Tag Archives: Research Blogging

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

Christ Church as it is: Creationist Credentials

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A couple of weeks ago, I introduced Christ Church, Moscow, Idaho’s friendly neighborhood theocracy-in-embryo, which weds garden-variety Christian Right hypocrisy with creepy, racist Neo-Confederate overtones. Today, I’m going to have a look at the Christ Church-affiliated New Saint Andrews College.

NSA cultivates a reputation as the ivory tower’s ivory tower – the curriculum includes lots of Classical studies, including Greek and Latin; the school’s vision statement puts much emphasis on the supremacy of Western Culture (or “Traditio occidentalis“). Zombie C.S. Lewis could totally be a member of the faculty, if he were into theocratic fundamentalism. Said faculty are all wearing Scholarly Robes in the group photo.


The original ivory tower is at the
University of Pittsburgh
Photo by Jeremy B. Yoder.

There’s nothing wrong with focusing on classical studies. NSA’s air of musty erudition has attracted a mostly positive profile by the New York Times Magazine and a favorable rating from the conservative Intercollegiate Studies Institute. (Full disclosure: my alma mater, Eastern Mennonite University, was also recognized by ISI.)

But, basically by their own admission, Christ Church’s theology is strongly right-wing. Is NSA’s ivory tower secure against the ideology of the church that founded it? The evidence is, not so much. NSA’s Code of Conduct sounds all sorts of alarm bells:

“The College seeks to recover true academic freedom, that is, submission to God’s Word in all our actions and attitudes in and out of the classroom.

As does the NSA Students’ Pledge:

I pledge to maintain sound Christian doctrine, to regularly attend an orthodox church, and to maintain a teachable spirit. I pledge to abstain from actively promoting doctrines contrary to the mission and goals of the College.

Who decides what is “God’s Word” and “sound Christian doctrine?” Conveniently, Doug Wilson, the pastor of Christ Church, is both a Board of Trustees member and a “Senior Fellow” at NSA. In fact, of seventeen faculty members, three are Wilsons. That’s DW, his son (if I’m not mistaken) Nathan, and brother Gordon.

Gordon L. Wilson, the “Senior Fellow of Natural Philosophy,” is actually my closest contact to NSA. Last fall I attended a debate on the topic of intelligent design between GLW and Washington State University biologist Mike Webster. It wasn’t pretty. GLW, who is basically miles to the right of Michael Behe, didn’t make a very good impression on behalf of NSA’s high-minded curriculum in rhetoric and philosophy – he dodged questions, failed to support his assertions, and generally displayed an inability (or unwillingness) to comprehend the logical underpinnings of the Scientific Method. In a particularly telling moment, he asserted that the reason ID/Creationists haven’t developed any testable hypotheses is because biased funding agencies won’t give them money.

That, of course, is laughable to anyone who does science for a living (i.e., a sizable chunk of GLW’s audience), because no one gets grant funding to develop hypotheses. Funding requests are descriptions of how you will test a hypothesis through a specific program of experiments or data collection. In other words, scientists receive funding after they develop hypotheses and convince funding agencies that they have a good way to test them.


The Eastern Box Turtle,
Terrapene carolina
Photo by West Virgina Blue.

It’s entirely possible that Gordon Wilson doesn’t actually know how scientific funding works. Which is consistent with the hypothesis that he’s more interested in adhering to his concept of “sound Christian doctrine” than doing science. The only published peer-reviewed research NSA’s Senior Fellow of Natural Philosophy has produced is a 2005 paper on the breeding ecology of box turtles [$-a]. (GLW’s NSA profile also mentions published “research, field notes, and abstracts,” but this is the only paper that comes up in a Google Scholar search.) It’s basically a census, although there are some t-tests. And it was funded not by an outside grant, but by what seems to be a donation from the biology department where GLW was an instructor when he did the study. Here’s the only mention of funding in the Acknowledgments section:

We would like to thank Paul Sattler (Chair) for allocating Liberty University Biology funds for the purchase of much of the field equipment necessary for this study.

To put this in perspective: I’m now a fourth-year doctoral student, and I’m not nearly to the point of having enough published work on my CV to say I’ve earned my doctorate yet, much less apply for a faculty position at a good university. I’ve personally written (as near as I can recall) four major grant requests, and contributed to a fifth; I’m a coauthor on a review article, one published original research article [$-a], and a third in press; I’m a coauthor on two more articles that are submitted for review, and I’m waiting for my first first-authored paper to go out to reviewers. And (what the heck) I’ve been published in the letters column of Science. Let me repeat: my pubs list is piddly. But it’s bigger than Gordon Wilson’s, and he’s somehow on the faculty at NSA. With the word “senior” in his title.

NSA might have a bang-up program as far as Latin studies go, but its resident “biologist” is clearly more interested in ideology than biology. I can’t say that bodes well for the “intellectual rigor” of the rest of the curriculum.

Edit, 7 Sept. 2008:
Added a couple of links to the NSA faculty pages in references to Doug Wilson’s positions at NSA and the number of Wilsons on the faculty.

Correction, 9 Sept. 2008:
Corrected the relationships between the Wilsons on the NSA faculty.

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

R. Gomulkiewicz, D.M. Drown, M.F. Dybdahl, W. Godsoe, S.L. Nuismer, K.M. Pepin, B.J. Ridenhour, C.I. Smith, J.B. Yoder (2007). Dos and don’ts of testing the geographic mosaic theory of coevolution Heredity, 98 (5), 249-58 DOI: 10.1038/sj.hdy.6800949

G.L. Wilson, C.H. Ernst (2005). Reproductive Ecology of the Terrapene carolina carolina (Eastern Box Turtle) in Central Virginia Southeastern Naturalist, 4 (4) DOI: 10.1656/1528-7092(2005)004[0689:REOTTC]2.0.CO;2

J.B. Yoder, B. Shneiderman (2008). Science 2.0: Not So New? Science, 320 (5881), 1290-1 DOI: 10.1126/science.320.5881.1290

Species hiding in plain sight

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ResearchBlogging.orgIt’s a truism that biologists have cataloged only a fraction of the living things on Earth. This is a major problem for conservationists, ecologists, and evolutionary biologists, because many of the questions we want to answer (“Which parcel of rain forest should we preserve?” or “How do species interactions play out over millions of years?”) hinge how we count species.

One solution is DNA barcoding, which uses the evolutionary divergence encoded in DNA sequences to tell species apart [$-a]. Barcoding is supposed to help researchers identify species without being experts in the fiddly business of taxonomy based on physical traits. It can also differentiate species that might never be recognized as separate without a DNA analysis.


Caterpillar with braconid pupae
Photo by Anita Gould.

An open-access article in last week’s PNAS does exactly that for a group of wasps in the family Braconidae. Braconid wasps are parasitoids, laying their eggs in live hosts. Eventually the eggs hatch and the larvae eat their host alive, then emerge to form pupae like those on the Hog Sphinx Moth caterpillar in the photo. (Insert obligatory reference to Alien here.)

Parasitoid wasps are thought to be hugely diverse, in part because coevolutionary interactions between larvae and their hosts’ immune systems might force each wasp species to specialize on one or a few hosts. Smith and coauthors use barcoding based on nuclear and mitochondrial DNA to determine the diversity of braconid wasps within a Costa Rican conservation area, comparing the results to those produced from a traditional taxonomic survey. Traditional methods found 171 potential species – and barcoding turned up another 142! These additional species were basically identical to the eye, but in many cases they’re actually collections of similar species using different hosts.

So not only are there more wasp species than traditional methods would detect – they’re more specialized than we’d know without barcoding. DNA Barcoding can make some biologists (including me) a little squeamish; it’s worrying to picture a world where no one really knows the organisms they study except through DNA sequence data. But Smith et al. are applying the method to find diversity that would probably not be detected in any other way, with results that bear directly on how we think about the interactions between parasitoids and their hosts. That’s unquestionably a good thing.

References

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

M.A. Smith, J.J. Rodriguez, J.B. Whitfield, A.R. Deans, D.H. Janzen, W. Hallwachs, P.D.N. Hebert (2008). Extreme diversity of tropical parasitoid wasps exposed by iterative integration of natural history, DNA barcoding, morphology, and collections PNAS, 105 (34), 12359-64 DOI: 10.1073/pnas.0805319105

Big herbivores shape plant community response to global warming

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ResearchBlogging.orgThe cover article from this week’s PNAS has important implications for how we plan for, and deal with, climate change. Post and Pedersen report that the way an arctic plant community changes in response to warming depends heavily on the presence of large herbivores [$-a], like muskoxen and caribou.


Photo by Giant Ginkgo.

Previously, it was thought that one effect of global climate change would be for woody shrubs and dwarf trees to become more common in arctic and subarctic plant communities. This increase in woody plants could trap more atmospheric carbon and increase the albedo of the land – meaning more heat could be reflected back into space. Both of which effects might help slow a warming global climate.

However, Post and Pedersen show that large herbivores can reduce this shift in community composition. In huge five-year study, they set up experimental plots from which caribou and muskoxen were either excluded by fencing, or not excluded. Within each class of plot, they also placed 1.5-m “open-topped chambers” (OTCs) made of fiberglass – basically, cylinders that help trap solar heat, warming the ground inside. In the fenced plots, the plant communities inside the OTCs shifted toward more woody species; but in the unfenced plots, where large herbivores could reach in and graze inside the warmed cylinders, plant communities didn’t develop greater cover by woody species.

Now, it’s not surprising that large herbivores can have a profound effect on the plant species that grow in their grazing land. Where I come from, in the northeast U.S., large swaths of forest have been dramatically altered [$-a] by a population explosion of white-tailed deer freed from their natural predators. But Post and Pedersen have drawn a connection between this effect and the ways in which natural communities may respond to the most dramatic environmental change in human history. It just goes to show what a massively complex system we humans are tinkering with, and how little we know about what that tinkering may ultimately do.

References

E. Post, C. Pedersen (2008). Opposing plant community responses to warming with and without herbivores PNAS, 105 (34), 12353-8 DOI: 10.1073/pnas.0802421105

F.L. Russell, D.B. Zippin, N.L. Fowler (2001). Effects of white-tailed deer (Odocoileus virginianus) on plants, plant populations and communities: A review The American Midland Naturalist, 146 (1), 1-26 DOI: 10.1674/0003-0031(2001)146[0001:EOWTDO]2.0.CO;2

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