Thomas' Plant-Related Blog

On plant science. Mostly.

Posts Tagged ‘Evolution

Of broccoli, butterflies and Arabidopsis

with 3 comments

Today, I’m venturing into the world of Arabidopsis, a plant I usually leave to the geneticists. More specifically, into it and its relatives’ evolutionary past.

DNA sequences can be used to estimate how long ago species separated. Once they separate, they stop interbreeding, and their DNA sequences start to evolve separately. So the more differences there are in their DNA, the longer it is since they split. Different bits of DNA change at different speeds: from essential genes evolving very slowly, to so called ‘junk DNA’, which doesn’t code for anything, so can change much faster.

All the data needs calibrating, though. We’ve got to know how fast particular bits of DNA change, before we can use them to date anything. The key is fossils. Say you’ve got two groups of living species, one of which has a novel and distinctive feature that the other group lacks (and presumably never had). If you find a fossil that looks like your species, and you can see it has that key feature, then the two groups must have split by the time of the fossil. I won’t go into the various ways you might find the age of the fossil, but there’s info on Wikipedia.

Seed pods on stem

Thlaspi arvense seed pods. Photo by Matt Lavin (flickr)

The paper I’ve read today did this calibration for the cabbage family, Brassicaceae (which includes Arabidopsis, along with a number of vegetables including cabbage, broccoli, turnips and oilseed rape), and some related families, like that of capers, the little buds used in Mediterranean cooking. They used five fossils which have previously been found of these plants. Perhaps the most important was a fossil seed pod from a plant called Thlaspi primaevum, which lived about 30 million years ago. Under a scanning electron microscope, they could see a characteristic pattern of ridges that it shares with living Thlaspi species, meaning that they must have split off from a closely related genus at least that long ago.

Using these fossil dates, and a more flexible model of evolution, they estimated the age of various splits between species. They put the split between the model plant Arabidopsis thaliana, and its close relatives like A. lyrata back to about 13 million years ago, three times previous estimates, and reckon that those species separated from vegetables like cabbage (Brassica) about 43 million years ago, about twice previous estimates. There are big margins of error around those “optimal reconstructions”, though.

So what does that tell us? Apart from having to re-examine how quickly various genes evolved, it places the earliest split of the ‘Brassicales’, when the ancestors of the cabbage and the caper bush separated, back in the Cretaceous, before the mass extinction that killed the dinosaurs. That suggests that those plants, after surviving the mass extinction, began to diversify to take advantages of new opportunities afterwards. Their survival and diversification could also be connected with genome duplications, where the plants ended up with two copies of all their genes, which can open up new possibilities to evolution.

The authors also suggest that the timing matches up with speciation in a family of butterflies called the Pierids, which includes the cabbage white and the orange tip. Their caterpillars can munch on these plants, as gardeners know all too well, because they can break down the toxic chemicals which protect them (the same chemicals that give mustard its sharp flavour). That’s interesting, because it suggests that the plants and the butterflies might have diversified together. Perhaps the butterflies adapted to the diversification of their host plants, or perhaps each group drove speciation in the other.

Finally, it puts the origins of Arabidopsis thaliana, the favourite of geneticists, back in the Miocene, a somewhat warmer period than the Pliocene, when previous estimates had it splitting. That might change our ideas about how it evolved.


Beilstein, M., Nagalingum, N., Clements, M., Manchester, S., & Mathews, S. (2010). Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0909766107


Written by Thomas Kluyver

17 October, 2010 at 10:04 pm

Posted in Papers

Tagged with ,

On the evolution of toilets

leave a comment »

Nepenthes rajah pitcher

A pitcher of Nepenthes rajah, one of the 'toilet' plants. Image by NepGrower (Wikimedia).

Just when you think you’ve seen it all, you learn about something completely unexpected. In this case, it’s a new way to get nitrogen, an important nutrient for all living things. Where the soil is poor in nitrogen, various plants have developed ways to trap insects and the like, among them the pitcher plants. Now it seems that a few species have adapted their pitchers to get nitrogen another way.

Several pitcher species are large enough to trap small mammals, but the scientists noticed that this hardly ever happened. Why else might the plants grow such large pitchers? The poo inside was the giveaway. The scientists found that it was from the mountain tree shrew (Tupaia montana), and could be the major nitrogen source for some plants.

Nepenthes burbidgeae pitcher

Pitcher of Nepenthes burbidgeae, a conventional trap. Image by JeremiahsCPs (Wikimedia).

The plant needs to do a couple of things to succeed as a toilet. First, it needs to be large enough to accommodate a tree shrew. Measurements of the ‘toilet’ species showed that the size of the pitchers fitted neatly with the length of a tree shrew.

Second, the plant needs to entice the tree shrew into the correct position. The inner surface of the lid produces nectar, attracting the tree shrew to feed from it. Then the shape of the lid is critical: compare the concave, upright lid of a ‘toilet’ species in the top picture to the lid of another species in the lower picture. The best place to get at that lid is sitting on the pitcher itself. The lid even has a partition in the middle, so a tree shrew going in from the side can only get to part of it.

Cameras set up to film the pitchers caught several visits from tree shrews, although only one where it left a dropping. The scientists suggest that the tree shrew may also leave urine (which is rich in nitrogen), but that needs more study.

Of the three species studied, two (Nepenthes rajah and N. macrophylla) also still catch insects, while N. lowii seems to be more specialised. A fourth species (N. ephippiata) looks like it might have the same trick, but wasn’t studied.

If they’re right, evolution has produced the first chemical toilet. Which is pretty amazing. I’m reminded of the bit in The Last Continent, where bizarre plants evolve on spoken demand.


Chin, L., Moran, J., & Clarke, C. (2010). Trap geometry in three giant montane pitcher plant species from Borneo is a function of tree shrew body size New Phytologist DOI: 10.1111/j.1469-8137.2009.03166.x
Giant meat-eating plants prefer to eat tree shrew poo, BBC Earth News

Written by Thomas Kluyver

16 March, 2010 at 11:55 pm

Herbicide resistant weeds in a GM field

with 9 comments

ResearchBlogging.orgNot the way that you might think or fear, though.

Genetically modified crops face public resentment, especially in Europe, perhaps simply as a figurehead of big corporate agriculture. One concern that often comes up is the possibility that the foreign genes will escape, to non-GM crops nearby or to weed populations. It’s not as unlikely as it might sound: even quite distantly related plants will very occasionally interbreed, so some genes can swap between species.

Since some of the most important GM crops are herbicide resistant (so farmers can use powerful weedkillers that would normally kill the crop), the spectre of herbicide-resistant ‘superweeds’ is invoked. So when herbicide resistant amaranth appeared in fields of GM cotton in the US, it must have been worrying.

Palmer's amaranth

Palmer's amaranth, also pleasingly called 'carelessweed'. Image by pompilid (Wikipedia)

As it turns out, the amaranth isn’t using the gene that was engineered into the cotton. They developed their own resistance, a textbook example of evolution by natural selection (if artificial herbicides could be called natural). Of course, that doesn’t make the weed any less of a problem, but it does mean that GM isn’t directly to blame.

The herbicide in question goes by the chemical name glyphosate, while Monsanto sell it under the brand name Roundup (hence the Roundup Ready series of resistant, GM crops). It works by blocking an enzyme called EPSPS. What EPSPS does isn’t important to the discussion, but it is important to the plant. With that enzyme out of action, a key part of their metabolism is blocked, and they die.

Roundup Ready GM crops are given a different form of EPSPS which isn’t affected by glyphosate. But the amaranth hasn’t got that gene, and it hasn’t independently evolved a resistant EPSPS gene, either. It’s used a rather more interesting strategy, a kind of brute force approach.

The amaranth simply produces a lot of the enzyme, and swamps the herbicide. And it’s achieved that by copying the gene for the enzyme, anywhere from five to 160 times, splashing it around its chromosomes. Like photocopying a recipe and giving it to dozens of people, that’s a simple but effective way to get more enzyme (or cake) made. One of the plants they bred in the lab had the enzyme processing 20 times faster than normal.

That’s interesting in its own right as a simple evolutionary case study, but it’s got other implications. Copying genes is a key part of evolution, because you get ‘spares’. The plant with 160 copies of the EPSPS gene could likely survive with 159 of them, leaving one free to evolve into… who knows? An enzyme producing doing something different in a small but significant way, perhaps. And does this massive duplication of genes happen by chance from time to time, or was it somehow caused by the stress of herbicide applications? What would happen to all those extra genes if we stopped using glyphosate?

Finally, I said that GM isn’t directly to blame. You could make a case that it’s indirectly responsible, because it allows the widespread use of a single herbicide, which creates a strong selection pressure on weeds. But, even if they sound evil, powerful herbicides are economically useful (so long as they don’t kill the crop, of course). The herbicide resistant weeds don’t make it any harder for farmers, they just cancel out the benefit of using the herbicide in the first place. In the end, we find ourselves in an arms race against natural selection, which has already equipped amaranth with resistance to several other herbicides. So far, we seem to be keeping up.


Gaines, T., Zhang, W., Wang, D., Bukun, B., Chisholm, S., Shaner, D., Nissen, S., Patzoldt, W., Tranel, P., Culpepper, A., Grey, T., Webster, T., Vencill, W., Sammons, R., Jiang, J., Preston, C., Leach, J., & Westra, P. (2009). Gene amplification confers glyphosate resistance in Amaranthus palmeri Proceedings of the National Academy of Sciences, 107 (3), 1029-1034 DOI: 10.1073/pnas.0906649107

Written by Thomas Kluyver

26 January, 2010 at 10:29 pm

Posted in Papers

Tagged with , ,