Table 1.

The fate of the central tenets of (neo)Darwinism in the post-genomic era^a

(neo)Darwinian principles	Post-genomic view
Random (undirected), heritable variation is the principal material for natural selection	YES but the relevant random changes are extremely diverse: -nucleotide substitution, insertion and deletion -duplication of genes, genome regions, and whole genomes -loss of genes and, generally, genetic material -HGT including massive gene flux after endosymbiosis -invasion and transposition of mobile selfish elements and recruitment of sequences from these elements Moreover, the wide spread of stress-induced mutagenesis and related phenomena suggests the possibility of quasi-Lamarckian variation (a part of Darwin’s concept purged by the Modern Synthesis) 22
Fixation of beneficial changes by natural selection is the main driving force of evolution that tends to generate increasingly complex adaptations; hence progress as a general trend in evolution	NO. Darwinian (positive) selection is important but is only one of several fundamental forces of evolution, and not necessarily the dominant one. Neutral processes constrained by purifying selection dominate evolution. Genomic complexity is not intrinsically adaptive and probably evolves as a ‘genomic syndrome’ in populations with small effective size and accordingly weak purifying selection. There is no consistent trend towards increasing complexity and no progress in evolution
Natural selection operates on ‘infinitesimally small’ variations, so evolution never makes leaps - the principle of gradualism	NO. Even duplication and HGT of single genes are not ‘infinitesimally small’ genomic changes let alone deletion or acquisition of larger regions, genome rearrangements, whole-genome duplication, and of course, endosymbiosis. Evolutionary (or even revolutionary) leaps are possible, especially, during population bottlenecks, and are crucial for major evolutionary transitions
Evolutionary processes were, largely, the same throughout the evolution of life – the principle of uniformitarianism borrowed by Darwin from geology	YES and NO. The principal factors of evolution, diverse as they are, probably, all were in operation through most of life’s history. However, the earliest stages of evolution antedating the emergence of the three domains of cellular life should have involved processes distinct from ‘normal’ evolution. Furthermore, major transition in evolution, such as eukaryogenesis, occurred through unique events (e.g. endosymbiosis)
Species is a central unit of evolution, and speciation a key evolutionary process	NO. Species can be meaningfully defined only for organisms that engage in regular sex but not promiscuous HGT, ensuring reproductive isolation. In general, the species concept does not apply to prokaryotes and is of dubious validity for unicellular eukaryotes as well10
The entire evolution of life can be depicted as a single “big tree” that reflects the evolutionary relationships between organisms and species (species tree)	NO…and YES. The discovery of the key roles of HGT and mobile genetic elements in genome evolution deal a death knell to the traditional Tree of Life concept. Still, trees remain natural templates to represent evolution of individual genes and many intervals of evolution in groups of relatively close organisms15
All existing life forms descend from a single ancestral form, the Last Universal Common Ancestor (LUCA)	YES…but… Comparative genomics leaves no doubt of the common ancestry of all cellular life. However, there are strong indications that LUCA could have been quite different from modern cells23

^aThe table is based on the discussion in Ref. [11], with modifications and additions.