>>I don't think they were referring to geographic isolation, but rather reproductive isolation.>>

It is actually quite obvious they mean geographic isolation.

"Cave populations isolated underground gradually evolve to lose newly useless structures such as eyes and pigmentation."

In that statement, people originally thought that cave salamanders evolved because they were isolated geographically underground. Of course geographic isolation also precludes gene flow. Anyhow, the African cichlids have shown that reproductive isolation can evolve even without geographic isolation, and of course geographic isolation does not necessarily lead to reproductive isolation, contra the assumptions of many. The Eastern tiger salamander (A. t. tigrinum) has the exact same reproductive behavior as the California tiger salamander (A. t. californiense) despite millions of years of geographic isolation between them. Since mating behavior is a very important pre-mating isolation mechanism, the identical mating behaviors insure that there will be no barrier to interbreeding if the gametes are fertile. I read that some people were puzzled why introduced tiger salamanders would interbreed freely with the California tiger salamanders when they are supposed to be different species and therefore reproductively isolated. That is because these tiger salamanders do not even know that they are supposed to be different species. One way they can tell is if their mating behaviors are different. If their behaviors are not different, then they would treat each other as conspecific. So, no matter what the DNA says about their divergence times, they can still be conspecific if neither has changed.

>>I've been following Niemiller and Miller's work on Gyrinophilus for a while,and it just keeps getting more interesting.>>

There are a lot of assumptions made about speciation and gene flow between species and so forth, and these assumptions are getting shattered by new data. It has been known for a long time, for example, that coyotes interbreed with wolves and yet both maintain their distinctness as species. It is now known that the "red wolf" is in fact a hybrid species between the coyote and the Gray Wolf. Even more interesting is the revelation that Eumeces gilberti is not a true species in the classic sense, but an ecological race of Eumeces skiltonianus. Different E. gilberti populations are derived from different E. skiltonianus populations, and yet E. gilberti does not interbreed with E. skiltonianus but different populations of E. gilberti will interbreed among themselves despite their separate origin.

In all these cases, and in the case of the cave salamanders, it shows that natural selection plays a bigger role than gene flow in maintaining species distinctness. If gene flow results in hybrids with phenotypes that are less adaptive to the environment, then these will be weeded out. If not, then a species can and do maintain its species distinctness even if gene flow occurs. My guess is that the selective forces that shaped the cave salamanders would eliminate any hybrids which are phenotypically maladaptive. So, even though gene flow may occur, it may not change an animal's phenotype because of natural selection.

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