An amateurish Essay I wrote one evening.
Darwin (1859; Chapter 4, p.130) argued that there was a “great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications.”
Evaluate how well this metaphor stands up to the discovery that “the horizontal transfer of genetic material … … is a major source of evolutionary innovation” (Williams et al. 2011). In particular, for which organisms is it least appropriate?
Thanks to pioneers like Allan Maxam, Walter Gilbert and Frederick Sanger in the 1970’s, gene and protein sequencing eventually lead to the advent of molecular phylogenetics. The vast amounts of data now available from any and all organisms finally allowed for substantial leads in the vindication of Darwin’s tree of life model of phylogeny, which previously had been based purely on phenetics- classification by morphological differences/similarities. These powerful new tools have lead biologists to believe that time is the only limiting factor in establishing a true, historically accurate phylogeny.
“… There is, after all, one true tree of life, the unique pattern of evolutionary branchings that actually happened. It exists. It is in principle knowable. We don’t know it all yet. By 2050 we should - or if we do not, we shall have been defeated only at the terminal twigs, by the sheer number of species.” - (Richard Dawkins, 2003)
As computational powers have increased however, sequencing of many organisms and their lineages have been illuminating an increasing number of incongruities with the typical vertical, bifurcating phylogenetic tree model. The discovery that open reading frames, operons, plasmids and plastids all evolve independently (williams et al.) as well as anomalies like mutational Saturation and homoplasy accumulating in pylogenies over vast evolutionary timescales has lead to systemic problems in both the understanding and the resolution of phylogenies (Rokas et al.). Literature on the ubiquity of one previously overlooked homoplasy mechanism has been accumulating in the last ten years, Horizontal Gene Transfer (HGT). Williams et al. believes that an entirely new phylogenetic model is needed, but is one underappreciated evolutionary mechanism enough to upend the previously infallible tree of life model?
Horizontal gene transfer in prokaryotes is especially significant, and is possibly the dominant factor in bacterial evolution. This has been known for some time, indeed the large variation in bacterial genomes would otherwise remain unexplained due to their lack of sexual reproduction. The significance of this wasn’t appreciated though until the 1950’s when anti-bacterial resistance genes proliferated on a worldwide scale (Ochman et al.) Three main mechanisms are responsible for HGT in bacteria, transformation, conjugation, and transduction. Transformation is the uptake of ‘loose’ DNA from the surrounding environment, from lysed cells for example. Species like B subtilis and str. Pneumoniae (the bacteria responsible for pneumonia) are capable of taking up nearly any DNA (Dale et al.). Conjugation is the transfer of genetic material from one bacterial cell to another, normally in the form of plasmids. This has been confounding for phylogeny due to the capability of .plasmid DNA to cross large taxonomic areas. (Dale et al.) Transduction deals with bacteriophages that package bacterial DNA instead of phage DNA by mistake, before infecting other bacteria with the transduced DNA. This is particularly significant because transduction events can exceed 100 kilobases (Ochman et al.) due to the phage’s protein machinery aiding in the recombination of the DNA into the host’s chromosome. That horizontally transferred genes exist and continue to proliferate (antibiotic resistance for example) in spite of the difficulties of recombination of horizontally transferred DNA, intense environmental and competitive selection on prokaryotes, the minimal, efficient structure of their genome and their tendency to rapidly delete unnecessary sequences (Andersson et al.) Demonstrates its significance in blurring phlylogenies. Indeed, E Coli. have been estimated to receive as much as 16KB every million years from HGT (Ochman et al.).
Unicellular eukaryotes (and the multicellular eukaryotes that evolved from them) are thought to be the result of endosymbiosis, the induction of one prokaryote into another to become an organelle. These organelles, consisting mainly of Mitochondria, and various plastids (such as chloroplasts) in plants maintain their own stock of genetic material. This in itself is confounding to a tree of life model, but in the last 20 years studies have been increasingly showing that endosymbiont DNA sequences have migrated to the nucleus of the host eukaryote that are essential to the organelle’s construction and regulation (Timmis et al.). In humans for example, as many as 612 instances of mitochondrial DNA insertion have been tallied (Tourmen et al.)
Metazoan HGT events are generally quite rare, although evidence is increasing that they are more widespread than originally thought. This is because multicellular organisms have somatic cell lines, reducing the likelihood that horizontally transferred genetic material will be passed on (Williams et al.). This is not the case in the fascinating Bdelloid Rotifers, small invertebrates that reproduce asexually by parthenogenesis. Despite this mode of reproduction, the organism is highly successful, possibly entirely due to HGT events that occur regularly in its lifecycle. Bdelloids live in aqautic environments, but can survive long periods of desiccation by entering a dormant state called cryptobiosis. During their recovery period, they take up DNA while patching holes in their cell walls, incorporating plant, bacterial and fungal sequences. In just 1% of DNA, dozens of foreign sequences have been identified (Gladyshev et al.). It has been suggested that in the absence of sexually induced variation, recombined ‘scavenged’ DNA may have provided a crucial selection tool for their evolution and continued success (Gadyshev et al.). I would say this organism is a major departure from the standard tree of life idea of lineage.
The above show the ubiquity of HGT in the evolutionary process, which standard cladistics do not properly account for in the linear, vertical inheritance tree of life model. In addition, over-averaging of multiple phylogenetic signals has lead to incongruities and therefore distorted resolution in phylogenies. Williams et al. have proposed a ‘rooted net of life’ model, which is based around a tree of ribomsomal DNA with horizontal reticulations to account for HGT. Other ‘supertree’ and ‘super matrix’ models also have potential as alternatives. It seems clear that more data on the scope of HGT is required before alternative models are realistically considered. But even if HGT does bring about a new model, I’m of the opinion that Darwin’s quote hasn’t lost relevance. Vertical descent is still the most prominent form of descent, and Darwin should certainly not be chided for not including in his theory a mechanism that technological constraints would not have allowed him to be aware of. By including in a way of accounting for HGT such as Williams et al’s reticulations, I think Darwin’s tree of life iconography is still poignant and effective. A few HGT vines between the branches could perhaps be added as an addendum.
WORD COUNT: 1065
REFERENCES
1. Charles Darwin, 1859, The Origin of Species By Means of Natural Selection (6th edition, 1902).
2. Richard Dawkins, 2003, A Devil’s Chaplain.
3. Antonis Rokas, Sean B. Carroll, 2006, Bushes in the tree of Life.
4. Howard Ochman, Jeffrey G. Lawrence, Eduardo A. Grolsman, 2000, Nature volume 405, Lateral Gene Transfer and the Nature of Bacterial Innovation.
5. Jeremy Dale, Simon F. Park, 2010, Molecular Genetics of Bacteria, fifth edition.
6. Andersson, S.G.E and Kurland C.G. 1998, Reductive Evolution of Resident Genomes. Trends Microbiol.
7. Jeremy N. Timmis, Michaell A. Ayliffe, Chun Y. Huang, William Martin, 2004, Nature Reviews Volume 5, Endosymbiotic Gene Transfer: Organelle Genomes Forge Eukaryotic Chromosomes.
8. Yves Tourmen, Olivier Baris, Philippe Dessen, Caroline Jacques, Yves Malthièry, Pascal Reynier, 2002, Structure and Chromosomal Distribution of Human Mitochondrial Pseudogenes, Genomics, 80.
9. Eugene A. Gladyshev, Matthew Meselson, Irina R. Arkhipova, 2008, Massive Horizontal Gene Transfe In Bdelloid Rotifers, Science, volume 320.
