Digital Biology Friday: Monkeying around with mitochondrial DNA

The past few Fridays, we've been comparing human mitochondrial DNA with the mitochondrial DNA of different apes.

We started doing this here, where you can find directions for getting started.

And, we've found some interesting things.

In this installment, we found that humans have practically an entire mitochondrial genome stuck in chromosome 17.

Last week, we found that human mitochondrial DNA is more similar to that of chimpanzees than to gorillas. We found that 90.6% of the bases in human mitochondrial DNA match bases in the Bonobo chimp and 90.7% match bases in the Chimpanzee.

This week, we're going to compare all four species to each other.

The first thing that I did was to do blastn searches with the other mitochondrial sequences. First, I compared the mitochondrial sequence from Pan paniscus to that of Pan troglodytes and the gorilla. Notice, the two chimps match along the whole length of the mitochondria, but the gorilla sequence shows some gaps where the bases don't match.

i-d8d2a33d6e8b9c451bdd3e2cbd780953-pan_blast.gif

Then I compared Pan troglodytes to the gorilla, and added up the matching bases across the length of the mitochondria for each comparison and determined the fraction that matched for each comparison.

This gave me a matrix like this:

i-55512198b140a384ab879b3507b67054-pan_table.gif

That information was enough for me to draw a cladogram. Cladograms are graphs that show evolutionary relationships but they don't include information about time.

For my cladogram, I put the two species together that were most closely related - Pan paniscus and Pan troglodytes. Then I added humans, and last gorillas. i-5a95ce9a7bdaf0e4688c4ae88ab696c6-ape_tree.gif

Since I wanted a nicer picture, I also converted my matrix to a different file format and ran the neighbor joining program from Phylip (apparently there's a new version, 3.66, that just came out this month, but I doubt that would matter for this analysis). Then I used NJ plot to view the tree.

There you have it, Pan paniscus and Pan troglodytes are the most closely related.

For some reason I thought, ahead of time, that the mitochondrial DNA of chimps and gorillas would be more similar to each other than to humans, but I was wrong. Human and chimp mitochondrial DNA were both 87% similar to the mitochondrial DNA from gorillas.

Come back for next Friday, for more monkeying around.

Wink, wink, nudge, nudge.

technorati tags: ,
, , , ,

Copyright Geospiza, Inc.

More like this

During these past couple of weeks, we've been comparing mitochondrial DNA sequences from humans and great apes, in order to see how similar the sequences are. Last week, I got distracted by finding a copy of a human mitochondrial genome, that somehow got out of a mitochondria, and got stuck right…
Last week, we decided to compare a human mitochondrial DNA sequence with the mitochondrial sequences of our cousins, the apes, and find out how similar these sequences really are. The answer is: really, really, similar. And you can see that, in the BLAST graph, below the fold. A quick glance…
As many of you know, I'm a big fan of do-it-yourself biology. Digital biology, the field that I write about, is particularly well-suited to this kind of fun and exploration. Last week, I wrote some instructions for making a phylogenetic tree from mitochondrial genomes. This week, we'll continue…
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,…

Your results are what would be expected based on currently accepted phylogenies.

If you look at the estimated time of divergence of these four species from the ancestral ape lineage it makes sense.

Bonobos and Commom Chimps split 2 mya
Humans and Chimps split 6 mya
Human/Chimp lineage and Gorillas split 7 mya.

http://tolweb.org/tree?group=Hominidae

By Petewsh61 (not verified) on 23 Aug 2006 #permalink

It's always nice when you can arrive at the same conclusions by different methods, thanks!

I like using the molecular data because anyone with a computer can do the experiments and confirm the results. It's a lot easier to get DNA sequences than try to find the original papers with carbon dating and photos of fossils.