Simulating the evolution of neutrally evolving sequences in a population under environmental changes

We simulated the molecular evolution of a neutral nucleotide sequence using an individual-based model that involves disruptive selection. We show that the developed approach allows us to infer important details of evolutionary processes from a sub-sample of the sequences resulting from a simulation. This procedure permits one to estimate the confidence limits for the observed rate at which new sequences evolve by analysing the shape of frequency distribution curve of the pairwise genetic distances among all the sequences. It is shown that this approach allows to distinguish between different scenarios of environmental changes which are important for speciation or intraspecific genetic diversification. This method is proposed as an alternative to the lineage through time approach that analyses the number of lineages in a phylogenetic tree.