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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.

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Related in: MedlinePlus

Dependence between genome size and gene density for large viruses and diverse cellular life forms. The plot is semi-logarithmic. Points corresponding to selected organisms are marked: Af, Archaeoglobus fulgidus (archaeon), Cp, Cryptosporidium parvum (unicellular eukaryote, alveolate), Hs, Homo sapiens, Os, Oryza sativa (rice), Mg, Mycoplasma genitalium (obligate parasitic bacterium), Mv, mimivirus, Tv, Trichomonas vaginalis (unicellular eukaryote, excavate).
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Figure 2: Dependence between genome size and gene density for large viruses and diverse cellular life forms. The plot is semi-logarithmic. Points corresponding to selected organisms are marked: Af, Archaeoglobus fulgidus (archaeon), Cp, Cryptosporidium parvum (unicellular eukaryote, alveolate), Hs, Homo sapiens, Os, Oryza sativa (rice), Mg, Mycoplasma genitalium (obligate parasitic bacterium), Mv, mimivirus, Tv, Trichomonas vaginalis (unicellular eukaryote, excavate).

Mentions: There are major differences in the genome layouts between different lines of life evolution. Prokaryotes and, especially, viruses have ‘wall-to-wall’ genomes that consist, mainly, of genes encoding proteins and structural RNAs, with non-coding regions comprising, with a few exceptions, no more than 10–15% of the genomic DNA. The genomes of unicellular eukaryotes have lower characteristic gene densities but, on the whole, do not depart too far from the prokaryotic principles, with most of the DNA dedicated to protein-coding, despite the distinct, exon–intron gene architecture. The genomes of multicellular eukaryotes are drastically different in that only a minority (a small minority in vertebrates) of the genomic DNA is comprised of sequences encoding proteins or structural RNAs. Generally, across the entire range of life forms, there is a notable negative exponential dependence between the density of protein-coding genes and genome size although significant deviations from this overall dependence are seen as well, particularly, in prokaryotes (Figure 2).Figure 2.


Darwinian evolution in the light of genomics.

Koonin EV - Nucleic Acids Res. (2009)

Dependence between genome size and gene density for large viruses and diverse cellular life forms. The plot is semi-logarithmic. Points corresponding to selected organisms are marked: Af, Archaeoglobus fulgidus (archaeon), Cp, Cryptosporidium parvum (unicellular eukaryote, alveolate), Hs, Homo sapiens, Os, Oryza sativa (rice), Mg, Mycoplasma genitalium (obligate parasitic bacterium), Mv, mimivirus, Tv, Trichomonas vaginalis (unicellular eukaryote, excavate).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: Dependence between genome size and gene density for large viruses and diverse cellular life forms. The plot is semi-logarithmic. Points corresponding to selected organisms are marked: Af, Archaeoglobus fulgidus (archaeon), Cp, Cryptosporidium parvum (unicellular eukaryote, alveolate), Hs, Homo sapiens, Os, Oryza sativa (rice), Mg, Mycoplasma genitalium (obligate parasitic bacterium), Mv, mimivirus, Tv, Trichomonas vaginalis (unicellular eukaryote, excavate).
Mentions: There are major differences in the genome layouts between different lines of life evolution. Prokaryotes and, especially, viruses have ‘wall-to-wall’ genomes that consist, mainly, of genes encoding proteins and structural RNAs, with non-coding regions comprising, with a few exceptions, no more than 10–15% of the genomic DNA. The genomes of unicellular eukaryotes have lower characteristic gene densities but, on the whole, do not depart too far from the prokaryotic principles, with most of the DNA dedicated to protein-coding, despite the distinct, exon–intron gene architecture. The genomes of multicellular eukaryotes are drastically different in that only a minority (a small minority in vertebrates) of the genomic DNA is comprised of sequences encoding proteins or structural RNAs. Generally, across the entire range of life forms, there is a notable negative exponential dependence between the density of protein-coding genes and genome size although significant deviations from this overall dependence are seen as well, particularly, in prokaryotes (Figure 2).Figure 2.

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
Related in: MedlinePlus