The extinctions are clearly linked to a virulent fungal disease, but the paper finds a correlation between temperature and extinction events, and hypothesises that the warmer climatic conditions are favouring the fungus. Now climatic conditions certainly can have an influence on the virulence of fugal pathogens - anyone who's had mildew on their roses or a case of athlete's foot will recognise the influence of the local microclimate in modulating fungal growth - but the evidence for this actually having been the major cause in wiping out the frog populations seems slim to me. There is, as far as I can tell, no real epidemiological evidence that it is likely to be the case - indeed the authors themselves state (as does the Wikipedia page above) that warmer conditions should in principle favour the frogs, so they hypothesise further that the warmer conditions bring more cloud which results in less sun and lower peak temperatures. It's all very interesting, and I've nothing against interesting ideas, but it seems rather more tenuous than you'd think at a first glance.
What's clear is that this disease is a recently introduced one, which has been spread by human activity over recent decades. Whenever the disease reaches a new area, it has devastating effects. This paper makes a very strong case that the disease originated in Africa, where it happily coexists with its main host the African Clawed Toad. After 1934, it started to be spread around the world (by human activity, initially due to the ACT's use in pregnancy testing and other biomedical research, more recently the pet trade and perhaps even tourism) at an increasing rate, leaving a trail of devastation in its wake as it infected species which had no naturally-evolved resistance to it. I spotted this news item more recently, which talked about the same disease affecting a nearby area:
Researchers from Southern Illinois say the fungus, which causes the infectious disease chytridiomycosis that affects amphibians, arrived in Panama in 1993 and was detected in El Cope, an area near the Caribbean with many frogs, in October 2004.That's a 70% extinction in one area in 4 short months! And the researcher mentions another two threats, one of which must be fairly generic (habitat loss) even if most species are not directly collected as pets.
Within four months, it had wiped out 57 out of a total of 70 frog, toad and salamander species, including many golden frogs, in the area.
"The golden frog is already endangered because of habitat loss and collecting for the pet trade," Lips said.
The Nature paper doesn't attempt any balanced consideration of the various factors which might have been contributing to the extinctions they studied. The obviously dominant factor is the recent introduction of the disease, and it's hard to see how a 0.5C warming can have a large effect compared to the other threats. Note that these frogs live in mountainous areas where their natural range covers a vastly greater range of temperatures, and a 100m elevation change would more than compensate for the warming. I bet that if the climate had been cooling in recent decades, there would still have been many extinctions - I've really no idea if it would be more or fewer, but I'm sure there would have been researchers concerned about it in any case.
By the way, the disease now seems to be getting established in the UK, which is obviously very bad news for frogophiles.
For two more takes on it, have a look here and here. I should make it clear (before anyone accuses me of turning septic) that I'm not much of a fan of either of those authors, and indeed I've previously had a couple of run-ins with them myself (eg here and here). But that doesn't mean I will automatically reject everything they write, even though I do view their comments with a rather sceptical eye. It seems to me that their criticisms are generally well-founded in this case.
I've tried to encourage RealClimate to write something about this story, without success. My guess would be that they have similar reservations to me, but are too circumspect to voice them openly. RC authors are of course welcome to confirm or deny this either in the comments, or directly by email if they prefer :-)