What single element could destroy the world?

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Edit: When I first wrote this I didn't grok the "single element" statement fully.
I'm not really changing my answer, just changing the execution.
With the right planning and equipment, you could wipe out the majority of life on earth with only 120-210 kg of Uranium/Plutonium.

Take the uranium and shape it into cores for bombs of around 30kg, which IIRC can deliver a yield in the 50-100 kiloton range with the right design.

This is the most efficient way I can think of to trigger the release.

You could probably do the same job with less plutonium. It's surprisingly hard to find statistics for core sizes and weapon yields.

No one has mentioned Methane yet.
Methane is heavier than oxygen and nitrogen, which means that it stays close to the surface instead of rising into the atmosphere, and there is enough of it stored in hydrates under the ocean to cover the surface of the earth and suffocate the majority of people.

Methane is also a very powerful greenhouse gas, which means the earth would warm significantly very quickly, and so the oceans would rise, and the gas would rise...

The best part is that because the methane is already stored in the hydrates you wouldn't need to make any, you would just need a submarine to go down and release it with some digging or bombs, which is pretty Mad Science.
The scientist would only have to release a fraction of the stored methane, which would cause a lot of warming, which would heat the oceans, releasing more methane.

The idea that this could happen naturally is called the Clathrate Gun Hypothesis.

And then there would be the opportunity to ignite the methane...

The check list:

Natural elements only, and no anti-matter...nice try.

Just normal weapons grade uranium or plutonium...

Looking for the element that a mad scientist would need the least of to wipe out all vertebrate life.

This would wipe out all surface life, though the earth itself would remain. The majority of people/animals would suffocate very quickly, and the methane explosions would probably get the rest.
You might get a handful of survivors at high altitudes for a while, but not enough to sustain a population.

How much would they need? (This is the efficiency part. I want to use the least amount of element x as possible)

Not that much. Enough for 4-6 medium size bombs. Rough calculations say 120-210 kg of uranium (30 kg per core), 60-100 kg of plutonium (15-20 kg per core).

This needs to be achievable by near future means, no magi-tech, no hand-wavium.

We could do this now with simple technology. It would just take a bit of money to map out the richest deposits and then build the nuclear bombs. Probably dig a few oil well style holes down into deposits, and then insert the bombs into the wells. Like fracking the ocean floor.
This could happen by itself at any time, if there was an earthquake in the wrong place.

Where would the element come from? (can it be harvested or manufactured?)

Africa probably.
I have heard of a nice guy in Libya that can get you some if the price is right, and I've heard of a guy in Chad selling yellow cake over the internet...
Russia has potential too.