Is complexification the prevailing modality of evolution?
Phylogenomic reconstruction, at least for bacteria and Archaea, suggests otherwise. It is not surprising that differential gene loss dominates the evolution of commensal bacteria, such as Lactobacilli, from a complex free-living ancestor. A qualitatively similar pattern was detected in evolutionary reconstructions for all bacteria and archaea. Strikingly, more recent reconstructions that were performed using larger genome sets and more sophisticated computational methods confidently indicate that the genome of the last common ancestor of all extant archaea apparently was at least as large and complex as that of typical modern organisms in this domain of cellular life. Fully compatible reconstruction results have been reported for the expanded set of cyanobacterial genomes. Thus, counter-intuitively, at least in prokaryotes, genome shrinkage that is sometimes called streamlining and is attributed to increasing selective pressure in successful, large populations , appears to be is no less and probably more common than genome growth and complexification.
The modes of evolution of these relatively simple organisms that, as we now realize, have dominated the biosphere since its beginning about 4 billion years ago to this day (and into any conceivable future) are different from the evolutionary regimes of animals and plants, the traditional objects of (evolutionary) biology. The study of microbial evolution has shattered the classic idea of a single, all-encompassing tree of life by demonstrating that the evolutionary histories of individual genes are generally different.
Lamarck's view of the role of evolution in the history of life was severely limited: he did not postulate deep common ancestry of life forms but rather believed in multiple acts of creation, perhaps a separate act for each species. Prescient ideas on evolutionary changes of organisms actually have been developed centuries before Lamarck and Darwin, most notably by the great Roman thinker Titus Lucretius Carus.
By mid-twentieth century microbiologists had realized full well that microbes possess genomes and can mutate, and accordingly, should evolve, in principle, similarly to animals and plants, all attempts to infer microbial evolution from morphological and physiological characters had been unqualified failures
In Haeckel's tree, Protista (unicellular eukaryotes) and Monera (bacteria) occupied unspecified positions near the root.
The life forms formerly considered “important,” i.e., the complex multicellular organisms (animals and plants), represent only two among the numerous branches of eukaryotes.There is no denying the fact that the true biodiversity on this planet is the diversity of unicellular microbes.
Thus, “evolution of prokaryotes and the Tree of Life are two different things” (Bapteste et al., 2009; Martin, 2011). Then, the question arises: is there any substantial tree component in evolution at all ?
As Martin and Dagan wryly notice, if a model (in this case, the Tree of Life model) adequately describes 1% of the data, it might be advisable to abandon it and search for a better one (Dagan and Martin, 2006). Such an alternative indeed has been proposed in the form of a dynamic network of microbial evolution in which the nodes are bacterial and archaeal genomes, and the edges are the fluxes of genetic information between the genomes (Kunin et al., 2005; Dagan and Martin, 2009; Dagan, 2011; Kloesges et al., 2011)
Indeed, there is potential for tree-like patterns to emerge from relationships that have nothing to do with common descent Although any phylogenetic tree of a central, conserved component of the cellular information-processing machinery (such as rRNA or the set of universal ribosomal proteins) represents only a minority of the phylogenetic signal across the phylogenetic forest (see details below) and so by no account can be considered an all-encompassing “Tree of Life,” neither is such a phylogeny an arbitrary and irrelevant “tree of 1%.” Most of the prokaryotes do not engage in regular sex but instead exchange genes via HGT with diverse other microbes that they happen to cohabitate with. In general, in the prokaryote world, there are indeed no discrete, genetically isolated systems of panmictic populations but rather complex webs of gene exchange (Dagan et al., 2008; Koonin and Wolf, 2008). Thus, the very notion of species as a distinct biological category does not apply even though traditionally bacteria and archaea are still denoted by Linnaean species names
The Never-Ending Quest to Rewrite the Tree of Life
Woese’s success in using 16S rRNA to rewrite the tree of life no doubt encouraged its widespread use. But as Lloyd and other scientists began to realize, some microbes carry a version that is significantly different from that seen in other bacteria or archaea.2
In the 1980s, most of the bacteria and archaea that scientists knew about fit into 12 major phyla. By 2014, scientists had increased that number to more than 50. But in a single 2015 Nature paper , Banfield and her colleagues added an additional 35 phyla of bacteria to the tree of life.
A new view of the tree of life 11 April 2016