How Microbiology defines the Rhizome of Life (ID: 22346011 Tasmim Jahan Mumu)

 How Microbiology defines the Rhizome of Life

In contrast to the tree of life (TOF) theory, species are mosaics of gene sequences with different origins. Observations of the extensive lateral sequence transfers in all organisms have demonstrated that the genomes of all life forms are collections of genes with different evolutionary histories that cannot be represented by a single TOF. Moreover, genes themselves commonly have several origins due to recombination. The human genome is not free from recombination events, so it is a mosaic like other organisms' genomes. Recent studies have demonstrated evidence for the integration of parasitic DNA into the human genome. Lateral transfer events have been accepted as major contributors of genome evolution in free-living bacteria. Furthermore, the accumulation of genomic sequence data provides evidence for extended genetic exchanges in intracellular bacteria and suggests that such events constitute an agent that promotes and maintains all bacterial species. Archaea and viruses also form chimeras containing primarily bacterial but also eukaryotic sequences. In addition to lateral transfers, orphan genes are indicative of the fact that gene creation is a permanent and unsettled phenomenon. Currently, a rhizome may more adequately represent the multiplicity and de novo creation of a genome. We wanted to confirm that the term “rhizome” in evolutionary biology applies to the entire cellular life history. This view of evolution should resemble a clump of roots representing the multiple origins of the repertoires of the genes of each species.

Lateral Inheritance 

Lateral Sequence Transfers in Eukaryotes and the Human Rhizome

Two elements participate in eukaryotic genetic change. The first is sexuality. In 1889, August Weismann proposed that sex evolved because of the advantage in creating variation among siblings. Therefore, natural selection favors the parents who can produce a variety of offspring. A similar hypothesis was proposed by Darwin in his “Origin of Species” , which states that all sexually reproducing organisms are derived from a common, single-celled eukaryotic ancestor. Many protists reproduce sexually, as do multicellular plants, animals, and fungi. A few species, such as Bdelloidea and some parthenocarpic plants have secondarily lost this feature . Some species, such as arthropods, can reproduce sexually and asexually or undergo parthenogenesis, which is the development of embryos in the absence of male fertilization. Wolbachia are known to induce female parthenogenesis in infected arthropods .

Genome mixing has also occurred between archaic hominins and modern humans. Indeed, evidence for a notable presence of a Neanderthal-derived X chromosome segment among all contemporary human populations outside Africa has been presented. Another archaic hominin was recently discovered in the Denisovan cave in Siberia. This group is derived from a hominin migration out of Africa distinct from the Neanderthal ancestors and modern humans, as suggested by the highly divergent morphological features. Evidence suggests that this archaic human lived close in time and space with Neanderthals and modern humans and that its genome contributed 4–6% of its genetic material to the genomes of the present-day Malaysians , whereas Neanderthals contributed approximately 1–4% of their genetic material to modern Europeans.

The Mitochondrial Rhizome

Mitochondrial evolution has recently been demonstrated to constitute a rhizome . The results of this study suggest that the origins of mitochondrial genes are not limited to Rickettsiales and that their creation did not occur in a single event but through multiple successive events. Contrary to what has been believed until now, recent evidence strongly suggests that mitochondria do not have a single common ancestor  but likely numerous ancestors, including proto-Rickettsiales, proto-Rhizobiales, proto-alphaproteobacteria and current alphaproteobacterial species. 

Lateral Sequence Transfers in Archaea and Their Rhizome

Many Archaea inhabit extreme environments similar to those in which life originated. Although Archaea members may be seen as evolutionary relics of the earliest life forms, none of the organisms living today are primitive. All extant life forms are modern organisms that are well adapted to their ecological niches. Numerous authors have observed many horizontally transferred genes in Archaea, confirming that lateral sequence transfer is a wide-ranging phenomenon observed large fractions of genes of bacterial or eukaryotic origins in Archaea genomes, suggesting a chimeric origin for Archaea. The percentages of horizontally transferred sequences in bacteria and Archaea are similar, ranging from 5% in Methanococcus jannaschii to 14% in Aeropyrum pernix  Massive gene exchanges between the extremely thermophilic Archaea and the hyperthermophilic Aquifex have been suggested. 

 Lateral Sequence Transfers in Viruses and Their Rhizome

Viral genomes are not without lateral sequence transfers. A recently discovered virophage, Sputnik, was considered to be a vehicle that mediated lateral transfers between giant viruses . The Acanthamoeba polyphaga mimivirus has unique features, including the presence of dsDNA, which was previously undocumented in viruses. Phylogenetic analyses identified a large number of bacterial homologs, suggesting an acquisition by lateral inheritance. Most of these genes were related to the orthologs in bacterial species, such as L. pneumophila, that are known to grow within amoebae. Mimiviruses likely acquired these genes from degraded or live bacteria sharing the same environment, particularly within amoebae ). In mammalian Herpesvirus, 141 putative transferred genes were identified, of which 91 were from gamma-herpesvirus, 42 from beta-herpesvirus, and 8 from alpha-herpesvirus, suggesting that gene acquisition in gamma-herpesvirus was more active than in the others). 

Intragenic Recombination

Other than lateral sequence transfer and recombination between various organisms, the origin of some genes cannot be simply explained because of the occurrence of intragenic recombination . Different varying sites recombine within the same gene locus, and intragenic recombination can generate new allelic variation at a locus. New gene products with potentially new properties will then arise. Chimeric gene sequences that could result from recombination between divergent alleles have been detected in several species . felis genomes that occurred independently of gene function or sequence length. The apparent horizontal transfer of DNA segments with different sizes has been detected, thus indicating that any segment of DNA may be laterally transferred ..

Conclusion

Darwin's TOL presents a single common ancestor on the root and different species on the major branches that separate and continuously diverge. However, the history of life cannot be attributed to a single ancestral species that yielded descendants that have adapted to their environment and developed into various species completely distinct and different from each other in such a short time. Furthermore, new species are continuously created and are not necessarily derived from other species. Furthermore, recent and massive gene transfer events have been identified in all living organisms. A rhizome could more adequately represent the multiplicities of genomes and their de novo creations. Emerging species grow from the rhizome with gene repertoires of various origins that allow for the multiplication of species under permissive environmental conditions. This view of evolution should resemble a clump of roots representing the multiple origins of the genetic repertoire of each species .