Why does the Philippines have little fossil deposits?
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Are you completely sure the Philippines' amount of fossils are unusually small? I know of no less than 2 anthropological finds there, the oldest dating back nearly 50,000 years. That isn't bad at all, for a place that would have required boats (or a very unusual accident) to reach. Its thought that no hominid had boats before that time, so any significantly earlier hominid finds are unlikely.
If you were hoping for other megafauna (like mammoths), again you have the boat problem. Flying creatures can obviously get there, as can smaller creatures by hopping a ride on a lucky piece of flotsam. However, it would be difficult to picture the errant floating log big enough to provide survivable purchase for a pregnant mastodon. So the only way they could get there was wait until glaciers locked up enough ice to wade there.
But of course if you go back before the Pleistocene (about 2.5 million years ago), there were no convenient world-wide glaciations to suck up all that water.
Then again, it really could just be a matter of activity. The Philippines in the 20th century wasn't exactly the safest place for western paleontologists to work, both for political and health reasons. Not only that, but much of the islands are covered with a dense rainforest that it is exceedingly difficult to get around in, not to mention difficult to work in during the rainy season. It is probably no coincidence that the stereotypical paleontology site is in a desert or semi-arid climate.
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