How to evaluate confidence of migration events?

General
1

I merged the South America dataset with mine (South Brazil).
The problem is that I have hundreads of sequences for South Brazil, so some “mugration” events do not make sense, ie some lineages appear to have arisen in South Brazil (but I am not sure that this is true, I believe it is a problem of undersampling for the rest of Brazil).

I also performed an independent phylogenetic reconstruction using only samples of certain pango lineages. Bootstrap values are very low, as expected, considering the narrow timeframe and the slow-evolving virus.

However, it makes me consider how much I can rely on the ancestral reconstruction of the nextstrain tree. How do I know if the viral migration events are in fact representing the reality?

2

The migration analysis reports marginal probabilities for ancestral locations. But these probabilities assume similar sampling efforts across the tree. In absence of a carefully sampled data set, wouldn’t put much confidence in these reconstructions.

3

Thank you very much.