Saturday, July 25, 2009

I'm a scientist! Pt 4

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.

This is post 28 of 49 of Blogathon. Pledge a donation to the Secular Student Alliance here.


  1. That didn't bore me. It just confused me. I have done lots and lots of reading on biology...I was just never very good at it. Wow, Jen, you're damn smarter than I am in this field. I think I get it....but wow.

  2. The ability to count is the first to go. Thanks, UWC.

    Sorry if I didn't do a good enough job explaining it, Veritas =\ It probably would have been clearer if I had more than a half hour. Have any specific questions?

  3. Huh. Okay, I have to admit to being no great shake at biology, but how do you determine the rate of mutation of different genes in order to find these differences? Is it an average or a trend or something? Does the rate of mutation of a specific gene just pop out naturally from sufficiently large quantities of data?

    Sorry, I'm in physics... so my basis for comparison is radioactive decay, which is all based on probability and all works out when you deal with big enough quantities, so that's how I'm interpreting what you're saying on this. I'd just like to know whether that's what is really going on.

    (btw... isn't this part 4 of this series?)

  4. Nope, Jen. It's clear. It just takes me 3-4 read-throughs. I have a mind that works well in a thick dusty history book. Chromosomes and I need extra time to get along.

  5. Is this sort of like the salamanders in Central Valley of California? I know the cases are different, because that case dealt with ring species and this one is just separated populations (so far), but would I be right in saying that in time, you could end up with distinct species/varieties at each end of the valley, with transitional varieties along the length of the valley?

  6. Ian: Mutation rates are figured out by a lot of data and math and modeling that I do not fully understand. Aka, I look it up in a paper that already has it figured out. If you want to learn more you can try here though:

    UWC: You're very correct. Consider this project a smaller version of ring species. Since they're not as far apart as the Salamanders you're talking about, it's incredibly less likely that the krats at the tips would be different species - but it's a good analogy.

    The krats also have only been in this valley for the last 10,000 years or so (the end of the pleistocene made suitable krat habitat), so they haven't had enough time to make different species yet. Maybe if you checked back a long time from now, you'd see a ring species effect.

  7. Actually, this sounds pretty frickin' awesome. And reminds me of that ant supercolony thing, only smaller.

    (Yay, finally back! I was unaware "Let's go have dinner!" meant "Why don't you come to the store with me to keep me company, too!" Heinlein was right.)