Different divergence times with nDNA and mtDNA

[Marilia]

Hi all,

I´m working with a dataset consisting of resequencing of mtDNA, and 10 nuclear loci, sampled from 2 human populations. I made 3 different runs:  1) using only the mtDNA data, 2) using the mtDNA + nuclear data, and 3) using only the nuclear data, and these runs yielded different estimates . For example, the estimates for the time split parameter were 11kya, 7kya, and 1kya, for runs 1, 2, and 3, respectively. All the runs converged. It seems like the mtDNA contains much of my information and thus dominates the outcome. I´m not sure how to interpret these results, so any comments would help.

Thank you
Marilia

[jhey]

If you are sure that there is no mistake in interpretation and no
mixing issues, then it seems like you would want to find some way to
assess whether the mtDNA results are significantly different from the
nuclear results. At the very least you could use the confidence
intervals or HPD intervals to get some sense of whether the difference
is actually noteworthy

jhey