I have done both test with similar results (see attachment) using an alignment of 129 individuals and a part of COX1.
I have 4 different genus of 2 different subfamilies of midges. I don't understand why, if as I mention, I have different genus and even subfamilies, I can't see any gap that indicates intra and interspecific distances.
Thank you foe reading me, any answer/suggestion would be greatly appreciate