbia.
authors.forename: Natasa M
authors.initials: NM
authors.lastname: Milic
authors.affiliation: University Children's Hospital, University of Belgrade, Belgrade, Serbia.
authors.forename: Dejan
authors.initials: D
authors.lastname: Skoric
authors.affiliation: Institute of Hematology, University Clinical Center, University of Belgrade, ul. Dr. Koste Todorovica br. 2, 11000, Belgrade, Serbia.
authors.forename: Milorad
authors.initials: M
authors.lastname: Pavlovic
authors.affiliation: University Hospital of Northern Sweden, Umeå, Sweden.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Lazarevic
mesh_terms: D003062:Codon; D004247:DNA / Q000032:analysis; D019143:Evolution, Molecular; D016678:Genome; D008957:Models, Genetic; D009154:Mutation; D016366:Open Reading Frames / Q000235:genetics*; D010641:Phenotype
chemical_list: D003062:Codon; D004247:DNA