Phylodynamics of viruses

A review of: MV Gimenes et al (2011). Phylodynamics and movement of Phycodnaviruses among aquatic environments. The ISME Journal, 1–11.

In the past two decades scientists are realising the importance of phylogeny. This paper uses new techniques of DNA sequencing and computer models to create a potential evolutionary history tree for the aquatic virus Phycodnaviruse, in order to discover how the virus changed in abundance and distribution over the last 400 thousand years. The virus infects plankton and therefore has ecological effects in terms of nutrient cycling and atmospheric composition.

Samples were taken from three tributaries to the Amazon river all with different physical, chemical and biological differences. The study used a marker of DNA polymerase that was specific to the group of viruses and highly conserved. The DNA was first extracted with a PowerSoil DNA kit. This was then amplified using PCR. After denaturation the samples were electrophoresed. The target was checked by a nested second round. After purification the fragments of DNA were cloned using E.Coli and then sequenced. Using a computer model and previously gathered data, with optimised parameters phylogenies of the virus were then constructed. The size of the genomes of Phycodnaviruses and the rate of change can be compared to Herpes virus type 1, and this information was put into the computer program. Other software was also used to estimate rates of change in traits, the rate of movement of traits between the different sample sites and the state of the common ancestor.

Results indicated significant genetic exchange among rivers and lakes, but exchange rates between marine and fresh waters were very low, ranging from 100 to 10 000-fold less. This may be due to the fact that freshwater phytoplankton cannot tolerate salinity and therefore the virus would not have followed. The study also suggested that the virus fluctuated in abundance by a boom and bust process. This may have an important role in controlling the algal population and abrupt bloom termination. It was found that there was a reduction in the virus population around 300 thousand years ago in most sample areas but in a couple areas this trend was not shown. The trend could be explained by the change and extinctions of species including planktonic species during the Pleistocene, 1.5 million to 300 thousand years ago.

The study is important because it constitutes the first report on the composition of Phycodnaviruses of tropical waters in South America from the Amazon Basin. But it also contributes to phylogeny information for future use. The paper is good in that it points out its limitations, which is important in the subject of evolution. But consideration of the paleotological records to add to possible explanations shows how microbiology is a subject of many disciplines.