Category Archives: evolution

The smallest possible eye

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ResearchBlogging.orgThe eye is the original instance of “irreducible complexity,” a biological structure supposedly too complicated to have evolved by undirected mutation and natural selection. Darwin made a point to deal with the evolution of the eye in The Origin of Species. He argued that, in spite of appearances, a surprisingly complete gradation of eye complexity is seen in nature, and it’s not too hard to connect the dots. Brace for Victorian prose:

In the Articulata [Arthropods] we can commence a series with an optic nerve merely coated with pigment, and without any other mechanism; and from this low stage, numerous gradations of structure … can be shown to exist, until we reach a moderately high stage of perfection. In certain crustaceans, for instance, there is a double cornea, the inner one divided into facets, within each of which there is a lens-shaped swelling. In other crustaceans the transparent cones which are coated by pigment, and which properly act only by excluding lateral pencils of light, are convex at their upper ends and must act by convergence; and at their lower ends there seems to be an imperfect vitreous substance. With these facts … I can see no very great difficulty (not more than in the case of many other structures) in believing that natural selection has converted the simple apparatus of an optic nerve merely coated with pigment and invested by transparent membrane, into an optical instrument as perfect as is possessed by any member of the great Articulate class.

Since Darwin’s day, biologists have developed much more detailed descriptions of how eyes might have evolved [$-a] from simple light-sensitive “eyespots” all the way up to the complex structure of mammalian eyes. But we haven’t had a good description of how those original, hyper-simple eyes actually work. Light hits them, and their owner responds to it – but what’s the connection between stimulus and response?


Photo by wakima.

As part of an early kickoff for Darwin’s 200th birthday celebration next year, this week’s issue of Nature has a paper that provides the answer: eyespots directly control how their owners move [$-a]. The authors, Jékely et al., use a variety of molecular biology methods to dissect the connection between eyespots and movement in the larvae of a marine flatworm, Platynereis dumerilii. Most of the experimentation wasn’t too kind to the larvae.

Platynereis larvae are tiny spheres with belts of cilia, their only means of propulsion, and an eyespot on either side of one hemisphere. The eyespots consist of only two cells each, a pigment cell and a photoreceptor, and they seem to be useful in helping the larva move toward light sources (i.e., further up in the water column). This tendency to move toward light is called “phototaxis.”

First, the authors burned off one eyespot or the other using a laser, and showed that larvae missing both eyespots were unable to move toward light, but those missing only one were mostly able to do so. Then they cut larvae in cross sections and, under an electron microscope, traced the body of an eyespot’s photoreceptor cell – which turned out to extend all the way to the cells in the equatorial cilia. It’s as if a human’s eyes were directly connected to her legs. The authors further show, in fact, that the Platynereis larvae swim in a manner perfectly adjusted for steering by eyespots; when one spot receives light, it makes the cilia on its side beat harder, and the larva banks toward the light source.

Like evolution itself, science proceeds slowly, step by tiny, hopefully useful step. This paper is one more piece in the enormous puzzle of life on Earth – the kind of work that has moved biology as far beyond Darwin’s first conjectures as the human eye is from a flatworm’s.

References

G. Jékely, J. Colombelli, H. Hausen, K. Guy, E. Stelzer, F. Nédélec, D. Arendt (2008). Mechanism of phototaxis in marine zooplankton. Nature, 456 (7220), 395-9 DOI: 10.1038/nature07590

T. Lincoln (2008). Cell biology: Why little swimmers take turns. Nature, 456 (7220) DOI: 10.1038/456334b

Sympatric skepticism

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ResearchBlogging.orgThe new issue of The Journal of Evolutionary Biology has a great article on a question that dates back to Darwin: sympatric speciation[$-a].

Sympatric speciation is simply speciation that occurs when a species splits into two reproductively isolated groups without any physical barrier arising between those groups. It’s often treated as the opposite of allopatric speciation, in which a species is split by some external barrier (a new mountain range, a river, &c) and the separated populations evolve on different trajectories until they’re unable to exchange genes even if the barrier is removed. There are a number of ways biologists think this can happen – for instance, a population of insects using two different, co-occurring host plants, might split into two species on the different hosts – but not many good cases where we’re pretty sure that it has happened.

In the new article, Kirkpatrick and his coauthors argue that the problem is one of definition. Sympatic speciation, as a concept, is set up to be impossible to test conclusively: Although it’s easy to show that two closely-related species occupy the same territory in the present, it’s rarely possible to show that they became different species while they were occupying the same territory at some point in the past, much less that they were “panmictic,” or freely interbreeding.

The problem for empiricists is that biogeographical sympatry is relatively straightforward to diagnose, but the initial condition of panmixia specified by population genetic models is virtually impossible to test.

As an alternative, the authors suggest ignoring the Platonic ideals of “allopatric” versus “sympatric” speciation, and instead concentrating on the interaction between divergent natural selection and gene flow in causing or preventing speciation. Not only is this sensible, it’s what most evolutionary ecologists are doing right now, anyway.

Reference

B.M. Fitzpatrick, J.A. Fordyce, S. Gavrilets (2008). What, if anything, is sympatric speciation? Journal of Evolutionary Biology, 1452-9 DOI: 10.1111/j.1420-9101.2008.01611.x

Joshua tree genetics suggest coevolutionary divergence

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ResearchBlogging.orgThe latest results from the Pellmyr Lab’s ongoing study of Joshua tree and its pollinators are online as part of the new October issue of Evolution. It’s the cover article, no less. The study, whose lead author is Chris Smith (now on the faculty at Willamette University) compares patterns in the population genetics of Joshua trees and the moths that pollinate them, and shows that although the moths have become two separate species, the trees may not have followed suit [PDF].

Evolution cover
Photo by Chris Smith.

Female yucca moths carry pollen between Joshua tree flowers in special mouthparts. When she arrives at a new flower, the female moth lays her eggs inside it, then deliberately applies pollen to the flower’s receptive surface. When the fertilized flower develops into a fruit, the moth eggs hatch, and the larvae eat some of the seeds inside the fruit.

Among the yuccas, Joshua trees are unique because they’re pollinated by two species of moths, which are each other’s closest evolutionary relative. One species is found in the eastern part of Joshua tree’s range, the other in the west. Joshua trees from the east and west have differently-shaped flowers [PDF], which is consistent with the hypothesis that coevolution between moths and trees has driven both toward an evolutionary split.

“Western” Joshua trees at Joshua Tree National Park. Photo by me.

The new study goes deeper to look at genetic relationships between different populations of the moths and the trees, and what it finds isn’t as tidy as the earlier work might suggest: While Joshua trees’ morphology corresponds nicely to the split in the pollinators, the patterns visible in their chloroplast DNA does not. In some populations, trees look “eastern,” but have chloroplast DNA more closely related to “western” populations. This suggests that, although the moths have become separate species, they’re still moving between the two kinds of Joshua tree frequently enough that the trees haven’t quite split. Why do the two tree types look different, then? One possibility is coevolution with the two moth species, which might exert selection the trees in different ways.

There’s still a lot of work to do before we fully understand what’s going on here. Will Godsoe, the other doctoral student in our lab, is doing some intensive niche modeling to see how much environmental differences might be contributing to the patterns we see here. My own dissertation will look at whether the same incongruities turn up in nuclear DNA, which can have a different evolutionary history than that in the chloroplast.

References

W. Godsoe, J.B. Yoder, C.I. Smith, O. Pellmyr (2008). Coevolution and Divergence in the Joshua Tree/Yucca Moth Mutualism The American Naturalist, 171 (6), 816-23 DOI: 10.1086/587757

C.I. Smith, W.K.W. Godsoe, S. Tank, J.B. Yoder, O. Pellmyr (2008). Distinguishing coevolution from covicariance in an obligate pollination mutualism: asynchronous divergence in Joshua tree and its pollinators. Evolution, 62 (10), 2676-87 DOI: 10.1111/j.1558-5646.2008.00500.x

Ecological differences divide Mimulus guttatus

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ResearchBlogging.orgReproductive isolation is the engine of evolutionary diversification. When two populations become unable to exchange genes, they’re effectively separate species, free to evolve on independent trajectories.

Biologists have documented many examples of reproductive isolation arising from all sorts of different interactions between organisms and their environments, including incompatibilities between gametes, adaptation to different pollinators (in plants), or the evolution of different sexual characteristics. The cover article for this month’s issue of Evolution describes another way reproductive isolation can arise – adaptation to different environments.


Mimulus guttatus
Photo by Dawn Endico.

The new paper, by Lowry et al., describes how different ecological conditions create reproductive isolation where there would otherwise be none [$-a]. The wildflower Mimulus guttatus grows all along the U.S. Pacific Coast. Some Mimulus populations grow inland, in coastal mountains, where the summers are hot and dry; others grow right on the coast, where fog provides moisture but plants have to tolerate salt spray from the sea. Plants from inland and coastal populations look quite different (inland = tall with big flowers; coastal = short with small flowers), and have previously been separated out into different subspecies. But are they actually isolated?

Lowry et al. found that inland and coastal plants perform poorly when transplanted to the others’ habitats, and that they flower at significantly different times. A population genetic analysis shows that the coastal and inland populations don’t exchange genes very often. But it’s possible to hybridize the two types in the greenhouse. In short, it looks like Mimulus is a case of what Nosil et al. called “immigrant inviability” [$-a]. Immigration between inland and coastal sites may be possible, and immigrants would (theoretically) be able to reproduce if they mated with plants from the local population – but before they get a chance, they’re nailed by summer drought (at inland sites) or salt spray (at coastal sites). So even before they’ve evolved fundamental incompatibilities, these two types of Mimulus are well on their way to being separate species.

References

D.B. Lowry, R.C. Rockwood, J.H. Willis (2008). Ecological reproductive isolation of coast and inland races of Mimulus guttatus. Evolution, 62 (9), 2196-214 DOI: 10.1111/j.1558-5646.2008.00457.x

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

DNA barcoding: A glitch in the system?

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ResearchBlogging.orgFollowing up on last week’s post about uncovering hidden species using DNA diversity (or “DNA barcoding”), an open-access paper in this week’s issue of PNAS demonstrates a potentially significant glitch in the system: mitochondrial pseudogenes.

The original DNA barcoding concept is straightforward, if not uncontroversial – use a standard DNA sequence marker to identify (“barcode”) species that might be challenging to ID otherwise, or previously not known as separate species. The proposed standard marker is a mitochondrial gene that codes for the protein cytochrome oxidase I (COI), which varies quite a bit between animal species (though it wouldn’t work for plants, whose mitochondrial DNA mutates very rarely). The lab where I work has used COI for a lot of studies in yucca moths, though not barcoding per se.


Photo by fabbio.

One potential problem with barcoding is that sequencing any gene in one species using procedures derived from another species is always a bit risky. DNA sequencing relies on primers, short snippets of DNA that bind to a region near the target gene as part of the reaction that makes lots of copies of that gene for analysis (this is called PCR, for polymerase chain reaction). The easiest way to get sequence data for a new species is to try and use primers from a close relative – if there aren’t any mutations at the primer site, they should carry over. But mutation happens, and it can definitely happen at primer sites.

Primer site mutations are a minor problem compared to pseudogenes, the focus of the new paper by Song et al. Pseudogenes are a result of gene duplication, a mutation in which an extra copy of a gene is accidentally created during DNA replication. Because it’s redundant, the extra copy can absorb mutations that destroy its function without harming individuals who carry it. The duplicate is then “junk DNA,” free to accumulate mutations – a pseudogene. (Gene duplication is also one way that new proteins and gene functions can evolve – but that’s beyond the scope of the present post.) A primer site mutation just means that primers from one species won’t work on another, but a pseudogene might still bind to primers. And then you can get sequence data from the pseudogene instead of the target gene.

DNA barcoding identifies species based on how many mutations have accumulated since they split from a common ancestor; a pseudogene, which mutates faster, can make two samples look further apart then than they are. So barcoding studies that accidentally use pseudogenes may identify two species where only one exists. Song et al. use data on mitochondrial pseudogenes in insects and crustaceans to argue that pseudogenes are both common and unpredictable. They also perform barcoding on grasshoppers and crustaceans using data “contaminated” with pseudogenes and data without – unsurprisingly, pseudogenes inflated the number of species detected by barcoding. Although Song et al. suggest a few ways to reduce the odds of interference from pseudogenes, they conclude that there is no way to completely eliminate this problem.

Last week’s paper by Smith and colleagues showed the importance of species identification for conservationists, ecologists, and evolutionary biologists. This new result suggests that DNA barcoding may not be the best way to identify species.

References

P.D.N. Hebert, A. Cywinska, S.L. Ball, J.R. deWaard (2003). Biological identifications through DNA barcodes Proc. Royal Society B, 270 (1512), 313-21 DOI: 10.1098/rspb.2002.2218

H. Song, J.E. Buhay, M.F. Whiting, K.A. Crandall (2008). Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified PNAS, 105 (36), 13486-91 DOI: 10.1073/pnas.0803076105

Birds converge on flightlessness

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ResearchBlogging.orgWhen two organisms evolve in similar ways independently, we call it convergent evolution. Classical examples include the fish-like shape of whales and the separate evolution of flight by both bats and birds. Now, in this week’s PNAS, a (huge) group of scientists report that ratites, the group of flightless birds including emus, ostriches, rheas, cassowaries, and kiwis, lost the ability to fly at least three separate times in their evolutionary history [$-a].


Photo by Morti Riuuallon.

The key question this paper addresses is whether ratites are all the descendants of a single common ancestor (a “monophyletic” grouping) – if they are, then chances are that flightlessness only evolved once, and in that ancestor. The new paper’s authors use a large DNA sequence data set to show that that tinamous, the group of flying birds most closely related to ratites, actually arose within the monophyletic group of the ratites. This makes the ratites polyphyletic, not monophyletic. Since the next-most-closely related birds fly, and it’s probably easier to lose the ability to fly than it is to regain it, this suggests that the common ancestor of the ratite-tinamou group could fly, and that ratites probably lost the ability to fly multiple times.

Reference

J. Harshman, E.L. Braun, M.J. Braun, C.J. Huddleston, R.C.K. Bowie, J.L. Chojnowski, S.J. Hackett, K.-L. Han, R.T. Kimball, B.D. Marks, K.J. Miglia, W.S. Moore, S. Reddy, F.H. Sheldon, D.W. Steadman, S.J. Steppan, C.C. Witt, T. Yuri (2008). Phylogenomic evidence for multiple losses of flight in ratite birds PNAS, 105 (36), 13462-7 DOI: 10.1073/pnas.0803242105

Blessed be Darwin

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The Onion reports: Evolutionists flock to Darwin-shaped wall stain.

Since witnesses first reported the unexplained marking—which appears to resemble a 19th-century male figure with a high forehead and large beard—this normally quiet town has become a hotbed of biological zealotry. Thousands of pilgrims from as far away as Berkeley’s paleoanthropology department have flocked to the site to lay wreaths of flowers, light devotional candles, read aloud from Darwin’s works, and otherwise pay homage to the mysterious blue-green stain.

Stop trying to overturn the Modern Synthesis

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There’s a great letter in this week’s Science, which points out the absurdity of talking about new “theories” of evolution [$$]. Writing in response to a recent “news focus” article on the subject [$-a], U. Kutschera argues that, because it is such an interdisciplinary field, modern evolutionary biology isn’t supplanted by new ideas of how life changes over time, but instead absorbs them into its broad synthesis.

Reference

U. Kutschera (2008). From darwinism to evolutionary biology Science, 321, 1157-8 DOI: 10.1126/science.321.5893.1157

Magpie, know thyself

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Photo by p_adermark.

New in PLoS Biology: European Magpies can recognize their own reflection in a mirror. Self-recognition in a mirror is used as a test of self-awareness in non-human animals, so this suggests that magpies, and maybe other birds, are conscious of themselves as separate from other members of their species.

To see if a magpie knew that a reflection in a mirror was an image of itself, the study’s authors glued a colored paper spot to the feathers below a magpie’s “chin”, then allowed the bird to see itself in a mirror. The magpie would have no way of seeing the spot except in the mirror, so if it reacted to the mirror image by trying to remove the mark from itself, it can be said to have recognized its own reflection. (And, presumably, thought something like “What the heck is this on my chin?”)

The supplementary materials for the paper include a number of videos of the test in action: here’s a magpie reaching for the mark with its foot [.wmv file], and here’s one using its beak [.wmv file]. Black spots, which wouldn’t be visible against the birds’ black chin-feathers, served as a control.

This is the first time that a non-mammal has been shown to be self-aware, and (in this one regard, anyway) it means magpies are smarter than monkeys. (Great apes recognize themselves in mirror tests; monkeys don’t.) It’s also more evidence that what we think of as consciousness, that nebulous quality that separates humans from the rest of the animal kingdom, isn’t as clear-cut as we used to think. Human intelligence most likely evolved by the incremental assembly of different mental skills – including self-awareness, but also tool use and language – that we see in other smart animals.

Reference

Helmut Prior, Ariane Schwarz, Onur Güntürkün, Frans de Waal (2008). Mirror-Induced Behavior in the Magpie (Pica pica): Evidence of Self-Recognition PLoS Biology, 6 (8) DOI: 10.1371/journal.pbio.0060202

Against specialist herbivores, plants give up

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Plants put up with a lot – everyone wants to eat them! And, basically, there are two ways a plant might respond to being eaten. They can put energy into regrowing bits that get eaten, or they can put energy into making a lot of some nasty chemical, like the milky sap in milkweed. The trouble with the first option is obvious – it doesn’t do anything to stop the damage. But the trouble with the second is that, whenever plants evolve a new defensive strategy, herbivores evolve a way around it. Often, these herbivores do very well, because they can eat something no one else can – and they become specialists on their new favorite food.


Photo by Melete.

Evolutionary ecologists have been thinking about this plant-herbivore arms race ever since Darwin. Back in 1964, Paul Erhlich and Peter Raven proposed that plants and insects might go through alternating cycles of diversification [$-a] driven by the evolution of new plant defenses and insect counterdefenses. Now, in a new paper in last week’s PNAS, Anurag A. Agrawal (who is at the top of everyone’s reference list) and Mark Fishbein show that sometimes, plants just throw in the towel [$-a].

Agrawal and Fishbein examine the evolutionary history of milkweed, which has a number of interesting anti-herbivore defenses besides the eponymous sap – and a number of specialized herbivores, like the red milkweed beetle pictured here. Their analysis looks for long-term evolutionary trends in the degree to which milkweeds put their energy into defenses, and the degree to which they put energy into regrowth. Over evolutionary time, it seems that milkweeds have reduced their defenses, and increased their regrowth efforts.

References

A. A. Agrawal, M. Fishbein (2008). Phylogenetic escalation and decline of plant defense strategies PNAS, 105 (29), 10057-10060 DOI: 10.1073/pnas.0802368105

P.R. Ehrlich, P.H. Raven (1964). Butterflies and plants: A study in coevolution Evolution, 18 (4), 586-608