Archive for July, 2007

Mastodon genetics paper in PLOS

By Razib Khan | July 23, 2007 6:35 pm

The Mastodon paleogenomics paper is out on PLOS:

We obtained the sequence from a tooth dated to 50,000-130,000 years ago, increasing the specimen age for which such palaeogenomic analyses have been done by almost a complete glacial cycle. Using this sequence, together with mitochondrial genome sequences from two African elephants, two Asian elephants, and two woolly mammoths (all of which have been previously sequenced), we show that mammoths are more closely related to Asian than to African elephants. Moreover, we used a calibration point lying outside the Elephantidae radiation (elephants and mammoths), which enabled us to estimate accurately the time of divergence of African elephants from Asian elephants and mammoths (about 7.6 million years ago) and the time of divergence between mammoths and Asian elephants (about 6.7 million years ago). These dates are strikingly similar to the divergence time for humans, chimpanzees, and gorillas, and raise the possibility that the speciation of mammoth and elephants and of humans and African great apes had a common cause. Despite the similarity in divergence times, the substitution rate within primates is more than twice as high as in proboscideans.

I don’t know much about paleobiology, but the idea that there might be correlated speciation events across multiple taxa sounds like the Turnover Pulse Hypothesis.


130,000 year old Mastodon DNA?

By Razib Khan | July 22, 2007 3:45 am

Science makes DNA breakthrough in the tooth of a mastodon:

…after finding DNA preserved in the fossilised tooth of a beast that died up to 130,000 years ago.

Researchers were hoping its teeth might have preserved enough of the DNA for them to recover lengthy chunks of it, and this week they will publish research detailing how their hunch has paid off. The find has allowed them to reconstruct the entire sequence of the DNA found in the creature’s mitochondria, the parts of cells concerned with energy production. It is thought to be the oldest DNA ever to have been recovered and decoded in this way.

The exciting: 130,000 years is pushing it really far. Elephants and their cousins are great, but of course it would real cool if we could push genetic retrieval techniques to snatch material from hominids of this vintage. After all, this is a period when anatomically modern humans were simply an African phenomenon (everywhere else they were “archaics”), but there were no behaviorally modern humans extant. The less exciting, well, it is mtDNA. OK for phylogenetics, perhaps, but not that informative otherwise and convenient mostly because of its abundance (cells have lots of mitochondria).



By Razib Khan | July 21, 2007 1:17 pm

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Mike on group selection

By Razib Khan | July 21, 2007 12:15 pm

Mike offers his 2 cents on the levels of selection debates. He says:

If it doesn’t provide me with testable hypotheses and the conceptual tools to do so, it’s just not useful. That’s what happened the last go around with this in the late 80s and early 90s. Do the experiments and I’ll be interested, because the last time it was a lot of yak and very little data.

Focusing on the “replicators” as opposed to the “vehicles” is so appealing because the former is so easier to grasp on to than the latter.


Terrence Tao on introgression

By Razib Khan | July 20, 2007 6:56 pm

A reader points out that Fields Medalist Terrence Tao has a post on introgression in Darwin’s Finches.


Out of Africa: by the skulls?

By Razib Khan | July 20, 2007 3:13 pm

Update: John Hawks weighs in. Here is the abstract.
Several people have asked about a new paper coming out that uses the diversity in skulls to “prove” the Out of Africa hypothesis. The paper is going to be out in Nature yesterday. Yes, you read that right, it was supposed to be on the site on the 19th, but it still seems embargoed. But here is the headline from ScienceDaily, New Research Proves Single Origin Of Humans In Africa. Press releases are generally a little inflated, so no worries.
The basic gist is that the authors used the variation in skulls to trace population bottlenecks due to migration. Generally a good assumption is that the region which exhibits the most variation is the region from which the population expanded, as expansions by their nature tend to result in loss of genetic information via bottlenecks. Just as much of the genetic data suggests Africa tends to have more variation, implying that the longest lineages in this region, so the variation in skull morphology points in the same direction. Does this “prove” that humans emerged out of Africa? Historical sciences are more about inference than “proof,” so I think the terminology is rather strong. One could posit, for example, that there were powerful selection pressures in Eurasia which resulted in the homogenization that we see. But in any case, I tend to lean toward the opinion that the preponderance of evidence does imply an overwhelming demographic expansion Out of Africa in the past 100,000 years. Nevertheless, I must object a bit to the framing of the issue in such a manner:

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Cognitive morphs in Drosophila

By Razib Khan | July 19, 2007 1:07 pm

Natural polymorphism affecting learning and memory in Drosophila:

Knowing which genes contribute to natural variation in learning and memory would help us understand how differences in these cognitive traits evolve among populations and species. We show that a natural polymorphism at the foraging (for) locus, which encodes a cGMP-dependent protein kinase (PKG), affects associative olfactory learning in Drosophila melanogaster. In an assay that tests the ability to associate an odor with mechanical shock, flies homozygous for one natural allelic variant of this gene (forR) showed better short-term but poorer long-term memory than flies homozygous for another natural allele (fors). The fors allele is characterized by reduced PKG activity. We showed that forR-like levels of both short-term learning and long-term memory can be induced in fors flies by selectively increasing the level of PKG in the mushroom bodies, which are centers of olfactory learning in the fly brain. Thus, the natural polymorphism at for may mediate an evolutionary tradeoff between short- and long-term memory. The respective strengths of learning performance of the two genotypes seem coadapted with their effects on foraging behavior: forR flies move more between food patches and so could particularly benefit from fast learning, whereas fors flies are more sedentary, which should favor good long-term memory.


Tuning in & out-by the genes

By Razib Khan | July 18, 2007 6:55 pm

Go Ahead, Everyone Talk at Once:

People who can’t follow a movie when someone else is talking can blame their genes. The ability–or inability–to listen to more than one thing at once is largely inherited, according to a study of twins. The finding could help scientists better understand disorders that involve problems in auditory processing.

“This is the first study to show that [normal] people vary widely in their ability to process what they hear, and these differences are due largely to heredity,” NIDCD director James Battey said in a statement. That’s important, says Deborah Moncrieff, an audiologist at the University of Connecticut, Storrs, because skeptics had questioned attributing difficulties in listening, learning, and reading to problems in the auditory pathway. Moncrieff has developed a method for training children to strengthen the transmission of signals from the ear to the speech center of the brain

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Who were the ancient Hungarians?

By Razib Khan | July 18, 2007 1:24 pm

We know that the Magyars originated from Inner Eurasia. They were one of the long line of steppe peoples who conquered and settled central Europe, the Avars being their local predecessors. But unlike the Avars, or the Bulgars or the Huns, the Magyars left a cultural imprint: their language. And yet physically and genetically the current Hungarian population seems to exhibit continuity with their European neighbors (in contrast, Gypsies show evidence of haplotypes normally found in the Indian subcontinent). Dienekes points me to some new data:

Strong differences appear when the ancient Hungarian samples are analyzed according to apparent social status, as judged by grave goods. Commoners show a predominance of mtDNA haplotypes and haplogroups (H, R, T), common in west Eurasia, while high-status individuals, presumably conquering Hungarians, show a more heterogeneous haplogroup distribution, with haplogroups (N1a, X) which are present at very low frequencies in modern worldwide populations and are absent in recent Hungarian and Sekler populations.

In other words, the genesis of the modern Hungarian ethnicity occurred via elite emulation as well as assimilation of the that elite by the substrate. Though the Hungarian language is very unique, most other aspects of their culture reflect the region’s assimilation toward Latin Christian norms. Note that mtDNA is normally the weaker signal when it comes to the genetic impact of nomads, who are likely to “pick up” women from the conquered peoples during their travels while their patrilineages remain more or less unbroken.


Harun Yahya – who is funding him?

By Razib Khan | July 17, 2007 9:52 pm

As a follow up to my post mocking Harun Yahya, check out Ali Eteraz’s impressive post exploring his possible sources of funding and affiliations. My own immediate instinct was to assume that he was a front for Saudi $$$; Ali points to reasons why this is unlikely. The argument is circumstantial and based on elimination of possibilities, but at least it pushes the ball forward.


Non-coding, but fitness implicating?

By Razib Khan | July 17, 2007 6:19 pm

Widely distributed noncoding purifying selection in the human genome (PNAS):

It is widely assumed that human noncoding sequences comprise a substantial reservoir for functional variants impacting gene regulation and other chromosomal processes. Evolutionarily conserved noncoding sequences (CNSs) in the human genome have attracted considerable attention for their potential to simplify the search for functional elements and phenotypically important human alleles. A major outstanding question is whether functionally significant human noncoding variation is concentrated in CNSs or distributed more broadly across the genome. Here, we combine wholegenome sequence data from four nonhuman species (chimp, dog, mouse, and rat) with recently available comprehensive human polymorphism data to analyze selection at single-nucleotide resolution. We show that a substantial fraction of active purifying selection in human noncoding sequences occurs outside of CNSs and is diffusely distributed across the genome. This finding suggests the existence of a large complement of human noncoding variants that may impact gene expression and phenotypic traits, the majority of which will escape detection with current approaches to genome analysis.

Purifying selection basically works against mutations which result in functional changes which might be deleterious; so it operates as a constraining force upon genetic diversification.
Related: This post from RPM, The Frailty of Nearly Neutral Hypotheses, is highly recommended.


Muslim Creationism: morons a publishin'

By Razib Khan | July 17, 2007 3:14 am

The New York Times has a funny article up, Islamic Creationist and a Book Sent Round the World, which recounts the mass distribution (gratis) of Harun Yahya’s latest tract, a lavishly illustrated and packaged glossy book which aims to show that evolution didn’t occur. This is chuckle worthy:

He said people who had received copies were “just astounded at its size and production values and equally astonished at what a load of crap it is.
“If he sees a picture of an old fossil crab or something, he says, ‘See, it looks just like a regular crab, there’s no evolution,’ ” Dr. Padian said. “Extinction does not seem to bother him. He does not really have any sense of what we know about how things change through time.”
While they said they were unimpressed with the book’s content, recipients marveled at its apparent cost. “If you went into a bookstore and saw a book like this, it would be at least $100,” said Dr. Miller, an author of conventional biology texts. “The production costs alone are astronomical. We are talking millions of dollars.”

Check out Harun Yahya’s extended biography (this is under his real name). Jump down to the “Cocaine Conspiracy” section, it’s pretty bizarre. Harun Yahya is obviously a major league tard, and he is clearly dull and deluded enough he doesn’t know how transparent his tardation is. The gaudy bling-bling Creationism is similar to the pap put out by the Institute of Creation Science, and his attempts to promote himself as a Renaissance Man who is the master of all he surveys are Dembski worthy. My main question is this: who is funding this trash?
Update: Hey, I have a life so I can’t monitor this weblog 24-7. I suspect that the influx of tards has been triggered by people coming through the trackback to the original article in The New York Times (this weblog is heavily linked to on “The Sphere” service that The New York Times uses). I’m going to close comments, though I invite regular readers to check out some of the tardish comments that popped up. They’re almost as hilarious as Harun Yahya’s website. I mean, yes, Creationism is bad; but such sincere morons are an exotic species to me since I am careful to avoid people at the first sign of tardation. It’s been a long time since I expended time arguing with Creationists, but at least “Yahya” and his tardish followers are too dumb to engage in serious sophistry. An analogy would be holding minors and adults accountable for crimes. Obviously minors should be held accountable in some manner, but not to the same extent or degree as adults who are presumed to be able to make more rational and premeditated choices. Though honestly, I feel like I’m insulting children by comparing them with the tard mentalities on display here.


Thank Jumala for Finnish record keeping!

By Razib Khan | July 16, 2007 2:03 pm

You might not be able to do controlled experiments on humans for evolutionary biological purposes (not only is it unethical, the leisurely rate of human reproduction doesn’t make it viable for cranking out Ph.D.s), but you can analyze our pedigrees! Scientific American has a long article, What Finnish Grandmothers Reveal about Human Evolution, about Virpi Lummaa’s research program. It’s a “sexy” one, I’ve blogged her research several times, it has pretty deep appeal, focusing on humans & evolution. For you religion haters out there, I do have to point out that it is enabled by the thoroughness and time depth of Scandinavian record keeping under the auspices of the Lutheran Church and its baptismal and death records. In any case, this part is new to me:

Lummaa has now turned her attention to the effect of grandfathers on grandchildren. If grandmothers improve survival odds, what do elderly males contribute? “If anything there’s a negative effect,” she says. This could be because of the cultural tradition of catering to men, particularly old men. “Maybe if you had an old grandpa, he was eating your food,” she speculates. Or it could be that because men can continue to reproduce, they are less vested in anyone other than their own children. Another possible reason is that women can be sure that a grandchild is their genetic descendant, but it is more difficult for grandfathers. This may also have spurred them to seek second and even third wives rather than focusing on their children. “We are comparing men who married once in their lifetime[s] with men who are married several times,” Lummaa says.

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Is the Academy liberal?

By Razib Khan | July 14, 2007 3:20 pm

I think the answer to the question posed in the title is “Yes.” But I’m more interested in the break down of disciplines. Below the fold is some data I’ve collated.

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Plugging the "gaps" in the fossil record

By Razib Khan | July 13, 2007 3:17 pm

Ethiopia unveils new find of ancient fossils:

Ethiopian scientists said on Tuesday they have discovered hominid fossil fragments dating from between 3.5 million and 3.8 million years ago in what could fill a crucial gap in the understanding of human evolution.



By Razib Khan | July 13, 2007 2:12 am

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Sexual selection @ Chernobyl

By Razib Khan | July 12, 2007 3:14 pm

About one month ago Ruchira Paul posted on the ecology around Chernobyl and the surprising bounce back of some taxa. The Economist has some interesting detail about the nature of this revival:

…they found that species which relied on a class of chemicals called carotenoids to tint their feathers fared worse when there was more radioactivity around. Intriguingly, that did not apply to birds that used melanin….
Besides acting as pigments, carotenoids are antioxidants that have an important role in protecting DNA from harm. One of the ways that radiation causes harm is by generating molecules that promote oxidation, so a good supply of carotenoids protects against such damage. Using them to make feathers pretty instead of mopping up oxidative molecules thus has a significant cost–as this result shows.
The reason this is interesting is that there is a debate in biology between those who think signals such as flashy feathers are essentially arbitrary and those who think they are signs of underlying health and good genes. Dr Moller’s and Dr Mousseau’s result shows that the bright reds and yellows of carotenoid-based plumage really do come at a price, and thus indicate underlying health. The unusual circumstances of Chernobyl have exposed that price to human observers, but it will have to be paid all the time, even in places that have not fallen foul of radioactive plumes.

Too much in discussion about sexual selection in the context of evolutionary biology operates so that it appears like a deux ex machina to rescue us. Like genetic drift too often people use sexual selection as a catchall explanation for traits which they can’t understand in an adaptive context. But though drift and sexual selection are real evolutionary forces it is important to remember that both are subject to conventional population genetic parameters. Additionally, theories of sexual selection come in varieties, with some being rather more arbitrary than others. Sexual selection maybe stochastic, but the sample space of possibilities does not seem infinite or unconstrained.


Levels of selection – the coming debate

By Razib Khan | July 11, 2007 3:33 pm

Wired has a blog entry up where they reproduce the text of an email exchange with Bert Hoelldobler, an entomologist who is collaborating with E.O. Wilson on a new book which will argue for the relevance of higher levels of organization in evolutionary processes. In The Cooperative Gene evolutionary biologist Mark Ridley elucidates how multicellular organisms emerge from a coalition of genes all with the same interest because of their imprisonment within the individual (their replication being mediated by the sex gametes). I’m assuming that Wilson & Hoelldobler are going to attempt something similar for social organization. As I have noted before E.O. Wilson is now making a big push for higher level selection dynamics, but his own sentiments have always been favorable toward this idea. Eusocial insects are probably some of the best cases for an empirical assessment and examination of the theoretical possibilities within the multi-level selection paradigm. Richard Dawkins and his fellow travelers have never denied that levels of selection higher than the individual may occur, they have questioned its power in shaping evolution over the long term. In the case of eusocial insects I think the counter-argument is on its strongest ground because of the peculiarities and regularities of insect societies; but the larger project of expanding outside of the domain of this branch of the tree of life is I think going to be more difficult. Like the meme meme (so to speak) the idea of a super-organism is analogically appealing, but its tractability and utility in day to day evolutionary biology has often been less than evident. As they say, you shall know it by its fruits.
Update: Part II of the correspondence is up.
Note: Readers not familiar with the debate between the “British School” and the Americans should read Richard Dawkins’ essay Burying the Vehicle.
Related: Cooperation and multilevel selection.


Chili peppers go way back

By Razib Khan | July 11, 2007 2:41 pm

beyonce-781573.jpgAncient Americans Liked It Hot: Mexican Cuisine Traced To 1,500 Years Ago:

Plant remains from two caves in southern Mexico analyzed by a Smithsonian ethnobotanist/archaeologist and a colleague indicate that as early as 1,500 years ago, Pre-Columbian inhabitants of the region enjoyed a spicy fare similar to Mexican cuisine today. The two caves yielded 10 different cultivars (cultivated varieties) of chili peppers.
“This analysis demonstrates that chilies in Mexican food have been numerous and complex for a long period of time,” said lead author Linda Perry, of the Smithsonian’s National Museum of Natural History. “It reveals a great antiquity for the Mexican cuisine that we’re familiar with today.”


Dark eyed lady

By Razib Khan | July 11, 2007 4:32 am

heigl.jpgA commenter below observed that both the Sami and the Finns are cases where females tend to have darker eyes than males. He chalked this up to sexual selection. I was skeptical a priori because 3/4 of the time the variation between blue and brown eyes within the population can be explained by one genetic locus, and this is a region (OCA2) that seems to have been under massive recent selection. Sexual dimorphism tends to emerge slowly within populations because it takes time for modifier loci which express themselves conditionally in response to sex hormones to scaffold the initial gene under selection. But, I am under the impression that the eye color difference is well documented in other populations, so it might be an older variant attached to the secondary loci (the other 1/4 difference) affecting eye color.

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