Category Archives: science

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

Blogging research

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ResearchBlogging.orgWondering what’s with these check-mark icons that have started popping up on my posts? They’re part of my new membership in the Research Blogging community, which aggregates ‘blog posts about peer-reviewed scientific literature.

Members use the Research Blogging online tool to create citations for papers they’re blogging about, and they copy the citation code into the relevant post to create a stylish reference list. The citation code includes tags that are picked up by Research Blogging’s web crawler, which then links the page containing the citation to Research Blogging’s relevant topic pages (such as biology) and RSS feed. Posts that I submit to Research Blogging will also be marked with the aggregator’s icon, so someone arriving directly at Denim & Tweed can quickly scan for posts about peer-reviewed papers. It’s a great way to find out what other science bloggers are reading, and it’s boosted my traffic to values that are statistically distinguishable from zero. If you like reading about science, or if you blog about it, Research Blogging is extremely useful.

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.

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

The evolution of offspring size

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ResearchBlogging.orgThe question of offspring size – that is, how big a child is relative to its parent – can seem downright absurd. In fact, it was the subject of the only paper (to my knowledge) ever published in the journal Evolution that ends with a punch line. That piece, written by Ellstrand in 1983, pretended to seriously address the question of why juveniles are smaller than their parents [$-a]. It was basically pointing out the absurdity of assuming that every trait we observe in a living organism has evolved adaptively, or specifically because natural selection favors it. Clearly, not all traits are adaptive – juveniles are smaller than their parents because, universally, a child has to emerge from its mother. It’s a basic fact of the conservation of mass-energy.


Photo by TIO….

On the other hand, the size of a child as a proportion of its mother’s body size varies tremendously in the natural world. Mushrooms release nearly-invisible spores, while kiwis lay eggs equal to a quarter of their body mass. There seem to be clear benefits to making bigger offspring – they should be better competitors against their peers, they may be more likely to survive to reproduce, and they may reach reproductive maturity faster. But there are also costs, in terms of the energy a parent uses to either produce an egg with a bigger yolk, or to provision a bigger embryo in the uterus, or to feed a juvenile in the nest.

The classic description of this trade-off is a mathematical model developed by Smith and Fretwell in 1974 [$-a]. But the Smith-Fretwell model doesn’t explain the wide variety of offspring sizes we see in nature, especially among species that seem to have more or less the same ecological requirements. In the current issue of The American Naturalist, Falster et al. propose an extension of Smith-Fretwell to better capture this variation, which follows juveniles from the moment they leave their parents, through a phase of establishment and growth, and then through a period of competition with their peers. Which juveniles survive to adulthood is determined by body size – in the final period of competition, big individuals win.

Falster et al. then use the parameters of the model – adult body size, total adult lifespan, and energy used for reproduction – to predict juvenile body sizes for mammals and plants. The model seems to predict the relationship between parental size and offspring size pretty well for mammals, not so much for plants. Which is actually not all that surprising. In mammals, adult and juvenile body sizes probably have a lot less “wiggle room” relative to each other; but adult plants can be multiple orders of magnitude bigger than the seeds they produce. So there’s just a lot more variation to try and explain in plants than there is in mammals.

References

N.C. Ellstrand (1983). Why are juveniles smaller than their parents? Evolution, 37, 1091-4 URL: http://www.jstor.org/pss/2408423

D.S. Falster, A.T. Moles, M.Westoby (2008). A General Model for the Scaling of Offspring Size and Adult Size. The American Naturalist, 172 (3), 299-317 DOI: 10.1086/589889

C.C. Smith, S.D. Fretwell (1974). The optimal balance between size and number of offspring The American Naturalist, 108, 499-506 URL: http://www.jstor.org/stable/2459681

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

So that’s why my front door is covered in beak scratches …

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New York Times: University of Washington scientists have shown that crows can recognize individual humans. Regrettably, I see no reference to the peer-reviewed publication.

How the chili got its hots

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In this week’s PNAS: capsaicin, the stuff that makes chili peppers hot, may have originally evolved as an anti-fungal agent [$-a].


Photo by bleu celt.

Tewksbury et al. examine variation in “pungency” (that is, concentration of capsaicin) in wild populations of the chili Capsicum chacoense and compare it to rates of fungal infection in the fruit. The result is interesting, and not necessarily clear-cut: more-pungent fruits are less frequently attacked by an assortment of true bugs, and when these bugs attack, they can introduce fungal spores into the fruit, which ultimately destroys the seeds inside. So more pungency means less bug damage, and lower rates of fungal infection, and potentially more seeds.

But the story of chili pungency is more complicated than that. Back in 2001, Tewksbury and Nabhan showed that capsaicin helps ensure that chilis are eaten by birds instead of mammals [$-a]. Birds make good seed dispersers – they eat a fruit, then, um, pass the seeds on undigested; mammals, on the other hand, like to eat the seeds specifically. Capsaicin irritates mammals, but doesn’t bother birds.

To complicate things still further, there’s a downside to producing capsaicin. In this January’s issue of the journal Ecology, Tewksbury and his coauthors showed that Capsicum chacoense seeds from more-pungent fruits also had thinner seed coats, which meant they were more likely to suffer damage in birds’ digestive tracts [$-a].

So why are chilies spicy? The answer is, probably for all these reasons, and maybe more that haven’t been discovered yet. This is a common situation in evolutionary biology – in many organisms, the traits that scientists find interesting may be useful in several different ways, and unhelpful in others. Very few traits experience natural selection in only one direction, as it turns out. The traits that we observe in nature are usually compromises between many different, sometimes directly conflicting, sources of natural selection.

References

J. J. Tewksbury, D. J. Levey, M. Huizinga, D. C. Haak, A. Traveset (2008). Costs and benefits of capsaicin-mediated control of gut retention in dispersers of wild chilies Ecology, 89 (1), 107-17 DOI: 10.1890/07-0445.1

J. J. Tewksbury, G. P. Nabhan (2001). Seed dispersal: Directed deterrence by capsaicin in chilies. Nature, 412 (6845), 403-4 DOI: 10.1038/35086653

J. J. Tewksbury, K. M. Reagan, N. J. Machnicki, T. A. Carlo, D. C. Haak, A. L. C. Penaloza, D. J. Levey (2008). Evolutionary ecology of pungency in wild chilies PNAS, 105 (33), 11808-11 DOI: 10.1073/pnas.0802691105