New blog on the block: Natural Current Events

Western conifer seed bug. Photo by Emily Jones at Natural Current Events.

I’ve been meaning for quite some time to point readers to Natural Current Events, the photoblog by Emily Jones (who, to disclose fully, is a postdoc with one of my doctoral committee members). It’s a photoblog with nice natural history notation, mainly focused on insects, their host plants, and their predators — but really covering anything that will stand still long enough for Emily to catch a photo. Each post is like a short walk through your neighborhood woodlot with a natural-history-savvy friend.◼

Share

Science online, “CSI: nowhere” edition

. . . and that's how i went insane Cruel and unusual education. Photo by Lee Nachtigal.
  • Zeno’s pinkeye. A woman fails to keep her contacts clean, ends up with eyes infected by an amoeba, which is infected by a virus, which is infected by a smaller virus, which is infected by sub-viral DNA particles.
  • So that works out even? African spiny mice have fragile skin, but that’s okay—it grows back super-fast.
  • Fishing trips. If you do enough different tests, eventually something will come up significant.
  • Or, you know, just more funding for all science? Do we need a NASA for the ocean?
  • CSI it ain’t. U.S. forensics doesn’t just need better technology; it needs a better scientific culture.
  • Let’s teach a chimp sign language, then ask it. Are humans really the only animals with language?
  • Oops? A new report from personal genomics company 23andMe suggests that family history may tell you more about disease risk than, um, personal genomics.
  • Or developing them. Why more ecologists should consider using model systems.
  • The horror! A “former philosophy major” is very upset that his son has to take high school chemsitry.
  • Alongside many other computers. The many movie roles of the IBM AN/FSQ-7.

Share

Many genes, but two major roads to adaptation

Fruit fly (Drosophila melanogaster, male) Drosophila melanogaster. Photo by Max xx.

Cross-posted at Nothing in Biology Makes Sense!

In the course of adaptive evolution — evolutionary change via natural selection — gene variants that increase the odds of survival and reproduction become more common in a population as a whole. When we’re only talking about a single gene variant with a strong beneficial effect, that makes for a pretty simple picture: the beneficial variant becomes more and more common with each generation, until everyone in the population carries it, and it’s “fixed.” But when many genes are involved in adaptation, the picture isn’t so simple.

This is because the more genes there are contributing to a trait, the more the trait behaves like a quantitative, not a Mendelian, feature. That is, instead of being a simple question of whether or not an individual has the more useful variant, or allele, at a single gene — like a light switch turned on or off — it becomes possible to add up to the same trait value with different combinations of variants at completely different genes. As a result, advantageous alleles may never become completely fixed in the course of an adaptive evolutionary response to, say, changing environmental conditions.

That principle is uniquely well illustrated by a paper published in the most recent issue of Molecular Ecology, which pairs classic experimental evolution of the fruitfly Drosophila melanogaster with modern high-throughput sequencing to directly observe changes in gene variant frequencies during the course of adaptive evolution. It clearly demonstrates that when many genes contribute to adaptation, fixation is no longer inevitable, or even necessary.

Turning up the heat, homogenizing flies

The authors of the new study, a team from the Institut für Populationsgenetik led by Pablo Orozco-terWengel, conducted what would otherwise be a rather simple experiment in evolutionary change in the laboratory. Starting with fruitflies collected from a wild population in Portugal (yes, Virginia, Drosophila melanogaster has wild populations!) they established three replicate populations of about 1,000 flies, which they put in temperature-controlled conditions somewhat warmer than the original collection location, and allowed them to propagate for 37 generations. Exensive previous work with Drosophila has established that simply moving the flies into a laboratory setting — where they live in bottles, and eat prepared food — exerts natural selection on them, and the increased temperature added a little bit more novelty to the lab environment to make it more likely adaptation would occur.

This experiment is different from all that previous experimental evolution of Drosophila, though, is that the coauthors tracked allele frequencies at thousands of markers during the course of those 37 generations of adaptation to the lab. To do this efficiently, they used an approach called “pooled sequencing.”

The principle behind pooled sequencing is that, if all you care about is the relative frequency of a gene variant in a whole population, you don’t need to know the genotype of any specific individual in that population. So to track changes in allele frequency, the team sampled hundreds of flies from the experimental population, and ground them all up together. (The polite, technical term used here is “homogenized.”) They then extracted DNA from this “pooled” sample, and used a high-throughput sequencer to collect millions of reads — short snippets of DNA sequence — out of the pool as a whole.

To extract allele frequencies from all of those sequence reads, the team identified where each read matched the Drosophila melanogaster reference genome. When multiple reads matched to the same location, but differed in one or more DNA nucleotide bases, they identified those bases as variable markers — single-nucleotide polymorphisms, or SNPs. Because the original DNA sample was pooled from many mashed-together flies, the relative frequency of each different variant of a SNP in the Illumina output should reflect the relative frequency of that SNP variant in the population as a whole.

Using this approach, Orozco-terWengel et al. could track allele frequency changes across more than a million SNP markers by taking these pooled samples from the intial population of flies, then at multiple points during the 37-generation evolutionary experiment. By comparing the allele frequencies in samples taken during the course of adaptation to the allele frequencies in the sample from the starting population, they could identify SNPs that became more common as the population adapted — and, because they had a big sample from across the genome, they could identify those SNPs whose allele frequencies had changed more than would be expected due to genetic drift. They examined samples taken after 15 and 27 generations of evolution, and at the end of the 37-generation experiment.

Two paths to adaptation

Fruit fly (Drosophila melanogaster, male) Allele frequency changes (AFC) in SNPs showing significant change by generation 15 (a) and by generation 37 (b). Image from Orozco-terWengel et al. (2012), figure 3.

What they found was largely in line with the verbal model I outlined at the beginning of this post. Over the course of experimental evolution, significant increases in allele frequency occurred at thousands of SNPs — suggesting that a great many genes are involved in the process of adaptation to life in the lab. Accordingly, very few of those allele frequency changes (in about 0.5% of the 2,000 SNPs that showed the greatest change from start to finish) represented complete or near-complete fixation.

More interestingly, comparison of allele frequency changes at the 15th generation and at the end of the experiment revealed two major “paths” taken by alleles. In the first case, the SNPs with strongest allele frequency changes by generation 15 all hit a “plateau” in subsequent generations — they didn’t see any significant increase in frequency between generations 15 and 37. In the second case, SNPs with the strongest allele frequency changes by generation 37, the end of the experiment, had increased steadily from the beginning population through the samples taken at the 15th and 27th generation. The SNPs in this second set had not shown significant allele frequency increases by generation 15 — which means the SNPs underlying most of the adaptive change in the first half of the experiment were a completely different set than the SNPs underlying adaptive change in subsequent generations.

If it’s already adapted, don’t fix it.

On the one hand, that suggests that Orozco-terWengel et al. managed to capture SNPs with a range of different contributions to the adaptation the observed by the end of the experiment. The SNPs with the biggest contribution showed rapid initial increases in allele frequency, then leveled off; SNPs with weaker effects showed slower, steady increases that continued for the entire experiment. But if it’s that simple, why didn’t the large-effect SNPs show continuing allele frequency change after the midpoint of the experiment?

It may be, as the coauthors speculate, that the two classes of SNPs identified in their experiment are separated by more than just the size of their respective contributions to adaptive change. There could be interactions among the alleles at these SNPs, such as overdominance, in which an individual is most fit when he or she carries two different alleles at a locus, rather than two copies of either allele. Overdominance would explain why most of the SNPs showing rapid initial increases in allele frequency then leveled out at intermediate frequencies.

So this combination of experimental evolution and modern sequencing technology raises some interesting questions even as it supports a lot of previous thinking about how natural selection acts on traits that are created by the collective action of many genes. It’s an exciting result, and, I hope, inspiration for much more work digging into the details of such “polygenic” adaptation.◼

References

Burke, M. and A. Long. 2012. What paths do advantageous alleles take during short-term evolutionary change? Molecular Ecology 4913–4916. DOI: 10.1111/j.1365-294X.2012.05745.x.

Orozco-Terwengel, P., M. Kapun, V. Nolte, R. Kofler, T. Flatt and C. Schlötterer. 2012. Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles. Molecular Ecology 4931–4941. 10.1111/j.1365-294X.2012.05673.x.

Pavlidis, P., D. Metzler and W. Stephan. 2012. Selective sweeps in multi-locus models of quantitative traits. Genetics 192:225–239. DOI: 10.1534/genetics.112.142547.

Share

Science online, tone-deaf parasitoids edition

Sneaking cat Be vewwy vewwy quiet. I’m hunting … everything. Photo by Hans Pama.
  • This week at Nothing in Biology Makes Sense! An army of cloned wasps demonstrates the importance of host-parasite specificity.
  • And at the Molecular Ecologist: Best practices for scientific programming.
  • How to be a queer ally — in science! An upcoming Q&A and/or discussion.
  • What about “Caution: not actually science”? Guest editor abuses his position to publish anti-feminist screed in a scientific journal. Journal apologizes badly, retracts screed, apologizes again, and then doesn’t mark the paper’s online copy — until someone tweets about it.
  • Paging Dr. Pangloss. Researchers shocked to discover that their adaptive storytelling doesn’t explain women’s taste in male body hair.
  • It just means you’re a lousy singer. If you can’t sing, it may not be because you’re tone deaf.
  • Well, a model Iguanodon. The time Victorian scientists celebrated New Year’s Eve inside an Iguanodon.
  • Most specific sample ever? Gay men found to be happier than their straight twin brothers.
  • Misremember me, maybe? Carly Rae Jepsen is on to something besides a catchy tune.
  • Furry murderers. That study about cats’ nocturnal hunting, as an infographic.
  • The reports of Solenodon‘s extinction were slightly exaggerated. The venemous, shrew-like mammal has been rediscovered in Cuba.

Share

Nothing in Biology Makes Sense: The vital importance of genetic variation

Black Bean Aphid Aphis fabae. Photo by robbersdog.

Over at Nothing in Biology Makes Sense!, Devin Drown describes an interaction between aphids and a species of wasp who lay their eggs in the aphids so their larvae can eat the aphids alive. A new study tests whether the success of a wasp larva infecting an aphid depends on the specific genetics of the wasp, and of a bacterial symbiont the aphid carries:

The Vorburger group studies a crop pest aphid, Aphis fabae, and its common wasp parasitoid, Lysiphlebus fabarum. The adult parasitoids lay their eggs in unsuspecting aphid hosts. As the parasitoids develop they battle the hosts defenses. Some aphid hosts are also infected with a bacterium symbiont, Hamiltonella defensa, which can provide protection against the parasitoid by releasing bacteriophages that target the parasitoid invader (Vorburger et al 2009; Vorburger and Gouskov 2011). If the wasp parasitoid can evade all the host defenses then eventually it develops inside the still living aphid. Eventually, as the authors describe in grisly detail

“metamorphosis takes place within a cocoon spun inside the host’s dried remains, forming a ‘mummy’ from which the adult wasp emerges” (Rouchet and Vorburger 2012).

To learn how Vorburger et al. evaluated the importance of wasp genetics for successfully mummifying aphids, go read the whole thing.◼

Share

Oh, hey. This sounds familiar.

Minnesota’s not the only state putting people’s civil rights up for a majority vote this election. Over on the Slog, Eli Sanders reports on working the phones with the campaign in support of Washington’s initiative R-74, which would make civil marriage available for same-sex couples in that state. (Contrast with Minnesota: here, we’re fighting against a ballot initiative that would put a ban on same-sex marriage in the state constitution.)

Sanders goes into rather more detail about specific calls than I did, probably because he’s a real journalist. I like this one:

Then, Ronald in Suquamish. I apologized for calling him during the dinner hour.

“Go ahead,” he replied. “I’m old, I like to talk.”

Ronald is 80. He told me that if I promised not to vote for Republicans “who are going to cut my Social Security,” he’d promise to vote to approve R-74.

But this wasn’t really a “persuasion” type of situation. Ronald had already come around to supporting marriage equality on his own. He’d met his first gay people while serving in the Navy, where he worked on submarines. “In fact, I got knocked on my butt by a lesbian in a bar in New York, in my uniform,” he told me. “I asked her girlfriend to dance. She let me have it. Knocked me right on my can.”

This is probably as good a time as any to note that my little fundraising project, in which I’m running the Mankato Marathon (in less than two weeks!) in support of the marriage-equality campaign here in Minnesota, Minnesotans United for All Families, is over halfway to my goal of $500! Thanks yet again to everyone who chipped in — and the rest of you, what’re you waiting for?◼

Share

Science online, Friday coffee break edition

Scream Someone just saw his report from “23andMe,” I guess. Photo by CHRISTOPHER MACSURAK.
  • At Nothing in Biology Makes Sense! God fails a standard information-theoretic test.
  • At the Molecular Ecologist: Reduce sequencing error with a new “duplex tag” method.
  • The only thing we have to fear is variation at adrenaline receptor loci. Against fearmongering over personal genomics.
  • Encouraging words for job application season. You don’t know how your story ends.
  • We’re number one? Study by Dunkin’ Donuts concludes that scientists drink more coffee than members of any other profession.
  • So say we all. Space operas, graded by accuracy of physics portrayed.
  • Three out of four cases. A large majority of scientific paper retractions are due to fraud.
  • Jumping gigawatt! Experiments that are so crazy, they just might work.
  • Proposed, then scuttled in Congressional absurdity. A multi-location National Park to commemorate the Manhattan Project.
  • Or, you know, human. Ayn Rand’s individualism doesn’t work so well if you’re a hunter-gatherer.
  • The early bug gets the bite. The use of insecticide-infused bed nets at night prompts mosquitoes to bite during the morning.
  • Historical contingency. What killed the electric car, the first time around.

Share

Notes on a model species

2012.09.20 - Seeds

Seeds. (Flickr: jby)

There are a couple of neat racks on my desk containing rows of plastic tubes, each tube with a drift of tiny, kidney-bean-shaped seeds at the bottom. These are seeds of Medicago truncatula, barrel medick. When I tell people about this plant I’m currently studying, I usually describe it as an unremarkable wildflower native to the Mediterranean. Or I note that it’s a close-ish relative of alfalfa (Medicago sativa).

Medicago truncatula does not have an especially grand heritage. It grows in dry, sunny places throughout the dry, sunny Mediterranean region, forming low tangles of trifoliate leaves and small yellow flowers that eventually ripen into tough, spiky, vaguely barrel-shaped fruits full of those tiny seeds. Some of the seeds on my desk are descended from plants that grew in places like the Temple of Apollo at Curium, Cyprus; but most are from less distinguished locales. In his 2011 monograph on the genus Medicago, Ernest Small quotes a description of M. truncatula‘s habitat as “sandy fields, wet grasslands, wet meadows, strongly overgrazed and degraded garrique, coniferous forests, grasslands, fallow fields, olive groves, and as a weed in cereal and crops and waste places.”

Continue reading

Share

Nothing in Biology Makes Sense: God’s AIC score

The creation of Adam. Image via Web Gallery of Art.

This week at Nothing in Biology Makes Sense! Noah Reid takes a cue from Bill Nye the Science Guy and applies information theory to test whether a model of divine intervention fits a simple phylogenetic dataset.

Without getting into the details, we can think of information theoretic criteria for model selection as formally implementing Occam’s Razor: the simplest model with the most explanatory power is to be preferred. By preferring simple models, you guard against overinterpreting data, a pitfall that can make models poor predictors of new observations.

So, I realized as long as we can formulate any mathematical model of “The Hand of God”, rejectable or not, we can compare it to an evolutionary model in this framework. If, as Nye suggests, evolutionary theory is simple and powerful, and creationism is a model of fantastical complexity that doesn’t much improve our understanding of the data, information theory would help us sort that out.

If you want to settle the whole evolution-versus-creationism thing once and for all (okay, not really), or just learn how biologists use information theory to select models (really!), go read the whole thing.◼

Share

5k down, 42 to go

2012.09.29 - Big Gay Racers Big Gay Racers. Photo by jby.

Saturday morning, I ran Big Gay Race with a whole bunch of friends and thousands of other Minnesotans. In spite of an early-season cold, I did the 5k run in 20:08, nine tantalizing seconds from a personal record. (Is Pseudophed a performance-enhancing drug? If so, it’s not performance-enhancing enough.)

The BGR was the first of two events I’m running in support of Minnesotans United for All Families and the fight against the proposed anti-gay-marriage amendment to the state constitution. With a bit more than a month to go before the vote, polling on the amendment is also tantalizingly close, a statistical dead heat at 49% for, 47% against, and 4% undecided.

Meanwhile, I’m just about ready to take something a little bit longer—the Mankato Marathon. I did what will probably be my longest pre-marathon training run—19 miles un-enhanced by cold medicine in beautiful autumn weather—on Sunday, and I do believe I’m ready to survive 26.2 miles (or about 42k) less than three weeks from now.

Denim and Tweed readers have already given $205 to MNUnited, for which I’m mighty grateful. But if you haven’t given yet, please help us make it to $500 with a donation of $5, or $10, or $25—we’re on the home stretch, and every little bit will make a difference.

Donate here.◼

Share