Wednesday, November 25, 2015

Sporadic blog posts from now on?

After a bit more than 400 posts, in general with regular posts on Mondays and Wednesdays, this blog is about to become more sporadic.

As many of you will know, last year the Swedish University of Agricultural Sciences realized that building two new buildings (one of them solely for administrators) was not a smart thing to do during a recession. Consequently, 200 people were asked to find employment elsewhere, one of whom was me. Since then, I have been a Guest Researcher in the Systematic Biology section at Uppsala University.

As of this week, I have started a training program that will occupy me full-time. I will therefore no longer be able to post here regularly. I hope to be able to continue posting intermittently, as do my blog co-contributors, but I am not sure how much time I will have to keep up with developments in phylogenetics.

Monday, November 23, 2015

The history of HGT

Because it seems to be an interesting topic, I have written a number of posts about the history of horizontal gene transfer (HGT) in phylogenetics, including:
The first gene transfer (HGT) network (1910)
The first paper on HGT in plants (1971)
HGT networks
The first HGT network
Recently, Nathalie Gontier has produced a comprehensive history of HGT, which makes a major contribution to the field:
N. Gontier (2015) Historical and epistemological perspectives on what horizontal gene transfer mechanisms contribute to our understanding of evolution. In: N. Gontier (ed.) Reticulate Evolution, pp. 121-178. Springer, Switzerland.
In this book chapter, she contemplates why the evidence for HGT was ignored for most of the 20th century:
Many of the mechanisms whereby genes can become transferred laterally have been known from the early twentieth century onward. The temporal discrepancy between the first historical observations of the processes, and the rather recent general acceptance of the documented data, poses an interesting epistemological conundrum: Why have incoming results on HGT been widely neglected by the general evolutionary community and what causes a more favorable reception today? Five reasons are given:
(1) HGT was first observed in the biomedical sciences and these sciences did not endorse an evolutionary epistemic stance because of the ontogeny / phylogeny divide adhered to by the founders of the Modern Synthesis.
(2) Those who did entertain an evolutionary outlook associated research on HGT with a symbiotic epistemic framework.
(3) That HGT occurs across all three domains of life was demonstrated by modern techniques developed in molecular biology, a field that itself awaits full integration into the general evolutionary synthesis.
(4) Molecular phylogenetic studies of prokaryote evolution were originally associated with exobiology and abiogenesis, and both fields developed outside the framework provided by the Modern Synthesis.
(5) Because HGT brings forth a pattern of reticulation, it contrasts the standard idea that evolution occurs solely by natural selection that brings forth a vertical, bifurcating pattern in the “tree” of life.
These are important points, and it is interesting to have so much of the history and epistemology gathered into one place.

Gontier notes:
In prokaryotes, HGT occurs via bacterial transformation, phage-mediated transduction, plasmid transfer via bacterial conjugation, via Gene Transfer Agents (GTAs), or via the movement of transposable elements such as insertion sequences ... In eukaryotes, HGT is mediated by processes such as endosymbiosis, phagocytosis and eating, infectious disease, and hybridization or divergence with gene flow, which facilitates the movement of mobile genetic elements such as transposons and retrotransposons between different organisms.
In this context, knowledge of HGT extends back a long way. Transformation was first observed by Griffith (1928), conjugation was discovered by Lederberg and Tatum (1946), and Freeman (1951) reported on HGT from a bacteriophage. Information about endosymbiosis and phagocytosis extends back even further.

Unfortunately, the history presented is incomplete, because it focuses on microbiology (possibly because the timeline around which the chapter is written "is based upon the timeline provided by the American Society for Microbiology"). The possibility that the asexual transfer of genetic units may be of more general occurrence than just prokaryotes dates back to at least Ravin (1955), who is not mentioned. Thus, for example, the early phylogenetic work of Jones & Sneath (1970) on bacteria is included, but the works of Went (1971) on plants and Benveniste & Todaro (1974) on animals are not referenced. Similarly, the discussion of gene trees versus species trees in bacteria by Hilario and Gogarten (1993) is quoted but not that of Doyle (1992) regarding plants. Thus, there is more history to be written.

The book itself (Reticulate Evolution) is mostly about the broader fields of symbiosis and symbiogenesis, rather than about more specific topics like lateral gene transfer and hybridization.


Benveniste RE, Todaro GJ (1974) Evolution of C-type viral genes: inheritance of exogenously acquired viral genes. Nature 252: 456-459.

Doyle JJ (1992) Gene trees and species trees: molecular systematics as one-character taxonomy. Systematic Botany 17: 144-163.

Freeman VJ (1951) Studies on the virulence of bacteriophage-infected strains of Corynebacterium diphtheriae. Journal of Bacteriology 61: 675-688.

Griffith F (1928) The significance of pneumococcal types. Journal of Hygiene 27: 113-159.

Hilario E, Gogarten JP (1993) Horizontal transfer of ATPase genes — the tree of life becomes a net of life. Biosystems 31: 111-119.

Jones D, Sneath PH (1970) Genetic transfer and bacterial taxonomy. Bacteriology Reviews 34: 40-81.

Lederberg J, Tatum EL (1946) Gene recombination in E coli. Nature 158: 558.

Ravin AW (1955) Infection by viruses and genes. American Scientist 43: 468-478.

Went FW (1971) Parallel evolution. Taxon 20: 197-226.