question about studying virus evolution using BAMM

[Centurion Cacau]

Hello,

I want to ask a conceptual question. I see bamm is often used to study animal or plant diversification across millions of years. I want to study virus diversification in which I have sampled a lot of virus sequence and know the sampling date. Is it possible to apply bamm? Or is the timescale too small to use bamm or other software?

Yours faithfully,

Cacau

[Dan Rabosky]

Hi Cacau-

I would say that BAMM, and most other diversification models, are poorly suited to studying virus diversification. The problem comes from the fact that it's almost impossible to know how to account for sampling, and the assumptions we make about sampling have a big impact on results. With typical animal/plant taxa, we can plausibly claim to have a rough understanding of the true number of species-level lineages that exist in our focal clades (e.g., "10,000 species of birds"). And diversification inferences perform better if sampling is (1) more complete, and (2) phylogenetically unbiased across our focal clade. Both of those assumptions are likely to be strongly violated in the case of viruses: the OTUs themselves are hard to define, we probably don't have a good handle on how many such OTUs (even if defined comparably) exist, and also the sampling itself would likely be biased for many reasons. There are phylodynamic approaches that have more promise than BAMM-type methods for this question but there are also many caveats that come with applying those types of approaches.

In short, virus diversification is a pretty hard problem.

Hope this helps,

~Dan Rabosky