Size of the protein-coding genome and rate of molecular evolution.
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.
Rajic
Zoran A
ZA
Institute of Hematology, University Clinical Center, University of Belgrade, ul. Dr. Koste Todorovica br. 2, 11000, Belgrade, Serbia.
Jankovic
Gradimir M
GM
Institute of Hematology, University Clinical Center, University of Belgrade, ul. Dr. Koste Todorovica br. 2, 11000, Belgrade, Serbia. gradjank@EUnet.yu.
Vidovic
Ana
A
Institute of Hematology, University Clinical Center, University of Belgrade, ul. Dr. Koste Todorovica br. 2, 11000, Belgrade, Serbia.
Milic
Natasa M
NM
Faculty of Medicine, Institute for Medical Statistics and Informatics, Belgrade, Serbia.
Skoric
Dejan
D
University Children's Hospital, University of Belgrade, Belgrade, Serbia.
Pavlovic
Milorad
M
Institute of Hematology, University Clinical Center, University of Belgrade, ul. Dr. Koste Todorovica br. 2, 11000, Belgrade, Serbia.
Lazarevic
Vladimir
V
University Hospital of Northern Sweden, Umeå, Sweden.
D003062:Codon; D004247:DNA / Q000032:analysis; D019143:Evolution, Molecular; D016678:Genome; D008957:Models, Genetic; D009154:Mutation; D016366:Open Reading Frames / Q000235:genetics*; D010641:Phenotype
D003062:Codon; D004247:DNA