Category Archives: science

How I spent (the first weekend) of my summer not-quite-vacation

Posted on by
Phylogeny of the Prodoxidae, the family of the yucca moths, with a (very basic) reconstruction of pollinator life habits. Image by jby.

Late last night I made it back to Moscow from (mostly) sunny Santa Barbara, California, where I was lucky enough to attend a summer short course in phylogenetic comparative methods using R, sponsored by NESCent, hosted by NCEAS, and helmed by Luke Harmon and Mike Alfaro. I came into the seminar as a big fan of the programming language R already, and it was great to learn about a whole new range of tools available for the platform. It was even better to learn about those tools in a group of really smart colleagues, all of whom were thinking about how best to use R in their own projects. It was like a warm-up for the Evolution meetings, which start this Friday.

Like the meetings, one of the principal pleasures was learning about everyone else’s study organisms, the best example being the wrinkle-faced bat, which has the strangest trait I think I’ve ever seen in a mammal: a bald face, and a “mask” of furry skin it can pull over said face. Flickr has photos! I’ll put one below the fold in deference to the squeamish.

Eat your heart out, George Lucas. Photo by Evets Lembek.

With conspecifics like these, who needs predators?

Posted on by

Update, 19 July 2011: More than a year after this study was published, some important objections have been made about very basic assumptions of the experiment presented. Also, I’ve fixed the first link the original article.

ResearchBlogging.orgThere’s something special about islands. After moving to islands, plants adapted to rocky outcrops evolve to grow in rainforests and alpine meadows, and finches evolve to behave like woodpeckers. But why? Islands contain new food sources and habitats, they often lack predators, and they can provide more geographic barriers to generate reproductive isolation—to name just a few possibilities. A newly published ecological experiment now provides evidence that one group of island lizards diversfied because islands are crowded [$a].

There’s something about islands. Photo by Storm Crypt.

Diversification on islands may be related to density compensation, the frequently-observed principle that islands often support fewer species than mainland sites of the same area, but contain more individuals of each species—that is, island populations are usually at higher density than their mainland counterparts [$a]. Density compensation seems to arise both from lack of predators on islands, and because island populations have fewer competitor species. This may mean that, compared to mainland populations, island populations are under weaker natural selection from other species, and stronger selection from competition with other members of their own species.

A somewhat strained analogy

How could that difference in selective regimes spur diversification? Imagine two towns, one surrounded by other settlements, the other on its own in the middle of the wilderness. The town in densely-populated country is probably best off doing one thing well—to have, say, most of its inhabitants working at a factory making (to pick a product at random) sausages for trade with other towns. People living in this first town might want to start up a factory making a different product, but odds are good there’s strong competition from another town nearby, so it’s hard to get the new business off the ground—it’s really just better to invest in the existing factory.

On the other hand, the inhabitants of the town in a lightly-populated district might need more products made locally because it costs too much to import. A businesswoman in the isolated town is probably better off starting a factory that makes a product no-one is making locally—if sausages are already accounted for, there might be a market for (to pick another product at random) pharmeceuticals.

In this scenario, competition from outside exerts economic pressure to do one thing well; competition from within exerts pressure to do many different things. Both kinds of competition are present in each town, but outside competition is stronger in the town surrounded by other towns, and competition from within is stronger in the isolated town.

Anole vs. anole

The density compensation hypothesis proposes that something similar happens on islands. With fewer predators or competitor species, island populations are able to maintain higher densities of individuals. That increased density means that competition within the species becomse stronger, creating natural selection that favors individuals who can use new food resources or live in new habitats.

Density compensation seems likely to be responsible for the diversification of anole lizards on the islands of the Caribbean. In the course of colonizing Caribbean islands, anoles have repeatedly evolved into a handful of different niche specialists [PDF] called “ecomorphs,” ranging from “giant” species that live high in the forest canopy, to small species that can navigate and perch on fine twigs, and intermediate species that live on and around tree trunks. Anoles on the mainland of Central America are no less diverse than their Caribbean congeners, but they haven’t evolved mini-radiations of replicated ecomorphs—and their population densities are much lower than those of the island species.

Anolis sagrei, the brown anole. Photo from WikiMedia Commons.

If release from predators, and the ensuing increase in population density, drove the diversification of island anoles, then we might expect that natural selection from predators has less effect on the traits that differentiate the anole ecomorphs than natural selection from other anoles. Testing that hypothesis experimentally is ambitious to say the least, but that’s what the new study attempts to do.

The authors, Calsbeek and Cox, identified six very small, similar islands off the coast of the Bahamian island Greater Exuma, and introduced varying numbers of brown anoles (Anolis sagrei) onto them at the beginning of the summer. The islands were small enough that Calsbeek and Cox could selectively exclude birds by enclosing the islands in netting; by introducing predatory snakes onto some islands, they could then generate three selective regimes: no predators, birds only, and birds plus snakes. Before introducing them into these experimental setups, the authors measured each anole’s body size, hind-leg length, and running stamina, and marked each lizard so they could estimate selection acting on the three traits based on which lizards survived to be recaptured at the end of the season. (The experiments were carried out over two years, with both years’ results compiled at the end.)

The results suggest that competition makes a bigger difference for the experimental populations than predation—while the strength of natural selection acting on all three traits increased with the anoles’ population density, it didn’t change when predators were allowed access to the islands. If the levels of predation simulated on the micro-islands accurately reflect what anoles experience throughout the Caribbean, then the result is, I’d say, pretty good evidence that competition is the most important evolutionary force acting on island anoles.

I should note that, although Calsbeek and Cox’s raw result is suggestive, it’s not clear that their sample size is big enough to support all the statistical analyses they perform on the data. On balance, I think they deserve a lot of credit just for tackling this question experimentally.

References

Calsbeek, R., & Cox, R. (2010). Experimentally assessing the relative importance of predation and competition as agents of selection. Nature, 465 (7298), 613-6 DOI: 10.1038/nature09020

Givnish, T., Millam, K., Mast, A., Paterson, T., Theim, T., Hipp, A., Henss, J., Smith, J., Wood, K., & Sytsma, K. (2009). Origin, adaptive radiation and diversification of the Hawaiian lobeliads (Asterales: Campanulaceae). Proceedings of the Royal Society B: Biological Sciences, 276 (1656), 407-16 DOI: 10.1098/rspb.2008.1204

Losos, J. (1990). Ecomorphology, performance capability, and scaling of West Indian Anolis lizards: an evolutionary analysis. Ecological Monographs, 60 (3), 369-88 DOI: 10.2307/1943062

MacArthur, R., Diamond, J., & Karr, J. (1972). Density compensation in island faunas. Ecology, 53 (2) DOI: 10.2307/1934090

Pinto, G., Mahler, D., Harmon, L., & Losos, J. (2008). Testing the island effect in adaptive radiation: rates and patterns of morphological diversification in Caribbean and mainland Anolis lizards. Proceedings of the Royal Society B: Biological Sciences, 275 (1652), 2749-57 DOI: 10.1098/rspb.2008.0686

Science online, southward bound edition

Posted on by
I’ll take the high road, you take the low road … Photo by gwgs.
  • Still gushing. The Deepwater Horizon well is still not contained. Wednesday BP agreed to set aside $20 billion for an independent reparations fund.
  • Got ’em coming and going. Even if they escape being soaked in oil themselves, seabirds are at considerable risk of eating oil-soaked prey. (Deep Sea News)
  • Me, I just turn left by default. Given a choice between a southern route and a northern route of equal length, people will choose the southern route—apparently because it feels easier. (Wired Science)
  • Who doesn’t want a view of the park? The conservation benefits of protected land can be offset if nearby real estate becomes popular. (Conservation Maven)
  • This is why I’m not a neurologist. Remember all those papers based on fMRI brain scans? Yeah, apparently we’ve only just discovered what fMRI scans actually mean. (Neurotopia)
  • Looking for an open alternative to MatLab? Try Python. (U+003F)
  • What is “forty-two,” Alex? IBM’s next advance in artificial intelligence centers on teaching a supercomputer to answer “Jeopardy” questions. (NY Times)

This week’s video from BBCEarth: David Attenborough says “boo” to a sloth.

Not just babble: Cooperating birds talk it through

Posted on by

ResearchBlogging.orgFor cooperation to work, everyone involved needs to know what the others are willing to contribute in order to decide what she will contribute. You might think that only humans can achieve that kind of back-and-forth negotiation, but a paper recently published online by Proceedings of the Royal Society suggests otherwise. In it, ornithologists decode the negotiations [$a] that allow sociable birds to share the task of watching for predators.

The southern pied babbler, Turdoides bicolor. Photo by Blake Matheson.

Pied babblers (Turdoides bicolor) are sociable South African songbirds, which live and forage for food in groups. During foraging, some adult babblers act as sentinels, perching above the ground to scan for predators, and alerting the rest of the foragers if any danger shows up. Sentinel behavior is cooperative—sentinels free the rest of the group to concentrate on feeding, but sentinels themselves cannot forage. The study’s authors, Bell et al. hypothesized that sentinels might communicate how long they’re willing to stand watch to the rest of the group, so as to prompt new birds to take up watch and given the current sentinels a break to feed.

The authors first established that how hungry a babbler is determines how long he or she is willing to stand watch, which they did by feeding the birds with meal worms immediately after they concluded a period of sentinel duty. Babblers receiving ten worms returned to duty faster than those receiving just one, and stayed on duty longer. Further feeding experiments and observations established that both foragers and sentinels called to each other less frequently when they were well fed, that sentinels called more frequently the longer they stayed on watch, and that sentinels who ultimately stayed on watch the longest also called the least frequently in their first minute on watch.

So call frequency is the babblers’ signal for how badly they want to forage—foragers hearing higher-frequency calls from sentinels should take them as a call for relief; and sentinels hearing lower-frequency calls from foragers should take them as permission to leave the watch and start foraging. To test this hypothesis, the authors played recorded calls to foragers and sentinels, and found that the birds responded as I’ve just described. The apparent babble of the babblers, then, is actually a perpetual negotiation about who should be on sentinel duty—sentinels complaining when they get hungry, and foragers telling the sentinels, “Not yet! I just need to catch a few more worms.”

Reference

Bell, M., Radford, A., Smith, R., Thompson, A., & Ridley, A. (2010). Bargaining babblers: vocal negotiation of cooperative behaviour in a social bird. Proc. Royal Soc. B DOI: 10.1098/rspb.2010.0643

Science online, phylogenetically distant edition

Posted on by
Louisiana Fish and Wildlife staff rescue an oil-coated pelican. Photo by The News Hour.

As of Thursday night, the Gulf of Mexico oil gusher is capped, but still gushing—and new reports suggest even more oil than previously thought has escaped. Plumes of oil are spreading under the surface of the Gulf. Reports from the American Birding Association are pessimistic at best. On the bright side, an environmental law expert told NPR earlier in the week that criminal prosecution arising from the spill will be “a slam dunk.” Southern Fried Science has compiled the best online sources for oil spill news, including this salty primer on oil containment with booms. I’d add ProPublica’s excellent coverage to the list—and you should go hear ProPublica’s Abrahm Lustgarten tell Terry Gross about BP’s dismal safety record in case you feel your outrage flag.

In non-catastrophic science news:

  • Darwin was right. Again. Confirming a prediction made in The Origin of Species, a recent study shows that bacterial strains are better able to invade cultures of distantly-related strains than closely-related ones. (The EEB & flow)
  • Surprising it’s not higher, really. A survey of marine biology papers suggests that about 25 percent of literature citations are “inappropriate”—but apparently considers citing review articles “inappropriate.” (Neurodojo)
  • Because men are shallow, whatever our orientation. Gay men are 50 percent less likely to be obese than straight men; the reverse is true for women. (Slog)
  • Really, it’s a shame to waste so much neck. Contrary to the current prevailing thinking among paleontologists, at least one sauropod species seems to have used its long neck to reach high-up foliage. (Dinosaur Tracking)
  • Somewhere in here is an episode of Star Trek. Unlike males, female jumping spiders will fight to the death in confrontations over territory—especially if they’re almost ready to lay eggs. (EcoTone, Wired Science)
  • Accidental complexity in the genetic code. Introns, snippets of non-protein-coding DNA interspersed within protein-coding DNA, may have originated as “selfish genes” in our bacterial ancestors. (Wired Science)

This week’s video: BBC footage of aphids’ peculiar lifestyle.

The “Big Four,” part IV: Migration

Posted on by

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

Edited 8 April 2011: Following some interesting comments from population geneticist Lou Jost, I’ve edited my characterization of the rule of thumb that one migrant per generation is generally enough to prevent populations from differentiating.

It’s the little differences. I mean, they got the same shit over there that we got here, but it’s just—it’s just there it’s a little different.
— Vincent, Pulp Fiction

ResearchBlogging.orgDifferent places are different from each other. This is a truism bordering on tautology, but it also has real implications for the ways in which life evolves and diversifies. The specific differences between one environment and another shape how well living things can move between those environments, and what happens when they do—the evolutionary consequences of migration.

Canada geese on the wing. Photo by Brian Guest (giant rebus).

Individuals moving between populations can alter the evolution of those populations in a number of ways [$a]. Migration introduces traits from one population into another, making it a source of variation not unlike mutation. Migration can swamp out the effects of local natural selection, if enough migrants come from a population experiencing a different selective regime. Migration from a larger population to a smaller one can offset the loss of variation to genetic drift; but a small group of individuals migrating to an empty habitat can be strongly affected by drift. Depending on what species concept you prefer, migration between two populations is either what prevents them from becoming separate species, or what conclusively proves that they are the same species.

Migration mixes things up

Strictly speaking, I’m not talking simply about the movement of living things from place to place, but about gene flow, which also requires interbreeding between migrants and the populations to which they migrate. Individuals might be able to travel to another environment, and even do so frequently, but fail to survive when they get there [PDF], or fail to find a mate in the local population, or have offspring that are themselves less fit than the offspring of the locals. Because tracking each of these steps directly is daunting at best, most population biology studies estimate the rate of successful migration by proxy, using some measure of the genetic similarity of populations—the more migrants successfully move between populations, the more similar the traits and gene frequencies of those populations will be.

The rate of gene flow between two populations is essentially a measure of how much those populations evolve as a single unit—if there’s no gene flow, selection or drift can eventually make the two populations into completely different things. An effective migration rate of one migrant per generation is has been generally understood to be enough to prevent drift from causing populations to diverge [$a]. (But there are significant objections to the one-migrant-per-generation rule of thumb, including the question of how we determine that populations have differentiated! See the discussion of this in the comments.) Populations linked by migration along several intervening populations may be isolated by distance [PDF] if the line of connecting populations is long enough.

If natural selection is operating in different directions in the two populations, more migration is necessary to prevent them evolving different traits. If individual genes experience different selection in each population, then those genes may still evolve differently even as migration continues to mix in neutral genes [PDF]. This movement of genes across recognized population and species boundaries is called introgression.

Gene flow versus selection

The bird-pollinated Iris fulva (left) can sometimes hybridize with bee-pollinated I. brevicaulis, but pollinators favor hybrids that look more like the parent species. Photos by Matt N Charlotte and Jim Petranka.

One well-documented case of gene flow between apparently “good” species is that of the Louisiana irises Iris fulva and I. brevicaulis. These two species fill fairly distinct ecological niches: red-orange I. fulva is mainly pollinated by hummingbirds, and grows in very wet conditions; blue I. brevicaulis is pollinated by bees, and grows best in drier habitats.

Yet when the two species co-occur, they sometimes do cross-pollinate. What prevents the two species from merging into a single iris? (Perhaps it would have purple flowers.) Natural selection, in this case, overwhelms migration. Experimentally created fulva–brevicaulis hybrids grown in wet conditions are more likely to survive if they carry specific genes from wet-tolerant fulva; and pollinators tend to favor hybrids that look more like their preferred parent species. I. fulva and I. brevicaulis share some genes that don’t affect wet tolerance or pollinator attraction, but generally remain separate evolutionary entities.

This kind of partial reproductive isolation is most widely documented in plants, but it has been found in all sorts of organisms—even the chipmunks Tamias ruficaudus and T. amoenus [PDF]. In an evolving world, this shouldn’t be surprising—it makes sense to find many cases of partial reproductive isolation as populations evolve toward the point of being separate species. Sometimes, of course, divergent selection weakens, or previous barriers to migration are removed, and populations re-merge into single evolutionary entities. But sometimes, the balance of the selection, mutation, drift, and migration is just right for just long enough to create a new, independently evolving form of life. And thus, as Darwin wrote, “endless forms most beautiful have been, and are being, evolved.”

References

Arnold, M., Hamrick, J., & Bennett, B. (1990). Allozyme variation in Louisiana irises: a test for introgression and hybrid speciation. Heredity, 65 (3), 297-306 DOI: 10.1038/hdy.1990.99

Good J.M., Hird S., Reid N., Demboski J.R., Steppan S.J., Martin-Nims T.R., & Sullivan J. (2008). Ancient hybridization and mitochondrial capture between two species of chipmunks. Molecular ecology, 17 (5), 1313-27 PMID: 18302691

Hedrick, P.W. (2005). Genetics of Populations. Boston: Jones and Bartlett Publishers. Google Books.

Martin, N.H., Bouck, A.C., & Arnold, M.L. (2005). Detecting adaptive trait introgression between Iris fulva and I. brevicaulis in highly selective field conditions. Genetics, 172 (4), 2481-9 DOI: 10.1534/genetics.105.053538

Martin, N., Sapir, Y., & Arnold, M. (2008). The genetic architecture of reproductive isolation in Louisiana irises: Pollination syndromes and pollinator preferences. Evolution, 62 (4), 740-52 DOI: 10.1111/j.1558-5646.2008.00342.x

Nosil, P., Egan, S., & Funk, D. (2008). Heterogeneous genomic differentiation between walking-stick ecotypes: “Isolation by adaptation” and multiple roles for divergent selection. Evolution, 62 (2), 316-36 DOI: 10.1111/j.1558-5646.2007.00299.x

Nosil, P., Vines, T., & Funk, D. (2005). Reproductive isolation caused by natural selection against immigrants from divergent habitats. Evolution, 59 (4), 705-19 DOI: 10.1554/04-428

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

Wang, J. (2004). Application of the one-migrant-per-generation rule to conservation and management. Conservation Biology, 18 (2), 332-43 DOI: 10.1111/j.1523-1739.2004.00440.x

Wright, S.J. (1943). Isolation by distance. Genetics, 28, 139-56 PMCID: PMC1209196

University of California system vs. Nature

Posted on by

Holy cow is right. In response to a threatened 400 percent increase in institutional subscription fees for 2011, the University of California system is threatening to boycott Nature and its sister journals [PDF].

… unless NPG [Nature Publishing Group] is willing to maintain our current licensing agreement, UC Faculty would ask the UC Libraries to suspend their online subscriptions entirely, and all UC Faculty would be strongly encouraged to:

  • Decline to peer review manuscripts for journals from the Nature Publishing Group.
  • Resign from Nature Publishing Group editorial and advisory boards.
  • Cease to submit papers to the Nature Publishing Group.
  • Refrain from advertising any open or new UC positions in Nature Publishing Group journals.
  • Talk widely about Nature Publishing Group pricing tactics and business strategies with colleagues outside UC, and encourage sympathy actions such as those listed above.

UC scientists will still get Nature articles—but now via e-mail from colleagues with personal subscriptions or access through non-UC libraries—and NPG will make nothing on those transactions. Refusal of peer review services—free labor provided to journals as a sort of scientific civil duty—also seems like it could reasonably inconvenience NPG. The full text of the memo mentions a similar successful boycott of Elsevier and Cell Press back in 2003, so clearly withdrawing the collective scholarly involvement of the UC scientific community can make a journal publisher take notice.

“What are birds? We just don’t know.”

Posted on by

The British are still light-years ahead of us Yanks when it comes to deadpan silliness.

And yes, there’s a whole series. I recommend Maths and Iron.

Science online, short work-week edition

Posted on by
Make mine a double. Photo by Ballistik Coffee Boy.
  • Not as obvious as it seems. Computer modeling suggests that giraffes are much worse swimmers than other ungulates—which suggests that giraffe populations should be easily isolated by water barriers. (Tetrapod Zoology)
  • Guess it’s time for that second cup. Regular coffee drinkers need their morning dose of caffeine just to achieve the baseline alertness of non-coffee-drinkers. (Yahoo! News)
  • Jet-setting dinos. New fossils show that ceratopsian dinosaurs (the group including Triceratops) had a wider range than previously thought, colonizing the landmass that would become modern Europe. (Smithsonian.com)
  • No carbon-free lunches. A new analysis of plant communities’ ability to absorb carbon dioxide suggests that managed landscapes like cropland may emit more of the greenhouse gas than they absorb. (Conservation Maven)
  • They still haven’t explained why Justin Bieber is so popular. As with biological evolution before it, the study of cultural evolution is advancing as scientists develop methods to directly experiment with cultural transmission. (A Replicated Typo)
  • More bad news. Computer simulations suggest that the Gulf of Mexico oil spill, now in its sixth week, will probably spread to the Atlantic by the end of the year. (Wired Science)

Here’s video of one scenario from the oil-in-the-Atlantic study.

Freeloading cuckoos force their hosts to diversify

Posted on by

ResearchBlogging.orgAshy-throated parrotbills have a problem every time breeding season rolls around: how do they know whether the eggs in their nests are their own, or those of the common cuckoo? A study recently released in PLoS ONE suggests that one population of parrotbills fights this brood parasitism by laying eggs of different colors.

Common cuckoos lay eggs that mimic those of the host birds they trick into raising cuckoo chicks. Photo by Sergey Yeliseev.

Brood parasitism, in which one bird species lays its eggs in another bird’s nest, has long been considered a likely cause of coevolution [$a] between brood parasites and their hosts, because the interaction exerts strong natural selection on both species. Hosts suffer major fitness consequences if they take on the raising of another bird’s chick—and brood parasite chicks are often bigger, and more aggressive, than their adoptive “siblings,” sometimes pushing them right out of the nest. On the other hand, brood parasites run the risk of losing their offspring to hosts who can recognize a strange egg and eject it from the nest.

One way to avoid raising a cuckoo chick is to lay eggs that look different from cuckoo eggs. Cuckoos counteract this defense by evolving eggs that match their most common hosts—a selective regime proposed to explain rapid rates of species formation in parasitic cuckoo lineages. In the new study, Yang et al. show that this pattern plays out within a single population of ashy-throated parrotbills and the cuckoos that parasitize them. At a forested nature reserve in southwestern China, the team found that parrotbills lay eggs of three different colors: white, blue, or (rarely) pale blue. Common cuckoos in the same area also laid eggs of those three colors, in about the same proportions as the parrotbills—and cuckoo eggs were usually found in host nests with eggs of the same color. Experimental introduction of eggs into parrotbill nests confirmed that parrotbills were more likely to reject eggs colored differently from their own.

That result captures many of the necessary conditions for coevolution between ashy-throated parrotbills and the local cuckoo population; the frequency with which parrotbills reject eggs unlike their own should exert strong selection on the cuckoos, and (conversely) the frequency with which parrotbills fail to reject cuckoo eggs that look like their own should exert selection on the hosts. This isn’t the first case in which brood parasites have apparently forced their hosts to diversify, however—notably, African village weaverbirds evolved less varied egg patterning after being introduced into parasite-free habitats on Mauritius and Hispaniola.

References

Krüger, O., Sorenson, M., & Davies, N. (2009). Does coevolution promote species richness in parasitic cuckoos? Proc. Royal Soc. B, 276 (1674), 3871-9 DOI: 10.1098/rspb.2009.1142

Lahti, D. (2005). Evolution of bird eggs in the absence of cuckoo parasitism. Proc. Nat. Acad. Sci. USA, 102 (50), 18057-62 DOI: 10.1073/pnas.0508930102

Rothstein, S. (1990). A model system for coevolution: Avian brood parasitism. Ann. Rev. Ecology and Systematics, 21 (1), 481-508 DOI: 10.1146/annurev.es.21.110190.002405

Yang, C., Liang, W., Cai, Y., Shi, S., Takasu, F., Møller, A., Antonov, A., Fossøy, F., Moksnes, A., Røskaft, E., & Stokke, B. (2010). Coevolution in action: Disruptive selection on egg colour in an avian brood parasite and its host. PLoS ONE, 5 (5) DOI: 10.1371/journal.pone.0010816