Limits...
Darwinian evolution in the light of genomics.

Koonin EV - Nucleic Acids Res. (2009)

Bottom Line: There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation.Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate.Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future.

View Article: PubMed Central - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA. koonin@ncbi.nlm.nih.gov

ABSTRACT
Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or 'forest' of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future.

Show MeSH
Universals of evolution. (A) Distributions of evolutionary rates between orthologs in pairs of closely related genomes of bacteria, archaea and eukaryotes. The evolutionary distances between aligned nucleotide sequences of orthologous genes were calculated using the Jukes–Cantor correction and standardized so that the mean of each distribution equaled to 0, and the standard deviation equaled to 1. The plot is semi-logarithmic. Metma—Methanococcus maripaludis C5 versus M. maripaludis C7 (Euryarchaeota); Bursp—Burkholderia cenocepacia MC0-3 versus B. vietnamiensis G4 (Proteobacteria); Salsp—Salinispora arenicola CNS-205 versus S. tropica CNB-440 (Actinobacteria). All sequences were from the NCBI RefSeq database. The probability density curves were obtained by Gaussian-kernel smoothing of the individual data points. (B) Fit of empirical paralogous gene family size distributions to the balanced birth-and-death model. The results are shown for yeast Saccharomyces cerevisiae (Sc, left) and humans (Hs, right). Upper panels, binned distributions of paralogous family sizes; middle panels, paralogous family size distributions in double logarithmic coordinates; bottom panels, cumulative distribution function of paralogous family sizes. The lines show the predictions the balanced birth-and-death model. The figure is from (204).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2651812&req=5

Figure 4: Universals of evolution. (A) Distributions of evolutionary rates between orthologs in pairs of closely related genomes of bacteria, archaea and eukaryotes. The evolutionary distances between aligned nucleotide sequences of orthologous genes were calculated using the Jukes–Cantor correction and standardized so that the mean of each distribution equaled to 0, and the standard deviation equaled to 1. The plot is semi-logarithmic. Metma—Methanococcus maripaludis C5 versus M. maripaludis C7 (Euryarchaeota); Bursp—Burkholderia cenocepacia MC0-3 versus B. vietnamiensis G4 (Proteobacteria); Salsp—Salinispora arenicola CNS-205 versus S. tropica CNB-440 (Actinobacteria). All sequences were from the NCBI RefSeq database. The probability density curves were obtained by Gaussian-kernel smoothing of the individual data points. (B) Fit of empirical paralogous gene family size distributions to the balanced birth-and-death model. The results are shown for yeast Saccharomyces cerevisiae (Sc, left) and humans (Hs, right). Upper panels, binned distributions of paralogous family sizes; middle panels, paralogous family size distributions in double logarithmic coordinates; bottom panels, cumulative distribution function of paralogous family sizes. The lines show the predictions the balanced birth-and-death model. The figure is from (204).

Mentions: Other potentially important regularities come in the form of conserved distributions of evolutionary and functional variables. Strikingly, the distributions of the sequence evolution rates of orthologous genes between closely related genomes were found to be highly similar in distant taxa (271); when standardized, these distributions are virtually indistinguishable in bacteria, archaea and eukaryotes and are best approximated by a log-normal distribution (Figure 4A). Considering the dramatic differences in the genomic complexity and architecture (see above) as well as the biology of these organisms, the near identity of the rate distributions is surprising and demands an explanation in terms of universal factors that affect genome evolution. Robustness to protein misfolding discussed above seems to be a good candidate for such a universal factor although quantitative models explaining the rate distribution remain to be developed.Figure 4.


Darwinian evolution in the light of genomics.

Koonin EV - Nucleic Acids Res. (2009)

Universals of evolution. (A) Distributions of evolutionary rates between orthologs in pairs of closely related genomes of bacteria, archaea and eukaryotes. The evolutionary distances between aligned nucleotide sequences of orthologous genes were calculated using the Jukes–Cantor correction and standardized so that the mean of each distribution equaled to 0, and the standard deviation equaled to 1. The plot is semi-logarithmic. Metma—Methanococcus maripaludis C5 versus M. maripaludis C7 (Euryarchaeota); Bursp—Burkholderia cenocepacia MC0-3 versus B. vietnamiensis G4 (Proteobacteria); Salsp—Salinispora arenicola CNS-205 versus S. tropica CNB-440 (Actinobacteria). All sequences were from the NCBI RefSeq database. The probability density curves were obtained by Gaussian-kernel smoothing of the individual data points. (B) Fit of empirical paralogous gene family size distributions to the balanced birth-and-death model. The results are shown for yeast Saccharomyces cerevisiae (Sc, left) and humans (Hs, right). Upper panels, binned distributions of paralogous family sizes; middle panels, paralogous family size distributions in double logarithmic coordinates; bottom panels, cumulative distribution function of paralogous family sizes. The lines show the predictions the balanced birth-and-death model. The figure is from (204).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2651812&req=5

Figure 4: Universals of evolution. (A) Distributions of evolutionary rates between orthologs in pairs of closely related genomes of bacteria, archaea and eukaryotes. The evolutionary distances between aligned nucleotide sequences of orthologous genes were calculated using the Jukes–Cantor correction and standardized so that the mean of each distribution equaled to 0, and the standard deviation equaled to 1. The plot is semi-logarithmic. Metma—Methanococcus maripaludis C5 versus M. maripaludis C7 (Euryarchaeota); Bursp—Burkholderia cenocepacia MC0-3 versus B. vietnamiensis G4 (Proteobacteria); Salsp—Salinispora arenicola CNS-205 versus S. tropica CNB-440 (Actinobacteria). All sequences were from the NCBI RefSeq database. The probability density curves were obtained by Gaussian-kernel smoothing of the individual data points. (B) Fit of empirical paralogous gene family size distributions to the balanced birth-and-death model. The results are shown for yeast Saccharomyces cerevisiae (Sc, left) and humans (Hs, right). Upper panels, binned distributions of paralogous family sizes; middle panels, paralogous family size distributions in double logarithmic coordinates; bottom panels, cumulative distribution function of paralogous family sizes. The lines show the predictions the balanced birth-and-death model. The figure is from (204).
Mentions: Other potentially important regularities come in the form of conserved distributions of evolutionary and functional variables. Strikingly, the distributions of the sequence evolution rates of orthologous genes between closely related genomes were found to be highly similar in distant taxa (271); when standardized, these distributions are virtually indistinguishable in bacteria, archaea and eukaryotes and are best approximated by a log-normal distribution (Figure 4A). Considering the dramatic differences in the genomic complexity and architecture (see above) as well as the biology of these organisms, the near identity of the rate distributions is surprising and demands an explanation in terms of universal factors that affect genome evolution. Robustness to protein misfolding discussed above seems to be a good candidate for such a universal factor although quantitative models explaining the rate distribution remain to be developed.Figure 4.

Bottom Line: There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation.Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate.Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future.

View Article: PubMed Central - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA. koonin@ncbi.nlm.nih.gov

ABSTRACT
Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or 'forest' of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future.

Show MeSH