July 19, 2013

Weed evolution in the New York Times

Carl Zimmer, author of several evolution-themed books and an interesting blog, published an article on weed evolution in Tuesday's New York Times. He used one of my favorite examples of rapid evolution of complex traits (flooding tolerance and crop mimicry in Echinochloa barnyardgrass/watergrass in <1000 years) to make the point that evolution of herbicide resistance (a much-simpler trait) in only a few years shouldn't have been a surprise.
(Left) Under selection pressure imposed by farmers with hoes, Echinochloa watergrass evolved to resemble rice more than it resembles its own recent ancestor, barnyardgrass (Barrett, 1983). I discussed this example near the end of this lecture at the International Rice Research Institute.

Glyphosate-resistant weeds are becoming increasingly common, just before the expiration of Monsanto's patent on Roundup-Ready soybeans. What does the US Constitution say about patents?

"The Congress shall have Power To...promote the Progress of Science and useful Arts, by securing for limited Times to Authors and Inventors the exclusive Right to their respective Writings and Discoveries...."
If the original intent was to give inventors short-term monopolies, in exchange for long-term benefits to society, should the duration of patent protection be shorter for inventions whose useful life is likely to be limited by evolution? For example, 17 years with a really good resistance-management plan, 5 years with no resistance-management plan.... Of course, the Patent Office might need to hire an evolutionary biologist or two.

I agree with the statement from David Mortensen that adding another resistance gene to glyphosate-resistant crops, and spraying with both herbicides, will be only "a short-lived solution," although it might last long enough to be worth patenting. If they had put two different herbicide-resistant genes into soybean from the start, and if evolution of resistance requires two or more independent mutations -- this isn't always true -- and if farmers growing that herbicide-resistant crop were somehow required to use both herbicides (so that mutants resistant to just one of the herbicides wouldn't have increased in frequency), evolution of resistance might have taken much longer.

Zimnmer quoted me and mentioned my book on Darwinian Agriculture, depleting Amazon's stock, though they still have a few copies left. You could try your favorite independent bookstore or library.

May 31, 2013

This week's picks

Functional Extinction of Birds Drives Rapid Evolutionary Changes in Seed Size "areas deprived of large avian frugivores for several decades present smaller seeds than nondefaunated forests, with negative consequences for palm regeneration"

Molecular evolution of peptidergic signaling systems in bilaterians "phylogenetic reconstruction tools... show that a large fraction of human PSs [peptide-based signaling systems] were already present in the last common ancestor of flies, mollusks, urchins, and mammals"

Honey constituents up-regulate detoxification and immunity genes in the western honey bee Apis mellifera "apicultural use of honey substitutes, including high-fructose corn syrup, may thus compromise the ability of honey bees to cope with pesticides and pathogens and contribute to colony losses"

Palaeontological evidence for an Oligocene divergence between Old World monkeys and apes" "the oldest known fossil 'ape', represented by a partial mandible... the oldest stem member of the Old World monkey clade, represented by a lower third molar... recovered from a precisely dated 25.2-Myr-old stratum in... the East African Rift in Tanzania."

Experimental evidence that evolutionarily diverse assemblages result in higher productivity "Species produced more biomass than predicted from their monocultures when they were in plots with distantly related species and produced the amount of biomass predicted from monoculture when sown with close relatives."

November 25, 2009

Not so fast!

I always enjoy Olivia Judson's columns in the New York Times, but today's post on evolution "failing" left out an important point. She referred to a paper published last year from Richard Lenski's long-term evolution experiment, showing that a bacterial population took 31,000 generations to evolve the ability to use citrate. Furthermore, although she didn't mention this, this trait has only evolved, so far, in one of their twelve replicate populations. If evolution is too slow to keep up with the changes we humans are making in the environment, then species that might evolve and survive if changes were slower will instead go extinct.

I agree that this is a significant problem, but I wouldn't assume that it would take polar bears, for example, 31,000 generations to evolve adaptations to warmer temperatures. The bacteria that Lenski's group studies don't have sex. So if one cell has a mutation that would allow it to use citrate, but only in combination with a second mutation found in another cell, they don't have any way to combine the two mutations in one citrate-using individual. If cells with only one mutation or the other have no advantage over cells with neither, then lineages with the first mutation will usually die out before acquiring the second mutation. A lineage could die out, for example, because the next mutation is gets is one of the many lethal ones, rather than one of the few beneficial ones.

Bacterial populations can sometimes evolve rapidly (with significant changes in only a few days) because their generation times are so short and because their large population sizes include many mutants. Evolution requiring a series of steps isn't a problem so long as each step is an improvement. But when a mutation is neutral or negative, except in the context of a second mutation, sexual species can evolve faster. Not necessarily fast enough to save the polar bears, though.

April 3, 2009

How fast can sexual traits evolve?

Experimental populations of hermaphroditic plants evolved a significant increase in male function in only three generations.

Many plant species are hermaphrodites, with each individual producing both pollen and seeds. Others species have separate sexes, as mammals and birds do, while still others have mixtures of unisexuals and hermaphrodites. Based on the distribution of these traits in the family tree of life, evolutionary transitions among these "lifestyles" appear to have been fairly common. This week's paper shows how hermaphrodites can evolve to be more female or, in this case, more male. Hermaphroditic Sex Allocation Evolves When Mating Opportunities Change was just published in Current Biology by Marcel Dorken and John Pannell.

Continue reading "How fast can sexual traits evolve?" »

December 30, 2008

This year in evolution, in Nature

The leading general-science journal, Nature, published many papers on evolution this year, two of which made it into their annual list of the editors' "favourites." One paper described laboratory experiments using the power of "directed evolution" to improve enzymes. The other explains the rapid evolution of new fish species in the wild. The editors also highlight two papers giving ice-core records of atmospheric carbon dioxide and methane over the last 800,000 years. These greenhouse gases both affect and are affected by life on earth, so they provide valuable context for recent evolutionary trends.

In a paper titled "Kemp elimination catalysts by computational enzyme design", Daniela Rothlisberger and colleagues started by designing enzymes using computer software. I don't know how the "RosettaMatch hashing algorithm" works, but the process seems to have a lot in common with natural selection's approach, selecting the best from "more than 100,000 possible realizations" rather than going directly from first principles to the ideal design. Furthermore, they noted that "our in silico design process seems to be drawn towards the same structural features as naturally occurring enzyme evolution."

Their next step was even closer to natural evolution. They started with their best design and generated lots of random mutants, testing each for activity. After seven rounds of this directed evolution, they got a 200-fold increase in enzyme activity. They noted that "in vitro evolution... is currently the most widely used and successful approach for refining biocatalysts."

Once again, nonrandom selection among random variants solves problems beyond the reach of (present) human ingenuity. How many more examples do we need before people stop saying "it's sophisticated, must have been designed" and instead say "it's sophisticated, must have evolved"?

In the second paper, Ole Seehausen and colleagues describe "Speciation through sensory drive in chichlid fish." For a species to split in two, interbreeding between two groups has to be low enough that they can evolve differences. This is easy if they are geographically separated, as on different islands or on continents drifting apart. But what if they're all fish in the same lake?

Even within a lake, there can be major differences in light conditions. Females often prefer brightly colored males, but the definition of "brightly colored" depends on lighting and on how sensitive female eyes are to different colors. They compared two related species, one with red males and one with blue males. These color differences in the males corresponded with differences in color perception by the females. The red fish were found at greater depth, where more red light penetrates.

Speciation depended on how rapidly light conditions changed with distance. If it didn't change at all, selection operated similarly across the range, giving no differences in light sensitivity. But apparently the same was true if light conditions changed too rapidly. In that case, fish had to cover a range of light conditions, so didn't evolve the specialization that would lead some females to prefer blue males and others to prefer red males.

April 12, 2008

Fear of flying -- in plants

“Every one is familiar with the difference between the ray and central florets of, for instance, the daisy… But with respect to the [two types of] seeds, it seems impossible that their differences in shape…can be in any way beneficial?—Charles Darwin

The theory of evolution is famously linked to the Galapagos Islands, but this week’s paper “Rapid evolution of seed dispersal in an urban environment in the weed Crepis sancta,? published in Proceedings of the National Academy of Science, studied much smaller “islands.? In an urban environment dominated by concrete, patches of soil around sidewalk trees (below left) are among the few places where plants can grow.
Photo credits: Gilles Przetak and Eric Imbert.

Members of the daisy or sunflower family (Asteraceae) often produce two types of seeds (above right) on the same disk-shaped composite flower head. Seeds from the center of the disk are light in weight and plumed, so they are easily dispersed by wind. Those from the outer edge of the disk are heavier and not plumed, so they tend to fall near the mother plant. Although Darwin apparently failed to see the benefit of having two types of seeds, this kind of diversity acts as a form of bet-hedging. Wind dispersal of seeds over a wide area decreases the chances that all of a plant’s offspring will be killed.

Then why not disperse all of the seeds? Because, given that the mother plant managed to reproduce -- many plants don't -- conditions near the mother plant may be better than where most wind-blown seeds might land. This was particularly true in the study discussed here. Earlier, Jonathan Silvertown pointed out, in an essay titled “When plants play the field," that the ratio of the two seed types changes in beneficial ways with changes in flower head diameter. The area of a disk increases four-fold as the circumference doubles, giving proportionally more of the wind-dispersed central seeds. So the plant will always drop some seeds in the same place that it managed to reproduce. But if favorable conditions lead to larger flower heads, more seeds will be dispersed by wind over a larger area, where they can compete with other plant's seedlings rather than with each other.

So, without any genetic change, this disk-size dependence adjusts the ratio of dispersing to nondispersing seeds to match current conditions. But what if conditions consistently favor more or less seed dispersal? Can this ratio also evolve, with a genetic change over generations?

Continue reading "Fear of flying -- in plants" »

April 7, 2008

Evolutionary trees

This week's paper is "Rapid evolution towards heavy metal resistance by mountain birch around two subarctic copper–nickel smelters", published in the Journal of Evolutionary BIology by J.K. Eranen.

Evolution is a change over generations, so evolution is typically faster (more change per year) in species with short generation times. Signficant evolutionary change in bacterial populations, therefore, can take only a day or two, under ideal conditions. Long-lived species like humans and trees evolve, too, but it takes much longer. So, for example, are trees likely to evolve fast enough to survive climate change?

Continue reading "Evolutionary trees" »

December 7, 2007

The ghost of infections past, present, and future

Summary: A 39-year record of host-parasite interaction, recovered from sediment layers in a pond, is consistent with rapid coevolution.
Link: Host-parasite /`Red Queen/' dynamics archived in pond sediment

As I've discussed previously, archival samples often prove useful for answering questions that weren't being asked when the samples were collected. But what if nobody collected and preserved the samples you need for your research? Maybe you can find a "natural archive" that has what you need.

Continue reading "The ghost of infections past, present, and future" »

September 11, 2007

Evolving enzymes in the lab

This week's paper is another example of how nonrandom selection from among random variants can solve problems so difficult that we are unable to "design" a solution. As in an earlier post, the selection process was automated, not requiring the human judgement used in breeding crops or dogs.

"Selection and evolution of enzymes from a partially randomized non-catalytic scaffold" was written by Burckhard Seelig and Jack Szostak, both of Boston, and published in Nature (448:828). Their goal was to evolve an enzyme to link two RNA bases together in a particular way, a reaction not found in nature.

Continue reading "Evolving enzymes in the lab" »

May 29, 2007

Coevolution and gene flow

Two species coevolve when changes in either lead to changes in the other. This includes “arms races? between species that compete with each other, but also interactions that benefit both species. “Gene flow? is the movement of genes from one population into another, of the same or related species. For example, some genes in modern cows seem to have come from mating with wild aurochs, before they went extinct. Gene flow often provides new genes; some may be useful to the recipient population. For example, pollen from transgenic sugar beets could transfer herbicide resistance (along with other crop genes) to related weed beets. More often, genes that were useful in the source environment may be harmful to the recipient population. Natural selection will tend to eliminate these, unless gene flow rates are too high. For example, if plants growing on toxic soil around an old mine are outnumbered by neighbors on nontoxic soil nearby, gene flow may swamp natural selection, preventing evolution of tolerance to toxic soil.

This week I’ll discuss a review article on coevolution and then an experimental paper showing how gene flow can affect coevolution. The review is “Variable evolution? by Elizabeth Pennisi, published in the May 4 issue of Science. It discusses coevolution of wild parsnip with the webworms that eat them and coevolution of pine trees with birds and squirrels, among other topics.

Continue reading "Coevolution and gene flow" »

May 6, 2007

How disturbed are most cheaters, really?

Yesterday, my wife asked, "why are there so many theoretical papers in evolutionary biology?" I suggested one reason may be that evolutionary theory is better developed, in the sense of making accurate predictions, than theory in much of biology. This week's paper, comparing results from an evolution experiment to predictions of a mathematical model, is a good example.

The paper is about the evolution of cooperation. This is a hot topic and also my own area of research. Humans enforce cooperation, to varying extents. For example, we often punish cheaters, those who try to benefit from cooperative activities of others without contributing anything themselves. Human cheaters are mostly pretty stupid -- don't even think about plagiarizing this blog for a term paper! -- but what about cheaters with no brains at all?

Continue reading "How disturbed are most cheaters, really?" »