Good points, Charles. I did say that I wasn't very familiar with the marmots, I just did a quick check on the web to find some info. I was wondering if anyone had looked into their genetics, and I'm not surprised by the results you posted. This often turns out to be the case when things are differentiated into species/subspecies simply on the basis of skin/fur colour & pattern, or location. I know of similar examples of snakes and fish (my two main areas), and also of cases where things that were considered similar have turned out to be quite different and ended up being split into different species.
With respect to extinctions (and though less definitive, exterminations of distinct populations is important as well), I was referring to "species which have shown declines in the last 200 years". Certainly, there are lots of things which declined in the past, and which are declining now that we don't even know about. We tend to only study things which are big enough to catch someone's interest, and even then, most of the resources get funnelled into a small number of species which are economically valuable or simply extremely charismatic. It goes without saying that these things are generally vertebrates. Other than some molluscs and arthropods (again generally those that are economically important or really pretty

), and a few pathogens and parasites that relate to humans, not many invertebrates get that much attention from a conservation perspective.
Of course, there is some validity to this approach. Bacteria, algae, flatworms, etc. generally have high reproductive capacities and short generation times, so they can adapt to changing circumstances faster than most vertebrates, and recover from declines quickly. Plus, it is very difficult to say "hey- the **** are all gone" when you can't see them anyway and would have a hard time knowing if you're just not looking in the right spot! (This happens with vertebrates from time to time as well, of course). I do recall one scientist who found a decline in a species of zooplankton in Pacific tide pools. As far as he could tell, they were all gone. As you've said, hardly anyone is likely to notice!
Parasite or pathogen invasion is an interesting theory regarding those mastodons. Certainly, such an example would qualify as natural. However, lots of parasites are now moved far more quickly by human activities, and while they rarely cause extinctions (this by nature eliminates the parasite if it is host specific) they certainly do cause declines, such as in the case of chestnut blight, dutch elm disease, and others (again, well studied due to their economic importance).
Declines in some frog populations/species have been traced to a chytrid fungus. One source of new infections- researchers tracking spores from one location to the next on their boots (now they sterilize or change them).
Anyway, so assuming we're talking about vertebrates, the list of things that we know have declined seriously or become extinct is hardly restricted to "mammals, some birds, maybe some frogs", though there are lots of these.
From a Canadian perspective, 62% of our reptile species are currently considered "at risk". Of the remaining 38%, quite a few have never been studied. Of course, many of our reptiles remain common in the US, but not all of them, such as the eastern fox snake, eastern massasauga rattlesnake, wood turtle, and Blanding's turtle. These species are in big trouble through most of their US range as well. Reptiles are a very ancient, very "successful" group of vertebrates, yet almost all taxa show some pretty serious declines for many or all of their species. Virtually every case appears to be traceable to human activities, though many have not been studied conclusively. If we separate them by group- crocodilians- many species in peril, turtles- serious declines for many species, most recently in Asia, due to overharvesting, snakes- perhaps the best off due to their secretive behaviour, but still many species showing dramatic declines in recent history based on anecdotal evidence, lizards- many species, especially long-isolated island forms that ARE genetically very different, are in big trouble. And then, there's the Tuatara, in a group of its own, nearly wiped out due to introduced species in New Zealand. Actually, much of the fauna of NZ has declined precipitously due to introduced species.
We could do a similar breakdown of fish, but it'd take too long. Some recent North American examples, though, that can be traced partly or mostly to human activities- mostly overharvesting, but also dam-building, logging (erosion and sedimentation), and introduced species:
Lake Erie blue walleye, deepwater cisco (both extinct), Lake Sturgeon (massive declines), Atlantic salmon and american eels (declines through much of their range).
And there are lots of frog examples, and yes, many mammals and birds as well, but I won't even get started on those.
"I also think that, in relation to extintion, that man is the dominant force on the planet. I think that the vast majority of extinctions among all species remain the result of original low population numbers coupled with climatic and other microevents and attrition through competition for resources. "
I'm guessing that you meant to say "man is NOT the dominant force" based on your second sentence.
Granted low population numbers, isolated distributions, etc. are a factor, especially for those species that have been 'human affected'. However, can you give me some examples of all these vertebrate species which are disappearing due to "climatic and other microevents and attrition through competition for resources"?
Jeff Hathaway