This Week in Evolution

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.

Posted by R. Ford Denison at 5:08 PM | Permalink | Comments (2)

Poster advertising Darwin symposium in Beckley, West Virginia, where I was a USDA researcher for several years.

Yesterday, I'm told, was the 150th anniversary of the publication of The Origin of Species. In honor of this occasion, and of the 200th anniversary of Darwin's birth, 12 February 1809, there were major symposia at the Universities of Cambridge and Chicago, and minor ones all over; I wasn't the only one to make a commemorative cake, although I thought mine was more scientific than most, but probably not as tasty as if it had evolved, with selection imposed by human preferences.

Posted by R. Ford Denison at 4:35 PM | Permalink | Comments (0)

When I was a grad student, I used to enjoy weekly play-along "jam sessions", where a group of people would get together and play old-time, bluegrass, or Celtic music. The better musicians were mostly pretty patient with us beginners, but I sometimes wished I could practice a bit beforehand, learning songs at my own speed. I could usually do fairly well on penny whistle, but could never keep up on banjo or hammer dulcimer. What I needed was Jam Hound, a free website set up by my brother, Glenn, a mandolin and guitar player and computer genius.

So far, the site includes:
* Rhythm Track Generator
* Ear Training
* Fingerboard Tutors
...mainly intended for musicians, including beginners, playing folk songs and fiddle tunes.

If you're interested, have a look and leave a comment if you have any suggestions for improvements.

Posted by R. Ford Denison at 8:06 PM | Permalink | Comments (0)

This week's paper, Symbiotic Nitrogen Fixation in the Fungus Gardens of Leaf-Cutter Ants, has already been discussed by Ed Yong, whose blog is among my favorites, and by the always-interesting Susan Milius of Science News. When she interviewed me, I endorsed the main conclusions of the article but expressed skepticism on one point.

The paper clearly shows that the fungus "gardens" cultivated by leaf-cutter ants contain bacteria that extract nitrogen from the air. The part I wondered about was their statement that:

Continue reading "Are ants' fungus gardens a source or sink for nitrogen?" »

Posted by R. Ford Denison at 6:18 PM | Permalink | Comments (2)

I just read a disturbing post on the amusingly-titled serious-science blog "Mystery Rays from Outer Space", discussing two examples of human pathogens that apparently escaped from laboratories. The key evidence, in each case, is evolution... or rather, lack of evolution....

Continue reading "Return of the viruses" »

Posted by R. Ford Denison at 3:51 PM | Permalink | Comments (0)

Guest blogger: Will Ratcliff

This week's paper, "Experimental evolution of bet hedging" by Hubertus Beaumont, Jenna Gallie, Christian Kost, Gayle Ferguson and Paul Rainey, published in Nature, shows that a trait that initially evolves for non bet hedging purposes can be maintained in the population through bet hedging.

The theory of bet hedging was first mathematically developed by Daniel Bernoulli (yes, the Bernoulli we all learned about in high school physics) in 1738. Because the basic idea is so simple - uncertain future conditions make conservative strategies beneficial - it is likely that folk wisdom advising bet hedging long predates Bernoulli's maths. The phrase "Don't put all your eggs in one basket" is one example of a widespread but anachronistic reminder to spread risk. Before we dive into this week's paper, I want to briefly cover the theory of bet hedging.

Like investing in the stock market, evolution is a multiplicative process, not an additive one. Steve Stearns (2000) illustrates this well....

Continue reading "Experimental evolution of bet hedging" »

Posted by R. Ford Denison at 7:42 PM | Permalink | Comments (7)

"Can you tell me, in lay language, what makes this achievement significant?"
"I can try", said Denison, cautiously.
-- The Gods Themselves (Asimov)

Ford Denison explains why eating more kale and less meat may trigger physiological changes that trade some of our potential reproduction for longevity (Ratcliff et al., 2009).

I usually discuss one scientific journal article per week, presenting new data on past evolution or ongoing evolution. My interests in the evolution of cooperation and in agriculture make me include more papers on microbes and plants than some other blogs with an evolutionary focus.

You know how evolution-deniers sometimes claim that they "used to believe in evolution", as if one person's changed opinion trumped the thousands of scientific articles on evolution published each year? For what it's worth, I didn't start as an evolutionary biologist. I earned a PhD in crop science from Cornell in 1983 and was a US Department of Agriculture researcher for several years, before becoming a professor of agronomy at UC Davis in 1993. There, I taught crop ecology, directed a major field experiment on agricultural sustainability (LTRAS), and did research on cover crops that get nitrogen from symbiotic rhizobium bacteria in their root nodules.

My interest in evolutionary biology developed gradually. I wanted my teaching to explain as many facts as possible, using a framework of universal principles, rather than jumping randomly from one fact to another. The universal principles that explained the most crop-ecology-related facts turned out to be conservation of energy, conservation of matter for each chemical element, and evolution by natural selection. Next, evolutionary ideas spread to my research, as I tried to answer a question few people had even asked: why do rhizobia invest their resources in taking up nitrogen from the atmosphere and giving it to their host plants, rather than using those resources for their own reproduction? Our 2003 paper in Nature, showing that soybean plants impose fitness-reducing sanctions on rhizobia that fail to fix nitrogen (as we had predicted, based on evolutionary theory), has been cited over 100 times and is probably my best-known contribution to science, so far.

In 2005, I took early retirement from UC Davis and a grant-supported adjunct position at the University of Minnesota, in order to live with my horticultural-scientist wife, after many years working in different cities. As long as the National Science Foundation keeps giving me grants, life is good.

Our most important recent paper, which began with an idea from grad student Will Ratcliff, explains increased longevity with dietary restriction (or with a diet containing toxins plants make to defend themselves against insects), based on the evolutionary benefit of delaying reproduction when the gene pool is shrinking.

I am writing a book, "Darwinian agriculture: where does nature's wisdom lie?" which is intended for an intelligent but nonspecialist audience. It should be published late in 2010, by Princeton University Press. When progress on the book is slow, I sometimes neglect this blog.

R. Ford Denison

Most significant publications:

Oono R., R. F. Denison, and E. T. Kiers. 2009. Tansley review: Controlling the reproductive fate of rhizobia: how universal are legume sanctions? New Phytologist 183:967-979.

Ratcliff W. C., P. Hawthorne, M. Travisano, and R. F. Denison. 2009. When stress predicts a shrinking gene pool, trading early reproduction for longevity can increase fitness, even with lower fecundity. PLoS One 4:e6055.

Sadras, V.O., R.F. Denison. 2009. Do plant parts compete for resources? An evolutionary viewpoint. New Phytologist 183:565-574.

Ratcliff, W.C., R.F. Denison. 2009. Rhizobitoxine producers gain more poly-3-hydroxybutyrate in symbiosis than do competing rhizobia, but reduce plant growth. ISME Journal 3:870-872.

Kiers E. T., R. F. Denison. 2008. Sanctions, cooperation, and the stability of plant-rhizosphere mutualisms. Annual Review of Ecology, Evolution, and Systematics 39:215-236.

Mitchell, A.E, Y.J. Hong, E. Koh, D.M. Barrett, D.C. Bryant, R.F. Denison, and S Kaffka. 2007. Ten-year comparison of the influence of organic and conventional crop management practices on the content of flavonoids in tomatoes. J. Agric. Food Chemistry 55:6154-6159

Kiers, E.T., M. Hutton, R.F. Denison. 2007. Human selection and the relaxation of legume defences against ineffective rhizobia. Proceedings of the Royal Society B 274: 3119-3126.

Denison, R.F., D.C. Bryant, and T.E. Kearney. 2004. Crop yields over the first nine years of LTRAS, a long-term comparison of field crop systems in a Mediterranean climate. Field Crops Research 86:267-277.

Martini E. A., J. S. Buyer, D. C. Bryant, T. K. Hartz, D. Barrett, and R. F. Denison. 2004. Yield increases during the organic transition: improving soil quality or increasing experience? Field Crops Research 86:255-266.

Okano, Y., K.R. Hristova, C. Leutenegger, L. Jackson, R.F. Denison, B. Gebreyesus, D. LeBauer, and K.M. Scow. 2004. Effects of ammonium on the population size of ammonia-oxidizing bacteria in soil -- Application of real-time PCR. Applied and Environmental Microbiology 70:1008-1016.

Kiers E. T., R. A. Rousseau, S. A. West, and R. F. Denison. 2003. Host sanctions and the legume-rhizobium mutualism. Nature 425:78-81.

Denison R. F., E. T. Kiers, and S. A. West. 2003. Darwinian agriculture: when can humans find solutions beyond the reach of natural selection? Quarterly Review of Biology 78:145-168.

Denison R. F., C. Bledsoe, M. L. Kahn, F. O'Gara, E. L. Simms, and L. S. Thomashow. 2003. Cooperation in the rhizosphere and the "free rider" problem. Ecology 84:838-845.

Kinraide T. B., R. F. Denison. 2003. Strong inference, the way of science. American Biology Teacher 65:419-424.

West, S.A., E.T. Kiers, E.L. Simms & R.F. Denison. 2002. Sanctions and mutualism stability: why do rhizobia fix nitrogen? Proceedings of the Royal Society 269:685-694.

Denison R. F. 2000. Legume sanctions and the evolution of symbiotic cooperation by rhizobia. American Naturalist 156:567-576.

Hasegawa, H., D.C. Bryant, and R.F. Denison. 2000. Testing CERES model predictions of crop growth and N dynamics, in cropping systems with leguminous green manures in a Mediterranean climate. Field Crops Research 67:239-255.

Jacobsen K. R., R. A. Rousseau, and R. F. Denison. 1998. Tracing the path of oxygen into birdsfoot trefoil and alfalfa nodules using iodine vapor. Botanica Acta 111:193-203.

McGuire, A.M., D.C. Bryant, and R.F. Denison. 1998. Wheat yields, nitrogen uptake, and soil moisture following winter legume cover crop vs. fallow. Agron. J. 90:404-410.

Denison R. F., R. Russotti. 1997. Field estimates of green leaf area index using laser-induced chlorophyll fluorescence. Field Crops Research 52:143-150.

Denison R. F., T. B. Kinraide. 1995. Oxygen-induced depolarizations in legume root nodules. Possible evidence for an osmoelectrical mechanism controlling nodule gas permeability. Plant Physiology 108:235-240.

Denison, R.F., and B.L. Harter. 1995. Nitrate effects on nodule oxygen permeability and leghemoglobin. Nodule oximetry and computer modeling. Plant Physiol. 107:1355-1364.

Denison R. F., J. F. Witty, and F. R. Minchin. 1992. Reversible O2 inhibition of nitrogenase activity in attached soybean nodules. Plant Physiology 100:1863-1868.

Denison, R.F., S. Hunt, and D.B. Layzell. 1992. Nitrogenase activity, nodule respiration, and O2 permeability following detopping of alfalfa and birdsfoot trefoil. Plant Physiol. 98:894-900.

Denison R. F., D. B. Layzell. 1991. Measurement of legume nodule respiration and O2 permeability by noninvasive spectrophotometry of leghemoglobin. Plant Physiology 96:137-143.

Denison, R.F., and R.S. Loomis. 1989. An Integrative Physiological Model of Alfalfa Growth and Development. Univ. Calif. Div. Agr. Nat Res., Publ. 1926, 73 pp.

Denison, R.F., and P.S. Nobel. 1988. Growth of Agave deserti without current photosynthesis. Photosynthetica 22:51-57.

Denison R. F., P. R. Weisz, and T. R. Sinclair. 1988. Oxygen supply to nodules as a limiting factor in symbiotic nitrogen fixation. Pages 767-775 In R. J. Summerfield, editor. World Crops: Cool Season Food Legumes, Kluwer Academic Plublishers, Dordrecht.

Weisz, P.R., R.F. Denison, and T.R. Sinclair. 1985. Response to drought stress of nitrogen fixation (acetylene reduction) rates by field-grown soybeans. Plant Physiol. 78:525-530.

Denison R. F., B. Caldwell, B. Bormann, L. Eldred, C. Swanberg, and S. Anderson. 1976. The effects of acid rain on nitrogen fixation in western Washington coniferous forests. Water Air and Soil Pollution 8:21-34.

Posted by R. Ford Denison at 4:38 PM | Permalink | Comments (0)

Richard Lenski and colleagues have been monitoring evolution of the bacterium Escherichia coli in his laboratory for 40,000 generations. Their latest paper, "Genome evolution and adaptation in a long-term experiment with Escherichia coli" was recently published in Nature.

One nice thing about E. coli is that they can freeze samples of their evolving populations every few thousand generations, for later analysis. So they were able to compare the fitness of different generations by competing each against a thawed ancestor. They also found the complete DNA sequence for many of these strains....

Continue reading "Experimental evolution meets genomics" »

Posted by R. Ford Denison at 9:37 PM | Permalink | Comments (0)

"I show that a similar cost of sex exists when asexual mutants arise... but not when the species is a self-fertile hermaphrodite.... Although individual fitness (expected reproductive success) is assumed to be equal for sexual and asexual females, the heritability of fitness is... twice as high in asexual females" -- Richard Michod, Darwinian Dynamics

I should be working on my book, but a paper that just came out in Nature got me thinking about sex. A population with half males and half females will grow only half as fast as one consisting only of females that self-fertilize or clone themselves. So, many people have asked why sex evolved.

That's an interesting question, but I'm not sure about the rationale. As noted by Michod, a population of self-fertilizing hermaphrodites doesn't have any intrinsic growth advantage over a population of hermaphrodites that mostly cross-fertilizes. So is the problem sex, or males?

Evolutionary changes in gene frequency over generations depend on whether individuals with a given gene survive and reproduce more than other members of their population, not on the consequences for overall population growth. (Individuals can move between populations.) So we really have two related questions:
1) why do genes for producing male offspring persist? and
2) why do genes for cross-fertilization persist in species that can self-fertilize?

From an individual perspective, it's not apparent that producing male offspring is always a bad idea. Do couples with two sons have fewer descendants than those with two daughters? It can depend on the sex ratio in the population. If a human couple produces one offspring of whichever sex is in the minority, their offspring may have an easier time finding a mate.

But what about cross-fertilization? If a female cloned herself, her offspring would have all of her genes, rather than just half of them. So the frequency of genes for self-fertilization would tend to increase, unless individuals resulting from cross-fertilization were more likely to survive and reproduce. An offspring with half as many of one's genes, but a 2.1-fold better chance of survival (maybe because a sexual partner contributes different disease-resistance genes) gives a greater increase in fitness. So, one key to understanding the evolution of sex (cross-fertilization) is to measure the survival of individuals with one parent versus two, under conditions that plausibly occurred at critical points in a species ancestry.

This week's paper, "Mutation load and rapid adaptation favour outcrossing over self-fertilization", set out to "recapitulate the evolutionary process under the specific conditions predicted to favour either selfing or outcrossing." Levi Morran, Michelle Parmenter, and Patrick Phillips used the nematode, C. elegans, which consists of males and hermaphrodites. (This mix, and the lack of pure females, suggests there can be individual benefits to maleness, whatever the consequences for the population as a whole.) They used genetic manipulation to make populations that only self-fertilized or never self-fertilized, exposed them to high mutation rates or to a bacterial pathogen, and let them evolve.

Continue reading "Experimental evolution of sex (revised)" »

Posted by R. Ford Denison at 7:29 PM | Permalink | Comments (4)

This week's paper, "Cheater-resistance is not futile" was published in Nature. It describes experimental evolution of the social amoeba Dictyostelium, whose propensity to cheat other members of its species was discussed by Will Ratcliff in a recent guest post titled "Sneaky slime molds."

When two Dictyostelium strains are mixed in a reproductive structure, cheaters contribute fewer cells to the stalk that holds up the reproductive spores. Could the presence of such cheaters select for cheater-resistance genes, just as the presence of owls or hawks selects for mouse genes that make their coats match the soil color?

Continue reading "Evolving resistance to cheaters" »

Posted by R. Ford Denison at 1:01 AM | Permalink | Comments (0)

I recently had two or three hours to spend at the Smithsonian, en route to the airport. I hadn't been to the natural history museum for awhile, and was interested to see how they were celebrating Darwin's anniversaries this year. Pretty well, it turns out. Banners outside advertised a Darwin exhibit and "Plants and butterflies: partners in evolution." Inside, there was apparently an organized "Evolution Trail", which I didn't have time to follow.

The Darwin exhibit is off the entrance hall with the elephant and has a mix of biographical and scientific exhibits. My main criticism was their definition of "co-evolution" as being limited to evolution for mutual benefit. Evolutionary arms races (e.g., between hosts and parasites) are also coevolution. The entrance hall on the other side, where I came in, has two display cases of Darwiniana.

The butterfly exhibit was dominated by a live butterfly room inside a larger room with displays on the coevolution of plants and butterflies, with fossils labeled "examine the evidence." I was happy to pay $6 admission to the butterfly room since I wanted to make a donation anyway and enjoyed having a frittilary land on my nose.

Near the Oceans exhibit was a display of Burgess Shale fossils I hadn't seen before, including Pikaia, a tiny 500-million-year-old chordate. We chordates have evolved a lot since then. Nearby were some fossil stomatolites.

The mammal room was great, focusing on adaptations in everything from bats to giraffes (splaying front legs to drink, with an explanation of adaptations to limit blood flow to head) to pangolins with termite mounds. Right in the middle of the floor was a window down to fossil hominid footprints.

I wish I could have stayed longer. One problem with a quick visit to the Smithsonian is that post9/11 hysteria has closed most of the bag-check rooms. You can't bring your luggage into the museum and if you leave it somewhere, they'll try to detonate it. (Luggage made of sapient pearwood can defend itself, but I wouldn't recommend bringing it to Washington!) But here's a secret tip for my regular readers only: the 4th St. entrance to the National Gallery still has a check room, complete with x-ray machine. Don't tell too many people, or they'll probably close it.

Coming up in March: the Hall of Human Ancestors!

Posted by R. Ford Denison at 7:29 PM | Permalink | Comments (1)

If you don't believe in evolution, you might not want to listen to this next story. Scientists reported this week on a new fossil, possibly a human ancestor, older than Lucy. The good news is, we're not descended from chimps after all. The bad news is, chimps and humans are descended from the same ancestor.

That's a paraphrase of how our local TV news covered Ardipithecus ramidus, the fossil hominid discussed in a series of papers in this week's issue of Science. Read all about it on Carl Zimmer's blog. The TV anchor didn't say which scientists claimed we are descended from chimps, perhaps because no scientist has made that claim. Chimps have evolved over the six million years or so since our last common ancestor, including their split with bonobos. Can we expect the story below on the TV soon?

Startling breakthrough in human genetics! You aren't descended from brother after all, or even from your cousin. You and your brother still have the same parents, and you and your cousin have the same grandparents, though. I hope that doesn't upset you too much.

We don't know for sure that present-day humans are descended from Ardipithecus . It's a reasonable hypothesis, but any hypothesis is, by definition, subject to possible disproof. For example, if we found another fossil that was clearly much more similar to modern humans, dating from the same time or earlier, then we'd conclude that Ardipithecus probably has no surviving descendants.

But this species probably isn't too far from the direct line of descent between our common ancestor with chimps and modern humans. Suppose you wanted to know what your great grandmother looked like, but there was no surviving picture of her. If you had pictures of her sister or her daughter, that would give you some idea, even if all her living descendants are descended from a son.

Of course, much of what we know about our ancestors now comes from analyzing DNA in humans and closely related species. We can figure out when vitamin C synthesis was lost or adult lactose tolerance gained, for example. But we don't yet understand development enough to predict height, foot shape, etc., from inferred DNA sequences of ancestral species. So keep those fossils coming!

Posted by R. Ford Denison at 4:32 PM | Permalink | Comments (1)

A couple of months ago, I read this New York Times article by economist Robert Frank, suggesting that Darwin's ideas may be a better guide to economics than (popularized versions of) Adam Smith's ideas. I was impressed and have been reading his books with considerable interest.

Many of his economic ideas parallel ideas I'm exploring in my book on Darwinian Agriculture. A singer, runner, or lawyer who's only 1% better may make ten times as much money, just as a leaf that's only 1 mm above the leaf of a competing plant may have ten times the photosynthesis. "Arms races" among humans -- working overtime will let you afford a house that is more expensive than average, so that your kids can go to a better-than-average school, but if everyone works overtime half the population still sends their kids to below-average schools -- parallel arms races among plants -- being taller than your neighbor means more photosynthesis and so more seed production, but if every plant grows taller that doesn't increase total photosynthesis and wastes resources on tall stems. And so on.

But today, in honor of Blasphemy Day, I want to summarize an interesting idea from his book, Choosing the Right Pond.

Freedom of speech is often presented as an "inalienable right", perhaps granted by (though never actively protected by) some hypothetical Creator. Frank suggests an alternative origin, based on freedom of association and economies of scale....

Continue reading "Off topic: Frank view of blasphemy" »

Posted by R. Ford Denison at 4:53 PM | Permalink | Comments (0)

Sears tricked customers into installing software that recorded:

"the contents of shopping carts, online bank statements, drug prescription records, video rental records, library borrowing histories, and the sender, recipient, subject, and size for web-based e-mails. The software would also track some computer activities that were not related to the Internet."

I hadn't seen anything about this in the news before reading about it on Bruce Schneier's blog. Why isn't he in charge of Homeland Security?

Posted by R. Ford Denison at 10:07 PM | Permalink | Comments (0)

Slime molds allocate less to costly public goods when sharing then when alone.

(Special Guest Blogger: Will Ratcliff )

The slime mold Dictyostelium discoideum ('dicty' for short) spends most of its life alone, hunting soil bacteria and yeast. But when food runs out, tens of thousands of individuals aggregate into a mobile slug (cool youtube video) which crawls to an advantageous place and differentiates into a ball of spores on top of a long stalk. Individual dicty either become a dead stalk cell or a reproductively viable spore.

© Copyright, Mark Grimson and Larry Blanton

What possible incentive could there be for a dicty to sacrifice its life (become a stalk cell) for the benefit of those that become spores? If you answered 'there is no direct advantage to dying for others', you're right! Nonetheless, kin selection can lead to this type of self-sacrifice if a) the dicty in the stalk are highly related to the dicty that form spores (so are highly likely to have the same "unselfish genes"), and b) spores benefit from being higher off the ground (better chance of dispersal?).

But what happens when slugs are composed of more than one genotype? Here stalk formation becomes a 'tragedy of the commons' in which it is in each clone's interest to cheat, letting the other clone form a greater fraction of the stalk. So do dicty cheat? If so, how do they do it?

The short answer, as reported by Buttery et al. in the paper Quantification of Social Behavior in D. discoideum Reveals Complex Fixed and Facultative Strategies recently published in Current Biology is that:

Yes, dicty cheat; they cheat like crazy.

There are two ways in which a dicty clone in a mixed slug could cheat, producing less stalk and leaving more spores than its competitor....

Continue reading "Guest Blog: Sneaky slime mold " »

Posted by R. Ford Denison at 6:22 PM | Permalink | Comments (1)