The Tuatara Genome Project

by Greg Mayer

We’ve had occasion to celebrate the completion of reptile genome projects before here at WEIT (including the first, the Anole Genome, and the recent turtle genomes), so it is especially notable that one of our favorite animals, the Earth’s Only Extant Non-Squamate Lepidosaur*, is now the subject on an ongoing sequencing project being led by Neil Gemmell of Otago University and the Allan Wilson Center for Molecular Ecology and Evolution (whose director is my old chum and fellow MCZ alum, Hamish Spencer). It is of course fitting that the genome project be based in the iconic animal’s native land, New Zealand. David Winter has begun a blog, Sequencing the Tuatara Genome, to document the project’s progress.

Why sequence the tuatara genome (other than just because they’re, you know, great)? This picture from David’s blog, should tell you. (BTW, back when the Anole Genome was completed, a reader asked, “What are the gaping holes in our genomic knowledge?”, and I presciently replied “Among tetrapods, the gaping holes are the tuatara,…”.)

Phylogeny of relationships of the tuatara, from David Winter's Sequencing the Tuatara Genome Project.

Phylogeny of relationships of the tuatara, from David Winter’s Sequencing the Tuatara Genome blog.

If it’s not clear, David spells it out (note that he uses the proper Maori “tuatara are“):

You sometimes hear people mistakenly call tuatara “living dinosaurs”.  In fact, as you can see in the figure above, tuatara are much more interesting than that. If you want to study a living dinosaur you only need to look out the nearest window. Modern birds descend from one branch in the diverse group we call dinosaurs, but each of those ten thousand species are dinosaurs. The tuatara, on the other hand, are the only living members of a lineage that separated from other reptiles more than 200 million years ago.

By placing modern organisms in the context of their evolutionary history, we can work out which traits were present in ancestral species, and reconstruct the changes that gave rise to modern ones. As the tuatara is the only living witness to hundreds of millions of years of evolution, its genome sequence will be immensely valuable in understanding the genetic changes that have allowed reptiles to evolve and diversify.

I urge you all to go take a look at David’s blog now, and check back in there now and again to see how things are progressing.

_______________________________________________

* I was going to say the Universe’s Only Extant Non-Squamate Lepidosaur, but I can’t quite rule out that some Vulcan survey craft, while cruising nearby waiting for Zefram Cochrane to release a warp signature, might not have decided to stop by for a bit and then taken some non-squamate lepidosaurs home (I know I would have).

31 Comments

  1. Posted July 10, 2013 at 6:45 am | Permalink

    One thing I don’t remember from previous discussions…prior to DNA sequencing, how did we figure out that what just looks like a typical lizard is hanging out there on an odd twig on the evolutionary tree?

    b&

    • Posted July 10, 2013 at 6:50 am | Permalink

      It only looks like a lizard on the outside. Its skull and other parts of its internal anatomy are quite distinct.

      GCM

      • gbjames
        Posted July 10, 2013 at 7:01 am | Permalink

        Very like me! I look like a lizard on the outside but inside I’m a handsome prince.

        • Diana MacPherson
          Posted July 10, 2013 at 7:22 am | Permalink

          I’m all lizard on the inside! :) Like in V

      • Posted July 10, 2013 at 7:26 am | Permalink

        Makes sense. Tanks!

        b&

      • Reginald Selkirk
        Posted July 10, 2013 at 1:02 pm | Permalink

        Does it taste like chicken on the inside?

  2. dhillis2013
    Posted July 10, 2013 at 6:49 am | Permalink

    Technically, though, there are two species of tuatara: Sphenodon punctatus and Sphenodon guntheri. The latter is endemic to North Brother Island in Cook Straight.

    • Posted July 10, 2013 at 1:12 pm | Permalink

      David–

      Guntheri was sunk back into punctatus in 2010 by the same people who had resurrected it in 1990. See the discussion here at WEIT. Has it been re-resurrected?

      GCM

    • David Winter
      Posted July 10, 2013 at 5:20 pm | Permalink

      Hi dhillis2,

      As greg says – the two species where sunk back to one in 2010. We are going to have a post about this hopefully next week, but the WEIT post sums up the research nicely.

      Having a draft genome will hopefully let us do some re-sequencing projects and get a good grip on the degree to which the remaining populations have distinct histories.

    • David Winter
      Posted July 18, 2013 at 7:37 pm | Permalink

      David,

      In case you’ve subscribed to follow-up comments here, we’ve got our posts on the history of the species problem and tuatara up now:

      http://sciblogs.co.nz/tuataragenome/2013/07/19/your-questions-how-many-species/

  3. Kevin
    Posted July 10, 2013 at 7:22 am | Permalink

    I want to know how they put dinosaurs where they did, with no DNA to guide them.

    Unless Jurassic Park is real.

    • truthspeaker
      Posted July 10, 2013 at 8:39 am | Permalink

      Morphology.

      • Kevin
        Posted July 10, 2013 at 10:26 am | Permalink

        Yes, but that’s not genetic analysis, then, is it?

        That’s a problem. I know you can say “well, the anatomy blah blah blah and all that”, but it’s supposed to be a genetic analysis.

        Isn’t. It’s guessing.

        • John Harshman
          Posted July 10, 2013 at 10:53 am | Permalink

          What’s supposed to be a genetic analysis? And why should morphological analysis be equated with guessing?

        • truthspeaker
          Posted July 10, 2013 at 11:21 am | Permalink

          The visual says phylogeny, not genetic analysis.

          Classifying phyla by morphology of fossil remains isn’t guessing. It’s how most of the phylogenetic trees we use today were developed.

        • David Winter
          Posted July 10, 2013 at 5:26 pm | Permalink

          Hi Kevin,

          The figure isn’t the result of a particular analysis – it’s a summary of the knowledge that we’ve gathered from many, many studies including those using genetic and morphological data.

          The relationship between birds and dinosaurs is supported by a bit more than a guess :)

  4. Diana MacPherson
    Posted July 10, 2013 at 7:26 am | Permalink

    I love that the Tuatara are getting their genome mapped mostly because tuatara are cute and awesome! The first time I saw one was at Rainbow Springs in New Zealand almost 20 years ago and I’ve loved them ever since! Cute little reptile!

    Loved the Zefram Cochrane reference. :)

    • Kelton Barnsley
      Posted July 11, 2013 at 9:32 am | Permalink

      So did I! First Contact is my favorite Star Trek movie (though I greatly enjoyed Into Darkness this year). I just love when Worf says to Picard: “If you were any other man, I would kill you where you stand.”

  5. RedSonja
    Posted July 10, 2013 at 8:52 am | Permalink

    WEIT – where I can get my evolutionary biology AND Star Trek jokes all in one place.

  6. Reginald Selkirk
    Posted July 10, 2013 at 10:18 am | Permalink

    Has anyone done a velvet worm genome?

    • John Harshman
      Posted July 10, 2013 at 11:01 am | Permalink

      Apparently not, but there’s a project just starting.

    • gravelinspector-Aidan
      Posted July 11, 2013 at 3:54 am | Permalink

      Someone has done their mitochondria :

      Podsiadlowski, L.; Braband. A.; Mayer, G. (2008). “The Complete Mitochondrial Genome of the Onychophoran Epiperipatus biolleyi Reveals a Unique Transfer RNA Set and Provides Further Support for the Ecdysozoa Hypothesis”. Molecular Biology and Evolution 25 (1): 42–51. doi:10.1093/molbev/msm223. PMID 17934206.

      http://www.hgsc.bcm.tmc.edu/content/i5k-velvet-worm tells me that another “G Mayer” (or the same one? Probable.) is the “man with a plan” for onchyphore genetics. Most recent data was posted on 21/03/13, so what they’ve been doing for the last 93 years isn’t clear [G].

  7. John Hunt
    Posted July 10, 2013 at 3:03 pm | Permalink

    I’m not Maori, so I’m just going to go ahead and pluralize words in the typical English fashion.

    • Diana MacPherson
      Posted July 10, 2013 at 3:23 pm | Permalink

      Okay Pakeha! :)

  8. David Winter
    Posted July 10, 2013 at 5:16 pm | Permalink

    Thanks very much for featuring the blog, Greg. We hope evolution, tuatara and genomics fans all get something out of the posts we publish :)

  9. Gayle
    Posted July 10, 2013 at 6:48 pm | Permalink

    It’s funny. When I was a PhD student in NZ back around 1999-2002 I distinctly recall a PhD student at University of Otago getting in a heck of a lot of trouble with the authorities for doing tuatara sequencing work (“Maori sensitivities”). It blew up in the media, her own institution behaved like cowards and refused to support her, and all of her material was confiscated and destroyed. All records of this happening seem to have been removed from the interwebs, but some vestiges remain. http://web.kuicr.kyoto-u.ac.jp/supp/hiranuka/pub/EGENES/animals/Sphenodon_punctatus/report I guess that scientists are assisted with iwi consultation these days and the project can go ahead with the blessing of Maori. I was stunned at the time both by the attitude of Otago University towards their student, but also because there was nothing in the world to stop researchers from outside of New Zealand sequencing the Tuatara genome and getting all the glory!

    • Gordon
      Posted July 10, 2013 at 9:02 pm | Permalink

      and that’s why academic freedom is important and more importantly an example of why the institution itself is usually the greatest threat to that freedom.

  10. lisa
    Posted July 10, 2013 at 8:03 pm | Permalink

    I see at least someone has watched some Star Trek.

  11. Diane G.
    Posted July 10, 2013 at 9:37 pm | Permalink

    sub

  12. marksolock
    Posted July 11, 2013 at 5:25 pm | Permalink

    Reblogged this on Mark Solock Blog.

  13. Posted April 9, 2014 at 3:31 am | Permalink

    Non squamate lepidosaurs don’t need aliens to survive. Some could develop advanced technology and fly to space when the Triassic-Jurassic extinction hit the Earth. In the other scenario, they might still be living. Maybe somewhere deep in the unexplored parts of New Guinea. I believe, as New Guinea is near Australia that had preserved many ancient forms, that somewhere in the deep forests or mountains of the country there might be living fossils waiting discovery. Other non squamate lepidosaurs, land crocodiles, meiolaniid turtles, or even premammalian synapsids.


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