Like biology, all bioinformatics is based on the idea that living things shared a common ancestor. I have posted, and will post other articles that test that notion, but for the moment, we're going to use that idea as a starting point in today's quest.
If we agree that we have a common ancestor, then we can use that idea as a basis to ask some interesting questions about our genomes. For, example, we know that genomes change over time - we've looked at single nucleotide changes here and here, and we've seen that large chunks of DNA can move around here.
So, it's interesting to consider how often different regions of DNA change relative to each other.
A few weeks ago we starting monkeying around with comparing human and primate sequences of mitochondrial DNA
Well, we're not done.
If you'd like to take a quick tour, here is a list of places that we've been and sequences we've explored.
Revisiting our blast results
This image shows where the mitochondrial DNA sequences of humans, bonobo chimps, chimpanzees, and gorillas match. A red bar indicates where the DNA sequences are very similar. Other colors or gaps show regions that are less similar or even missing from one or more sequences.
I circled 3 segments in this image and now, here's your chance to interpret the results and make a guess about what the results are telling you.
Think about why the sequences in section 2 show a different result than the sequences in section 3. It might be helpful to go ahead and do the experiment yourself, so that you can identify the matching sequences, the instructions are here and there are some helpful hints here.
Can you explain the results?
Let me know what you find!
Group 3 doesn't actually do anything and thus is prone to being overwritten with translocated chunks of mtDNA from elsewhere.
Given the compactness of the mitochondrial genome (which is a standard property of small genomes), there aren't going to be many places that aren't necessary for survival, and it's just our luck to have found one of them :-P
A better approach to determining phylogenetic distance might be to look at a strongly conserved region and count silent mutations. That won't have the same problem with natural selection rearing its ugly head.
Am I on track?
Sorry for the late reply.
You're definitely on track but I don't agree about needing to use silent mutations to detemine phylogenetic distance. I don't think natural selection and speciation can be separated since the two processes are intertwined.
I also disagree with this statement:
thus is prone to being overwritten with translocated chunks of mtDNA from elsewhere.
In order to be overwritten, this region would have to be accessible to the enzymes involved in recombination or gene conversion. But it's not. Mitochondrial DNA is sequestered inside the mitochondria, which are located in the cytoplasm and physically separated from the enzymes and translocated chunks of DNA that are involved in recombination and gene conversion.
Instead, I think that we see more mutations and deletions in this region because it's less important for survival.