March 20, 2009

No butterflies were harmed by this research

With a species using cryptic resemblance [camouflage] for its protection, the very existence of neighbours involves a danger to the individual, since the discovery of one by a predator will be a step in teaching it to recognize the crypsis. With an aposematic [bad-tasting, warning-coloration] species, on the other hand, the existence of neighbours is an asset, since they may well serve to teach an inexperienced predator the warning pattern. -- William Hamilton, 1964
This week's paper describes research that could have been a winning science fair project. "Does colour polymorphism enhance survival of prey populations?", published online by Lena Wennersten and Anders Forsman in Proceedings of the Royal Society, helps answer an interesting evolutionary question, using materials available in many kitchens.

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January 30, 2009

Inferring details of past evolution from DNA is tricky

Last week I discussed one of many papers that use the ratio of protein-changing to "neutral" genetic changes, along the branches of an evolutionary tree, to infer past natural selection. This week's paper presents data calling that approach into question. This does not necessarily undermine the overall conclusions of last week's paper, which were based on a variety of methods, including testing the actual performance of mutant proteins.

"Hotspots of biased nuclear substitutions in human genes" was published in PLoS Biology by Jonas Berglund and colleagues. I am not a molecular biologist, so will just summarize their main points. The paper is open access.

Most of our DNA does not code for proteins. Some of the noncoding DNA is known to have important regulatory functions. But there is lots of DNA whose function, if any, is unknown, but which is nonetheless highly similar among species, as if any change was lethal. Except, when someone tried deleting this DNA, a bit at a time, most of the deletions were not lethal or even (as far as they could tell) harmful. I discussed this work earlier.

Anyway, much of this noncoding DNA that differs little among most species is different in humans. Could these differences be what makes us different from other apes? Quite possibly. But are all these human-vs.-chimp differences important? Maybe not. An unexpectedly high fraction of the changes from the ape ancestor we share with chimps involved a change from A bound to T (a weak bond) to G bound to C (a strong bond). Unless noncoding DNA with stronger bonds is consistently better somehow (and only in humans!), this suggests that these changes are caused by some DNA-specific process and not by natural selection. In other words, these changes occurred whether or not they were beneficial, just as mutations do. Could similar AT=>GC changes have changed protein-coding sections of DNA?

The researchers compared 10,238 genes in humans, chimps, and macaques...

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January 23, 2009

Staying ahead in the evolutionary arms race with viruses

This week's paper uses molecular methods to reveal new details of the evolutionary arms race between primates, including humans, and viruses. "Protein kinase R reveals an evolutionary model for defeating viral mimicry" was published in Nature by Nels Elde and colleagues in Seattle.

Protein kinase R (PKR) is an important defense against viruses in many species, from humans to yeast. When it detects a virus inside a cell, it activates eIF2-alpha, which shuts down protein production in that cell. With protein production blocked, the virus can't replicate and spread to other cells. Viruses, however, have evolved counter-measures. These include molecules that resemble eIF2-alpha. These molecular mimics interact with PKR and prevent its normal defensive activity.

Viral epidemics can be a major cause of death, so we expect populations to evolve PKR resistant to the eIF2-alpha-mimics produced by viruses. Can we find evidence of such evolution in primates?

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August 30, 2008

How does gene duplication allow evolutionary innovation?

Genes with new functions do not magically appear from nowhere, or so most scientists assume. (If I thought that evolution, perhaps especially human evolution, was being guided by some supernatural individual or group, I would be looking for such “genes from nowhere? rather than whining that theories with no evidence should get equal time. Not that they want schools to teach all theories that lack evidence, of course, just ones favored by their particular religion or short-term economic interests.)

Random duplication of existing genes is often a key step, but there are at least two different ways in which gene duplication could facilitate evolutionary innovation. Once there are two copies of a gene, one could evolve a new function without interfering with the old gene’s function. Or, a single gene could evolve two different functions, doing neither of them particularly well. Then, gene duplication would allow the two copies to evolve separately, each being optimized for a different function. This week’s paper shows that evolution has followed this second pathway at least once, and perhaps often. The paper also provides yet another example of how molecular methods are providing new details on how evolution works.

Escape from adaptive conflict after duplication in an anthocyanin pathway gene? was published in Nature by David L. des Marais – apparently not the the David J. des Marais who has published on evolution of photosynthesis – and Mark Rausher, at Duke University in North Carolina. They looked at genes whose enzyme products make pigments for flower colors.

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February 11, 2008

Ancient temperatures inferred from DNA

“Where was you hid to see all that?? he cried. “It seems to me that you knows a great deal more than you should.? – The Complete Sherlock Holmes
“Our DNA is a coded description of the worlds in which our ancestors survived. And isn’t it an arresting thought? We are digital archives of the African Pliocene, even of Devonian seas; walking repositories of wisdom out of the old days. You could spend a lifetime reading in this ancient library and die unsated by the wonder of it.? -- Richard Dawkins, Unweaving the Rainbow

Like many of the characters baffled by Sherlock Holmes, I am repeatedly amazed by the detailed inferences my fellow scientists are able to draw about events in the distant past. This week’s paper:
Palaeotemperature trend for Precambrian life inferred from resurrected proteins
is a good example. Eric Gaucher and colleagues at the University of Florida and DNA2.0 Inc. used protein sequences from a variety of modern bacteria species to infer the protein sequences of their distant and more recent ancestors…

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December 07, 2007

The ghost of infections past, present, and future

Summary: A 39-year record of host-parasite interaction, recovered from sediment layers in a pond, is consistent with rapid coevolution.
Link: Host-parasite /`Red Queen/' dynamics archived in pond sediment

As I've discussed previously, archival samples often prove useful for answering questions that weren't being asked when the samples were collected. But what if nobody collected and preserved the samples you need for your research? Maybe you can find a "natural archive" that has what you need.

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July 09, 2007

Selection beats design, again

This week's paper is "HIV-1 proviral DNA excision using an evolved recombinase" by Indrani Sarkar and others, published in Science (vol.316, p.1912). This paper is yet another example showing that selection (natural or artificial) can outperform design.

To illustrate the point, let me start with a well-known example from plant breeding. Suppose you wanted to make broccoli, starting with its ancestor, wild kale? You could cross them, identify which genetic differences are most responsible for the large edible inflorescence, and transfer those genes to the wild kale. But what if broccoli didn't exist?

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June 30, 2007

Tracing the spread of agriculture with stone-age human DNA

This week's paper is "Palaeogenetic evidence supports a dual model of Neolithic spreading into Europe" by M.L. Sampietro and others, published online in Proceedings of the Royal Society. The paper is interesting both for its findings and for its methods.

We know that agriculture spread from the Near East -- do people in Asia call this the Near West? -- to western Europe, starting around 10,000 years ago. But did this mostly involve farmers moving, or the spread of agriculture without major movement of people?

People have tried to figure out past population movements using genetic differences among modern populations, but it would help to have genetic information from people who lived thousands of years ago, as well. This is technically challenging, however...

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May 02, 2007


What did our early ancestors and related species eat? Different data seemed to give different answers. This week’s paper may have helped to solve this mystery.

Isotope data suggest that tropical grasses were a big part of the diet of the hominins Australopithecus africanus and Paranthropus robustus. These grasses have CO2-concentrating C4 photosynthesis. As a result, they have a little more of the rare carbon-13 isotope, and a little less C12, relative to most other plants. So do the fossil teeth of these early human relatives, as if they ate these grasses. But the shape of their teeth, and wear patterns, are wrong if they mostly ate grass leaves or animals that ate grass. What about roots, or underground storage organs? These are an important food for some human foragers today, especially in dry climates. If our early relatives mostly ate these “USOs?, then the isotope ratios in their teeth should be like those of other species with a similar diet. Mole rats, for example.

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