setting parameters for ancient human mtDNA for a Coalescent Bayesian Skyline

[David]

Hey,

I am trying to create a Coalescent Bayesian Skyline plot for my samples, which consists of modern and ancient human mtDNA sequences from the same population. When setting up the parameters in BEAUti, I used "Taming the BEAST" (https://taming-the-beast.org/tutorials/Skyline-plots/) as a reference. "Taming the Beast" uses Hepatitis C sequences, so I did change the mean clock rate to 9.66E-8, but I am not sure if I need to modify any other settings. I'd appreciate any input on what parameters I need when using human mtDNA for a Coalescent Bayesian Skyline plot.

I have 42 samples in total (20 are modern and 22 are ancient). My ancient samples range from 835 to 1545 years old. I have changed the age of my samples in updates, so that modern samples have an Age/Height of 0. I am using a GTR submodel (all rates are set to 1.0) with a gamma category count of 4. The mean clock rate is set to 9.66E-8. My prior tree is changed to Coalescent Bayesian Skyline, and the clockrate is Uniform. bPopSize and bGroupsize have a dimension of 4 with a minordimension of 1. For the MCMC, I used 0 burning and 3,000,000 chain length; the "Log Every" in tracelog and treelog were changed to 3,000.