Posted by: salamandercandy | November 28, 2006

Copies

How genetically diverse is the human species? How genetically different are we from other species? You might think that scientists could spit out simple, single-number answers to these questions. However, measuring genetic variation and divergence is not as straightforward as it might seem.

To assess the genetic difference between two individuals, you could just align related DNA sequences from their two genomes, and calculate the percentage of nucleotide letters that differ between them. This is analogous to aligning two English phrases:

“Mary had a little lamb. Its fleece was white as snow. And everywhere that Mary went, the lamb was sure to go.”
“Mary had a little lamb. Its fleece was white as snot. And everywhere that Mary went, the lamb was sure to go.”

The above two phrases are 99% identical, due to a single typo (mutation). So, you might conclude that the books (genomes) in which you found these phrases are also 99% identical. But in reality, genomes don’t align so nicely. Chunks of DNA get copied and deleted pretty often, so you might find something like this:

“Mary had a little lamb. Its fleece was white as snow. And everywhere that Mary went, the lamb was sure to go.”
“Mary had a little lamb. Its fleece was white as snow. And everywhere that Mary went, the lamb had a little lamb was sure to go.”

These phrases also differ by single “mutation,” but this time it’s a copy-and-paste mutation, so the phrases are only about 92% identical.

Since “copy-and-paste” mutations can cause bigger changes than “typo” mutations, they are responsible for more genetic variation and divergence. According to a paper that just came out in the journal Nature, 12% of the human genome is variable in terms of the number of copies of DNA sections. In contrast, less than 1% of the genome is variable in terms of “typo” differences (called single nucleotide polymorphisms, or SNPs). So most of the genetic variation in our species is due to copy number, and it would be misleading to use the percentage of nucleotide letters that differ among sequences as an absolute measure of diversity. Similarly, you may have heard the oft-repeated factoid that humans and chimps are only 1% genetically different. This is true if you’re just talking about typos, but in terms of copying-and-pasting the difference is substantially greater. Many of the important adaptive phenotypic differences within and between species are probably due to differences in the copy number of chromosomal regions. Aligning related sequences and looking for typos is easy, but that method might miss most of the variation.

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