Skygrid interpretation in HPM

[geo]

Dear all,

I’ve run a BEAST analysis including five different datasets representing distinct clades of viruses sampled in a single country, some of which were collected in different time periods. Although each group of sequences is monophyletic, they are not monophyletic as a whole.

Since the number of sequences for each clade was limited, my aim was to maximize the information by analyzing them together, linking the substitution model, site heterogeneity model, and molecular clock using a hierarchical framework. To estimate population dynamics, I selected the Skygrid model.

In the end, I obtained a single population dynamic reconstruction.
How should this be interpreted? Does it reflect the overall dynamics of all viral clades circulating in the country, or would that be an overinterpretation?

Thank you very much for any advice you can provide.

Very best regards,

Giovanni