Yesterday, I presented some ideas about analyzing the spatial distribution of genetic variation in virus strains. Today, I am going to present some ideas on analyzing the genetic variations of virus over time, or to say, demographic history of virus. In doing so, we can understand the evolution of virus and identify some key genes associated with increased transmissibility and virulence.
First, window-based nucleotide diversity, Tajima’s D, Dxy and Fst analyses. Display these values along chromosomes as line plot and we may locate genomic regions showing distinctions.
Second, effective population size changes. Using PSMC and Dadi modelling methods, we can infer the changes of effective population size amongst different virus strains.
Third, gene birth and death analyses. We can use CAFE to analyze gene family evolution amongst virus strains. Then we can compare the enriched genes among the expansion and contraction families.
Fourth, detect positive selection markers. This step is the continuation of the first step. Along with some outgroup virus species, we can align orthologous genes, then run PAML to identify positive selection markers.
Taken together, we can use the above methods to detect, locate, pinpoint and understand some key genes which emerge in evolutionary process. These genes may be associated with increased transmissibility and virulence in host-pathogen interaction.