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Size of the protein-coding genome and rate of molecular evolution

Rajic, Zoran A; Jankovic, Gradimir M; Vidovic, Ana; Milic, Natasa M; Skoric, Dejan; Pavlovic, Milorad and Lazarevic, Vladimir LU (2005) In Journal of Human Genetics 50. p.29-217
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... (More)

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.

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author
publishing date
type
Contribution to journal
publication status
published
keywords
Codon, DNA, Evolution, Molecular, Genome, Models, Genetic, Mutation, Open Reading Frames, Phenotype
in
Journal of Human Genetics
volume
50
pages
13 pages
publisher
Springer
external identifiers
  • scopus:21544439044
ISSN
1434-5161
DOI
10.1007/s10038-005-0242-z
language
English
LU publication?
no
id
b4446af4-037e-4858-af0c-05e5aba3774c
date added to LUP
2016-05-24 17:21:35
date last changed
2017-02-02 11:54:14
@article{b4446af4-037e-4858-af0c-05e5aba3774c,
  abstract     = {<p>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&lt; 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.</p>},
  author       = {Rajic, Zoran A and Jankovic, Gradimir M and Vidovic, Ana and Milic, Natasa M and Skoric, Dejan and Pavlovic, Milorad and Lazarevic, Vladimir},
  issn         = {1434-5161},
  keyword      = {Codon,DNA,Evolution, Molecular,Genome,Models, Genetic,Mutation,Open Reading Frames,Phenotype},
  language     = {eng},
  pages        = {29--217},
  publisher    = {Springer},
  series       = {Journal of Human Genetics},
  title        = {Size of the protein-coding genome and rate of molecular evolution},
  url          = {http://dx.doi.org/10.1007/s10038-005-0242-z},
  volume       = {50},
  year         = {2005},
}