19 June 2008

Wait...did you say "eldritch?"

It's exciting to live in the era of evolutionary genomics, when new genomes are being published approximately once a week, and the light of genomic analysis is being trained on more and more branches of the tree of life. This week sees the unveiling of the genome of Amphioxus, a primitive vertebrate that has long been known to be a key piece of the puzzle of animal evolution, and the results are sharpening our hypotheses about the genesis of major animal groups.

First a little about the results published in this week's Nature. Amphioxus is the fancy name for lancelets, which are small and simple sea-going creatures that represent a very interesting branch on the tree of life: they constitute a group called the cephalochordates, which is one of the three living groups of chordates. (Remember "kingdom, phylum, class, order, family, genus, species"? Humans are vertebrates, and vertebrates are a subdivision of the chordates.) Vertebrates and tunicates (sea squirts) are the other two groups. Because the lancelets are similar in structure to vertebrates, more so than are the tunicates, they were long thought to be more closely related to vertebrates, and so it was postulated that tunicates were more "basal" on the evolutionary tree. But two years ago, new analyses strongly suggested that it is the lancelets that are the most basal group. And so the lancelets became even more interesting: understanding their genomic structure would surely provide clues to the nature of the original chordate genome.

The examination of the lancelet genome (well, it's the genome of one lancelet of one species) provides substantial new insight into vertebrate evolution. For some solid overviews, check out Nobel Intent at Ars Technica, and the press release from UC Berkeley. Here are just a few tidbits that got my attention:
  • The findings strongly support the hypothesis that the vertebrate gene set was diversified through two ancient whole-genome duplications. This phenomenon and its role in the generation of new gene functions have been discussed here before.
  • The lancelet genome contains roughly the same number of genes as the human genome.
  • Comparison of the various chordate genomes reveals that there are very few chordate-specific genes. Specifically, the authors described 239 "chordate gene novelties" out of 22,000 genes in the lancelet. The nature and function of these genes is intensely interesting, and indeed the authors devote a separate report to issues related to this. But think about it: only 1% of the genes in chordates (vertebrates and all their relatives) are "novel" among genes from all other organisms.
  • So if the toolbox isn't all that different between lancelets and lions, despite divergence at least 550 million years ago, then what is different? Anything? As John Timmer notes on Nobel Intent, the authors could find relatively few examples of regulatory DNA sequences that are conserved between lancelets and vertebrates, pointing to the likelihood that changes in regulation of a (mostly) common genetic toolkit is a major factor in evolution of form. (Okay, so that was just a plug for evo-devo. It's my blog.)
But one more thing. Why the bizarre title for this blog entry? Well, Henry Gee at Nature wrote a very nice News & Views summary of the genome report, and here are a few not-so-randomly-selected excerpts:
The age of genomics has rescued the amphioxus from chthonic obscurity, as new data — now including Putnam and colleagues’ paper and three companion reports in Genome Research — have reinvigorated the study of the origin of the vertebrates.
Is there a typo in there?
The 520-megabase genome of B. floridae would, therefore, be nothing much more than a curiosity without the comparative context offered by the increasing number of completed or draft animal genomes from humans to sea anemones... Such studies reveal the amphioxus genome to be, in fact, of preternatural importance.
But with Putnam and colleagues’ publication on page 1064 of the draft genome sequence of Branchiostoma floridae, one of the 25 or so recognized species of amphioxus, this eldritch organism is set to re-enter public life.
Eldritch? Eldritch?? What the heck?!

'Preternatural' I can handle, barely, but 'eldritch' and 'chthonic'... Yes, there's a story here, and it's very funny. Enjoy, and have fun in your next Scrabble game.


Martin LaBar said...

Interesting. Thanks for posting this.

Sparky said...

Now that makes me want to go grab my Lovecraft anthologies. A quick glance through Google images suggests the connection may be apropos -- that mouth is full of tentacles.

Jimpithecus said...

That's just goofy. I have read Henry Gee before and he has never been quite that over-the-top. This is my favorite:
"This extensive synteny has allowed substantive insight into a suspected episode in the early history of vertebrates when the genome underwent tetraploidization. "
The sad thing is that there is no other word for "synteny."

Jimpithecus said...

Although one wonders why "gene linkage" wouldn't have worked.

Anonymous said...

Henry is a scream. I can't wait to meet him in August.

If you follow the link at the Labrats to Henry's blog at Nature Network you'll see what I mean. And get the chance to read drafts of his epic space opera trilogy.