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July 31, 2010

Evolutionary history of yucca moths

I've written a few posts about ancestral-state reconstruction, where we use molecular or other information from living species to infer the traits of their shared ancestors. But I really like this post in which PhD student Jeremy Yoder describes his own work.

There's a nice diagram showing the general approach, then he looks at yucca moths and their relatives to figure out what their ancestors did. Yucca moths, like fig wasps, lay their eggs in flowers. Their larvae eat seeds, but the moths pollinate the flowers, so it's not too bad a deal overall. Their ancestors, he concludes, fed inside developing flowers, but without pollinating them. Maybe the world is getting a little more cooperative, after all.

July 27, 2010

A plague of "comments"

Here's a question for any fellow bloggers:

Has anyone else seen a huge increase in "comments" over the past few days?

These comments are mostly on older posts and are obviously intended to generate links to for-profit or crackpot websites. Usually there's some superficial reference to the post, enough to convince me the comment was left by a human, but not one with any particular expertise or interest in the topic of the post.

A quick Google search shows that people are selling this "service" for as little as 5 cents per "comment."

I am using Movable Type's "Report Spam" feature with these, hoping that will make it harder for them to spam others. Any other suggestions?

July 23, 2010

Reversing evolution: crops evolving into weeds

Evolutionary Applications will be publishing a special issue on evolution and agriculture. Some of the papers are already available online. One that caught my eye is "Crops gone wild: evolution of weeds and invasives from domesticated ancestors" by Norman Ellstrand and others. (Among Ellstrand's past contributions is work on gene flow from transgenic crops to their wild relatives.)

They looked for cases where long-domesticated crops (>1000 years) evolved into weeds. Of 13 cases, seven involved hybridization, mostly with a wild relative. Many cases involved reversal of evolutionary changes that had occurred during domestication. As I point out in my forthcoming book on Darwinian Agriculture, much of crop genetic improvement has involved reversing effects of past natural selection that are undesirable in agriculture.

For example, nine species re-evolved seed shattering (scattering seeds as soon as they're mature), a trait seen in many weeds and in the wild ancestors of crops, but often lost during domestication. With harvesting by humans, seeds scattered on the ground apparently have worse survival prospects than those that get harvested. Even though the majority of harvested seeds get eaten, some are saved, protected from animals, and carefully planted the next year.

Similarly, three species re-evolved seed dormancy. This trait of wild plants and weeds delays growth of some seeds for a year or more, decreasing the risk that all of a plant's offspring will be killed in a bad year. Dormancy in a crop, however, results in (for example) soybeans coming up in the corn and being killed by herbicides to which corn is resistant.

One trait that was rarely reversed was looking like the crop. A weed that resembles the crop is less likely to be killed by hand weeding. I was familiar with an earlier study by Barrett (1983)showing that the rice-field weed, watergrass, evolved to resemble rice more than its own recent ancestor, barnyard grass, presumably because weeds that look more like rice are less likely to be removed by human weeders (Ehara and Abe 1950).

Weedy rice appears to have evolved from cultivated rice several times, with at least one case involving hybridization between two different kinds of cultivated rice. Weedy rye, on the other hand, appears to have a single origin. Like many weeds, it has smaller seeds than its crop ancestor, so it can make more of them with a given amount of carbon and nitrogen. This smaller seed size (and other traits, such as shattering and smaller leaves) evolved in less than 60 generations. (For comparison, 60 human generations would be about 1500 years, allowing significant evolutionary change within recorded history.)

Among species recommended for further study is strawberry guava. Although it's a serious invader of natural areas, apparently nobody knows how much, if it all, the invasive version has evolved from its cultivated ancestor.

Finally, they note that weedy versions of crops typically occur in the same areas as the crops themselves. They may grow at the edge of the field or in the wrong year of a crop rotation, but they could still be inundated by pollen from nearby crop plants, which could tend to slow evolutionary change. This would only apply to cross-pollinated species, of course. And all of those species evolved an earlier or later flowering date than the crop, limiting gene flow.

LITERATURE CITED

Barrett S. C. H. 1983. Crop mimicry in weeds. Economic Botany 37:255-282.

Ehara G., S. Abe. 1950. Classification of the forms of Japanese barnyard millet. Proceedings of the Crop Science Society of Japan 20:245-246.


July 17, 2010

Directed evolution versus intelligent design of enzymes

"How have all those exquisite adaptations of one part of the organisation to another part, and to the conditions of life, and of one distinct organic being to another being, been perfected? We see these beautiful co-adaptations most plainly in the woodpecker and missletoe; and only a little less plainly in the humblest parasite which clings to the hairs of a quadruped or feathers of a bird; in the structure of the beetle which dives through the water; in the plumed seed which is wafted by the gentlest breeze; in short, we see beautiful adaptations everywhere and in every part of the organic world." -- Charles Darwin
Evolution denialists often claim that these adaptations must have come from an Intelligent Designer, who has apparently been too busy lately (protecting pedophile priests, maybe, or working to block gay marriage?) to come up with any new designs. They claim that natural selection (nonrandom proliferation of random variants) isn't up to the job.

But intelligent human designers are increasingly relying on processes similar to natural selection. The latest issue of Science discusses two examples of the use of selection-like processes for developing useful enzymes. One paper explicitly calls their approach "directed evolution." The other doesn't use the term, but what would you call generating billions of randomly varying designs in a computer and selecting those that meet certain criteria? Sounds like selection to me. In neither case did the researchers rely only on natural-selection-like processes. Instead, they used some combination of intelligent design and selection from among random variants. But nonrandom selection from among random variants was a key contributors in each case, solving problems beyond the reach of human reason or intuition.

July 1, 2010

Carnival of evolution

Lots of interesting blogs.

Earliest multicellular life? Maybe not.

This week's paper is "Large colonial organisms with coordinated growth in oxygenated environments 2.1 Gyr ago", published in Nature by Abderrazak El Albani and colleagues. These two-billion-year-old fossils are clearly the remains of something living, based on appearance, different carbon isotope composition from the surrounding rock. But are they colonies of unicellular organisms, or something more organized?

The authors note the resemblance to "bacterial colonies growing on surfaces" which they say are known to "coordinate their behavior" often via "repulsive chemotaxis." In other words, cells detect the presence of neighbors and tend to disperse in ways that can generate patterns similar to those seen in these fossils. Sometimes, bacteria may coordinate their activities in more sophisticated ways, which wouldn't leave fossil traces.

A commentary on the article is titled "Origins of multicellularity", but most people would expect more from a multicellular organism than a little coordination among cells. We expect differentiation, for example, where different cells specialize for different functions. Trichoplax is thought to have four different cell types, including cells with flagella that move these simple multicellular animals along, and cells that excrete digestive enzymes. In larger animals, a few cells specialize in reproduction, a potential source of conflict, especially if there are genetic differences among cells. I don't think we can tell from these fossils whether there was any such specialization.

A consistent size and shape is another criterion for true multicellularity, met by Volvox, for example. The fossils don't look any more consistent in size and shape than one would expect from bacterial colonies. On the other hand, Trichoplax individuals seems to vary somewhat, but I wouldn't argue against calling them multicellular organisms.

Interestingly, the authors found traces of the chemical sterane, which is typically found in eukaryotes. But apparently there's some possibility that it could have diffuses into the fossil rock from younger materials.

I've been reading about multicellularity recently and was particularly impressed by a 1998 paper by Boraas et al., in Evolutionary Ecology, and titled "Phagotrophy by a flagellate selects for colonial prey: a possible origin of multicellularity". (I would link to the paper, but the publisher Springer has this stupid system that sends you to their main web page.) Boraas et al. exposed unicellular algae to predators and evolved multicellular clumps in only 10-20 generations. The first clumps contained hundreds of cells, but eventually they evolved an 8-cell phenotype, too big for the predators to eat, but with better access to nutrients for each cell than if they were in a larger clump. Surprisingly, nobody seems to have done further evolution experiments with this system.