Genome research: good idea, bad idea

Good idea: A paper in the Journal of Heredity proposes sequencing 10,000 genomes...

Bad idea: ...of vertebrates.

Okay, I’ll admit that isn’t strictly a bad idea. But it certainly leaves something to be desired, given that a news article in Science characterized this plan as, “No genome left behind.” But of course, it leaves a tremendous number of genomes behind, namely, every single invertebrate. What are the current estimates for number of vertebrate species? Maybe 60,000 or so? The crustaceans alone probably have about the same number of species. The number of vertebrate species is not even close to the number of beetle species.

The paper provides no rationale for doing such a massive scan of the vertebrate genomes alone as opposed to a project that would include the invertebrates. Indeed, the word “invertebrates” appears only once, in reference to fisheries.

In fairness, I actually do think it’s great that these researchers are working together and suggesting a big, bold scheme. I’ve made no secret that I want a crayfish genome project. With this 10K genome paper, maybe it’s time to start thinking about a larger scale invertebrate genome sequencing project that will cover the rest of the animal kingdom, even though it’s obviously not possible to do the same level of coverage as the small vertebrate sub-phylum.

Reference

Genome 10K Community of Scientists. (2009). Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species Journal of Heredity, 100 (6), 659-674 DOI: 10.1093/jhered/esp086

Pennisi, E. (2009). No Genome Left Behind Science, 326 (5954), 794-795 DOI: 10.1126/science.326_794

Pic of the moment: 5 December 2009

This is a sick crayfish. As readers may know, I am not a pathologist or parasitologist, so I have little idea what these black spots may be or how to combat them. We’ve definitely had some animals die prematurely due to whatever these are. Any information would be most welcome!

Darwin on crayfish development

Today is the 150^th anniversary of the publication of On the Origin of Species. I’ve talked before about the monograph on crayfish by Darwin’s close friend, Thomas Henry Huxley, but Darwin himself did significant work with crustaceans, notably barnacles. But because this is a crayfish blog, I went looking through the massive online database of Darwin’s writing for references to crayfish.

In the Variation of Plants and Animals Under Domestication:, Darwin considers something near and dear to the heart of this blog, crustacean development:

We are led to the same conclusion, namely, the independence of parts successively developed, by another and quite distinct group of facts. It is well known that many animals belonging to the same class, and therefore not differing widely from each other, pass through an extremely different course of development. Thus certain beetles, not in any way remarkably different from others of the same order, undergo what has been called a hyper-metamorphosis—that is, they pass through an early stage wholly different from the ordinary grub-like larva. In the same sub-order of crabs, namely, the Macroura, as Fritz Müller remarks, the river cray-fish is hatched under the same form which it ever afterwards retains; the young lobster has divided legs, like a Mysis; the Palæmon appears under the form of a Zoea, and Peneus under the Nauplius-form; and how wonderfully these larval forms differ from each other, is known to every naturalist. Some other crustaceans, as the same author observes, start from the same point and arrive at nearly the same end, but in the middle of their development are widely different from each other.

In other words, Darwin has twigged to the important idea that each stage of the life-cycle of an organisms is under different selective pressures, and thus one stage can diverge while the others remain quite similar.

Crayfish are also mentioned in one of Darwin’s transmutation notebooks. In it, Darwin shows his admiration for the natural world (“beautiful adaptations”), and interest in explaining the non-adaptive features (“unintelligible structures”):

The question if creative power acted at Galapagos it so acted that birds with plumage and tone of voice purely American, North and South; so permanent a breath cannot reside in space before island existed. Such an influence must exist in such spots. We know birds do arrive, and seeds. (And geographical divisions are arbitrary and not permanent. This might be made very strong, if we believe the Creator created by any laws, which I think is shown by the very facts of the Zoological character of these islands.)

The same remarks applicable to fossil animals same type; armadillo-like cray [i.e., crayfish?] created; passage for vertebrae in neck same cause. Such beautiful adaptations, yet other animals live so well. This view of propagation gives a hiding place for many unintelligible structures; it might have been of use in progenitor, or it may be of use,—like mammae on man's breast.

In the Voyage of the Beagle, crayfish feature in a segment that shows the less enlightened aspect of Darwin’s cultural background, with the sort of references to “savages” that interested colonial powers.

The little stream, besides its cool water, produced eels and cray-fish. I did indeed admire this scene, when I compared it with an uncultivated one in the temperate zones. I felt the force of the observation, that man, at least savage man, with his reasoning powers only partly developed, is the child of the tropics.

More on Darwin’s ties to crustaceans can be found in today’s post on NeuroDojo.

For your consideration

The nomination deadline for The Open Laboratory anthology, the annual collection of science writing on blogs, is in two weeks. If there’s a post from this blog that you liked, I’d like to ask that you consider nominating it for the anthology. Posts from 1 December 2008 to 30 November 2009 are eligible.

Some suggestions, in chronological order:

• Stochastic resonance
• Haiku
• Muscle receptor organs
• Before he was famous

Click here to submit an entry. A Blog Around the Clock regularly updates the list of entries; here’s a recent one (probably out of date by the time you read this).

In case you’re wondering why I don’t just nominate myself, I think it’s better for readers to decide what’s good than writers. And because it feels gauche to nominate a bunch of your own stuff.

A whiter than white way to get rid of invasive crayfish

Got a crayfish invasion? Try bleach. A lot of it.

A panoply of embryos

The September 2009 issue of Genesis features a gorgeous array of animals early in their development, taken by students at the Woods Hole embryology course. The journal says that one of the images is of marbled crayfish, but doesn’t exactly provide a key.

I emailed the course organizers, and Nipam Patel got back to me, writing:

I should say that after looking again, it would be best to say that it is definitely a decapod crustacean, but it might actually be a crab larvae instead. I say this because the student who did the staining was working with a number of decapods (multiple crayfish and crab species) at the time and I am not certain that this image is actually Marmokrebs.

And, for the record, the crustacean is immediately under the words “Genetics and” in the subtitle, and is purple and green. Even if it isn’t Marmorkrebs... it’s still a superb cover.

Circus of the Spineless #44

Welcome to the 44^th and latest edition of Circus of the Spineless, the monthly celebration of animal diversity. Although this blog is devoted to just one invertebrate species, I’m pleased to host this carnival and showcase all the other wonderful forms that invertebrates take. Please take a moment to visit the home page and have look around.

I find the biggest problem is always how to sort the posts. Sadly, I am not imaginative, so I broke it down into the nicknames that I often hear my colleagues who study invertebrates: “crunchies” (things with exoskeletons) and “squishies” (things with soft bodies).

Crunchy posts

Because this is a crustacean blog, please forgive a little double favouritism by me starting off with a post from NeuroDojo (a sibling blog that I also author). In it, I take serious ethological research on hermit crabs, and turn it into a fairy tale.

Not only do I love fairy tales, I love mysteries, too. It can be a simple mystery, like “Who’s easting the Photinias?” Jason at Xenogere takes on the case and gets photographic evidence.

Adrian at The Bug Whisperer also tries to take photos, but seems to cause a crime rather than preventing one, as a fight breaks out between his ant subjects. Models can be such divas.

Staying with ants for the moment, the Wild About Ants blog shows ants visiting extrafloral nectaries on cacti. Roberta Gibson want to know if you’ve seen ants visiting nectaries; go help her out.

At Hill-Stead’s Nature Blog, Diane Tucker features dragonflies and envies their ability to rise above it all.

Trees, Plants and More catches photos of a lynx spider among some plant leaves.

Marcia Bonta looks at charismatic invertebrates. And I guess if you’re an invertebrate and want to be charismatic, it helps to have long legs, since she focuses in on daddy long legs and stick insects.

But if you want beautiful, Ted MacRae at Beetles in the Bush reckons he’s got the most beautiful beetle on the North American continent. I took the liberty of including a picture at right; isn’t it a beauty?

Wandering’ Weeta also has a gallery of insects who take advantage of her warm home in fall.

At The DC Birding Blog, John discusses and documents several insects lured by the promise of cheap beer. I am not making this up. If that’s a little to crazy for you, just look at the nice butterflies.

Another birding blog, 10,000 Birds momentarily joins the spineless celebration with carpet moths.

Dave Ingram, writing on the modestly titled Dave Ingram’s Natural History Blog, rounds out the crunchy section of our program with some pictures and note on millipedes.

Squishy posts

Wanderin’ Weeta finds a jellyfish in a tide pool, and gets the event on camera.

Trees, Plants and More serves up a hammerhead worm in the “More” category.

While I would never claim to have saved the best for last, I do think you’ll admit this last post is worth the wait. Hill-Stead’s Nature Blog brings us... slug poetry!

Next time, on Circus of the Spineless...

That concludes this installment of Circus of the Spineless! Please join us again in about 30 days over at Greg Laden’s Blog. Email your submissions to Greg. (And come on, squishy lovers, show your colours!)