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Interestingly, there are natural ways that differences in the abundance of isotopes can arise.

The obvious example is carbon, where the different abundances of carbon 14 are used to date archeological artifacts.

For most elements, the isotopes were determined billions of years ago when the Earth condensed out of the swirl of matter around the newly formed Sun, so the mix of isotopes then was what it is now and things were pretty well mixed then. Even if not, the process by which the isotopes were made is pretty much the same all over the universe so different stuff combined from different parts of the universe should still have about the same isotopic mix. (See related link to Nucleosynthesis.)

There are a couple of things that can cause the isotopic ratios to change. In the case of carbon, the cause is bombardment of the atmosphere by cosmic rays with enough energy to cause nuclear reactions. Carbon 14 and Iodine 129 are produced by this process and they are termed "cosmogenic nuclei." So, objects with old carbon, not having exchanged carbon with the atmosphere will have less carbon 14 because whatever was there decayed and was not replenished.

There is also the process of natural radioactive decay of things like uranium-235, uranium-238, and thorium-232 produce various elements. These elements will not necessarily have the same isotopic composition as the element that was naturally occurring at the time the Earth was created.

Of course, one might ask if materials that come to Earth from outer space, e.g. meteorites, count as "naturally occurring." One would not expect them to have the same isotopic composition exactly as what is on Earth originally.

There are other differences, such as the rate of diffusion that are different for different isotopes. A molecule of water with a deuterium diffuses at a different rate than one just a tiny bit lighter. Such processes may lead to depletion of lighter isotopes in samples.

Those are a few obvious mechanisms that may create different abundances of isotopes in different samples of the same element, but there are surely more. This answer has not given any indication of which might be the most common mechanisms, except for carbon 14.

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