A massive data dive proves that languages and genes evolve together
qz.com
qz.com
What GP is saying is that people with the same language interact more with each other and therefore reproduce, thus narrowing (averaging?) the gene pool to the speakers of that language.
Not that you'd be unable speak a language because of your genes! The cause-effect GP proposed would be language -> genes, not genes -> language (which is what I guessed you meant to refute).
Similarities in pronunciation between languages spoken over the same region are part of a phenomenon well known to linguists and do not imply that the languages are related. For example in terms of a pronunciation feature called coda devoicing, Slovene dialects near the Austrian border will pattern with German, those near the Croatian border will pattern with Croatian, while Standard Slovene will have something in the middle. Slovene and German are only very distantly related.
There may be something there about closely related population groups ending up using similar sounds even if their languages are not closely related, but I doubt the researchers even thought about that and used phonemic distance as a shorthand for actual linguistic distance.
I am not saying that this is the case for this paper. However, I note that there are no linguist authors, no linguist reviewers, and no linguist editors, involved in the process. And, as a linguist, I don't understand the motivation for this work. The presence of a phoneme in language X and language Y tells me next to nothing about the relationship between X and Y; there is no theory of "phoneme evolution" because the evolutionary metaphor is irrelevant at best (there is no analogue to selection). And we've known for centuries that unrelated languages in close contact may borrow phonemes from each other (retroflex t in South Asia being the parade example), and obviously close contact will lead to genetic transfer too.