If I understand what you are trying to say, you feel that all females in the previous single population responded to more than one call. If the females in one of the two populations only respond to one specific call, while females in the other group only respond to the other call, gene flow is disrupted and they are confirmed as two different species.
However, mating calls are very specific and generally tell a female which male belongs to her group and will not respond to other calls. Unless these particular frogs are an anomaly in this respect we conclude they had only one call. However, the number of initial calls is not relevant to speciation, the response or non-response to a call determines whether gene flow is disrupted.
DNA can not tell whether they had a single call or not, but that is not what I said. DNA will tell us if they in fact were a single intra-breeding population and mDNA will tell us when they separated. The thing about the genes was not a red herring, you simply didn't understand the significance of the mention of them.
No, my point was not about the science. It is more an issue of logic and assumptions. There are three frog populations discussed. A northern one, a southern one, and a small pocket of "southern" frogs in the northern region.
The assumption is, apparently, that because the frogs in the small pocket in the north and the larger population in the south appear to be the same (and, I assume, have very similar DNA), that therefore they came from the same original frog population and then developed along separate paths because they were geographically separated for a long time. I hope I am interpreting the article correctly.
The underlying assumption seems to go something like this: all animals originally came from a single source, and we can tell how closely related one group is to another by looking at DNA. In other words, it assumes Darwinism. So the conclusions can't be used to support Darwinism.
"Over several thousand years, this behavior created a reproductively isolated population - essentially a new species - that is unable to mate with either of the original frog populations."
This is a good story, which accommodates the observations and the accepted belief system. But since none of today's scientists were there 8000 years ago to verify that indeed all of the "southern" frogs were at one time part of the same population, had the same mating call, and could produce viable offspring with any combination of male and female, we should recognize that it is, after all, just a story.
The science of the article consists of the observations made in today's world. The speculation starts when the author tries to explain how it came about, assuming Darwinism is true.