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Base Composition as Recombinational Isolator

Posted by forsdyke on 03 Jun 2007 at 21:53 GMT

Samath and coworkers [1] report that differences in base composition can be used to differentiate influenza virus genotypes “with a specificity approximating sequence-level resolution.” Since sequencing is laborious, this rapid way to “identify all species of influenza viruses with clade-level resolution” and so monitor “new genetic variants without prior knowledge of viral sequence,” represents an important clinical advance. However, apart from surprise that “mutations became fixed rapidly in the viral populations,” there is no suggestion that base composition differences might have played a primary role in this fixation (i.e. prevented the recombinational blending of genomes in a shared host cell).
As noted by Bronson and Anderson for retrovirus evolution, meaningful phylogenetic trees can be constructed based on base composition differences alone [2]. The case has been made that the failure of recombination between clades (i.e. their reproductive isolation), is a result, not a cause, of primary differences in base composition [3, 4]. Thus, apart from its clinical significance, this paper appears of significance as a contribution to Darwin's great problem - that of the origin of species.

1. Sampath R, Russell KL, Massire C, Eshoo MW, Harpin V, et al. (2007) Global surveillance of emerging influenza virus genotypes by mass spectrometry. PLOS ONE 2: e489.

2. Bronson EC, Anderson JN (1994) Nucleotide composition as a driving force in the evolution of retroviruses. J Mol Evol 38: 506-532.

3. Forsdyke DR (1995) Reciprocal relationship between stem-loop potential and substitution density in retroviral quasispecies under positive Darwinian selection. J Mol Evol 41: 1022-1037.

4. Forsdyke DR (2001) The Origin of Species, Revisited. McGill-Queen’s University Press, Montreal.