A little while ago, I discovered a common error in jmodeltest is the error message that the number of sites appears to be wrong. I recently encountered this issue again. This is caused by single quotation marks on either side of tip names in a NEXUS file, which is a common form of the output/exported NEXUS file from DnaSP.
So, once you export a NEXUS from DnaSP, say after doing some population level genetic analyses or after defining sequence groups for setting up structure in ARLEQUIN, you should simply open your NEXUS file in a word processor or text editor and use the “Replace” command to remove all quotation marks from your file. Dots aren’t usually a problem, but spaces should probably also be avoided within sequence names. I never put spaces, only letters, numbers, dots, or underscores. And this has worked for me so far. Hope this helps.
~ J