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November 28, 2008

We cooperators need to stick together

Experiments on the evolution of cooperation can be simpler with microbes than with animals. Microbes do sometimes cooperate. For example, some amoebae get together and form a stalk (consisting of hundreds of individual cells) to elevate spores (many more individual cells) above the soil. Bacteria may collectively produce and release enough extracellular enzymes to make food available for all, when none of them could make enough enzyme alone. But why should an amoeba volunteer to be in the stalk (an evolutionary dead end) rather than becoming a spore? And why not save the cost of making expensive extracellular enzymes, by free-loading on enzyme production by others? Out of the goodness of their hearts? They don't have hearts.

Cooperation is easiest to understand among microbes that share the same allele (one of several alternative versions of a gene) for cooperation. Kin-selection theory says that an allele leading to some individually costly activity may spread if it preferentially benefits others with the same allele, relative to those with different alleles. Cooperation among relatives, who are more likely to share a given allele, is therefore easy to understand.

But can microbes recognize kin, i.e., whether another microbe has the same alleles? Sometimes, apparently. In this week's paper, Elizabeth Ostrowski and colleagues report in PLoS Biology that Kin discrimination increases with genetic distance in a social amoeba.

PLoS papers are open access and Robin Meadows has already written a nice summary of this paper, so I won't go into a lot of detail. Basically, they mixed a fluorescent lab strain with each of 14 wild strains. They used molecular methods to measure how genetically similar (related) each wild strain was to the lab strain.

When they mixed two closely related strains, neither strain took advantage of the other. That is, they made a fruiting body in which the two strains shared rewards (spore production) about equally. But when less-related strains were mixed, one or the other usually dominated spore production, at the expense of the other. In effect, these amoeba recognized close kin and cooperated with them. Recognition was apparently at the level of adhesion: related cells stuck together better than unrelated cells.

There are probably other cases where sticking together, literally, is the key to cooperation. For example, some bacteria stick together and form mats on liquid media, benefiting from additional oxygen at the surface.

But what about microbial cooperation without physical contact between cells? How does a bacterium investing in expensive extracellular enzymes know (to the extent that a cell with no brain can know anything) that is surrounded mostly by relatives? Or what about restraint in consumption of resources, when a cell becomes a metabolically inactive "persister"? This can free up resources for nearby cells, but what if those neighbors aren't relatives?

We just had a grant proposal to study persisters rejected by NSF, leaving us with no money to run our lab this year, so I've been thinking about this topic a lot. We assume that bacteria are often surrounded by relatives, because of how they reproduce. "Cooperate with neighbors" can be equivalent to "cooperate with kin." (It's a little more complicated than that, of course.) So we designed experiments in which spatial structure could favor cooperation among kin.

One of the reviewers of our grant pointed out that kin recognition might work just as well. But is kin recognition among bacteria actually possible? This week's paper suggests that it might be, if they're touching. That might sometimes happen in biofilms. But suppose a cell is touching one clonemate and one unrelated cell. Should it make extracellular enzymes, or not? If resources are scarce, should it restrain its own resource consumption, freeing resources for its neighbors? And what if the cells aren't quite touching? Bacteria produce and respond to various chemical signals. If each strain produces different signals, it's conceivable that they could assess their average relatedness to their neighbors. We have some ideas about that, but testing them will take money. I am hoping President Obama's efforts to stimulate the economy will include more funding for research.

November 21, 2008

November 21

Until I finish my book, Darwinian Agriculture, I am cutting back detailed posts to once or twice a month, but here are some links to papers that looked interesting this week.

Sustaining biodiversity in ancient tropical countryside
"arecanut palm (Areca catechu) production systems retain 90% of the bird species associated with regional native forest"

Selfish Genetic Elements Promote Polyandry in a Fly

[This "selfish gene" on the X chromosome refuses to share sperm with a Y chromosome. Female fruitflies mate with more males when more of them have this gene.]

Frequency-dependent selection maintains clonal diversity in an asexual organism

Reproductive constraint is a developmental mechanism that maintains social harmony in advanced ant societies

Finally, someone left a comment on an earlier post that used an out-of-context quote to claim evolutionary biologists are hiding from the fossil record. The truth is that fossils are less important to evolutionary biology today only because their contribution is diluted by new sources of information, especially comparisons of DNA sequences among species. But fossils are still a valued source of information. Here are two papers on fossils published this week in major journals. (How many papers did the "intelligent design" folks publish in major journals this week? This year? None?)

A new stem turtle from the Middle Jurassic of Scotland: new insights into the evolution and palaeoecology of basal turtles

Variation in Evolutionary Patterns Across the Geographic Range of a Fossil Bivalve

November 14, 2008

November 14

I need to spend more time working on my book, "Darwinian Agriculture: Where Does Nature's Wisdom Lie?" and don't want to neglect my grad students, who are getting some interesting results on evolutionary problems from symbiotic cooperation to aging. So I have decided to offer detailed analyses of papers less often (maybe once a month) for a while. But here are some links to papers I thought looked interesting this week.
Evidence for novel and specialized mycorrhizal parasitism: the orchid Gastrodia confusa gains carbon from saprotrophic Mycena



Mechanisms and evolution of hypoxia tolerance in fish



Recognition of other species' aerial alarm calls: speaking the same language or learning another?



A Female Homo erectus Pelvis from Gona, Ethiopia


Production of healthy cloned mice from bodies frozen at −20°C for 16 years

November 7, 2008

Can an NPR gene explain gregarious and solitary behavior?

This week's issue of Science has a special section on the genetics of behavior. In humans, at least, conflicting results seem to be common. According to the overview paper, one study found that people who were abused as children have a two-thirds chance of depression as adults, if and only if they also have a particular version of a serotonin transporter gene; an analysis of several studies on this gene rejected this conclusion, however. Other combinations of genes affecting testosterone and the rate at which certain brain chemicals break down may increase criminal activity, but maybe not. One company is already offering genetic testing of potential mates for a gene possibly linked to divorce. How soon will we see "in-vitro tourism", to countries that offer genetic modification of behavior-linked genes in human germ-line cells? Clinics that currently offer untested or dangerous "cancer cures" might not wait for answers to the many scientific, technical, and ethical questions that such services would raise. But genetic effects on behavior are complex and hard to predict, even in the simplest cases, as seen in this week's paper.

"npr-1 regulates foraging and dispersal strategies in Caenorhabditis elegans" was just published in Current Biology by Andrea Gloria-Soria and Ricardo Azevedo.
C. elegans is a tiny worm, barely visible without magnification. Two alleles of the npr gene produce two different versions of the NPR signal-receptor protein, differing in a single amino acid. (Despite the connection to signals, the NPR gene actually has as much to do with National Public Radio as the famous "sonic hedgehog" gene has to do with hedgehogs.)

Worms with different versions of npr have consistent behaviors referred to as "gregarious" and "solitary," but these traits may be rather different from their human equivalents. "Gregarious" worms appeared to hang out together more than "solitary" worms, but it's not clear that they necessarily enjoy each other's company more. The worms eat bacteria, which (in the lab), spread out from the center of a Petri dish. They used fluorescent bacteria as worm-food, so feeding locations could be measured from changes in fluorescence, controlling for bacterial reproduction.

When there were lots of worms on each Petri plate, 79% of "gregarious" worms apparently preferred the growing edge of the bacterial swarm, whereas "solitary" ones were indifferent to where they fed, with only 35% feeding on the edge. So "gregarious" worms might just end up relatively close to each other because they all like life on the edge. Similarly, if beer were only available in bars, we might see beer-lovers as gregarious, whether or not they actually enjoy socializing. But when they tested single worms, they found no genetic difference in the percent of time spent on the edge. "Solitary" worms appeared to dislike other worms: they spend most of their time on the edge, but not if there are other worms there. So maybe "tolerant of crowds" would a better description of the "gregarious" worms.

If "gregarious" worms are more tolerant of crowding, you might expect them to disperse less. But they found that the opposite was true. When worms started at the center of a Petri plate with rings of bacteria, most of the "solitary" worms stayed in the center, whereas the "gregarious" ones distributed themselves across the plate.

Groups of worms consume more oxygen, lowering its concentration. If "gregarious" worms are more tolerant of low oxygen, that could explain their apparent tolerance of crowding. But their greater dispersal tendency seems inconsistent with this, as dispersal takes them into regions of higher oxygen.

Bacteria may be younger and tastier at the growing edge. This may be less important to "solitary" worms, relative to their aversion to crowding or low oxygen. Could greater dispersal by "gregarious" worms also be a search for younger bacteria?

I have focused on behavioral issues in this paper, but the authors also asked an evolutionary question which comes up repeatedly whenever two or more genotypes persist over generations: why doesn't one genotype out-compete the other? They showed that spatial structure may be important, given differences in dispersal, etc. But the "gregarious" strain lost in competition, whether or not the environment was fragmented. Still, this paper is a nice illustration of the complexity of behavioral differences that can result from the simplest possible genetic difference.

Incidentally, they cite a paper by fellow blogger John Dennehy, whose summaries of keystone papers are themselves classic.

November 3, 2008

Ook! Another librarian for Obama

With the US election imminent, I interview the Librarian of Unseen University.

TWiE: Your endorsement of Obama has created quite a stir on this planet and might help swing the election. Were you influenced by Sarah Palin's firing a librarian for refusal to censor library books or for her views on evolution?

Librarian: Ook.

TWie: OK, but she would have limited power (you know, like Cheney) unless McCain dies in the next four years. Are you worried that some Christian terrorist would assassinate him to put her in power? Or are there problems with McCain as well?

Librarian: Ook!

TWiE: A macaca? But those aren't even apes; they're...

Librarian: Ook. Ook.

TWiE: OK, OK. Moving on to another topic, are you supporting anyone for Patrician?

Librarian: Eek. Ook.

TWiE: OK, thanks for your time. I did have a few more questions, but good luck straightening out Wall Street.