SPEEDEMON low coalescent rate ESS

[Nicola Zadra]

Good morning, everyone.

I would appreciate some advice regarding my analysis. I am currently using Snapper alongside SPEEDEMON for species delimitation. I've observed that prior, likelihood, posterior, and all collinearity rates have red effective sample sizes (ESS) well below 200. In contrast, the values utilized by SPEEDEMON—such as Tree Height, birth rate, and cluster count—exhibit very high ESS values.

I'm certain that the challenges I'm encountering stem from rapid radiation, along with potential incomplete lineage sorting (ILS) or introgressions in the tree topology, coupled with a limited number of markers available for the Snapper analysis. Despite increasing the number of SNPs (I tried with 3000), it hasn't resolved the issue.

Can we infer the number of species solely from SPEEDEMON parameters with high ESS values? I have included the Tracer window  below.

Thank you for considering my request.

Best,  
Nicola