Monthly Archives: May 2010

Science online, binge-drinking tree shrews edition

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Style over ecological substance? Maybe. But how can you say “no” to that face? Photo by rockabillyboy72.
  • Much like nectar-feeding bats, pentailed tree shrews drink alcoholic nectar from their favorite food plant, and get enough (by weight) to intoxicate a human. (Endless Forms)
  • “Due to its well-known song, the field cricket is a comparatively popular insect species.” Choosing a “flagship species” to promote conservation awareness involves thinking about image as well as ecology. (Conservation Maven)
  • Who knew that sharks like to climb? Undersea mountains are hotspots of biodiversity. (deep type flow)
  • Sadly, no mention of the fact that they ate Joshua tree fruit. Reconstructions of extinct giant ground sloths’ muzzles suggest a diversity of foraging habits. (Laelaps)
  • ArchaeopteryX-rayed. A new scanning technique applied to fossils of the feathered dinosaur reveals new detail. (Dinosaur Tracking)

And finally, via Observations of a Nerd, here’s none other than Douglas Adams discussing evolution and endangered species. (Be advised: It’s an hour and a half long. Worth every moment, though.)

The “Big Four,” part I: Natural selection

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This post is the first in a special series about four fundamental forces in evolution: natural selection, mutation, genetic drift, and migration.

This post was chosen as an Editor's Selection for ResearchBlogging.orgAmong non-biologists, the best-known of the Big Four forces of evolution is almost certainly natural selection. We’ve all heard the catchphrase “survival of the fittest,” and that’s a pretty good, if reductive, summing up of the principle. In more precise terms, here’s how natural selection works:

  • Natural populations of living things vary. Deer vary in how fast they can run, plants vary in how much drought they can tolerate, birds vary in their ability to catch prey or collect seeds—no two critters of the same species are exactly alike.
  • Some of those variable traits determine how many offspring living things have. How well you avoid predators, fight off disease, and collect food all determine how many babies you can make.
  • Many of those variable traits are heritable, passed on from parents to offspring. Faster deer usually have faster fauns; drought-tolerant plants make drought-tolerant seeds.

With these three conditions in place, natural selection occurs: heritable traits that help make more babies become more common. That is, if you have a trait that lets you support more offspring than your neighbor, you’ll have more children than your neighbor, and they’ll have more children than your neighbor’s children, and so on.

Fitness-versus-phenotype regressions for directional, stabilizing, and disruptive selection. Graphic by jby.

Measuring selection

Put this way, natural selection is simply a relationship between fitness, the number of offspring an organism can produce (often reported in comparison to the rest of the local population), and phenotype, the value of one or more traits of that organism (wing length, running speed, number of flowers produced, &c). Biologists can measure selection in natural populations by estimating this relationship between fitness (or a proxy for fitness, like growth rate), and phenotypes. Such an analysis should produce something like the regression graphs to the right, in which the relationship might be directional, with greater- (or smaller-) than-average phenotypes having greater fitness; stabilizing, with the average phenotype value having greater fitness; or disruptive, with extreme phenotype values having greater fitness. The slope of the line, or the shape of the curve, is a measure of the strength of natural selection [PDF] on an organism’s phenotype. This approach to measuring selection has been widely applied, and in 2001 a group of biologists led by Joel Kingsolver collected more than 2,500 estimates of the strength of natural selection [PDF].

How strong is selection?

Kingsolver et al. found that selection was usually surprisingly weak. Studies with the largest sample sizes, and the most statistical power to detect selection, mostly found directional selection strength (that is, the slope of the fitness-phenotype regression) less than 0.1, and the strength of stabilizing or disruptive selection was similarly low. Does this mean selection doesn’t matter in the short-term evolution of natural populations?

Probably not. The average selection strength estimates from the Kingsolver et al. dataset are actually stronger than selection strength assumed in most mathematical models of evolution. Furthermore, the collected estimates of selection had “long tailed” distributions—a small number of studies found quite strong selection, up to ten times as strong as the average. So maybe rare but strong bouts of selection have disproportionate impact over the long term.

Peter and Rosemary Grant have documented decades of shifting natural selection on Darwin’s finches (Geospiza spp.). Photo by Igooch.

Taking the finch by the beak

Part of the problem with assessing selection in nature is that most datasets measure selection over just one or a few years. One exception is the case of Darwin’s finches in the Galapagos Islands. The Galapagos offers a wide variety of habitat types, and experiences substantial year-to-year environmental variation—a landscape that should exert all sorts of natural selection on its occupants. Peter and Rosemary Grant have studied Galapagos finches for decades now, and found that selection is continuously at work on these unassuming birds. (The Grants’ book How and Why Species Multiply sums up their research program for a lay audience.)

Much of the Grants’ work has focused on the finches’ beaks, which largely determine what food the birds can eat. The distribution of seed sizes available on different Galapagos islands strongly predicts [PDF] the size of finches’ beaks on those islands. In 1989, the Grants published estimates of selection on beak size in the finch species Geospiza conirostris following a drastic wet-to-dry climactic shift that radically changed what foods were available to the finches. They found strong selection [$a], with fitness-phenotype regression slopes as high as 0.37. What’s more, the direction of selection changed dramatically from a very wet year to the dry year immediately afterward, as the finches were forced to move from feeding on small seeds and arthropods—which gave the advantage to shorter beaks—to hard-to-crack seeds, which required deep beaks.

The Grants’ longer-term study of selection on Galapagos finches confirms this image of selection swinging back and forth unpredictably [PDF]. From 1972 to 2001, they tracked populations of the finch species G. scandens and G. fortis, and saw both more gradual long-term changes in the finches’ body size and beak measurements as well as sudden sharp shifts. These changes continually altered the ability of the two species to hybridize, so that some years they were more reproductively isolated than others—and conditions in any one year were poor indicators of what would be going on five, ten, or twenty years later.

So when does selection matter?

The Grants’ study makes natural selection look as shifting and impermanent as the wind. How can it shape patterns of evolution over millions of years, then? One possibility is that trends may emerge over longer periods of time, as wobbly selection moves species in new directions in a drunkard’s walk, with two steps forward, then one step back, then four steps forward. Another is that lasting trends only occur when speciation intervenes to lock in fleeting changes due to variable natural selection [$a]. Much also depends on how selection interacts with mutation, genetic drift, and migration, as I’ll discuss in the rest of this series.

And here’s a shameless plug for a t-shirt. Photo by jby.

References

Futuyma, D. (1987). On the role of species in anagenesis. The American Naturalist, 130 (3), 465-73 DOI: 10.1086/284724

Grant, B.R., & Grant, P.R. (1989). Natural selection in a population of Darwin’s finches. The American Naturalist, 133 (3), 377-93 DOI: 10.1086/284924

Grant, P.R., & Grant, B.R. (2002). Unpredictable evolution in a 30-Year study of Darwin’s finches. Science, 296 (5568), 707-11 DOI: 10.1126/science.1070315

Grant, P.R. and B.R. Grant. (2008) How and Why Species Mutliply: The Radiation of Darwin’s Finches. Princeton University Press. Google Books.

Kingsolver, J., Hoekstra, H., Hoekstra, J., Berrigan, D., Vignieri, S., Hill, C., Hoang, A., Gibert, P., & Beerli, P. (2001). The Strength of phenotypic selection in natural populations. The American Naturalist, 157 (3), 245-261 DOI: 10.1086/319193

Lande, R. (1976). Natural selection and random genetic drift in phenotypic evolution. Evolution, 30 (2), 314-34 DOI: 10.2307/2407703

Johnson, T., & Barton, N. (2005). Theoretical models of selection and mutation on quantitative traits. Phil. Trans. R. Soc. B, 360 (1459), 1411-25 DOI: 10.1098/rstb.2005.1667

Schluter, D., & Grant, P. (1984). Determinants of morphological patterns in communities of Darwin’s finches. The American Naturalist, 123 (2), 175-96 DOI: 10.1086/284196

In which I provide something like an explanation

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Now that D&T has its own domain, Google hosting allows me a few dedicated pages apart from the blog itself. So I’ve written up an about the blog page with more information than you probably require. I’ve revised the “About me” blurb in the sidebar to reflect this.

We now return you to your regularly scheduled Internet.

Science online, cephalopod sensitivity edition

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This one is for PZ. Photo by Joachim S. Müller.

I spent my week readying another (!) manuscript for submission and doing large volumes of PCR. And, yes, surfing the web between thermal cycler loads. But! I read about science, so that’s mostly OK.

  • What we have here is a failure to communicate. With their complex nervous systems and surprising intelligence, octopuses ought to be as sensitive to pain as mammals—but there’s surprisingly little evidence to address that question. (NeuroDojo)
  • Where are all the men? Analysis of DNA from thousand-year-old “moa graveyards” in New Zealand finds female skeletons overwhelmingly outnumbering males. (Laelaps via @nerdychristie)
  • You can only preserve what you can get. Land protection efforts by NGOs fall short of established habitat protection goals, a case study in Maine finds. (Conservation Maven)
  • How long we have left is in-DEET-terminate. Laboratory selection experiments demonstrate that mosquitoes may be evolving resistance to the insect über-repellent. (Wired Science)
  • It only took 41 years longer than we needed to put a man on the moon. A Florida horticulture professor has bred what could be the first good-tasting mass-producible tomato. (The Washington Post)
  • We’re all Neanderthals now. Analysis of the first complete Neanderthal genome suggests that they interbred with modern humans. (Special feature in Science, NPR, John Hawks Weblog)

And for those of you who didn’t recognize the three-letter acronym in my introductory paragraph, this is what PCR does:

Four-part sheet music is a challenging read

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Via Kottke: Craig Fehrman has posted the complete text of a “lost” 1996 profile of David Foster Wallace written for Details magazine by David Streitfeld. It’s quite short, but it includes a couple of details about Wallace’s relationship with Christianity I hadn’t heard before, including one that really shouldn’t be surprising given how much of his life he spent in the Midwest:

Recently he found a Mennonite house of worship, which he finds sympathetic even if the hymns are impossible to sing.

Back to basics: The “Big Four”

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ResearchBlogging.orgThe nice thing about a field season away from all regular internet access is that it gives you a real sabbatical of a sort—a chance to reassess plans and set new goals. One of the new goals I set myself this last field season was to introduce a new kind of topic here at Denim and Tweed.

Most of my writing about science at D&T focuses on recently published discoveries in evolution and ecology. It’s fun writing, and it coincides neatly with my regular journal reading, and I intend to keep doing it. But I’ve discovered that when I want to put new work in context, I often need to discuss fundamental concepts of evolutionary biology that aren’t necessarily common knowledge, such as genetic drift or sexual selection. However, I rarely have room to explain these concepts in depth within a blog post devoted to something else.

So maybe the solution is to devote some posts to explaining these “basics.” I’m going to start with a series of posts on the “Big Four” processes of population genetics. These are the four processes that account, in one way or another, for every change in the frequency of genes within natural populations. In other words, the Big Four account for much of evolution itself. They are:

  • Natural selection, changes in gene frequencies due to fitness advantages, or disadvantages, associated with different genes.
  • Mutation, the source of new forms of genes;
  • Genetic drift, or changes in gene frequencies that arise from the way probability works in finite populations; and
  • Migration, or changes in gene frequencies due to the movement of organisms from site to site.

Lay readers may be surprised both by what we know, and what we don’t, about how these four processes operate in nature. Natural selection is relatively easy to measure, and apparently ubiquitous [PDF] in natural populations—but we don’t know how often the resulting short-term changes impact evolution over millions of years. Mutation, the source of variation on which natural selection acts, seems to vary widely among living things. Genetic drift means that a trait can come to dominate a population even if it has no fitness effect—or sometimes a deleterious one. Finally, migration across variable landscapes can interact with selection, drift, and mutation [$a] to completely alter their effects.

I’ll devote one post each to selection, mutation, drift, and migration, discussing classic findings as well as more recent scientific discoveries about each. They’ll arrive as my usual mid-week science posts for the next four weeks, and I’ll update this post with links to the others as they go online—so if this looks worth following, you can either bookmark this post, or subscribe to D&T’s RSS Feed.

Natural selection, mutation, genetic drift, and migration act together to shape the evolution of natural populations. Photo by jby.

References

Drake JW, Charlesworth B, Charlesworth D, & Crow JF (1998). Rates of spontaneous mutation. Genetics, 148 (4), 1667-86 PMID: 9560386

Kingsolver, J., Hoekstra, H., Hoekstra, J., Berrigan, D., Vignieri, S., Hill, C., Hoang, A., Gibert, P., & Beerli, P. (2001). The strength of phenotypic selection in natural populations. The American Naturalist, 157 (3), 245-61 DOI: 10.1086/319193

Slatkin, M. (1987). Gene flow and the geographic structure of natural populations. Science, 236 (4803), 787-92 DOI: 10.1126/science.3576198

Wright S (1931). Evolution in Mendelian populations. Genetics, 16 (2), 97-159 PMID: 17246615

Do I look “illegal”?

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Here’s a great American, fretting about immigrants:

Few of their children in the country learn English; they import many books from [their nation of origin] …. The signs in our streets have inscriptions in both languages, and in some places only [the other]. They begin of late to make all their bonds and other legal writings in their own language, which (though I think it ought not to be) are allowed good in our courts, where the [non-English] business so increases that there is continual need of interpreters; and I suppose in a few years they will also be necessary in the Assembly, to tell one half of our legislators what the other half say.

If I didn’t tip my hand with the use of the word “great,” it may surprise you to learn that the American doing that fretting is not a current member of the Republican Party, but Benjamin Franklin; and the immigrants occasioning that fretting are not Latinos but Germans. The above passage is a quote from one of Franklin’s letters, dated 9 May 1753, which I found in H.W. Brands’ excellent biography The First American.

These were my people Franklin was fretting about. Most of the time it’s easy to forget that I have an ethnicity, much less one that was once at odds with an English-speaking colonial culture. That’s my privilege as a white man in the twenty-first century U.S. Many folks don’t enjoy such a privilege—particularly not in Arizona, where a widely-discussed law will soon allow police to ask for proof of legal residence based on only a “reasonable suspicion” that someone is in the country illegally. It’s an invitation to racial profiling, aimed squarely at people of the current fret-worthy ethnicity, Hispanics.

Fortunately, the American Civil Liberties Union (among other organizations, including the federal government) will contest the law. In another 250 years, maybe this law will seem as quaint as Benjamin Franklin complaining about street signs in German—but before then, I’m sure the ACLU would appreciate your support.