So what do I specifically study about kangaroo rats using genetics? Well, there's been a long standing debate in our lab if our two study sites are actually separate genetic populations, or geographic locations. They're separated by about 30 miles, and krats don't disperse that far in a year - usually 100 meters. However, the sites are connected by a valley that's full of kangaroo rats. If they're a single population, their long term population histories and genetic variation would be similar. If they're two populations, you would see some difference. That's what I'm trying to solve.
How do you look thousands of years back into the past using just the DNA you have now? You use a molecular clock. DNA mutations accumulate at certain rates in certain areas, and you count the number of mutations. For example, if you know in one gene you get one mutation every ten million years, and you see three mutations, that probably took 30 million years to accumulate.
I specifically use the control region of mitochondrial DNA. The control region is a noncoding region that accumulates mutations quickly since it doesn't undergo any type of selection. It accumulated mutations so quickly that you can see differences within individuals in a single population by just looking at a couple hundred base pairs of sequence data. For example, these may be two individuals:
krat 1: AATCGTT
krat 2: GATCGTT
Each variation of sequence is called a haplotype. You may know the term "genotype" - the main difference here is that since we're dealing with mitochondrial DNA, it's haplod (only has one copy). More than one individual usually share haplotypes unless it's a rare one. If the two populations are isolated, you would expect to see differences in haplotypes. We didn't see any differences, which indicate these two locations aren't as isolated as we may have thought.
There's some more in depth analysis going on, but I'm not going to bore you with those bits.
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