This is usually the other way around: genetic divergence/distance on the x-axis and frequency (%) on the y axis, where frequency (%) refers to the percentage of alleles that have a given distance from one another,

Thank you very much Richard. That helps. Also, I have corrected the question.

One easy way of generating such histograms is using the ABGD online tool (https://bioinfo.mnhn.fr/abi/public/abgd/). You can use your alignment or precomputed paiwise genetic distances (e.g., from MEGA)

shamelessly promoting my own tool for this here: https://github.com/cdoorenweerd/PyCOIStats

It is better to focus on Dmin_NN (minimum distance to nearest neighbor) and Dmax (maximum intraspecific distance) values, which PyCOIStats also provides. Hope you find it useful