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Hi Nic. The first thing to clarify is that megapixels (informally abbreviated MP) and megabytes (MB) are not the same thing. I mention this because people often confuse the two, not because you've necessarily done so.
A megapixel is a million pixels (the digital dots that make up the image).
A megabyte is a million bytes (and a byte is in turn 8 bits, a bit being the most basic unit of information in digital systems, expressed as a 0 or 1 in binary notation).
Your EOS-1Ds Mark II has roughly 16 megapixels, but that doesn't mean you'd expect it to produce 16-megabyte files. Since it's a 12-bit camera, it produces 12 bits of information for each pixel, and it has 4992 × 3328 pixels (that's where the ~16 million comes from). If you multiply the pixel count (16 million) by the bit depth (12), you get a raw file size of about 190 megabits. Dividing that by 8 to get bytes, you get about 24 megabytes for the file size.
However, your camera compresses that information to save storage space, which is why Canon specifies an average raw file size of 14.6 megabytes (on page 45 of the EOS-1Ds Mark II user manual). You can think of this compression system as replacing all the "the" words in my message with the character z, which would make my message shorter without losing any information. Obviously it's a bit more sophisticated than that in practice, but that's the idea. The compression scheme works best if there is little detail to compress. If the photo has loads of identical blue pixels representing a large swathe of sky, for example, it's analogous to my message consisting of long sentences of "the the the the the the" – clearly very compressible information.
If, on the other hand, you're shooting dense forest full of tiny details, or shooting at a high ISO producing noisy images, the compression scheme is less effective. (The compression scheme can't tell the difference between noise and twigs: to it, they're both details that can't easily be compressed.)
Since you're shooting wildlife with a 300 mm lens, you probably have large out-of-focus areas in your photographs. These areas are easily compressible, since they're smooth and lacking in detail. Shooting at ISO 100 also means noise is kept to a minimum. Both of these factors contribute to smaller-than-average raw files, and would explain why your files are around 12 megabytes instead of Canon's conservative figure of 14.6 megabytes.