In his recent paper, Darwinian evolution in the light of genomics (Nucleic Acids Research, 2009, 1–24), Eugene Koonin outlines the principal concepts of the Modern Synthesis.
1. Undirected, random variation is the main process that provides the material for evolution.
2. Evolution proceeds by fixation of the rare beneficial variations and elimination of deleterious variations: this is the process of natural selection that, along with random variation, is the principal driving force of evolution according to Darwin and the Modern Synthesis.
3. The beneficial changes that are fixed by natural selection are ‘infinitesimally’ small, so that evolution proceeds via the gradual accumulation of these tiny modifications.
4. An aspect of the classic evolutionary biology that is related but not identical to the principled gradualism is uniformitarianism (absorbed by Darwin from Lyell’s geology), that is, the belief that the evolutionary processes remained, essentially, the same throughout the history of life.
5. Evolution of life can be presented as a ‘great tree’, as epitomized by the single, famous illustration of the Origin.
6. A corollary of the single tree of life (TOL) concept that, however, deserves the status of a separate principle: all extant diversity of life forms evolved from a single common ancestor.
Koonin then reviews how well these concepts (predictions?) have held up in light of the massive new information from genomics. His summary is below the fold.
1. True. The repertoire of relevant random changes greatly expanded to include duplication of genes, genome regions, and entire genomes; loss of genes and, generally, genetic material; HGT including massive gene flux in cases of endosymbiosis; invasion of mobile selfish elements and recruitment of sequences from them; and more.
2. False. Natural (positive) selection is an important factor of evolution but is only one of several fundamental forces and is not quantitatively dominant; neutral processes combined with purifying selection dominate evolution. Genomic complexity, probably evolved as a ‘genomic syndrome’ cause by weak purifying selection in small population and not as an adaptation. There is no consistent trend towards increasing complexity in evolution, and the notion of evolutionary progress is unwarranted.
3. False. Even single gene duplications and HGT of single genes are by no means ‘infinitesimally small’ let alone deletion or acquisition of larger regions, genome rearrangements, whole-genome duplication, and most dramatically, endosymbiosis. Gradualism is not the principal regime of evolution.
4. Largely, true. However, the earliest stages of evolution (pre-LUCA), probably, involved distinct processes not involved in subsequent, ‘normal’ evolution. Major transition in evolution like the origin of eukaryotes could be brought about by (effectively) unique events such as endosymbiosis.
5. False. The discovery of the fundamental contributions of HGT and mobile genetic elements to genome evolution invalidate the TOL concept in its original sense. However, trees remain essential templates to represent evolution of individual genes and many phases of evolution in groups of relatively close organisms. The possibility of salvaging the TOL as a central trend of evolution remains.
6. True. Comparative genomics leaves no doubt of the common ancestry of cellular life. However, it also yields indications that LUCA(S) might have been very different from modern cells.