Dating a virus evolutionary history

Hello everyone!

We are trying to understand the origin of a DNA virus. The genome is rather large (>100kb). We constructed the phylogenetic relationship between all existing genomes sampled from different geographic locations and historical time. We observed several important historical splits and population expansions. We wanted to date those important time points.

Due to large sample size and genome size, we tried two approaches

1. subsample the sequences and date those historical time points using BEAST.
2. subsample the loci (genes), one interesting observation is that, when we build local gene trees, the gene genealogies do not always reflect the global genome tree (either due to lower mutation rate or historical recombination). In this case, the historical splits we want to date is not identifiable in the local gene tree (due to change in gene genealogy). This becomes an issue preventing using local gene trees to date historical events when there are variations in gene genealogies across the genome.

I was wondering there are ways to come around this problem?

Dating the origins of viruses can be tricky, and recombination can often be involved and make it even more difficult. I have been studying the origins and evolution of lentiviruses for 30 years, and there have been many interesting developments along the way. I have also studied many other viruses, and have used mammalian mitochondrial DNA for comparison purposes because we have good fossils for mammals and because mammal mitochondrial are essentially free of recombination.

There are many goo recombination detection and analysis programs that should help you (RIP, RAPR, jpHMM, RDP4, SimPlot, etc…) but it may take some work to identify which, if any, of the genomes are non-recombinant in order to then map when and where recombination events took place.

Feel free to write to me, if you want some more help or advice.

Thank you so much for your reply. I have forwarded your message to my colleague. We are investigating the potential tools for this problem, will get back shortly once we encounter a deeper question.

find the non-recombinants as parents that can also be tricky.