Kristian G. AndersenGeverifieerd account

I am curious why the tree makes it look like the Thai strains have evolved from particular Wuhan strains when they don't share mutations?

That will be because they are both from a later time than all the rest. So , all else being equal the coalescent model will put them together because it infers a small population.

I think it is premature to be trying to reconstruct time-trees.

I wanted mainly to estimate TMRCA. I think the observation of early Dec ancestor fits with Poisson expectation given 5 zeros, 2 ones, 5 twos and 1 three mutation away from common ancestor and a genomic subs rate of 1.1 subs per site per month.

Right after a host switch the rate might well be different (higher). And the high fraction of non-syn mutations and residual clustering suggests this might be the case.

I'm concerned about ~ 50% of the SNPs in the tree, so I think there's a lot of spurious signal at this stage. Mainly based on the following: 1. Ends that don't match 2. Indels that break ORFs 3. Ts/Tv rate that is too low (too many transversions) 4. Unusual Non-synonymous Tv's