Mito Much?

mitochondrion_186.jpgA recently sweep of the literature (courtesy of my standing My NCBI search) led me to another mitochondrial resource that I thought I would mention. MITOMASTER is the resource, and you can find details about it in this paper:

MITOMASTER: a bioinformatics tool for the analysis of mitochondrial DNA sequences.

So of course I went to explore–I love a new database! Wandering around a bit, I find that they are the Molecular and Mitochondrial Medicine and Genetics Center (MAMMAG). I find this incredibly difficult to say–which is rather odd, since both my first and last name start with M you would think I would be better that this…

In any case, they are the home of a bunch of Mito features, it turns out. MitoMed, MitoMap, MitoWiki and MitoMaster. So I will now always think of it as the Mito4 place.

Mitomap is a database of human mitochondrial variations. You can access the existing site here: http://www.mitomap.org/ But it appears that they are planning a new version, and they are looking for input if you have some: http://mammag.web.uci.edu/twiki/bin/view/Mitomap/WebHome

The page had a number of links to other mito resources that were new to me–including the FBI Forensic mtDNA database. I have to admit, I went to peek at it to see what was in there. But it requires a download. I’m just not downloading stuff from the FBI….

You have to register to access part of the site, so I did. Then I tried out Mitomaster with a sequence I pulled out of GenBank. Quite a straighforward interface. It seemed to run fast and deliver interesting information about the variants. There was a button for each variant that quickly offered a more detailed look at any changes in a given gene. Seemed like a pretty useful option. I’ll try it out more soon–but I wanted to mention it while the paper was fresh in my mind.

9 thoughts on “Mito Much?

  1. Jeremy

    Just out of interest, what do you make of the idea that because some mt genes may not be neutral, therefore the mitochondrial Eve theory is not valid? I’ve just seen in on an anthro blog and I cannot for the life of me follow the logic.

  2. Mary

    Hmmm…I’m not sure I would have an opinion on that. I haven’t been following the mitochondrial Eve discussions at all.

    I’m more interested in analysis of contemporary sequences–I’m a lot more wigged out about that FBI database, frankly :)

    We would need to have the evolutionary biologists weigh in on the Eve issues.

  3. Trey

    Hmm, I haven’t kept up with that argument. Have any references?

    I’m sure I’d have an opinion after some reading :D

  4. Jeremy

    Well, there was a blog post here: The misleading concept of Mitochondrial Eve, but no references, yet. Having reread that, I think that Mathilda is just muddled about the different implications of MT genes being selected — which could affect the ticking of the molecular clock, but not necessarily — and the broader question of a single origin for modern Homo, which is not in the least bit affected by whether the MT genes are selected or not.

    I’ve just read a new article in Scientific American, The Migration History of Humans: DNA Study Traces Human Origins Across the Continents and I don’t honestly think that a multiregional hypothesis for human origins has much left going for it.

  5. Trey

    So Jeremy,

    I read the blog post you linked to. I do think she is muddling concepts concerning molecular evolution and her premise is basically a straw man.

    I’ll have to read it (and the rest of her site for that matter, because the post wasn’t particularly data or argument rich, so to speak) more in depth to give a more cogent response. I’ll put it in the que of things to think/write about.

    Just read the SciAm article too. Generally good, and I also think the multi-regional hypothesis is quite sickly, if not dead.

  6. Jim

    I believe that the mitochondrial Eve issues are only about the divergence estimate (the date put on her). Mark Stoneking just published a review on human evolution this year, and discusses some of this. I can’t find the reference at the moment, however…

  7. Jennifer

    Hi Jim,

    Thanks for the tip. I think it might be this review:

    Human origins. The molecular perspective
    Mark Stoneking
    EMBO reports 9, S46 – S50 (01 Jul 2008),
    doi: 10.1038/embor.2008.64,

    Let us know if that’s the one.

  8. Jim

    Jennifer,

    Yes… thanks for posting the link. It is a bit of an “easy” review of the details of the problem, but I think it is a great reference for those new to the field, or those not so into molecular clocks.

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