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September 4, 2009

Where do new genes come from?

When a few members of a family have a gene not found in most other members, one explanation is that the gene is newly evolved, rather than inherited from the common ancestor of that family. (The other possibility is that their ancestor had it, but most descendants lost it.)

New genes often turn out to be copies of old genes, sometimes with modifications that give them very different functions. But a paper just published in Current Biology reports "Emergence of a new gene from an intergenic region", rather than duplication of an existing gene....

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July 9, 2009

Has natural selection been asleep at the switch?

"This new forage has great insect resistance", effused a former colleague, "we just need to eliminate the toxins that keep sheep from eating it."

Genetically engineered drought-tolerant crops are introduced with great fanfare, only to disappear when they turn out to have low yield under nondrought conditions.

When natural selection falls short of perfection, it may be because "you can't get there (some desirable adaptation) from here (current genotypes)" without passing through a series of intermediate generations that would have lower fitness. Natural selection favors genotypes best-adapted to current conditions, which are not necessarily steps towards any long-term improvement.

But natural selection often seems to miss even "simple" improvements, that might be achieved by changing as little as one DNA base. Such small changes are often enough to increase or decrease expression of key genes, for example. This sort of evolutionary progress may be blocked by tradeoffs, e.g., between seed production under different conditions (e.g., wet vs. dry), or between the competitiveness of individual plants and their collective seed production.

So what are we to make of two recent papers (in Science and Nature, respectively, discussed in Science News) on extending lifespan, one using calorie restriction and the other using the antibiotic, rapamycin?

Calorie restriction has been shown to increase longevity in model species like nematode worms and mice, but this latest study shows clear benefits in monkeys. The obvious question -- at least, it was obvious to me -- is why has past natural selection given monkeys (and fruitflies, and nematodes, and mice...) appetites that make them eat more than is good for them?

At least, that seemed to be the question, until it was shown that food odors can reverse the beneficial effects of calorie restriction, at least in fruitflies and nematodes. In humans, soft drinks with artificial sweeteners turn out to be just as likely to cause "metabolic syndrome" (related to diabetes) as those with sugar. So apparently our lives can be shortened by a perception of abundance, not just by actually eating too much. What is going on here?

In this case, the evolutionary tradeoff seems to be between current and future reproduction. As discussed in last week's post, delaying reproduction usually decreases fitness (representation in the next generation, relative to others) when population is increasing, but delaying reproduction can increase fitness when population is decreasing. Calorie restriction predicts population decline, triggering physiological responses that delay reproduction and thereby increase longevity. So do bitter-tasting foods, traditionally eaten only during famines. Food odors or sweet tastes have the opposite effect, because they predict population increase.

But what about life extension by rapamycin? One known tradeoff is suppression of the immune system, so we might get longer lives only in a hypothetical germ-free environment. But could the protein target of rapamycin (TOR) also be important to reproduction? Is this yet another example of a longevity-vs.-reproduction tradeoff?

May 22, 2009

Oxytocin and the genetics of altruism

Where to publish a paper on the genetics of altruism? In an open-access journal, of course! One day after publishing the fossil primate paper that's creating so much excitement -- it's a great fossil, but too old to tell us anything about our recent ancestors, shared with other apes, or the less-recent ones shared with monkeys -- PLoS One published "The Oxytocin Receptor (OXTR) Contributes to Prosocial Fund Allocations in the Dictator Game and the Social Value Orientations Task", by Salomon Israel and colleagues. Like all papers in open-access journals, the full text is available on-line.

These researchers measured altruism in 200 students, based on how each chose to divide a pool of money with another unknown individual. Their hypothesis, based on various past studies, was that the hormone oxytocin is important for social interactions in general and for human altruism in particular. For example, Zak and colleagues showed that sniffing oxytocin made people offer a more generous split when the recipient had the chance to retaliate for a low offer (the "Ultimatum Game"), although not when there was no chance to retaliate, as in the Dictator Game used in the current study.

The researchers tested for statistically significant relations between and different variants of the oxytocin receptor gene, which codes for the protein that responds to this hormone signal in the brain, and "prosocial responses" (generosity) in the Dictator Game and a more-complex version, the SVO. Interestingly, none of the genetic differences they looked at were in the protein-coding part of the gene (orange). Most were in an intron, which would be transcribed from DNA into messenger RNA but then cut out before the mRNA is translated into protein. So I assume these genetic differences could affect how much oxytocin receptor protein is made where and when, but not the structure of the protein itself.
receptor.jpg

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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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November 3, 2008

Ook! Another librarian for Obama

With the US election imminent, I interview the Librarian of Unseen University.

TWiE: Your endorsement of Obama has created quite a stir on this planet and might help swing the election. Were you influenced by Sarah Palin's firing a librarian for refusal to censor library books or for her views on evolution?

Librarian: Ook.

TWie: OK, but she would have limited power (you know, like Cheney) unless McCain dies in the next four years. Are you worried that some Christian terrorist would assassinate him to put her in power? Or are there problems with McCain as well?

Librarian: Ook!

TWiE: A macaca? But those aren't even apes; they're...

Librarian: Ook. Ook.

TWiE: OK, OK. Moving on to another topic, are you supporting anyone for Patrician?

Librarian: Eek. Ook.

TWiE: OK, thanks for your time. I did have a few more questions, but good luck straightening out Wall Street.

September 26, 2008

Social intelligence

The other day, my brother was telling me about playing mandolin on songs he didn't know, with a band he'd just met. Then there are people who can play several chess games at once or write crossword puzzles for the New York Times. How did humans get so smart? Over most of our evolutionary history, mandolin players and crossword writers probably had a hard time making a living.

This week's paper tests the hypothesis that natural selection favored intelligence largely because it was important in social interactions. If that's true, then species that interact with more different individuals should evolve greater intelligence. Federica Amici and colleagues tested this hypothesis using apes and monkeys and reported their results in Current Biology. Their paper is titled "Fission-fusion dynamics, behavioral flexibility, and inhibitory control in primates."

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September 6, 2008

Brief note on thumbs and junk DNA

I was going to write about this paper about a gene that evolved rapidly in humans since our lineage split from that leading to chimps. But Ed Yong at Not Exactly Rocket Science has already done a great post on it, including a picture showing its likely link to thumbs.

Comments on Ed's blog and a more complete treatment on Carl Zimmer's "The Loom" (both favorites of mine) point out the fallacy of some popular press coverage claiming this is the first evidence that "junk DNA" isn't junk after all. They both make the important point that we've known for decades that some DNA that doesn't code for protein is nonetheless very important.

On the other hand, lots of our DNA really does seem to be junk. Much of it is the product of "jumping genes" that copy themselves and insert themselves into existing DNA. These are common because they copy themselves, not because they do us any good (although, just by chance, they may occasionally be beneficial).

About 5% of DNA that doesn't code for protein is nonetheless "highly conserved", as if it were somehow beneficial and therefore maintained by natural selection. But a paper I reviewed earlier showed that much of this conserved noncoding DNA can be deleted without apparent ill effects. So if it's beneficial, it's not very beneficial. Or maybe it's beneficial only under special circumstances.

August 21, 2008

The bird in the mirror

This week’s paper is “Mirror-induced behavior in the magpie (Pica pica): evidence of self-recognition?, by Helmut Prior and colleagues, available online in PLoS Biology.

When confronted with mirrors, apes (including humans) react very differently from monkeys. Monkeys never seem to recognize that they are seeing a reflection of themselves rather than another monkey. Recently, dolphins and elephants have been added to the list of species that can recognize themselves in mirrors and use them for self-exploration. Most other species can not. Is this because their brains are too small? Or is the tendency to self-exploration using a mirror a side-effect of a mental ability that evolved for other reasons? If the latter is true (even if there is also some minimum brain size requirement), then more species that need to pay more attention to what others of their species are doing might be more likely to evolve this mental ability.

Some birds, for example, hide food, raid each other’s food caches, and pay attention to who was around when they were hiding food. How do these birds respond to mirrors?

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May 3, 2008

Sharing diseases with relatives and neighbors

Not enough people voted on the Reader’s Choice, so this week’s paper is “Phylogeny and geography predict pathogen community similarity in wild primates and humans� by Jonathan Davies and Amy Pedersen, published in Proceedings of the Royal Society.

Many humans diseases, from flu to AIDS, come from other species. Similarly, diseases from dogs are an increasing threat to lions, while cat diseases kill sea otters. Are there general rules that predict how likely two species are to share diseases?

To find out, the authors analyzed several large data sets on diseases of humans and 117 other species of primate (apes, monkeys, etc.). They hypothesized that species are more likely to share diseases if they live near each other and/or if they are more closely related, that is if they share a more recent common ancestor. This is similar to how we define relatedness in humans: brothers and sisters have more recent common ancestors (parents) than cousins do (grandparents). Fortunately, the family tree for primates is relatively uncontroversial, at least among scientists.

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April 19, 2008

Separate vacations and other sexual differences

Three recent papers in Proceedings of the Royal Society discuss differences between males and females or, in one case, among males.

“The costs of risky male behaviour: sex differences in seasonal survival in a small sexually monomorphic primate� by Cornelia Kraus and others, is based on a 10-year study of differences between male and female behavior in grey mouse lemurs. During the breeding season, males had lower survival than females, despite any possible risks associated with pregnancy or raising young. The higher risk for males apparently resulted from their tendency to travel more, looking for females.

The sexes also differ in winter behavior: females hibernate, while males remain active. Is there something about female physiology that makes hibernation healthier for them than it would be for males? Maybe, but there was no difference in winter survival between the sexes, which don’t differ much in size in this lemur species. The authors suggest that hibernation might have longer-term benefits in females, such as increased lifespan, whereas males need to stay active to bulk up in preparation for the breeding season.

This paper reminded me of an earlier paper on albatrosses, in which "in each pair, the male spent the winter just north of the pack ice in Antarctic waters whereas the female stayed south of Madagascar." It’s not hard to understand why males and females might differ in various ways (size, color, etc.) but differences in behavior outside of the breeding season are more interesting.

The second paper addresses an old argument between Charles Darwin and Alfred Russel Wallace, who developed similar explanations of evolution by natural selection at about the same time.

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November 2, 2007

When did social learning evolve?

Two papers this week may shed some light on human evolution. We aren't descended from modern monkeys or lemurs, but we can often learn something about our ancestors by studying our distant cousins.

colugo.jpg

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September 14, 2007

Money for monkeys

This week's paper is "Do capuchin monkeys (Cebus apella) use tokens as symbols?" by E. Addessi and coauthors, published in Proceedings of the Royal Society.

Humans use symbols in various ways, from drawings that somewhat resemble the object represented to national flags and religious symbols that represent complex ideologies (or at least group identity). Is symbolic reasoning a uniquely human trait, at least on this planet?

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June 24, 2007

Trade-offs in defense against retroviruses

I have written about evolutionary trade-offs before, starting with early posts about trade-offs between seed size and seed number in plants, and trade-offs between the ability of insects to escape predators by flying away, versus the ability to hide from them by playing dead. I have also given some examples of the increasing use of sophisticated experimental (often molecular) methods in evolutionary biology. This week's paper combines both themes.

The paper is "Restriction of an extinct retrovirus by the human TRIM5-alpha antiviral protein" by Shari Kaiser, Harmit Malik, and Michael Emerman, published in Science (vol.316 p.1756).

Retroviruses are made of RNA, but make DNA copies of themselves that can insert into the DNA of host cells they infect. HIV, the cause of AIDS, is a well-known example, but there are many others. If DNA copies of the retrovirus are inserted into cells giving rise to sperm or eggs, they can be passed to the next generation, as endogenous retroviruses. If the DNA inserts somewhere where it turns an important gene on or off, it may kill the host. Or, once in a while, this change may turn out to be beneficial. The few beneficial changes are the ones that survive and spread, just as the few mutations that are beneficial are the ones that persist.

VWXYNot has an interesting discussion of how a creationist web site misused one of her papers as evidence of "intelligent design." She shows how shared endoviruses can be used to infer shared ancestry, providing yet more evidence that we share a recent ancestor with apes, less-recent ancestors with monkeys, etc. But that's not what this week's paper is about....

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March 7, 2007

Teenage chimps with spears and hammers

Two related papers this week: “Savanna chimpanzees, Pan troglodytes verus, hunt with tools� by Jill Preutz and Paco Bertolani, published in Current Biology (17:1-6), and “4,300-year-old chimpanzee sites and the origins of percussive stone technology� by Julio Mercader et al., published in Proceedings of the National Academy of Science (104:3043-3048).

Preutz and Bertolani report field observations of chimpanzees in Senegal making simple wooden spears and using them to kill bushbabies (sleeping in hollow trees) for food. Several individuals were seen making and using the spears, although apparently they only saw one successful “hunt.�

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