22 May 2008

Finches, bah! What about Darwin's tomatoes?

Charles Darwin collected all sorts of cool stuff (like a vampire bat, caught while feeding on his horse) on his journey aboard the Beagle, and it has to be said that he understood little of it until after he got back. The finches that bear his name were identified as such by someone else, and his own bird collections from the Galapagos were nearly worthless due to the fact that he hadn't bothered to label ResearchBlogging.orgspecimens as to their place of origin. It was only upon their correct identification as different species of finch that Darwin realized that the birds represented what we now call an adaptive radiation.

Darwin collected a lot of plant material, too, and much of it was completely new to science. J.D. Hooker was a botanist and contemporary of Darwin, and in 1851 he wrote a little paper, "An Enumeration of the Plants of the Galapagos Archipelago; with Descriptions of those which are new" describing his studies of Darwin's collection. It was more than 100 pages long.

One unique feature of the collection was a pair of species of tomato plant. Like all other species in the archipelago, the Galapagean tomatoes resemble South American species, but are subtly different. More interestingly, the two Galapagean species are highly similar to each other (and reproductively compatible), but occupy separate habitats and exhibit some odd variations, including a striking divergence in leaf shape.

Image from Figure 1 of Kimura et al., cited below. On the left is S. cheesmaniae; on the right is S. galapagense.

How might such a variation arise in evolution? A nice study published in Current Biology two weeks ago provides the interesting answer, and addresses an important question raised by evo-devo theorists. The article is "Natural Variation in Leaf Morphology Results from Mutation of a Novel KNOX Gene," by Seisuke Kimura and colleagues at UC Davis.

Look again at the picture: the leaves pictured on the left are "normal" tomato leaves, as one might see in a Michigan garden or on the South American plants thought to be the ancestors of the Galapagean species. The leaves on the right are significantly more complex. (For lovers of botanical detail, the "normal" leaves are unipinnately compound, while the S. galapagense leaves are three- or four-pinnately compound. For the botanically challenged like me, the leaves on the right are more snowflake-like.)

This trait has long been known to be under the control of a single gene, but the nature of that gene and its effects were unknown before the experiments of Kimura et al. They did some pretty intense genetic mapping, and zeroed in on a rather small piece of the genome. Specifically, they ended up examining a region 1749 base pairs in length. Inside that region, they found exactly one change that could account for the leaf variation: a deletion of a single base pair. One DNA letter, removed from the genome, makes all that difference.

But there's more. That change isn't in the coding region of a gene, meaning that the mutation doesn't affect the structure of any protein. Like the genetic variation that Cretekos et al. studied in their analysis of bat wing development, this is an example of a change in a regulatory region of the DNA, the kind of change that evo-devo theorists have predicted to be fairly common in the evolution of new forms.

The authors showed that the teeny little one-letter change results in a huge increase in the amount of a protein called TKD1. And they did a compelling experiment similar to the one that Cretekos and colleagues did with the bat and the mouse: they took that piece of regulatory DNA (with the one-letter change) and stuck it into a tomato plant, and showed that it could induce a complex-leaf trait all by itself. No change in protein structures, just a one-letter change in a regulatory DNA region. Isn't that cool?

Kimura et al. went on to show that TKD1 reduces the formation of a complex between two other proteins, and their data suggest that the levels of TKD1 constitute a dimmer switch-like (rheostat) control on that complex, which ultimately controls the development of leaf shape.

Now, here's why this result is interesting in the context of evo-devo. A structural mutation in a protein that controls development can result in dramatic changes in form, for sure. But such a mutation will likely alter all of the processes controlled by that protein, resulting in widespread developmental reorganization. (Think "hopeful monster" here.) Evo-devo thinkers assert that regulatory changes are better suited (in general) for the induction of evolutionary changes in form, because such changes can affect isolated developmental processes without affecting the overall development of the organism. In this case, the excess TDK1 protein is able to inhibit the action of a particular complex in particular areas at particular times, without interfering in the functions of those other proteins elsewhere and at other times. Here are the concluding sentences of the paper:
Mutations affecting the expression levels of transcription factors can modify the function of a major developmental regulatory complex in some organs without interfering with its other essential roles in morphogenesis. Such dosage-sensitive interactions may be broadly responsible for evolutionary change and provide a relatively simple mechanism for the generation of natural variation.
I hope you agree that studies like this one and the bat-wing story are inherently interesting. But I hope you also see how sadly foolish it is to disparage evolutionary science as mere mythology, or to pretend to invalidate a century of evolutionary genetic analysis with a few bogus calculations. Scientists are weird enough to think tomato plant leaves on the Galapagos are worth subjecting to detailed genetic analysis, and maybe that means we're a bit on the obsessive side. But come on: we're not stupid.

Article(s) discussed in this post:

KIMURA, S., KOENIG, D., KANG, J., YOONG, F., SINHA, N. (2008). Natural Variation in Leaf Morphology Results from Mutation of a Novel KNOX Gene. Current Biology, 18(9), 672-677. DOI: 10.1016/j.cub.2008.04.008


Karen James said...

Oh, applause, Steve. You've outdone yourself here. As far as I'm concerned, this post ticks all possible boxes: evo-devo, plants, Darwin, Galapagos, evolution, lovely leaf forms. I think I might have to go away to swoon now.

Jimpithecus said...

I find this sort of thing fascinating. I am trained in human evolution, so plants are a bit of a mystery to me. Thanks for all of the neat information.

Jimpithecus said...

Steve, I just posted this on my own blog:
"Steve Matheson, a professor of Biology at (where else) Calvin College, that oasis in the middle of the Christian intellectual desert, has a blog that is great to read. His two most recent posts on tomato leaf morphology and how the bat got its wing are concise, clearly written and (ought to be) compelling to anybody of a creationist bent. While my blog tends to be more newsy and less interpretive, Steve seems to have really gotten the feel for what a blog ought to be. Bookmark this one!"


John Farrell said...

Another great post--and more fodder for my "regulatory changes" folder!

Jim Lemire said...

Two excellent posts back to back. It is always great to read about the logic of evo-devo (or whatever) experimentally supported.

nice summaries.

Anonymous said...

Very interesting, the laws of variation which were a big unknown to Darwin emerging in fascinating ways. Unfortunately you start with an error, by saying "his own bird collections from the Galapagos were nearly worthless due to the fact that he hadn't bothered to label pecimens as to their place of origin"

He hadn't labelled the island of origin or the various birds Gould later identified as "finches", but did notice differences between mockingbirds in relation to islands, and labelled them. On the last lap of the voyage Darwin speculated that this, together with stories he'd heard about tortoises being identifiable by island and about the Falklands "Fox", would undemine the doctrine of fixity of species. The finches can hardly be said to have been nearly worthless – even without labels identifying them by island, Gould's revelation in the context of the ideas inspired by the mockingbirds was enough to suggest that the "finches" might vary by island, and inspired Darwin to find better labelled specimens in the collections that FizRoy and Covington had made when they were on the islands with Darwin.

So, though Darwin didn't label the "finches" by island, he did label other birds, and all these specimens played an important part in developing his ideas. Wonder if he noticed the tomatoes?

Anonymous said...

Some of the species of Galapagos finch are limited to very few islands, and some species are found on many islands. So even if "(Darwin) hadn't bothered to label specimens as to their place of origin" , labelling them as to their place of origin need not have shown "one species, one island". Present day species distribution data rather contradict that the "finches" might vary by island

Anonymous said...

For trying to be scientific, this post, and I'm sure the blog as a whole, is quite defensive. Why would you be so defensive if you were so sure of the science? I pray that through your research and honest searching you come to learn the true origins of life - God Himself, the maker of human life. Question: If we are nothing but the sum of our parts - some DNA structures - what makes us unique? Answer: Our soul. God created us in His image. Be awed and inspired by the majesty of His creation. You will not find peace and solace on your own but only through Him who is peace and solace. He created science and the brain that understands complex things.

John Farrell said...

For trying to be scientific, this post, and I'm sure the blog as a whole, is quite defensive.

And I'm sure being anonymous, this person really has the courage of his/her religious convictions.

Stephen Matheson said...

Thanks for reading and taking the time to comment. I long ago rejected the damaging false dichotomy that you are promoting, and my blog's chief purpose is not to "defend" science but to help liberate fellow Christians from dangerous errors, such as your apparent belief that scientific explanations are a hindrance to awe and wonder, or to an understanding of God as "the maker of human life."

Anonymous said...

I will read original paper.
But there is one thing really funny for me.
Why that damned English language violating common names of plants?
I guess, tomato = Lycopersicon esculentum. Solanum species = nightshade, e.g. common nightshade?
Why this paper tells Solanum = tomato? Bheh really funny :)

Anonymous said...

What is your question anonymous? Tomato = Solanum lycopersicum.