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."



Technically this is not geographic isolation, it is habitat partitioning. The animals are well within one another's geographic ranges (they are sympatric or parapatric in many areas) and dispersal areas. Besides, Gyrinophilus porphyriticus (the "surface species" ) is well known to use caves throughout its range.



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.



You seem hung up on the idea that the ability to interbreed is proof of conspecificity. This is not a species definition supported by any working biologists that I am aware of, not even the late great Ernst Mayr who first laid out the biological species concept. The fact that gene flow could occur if two populations (let's use your eastern and California tiger salamanders as an example) were sympatric does not reflect the fact that gene flow is not occurring. The two populations are as isolated from another as they are from pigeons or hedgehogs. Of course this reasoning can be taken too far (does each of the many isolated populations of four-toed salamanders deserve species status?), but I think you are in an indefensible position by claiming interbreeding=conspecificity.



Reproductive incompatibility, whether behavioral, physical, or genetic, is often evolved in closely related species that are sympatric to guard against hybridization; there is no reason for allopatrically distributed species to evolve such safeguards. This does not make them conspecific.



>>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.



It is my impression that the gray wolf/coyote hybrid origin for red wolves is speculative only; if you have links to any research on the issue I would be glad to read it. But certainly it would not be a unique situation; the European edible frog (Rana edulis) is a similar case. The hybrid Ambystoma of the northeast are even more peculiar. They have genomic components from four species, but their MtDNA is unrelated to any of the four; apparently all the 'hybrids' are the descendants of an ancestral stock whose nuclear genome has disappeared!



The Eumeces (I guess it's now Plestiodon) gilberti stuff is very interesting; it must be a fairly simple genetic cause to allow multiple independent origins from the E. skiltonianus stock. The same has been shown in the tetraploid gray tree frog Hyla versicolor.

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