Wednesday, December 27, 2006

Iran, oil and nuclear energy (or weapons?)

I thought it was interesting that a paper like this showed up in PNAS. Basically, maybe Iran's intentions really are good. (the paper is open access, so see link)

The Iranian petroleum crisis and United States national security

Roger Stern

PNAS Early Edition

Abstract: The U.S. case against Iran is based on Iran's deceptions regarding nuclear weapons development. This case is buttressed by assertions that a state so petroleum-rich cannot need nuclear power to preserve exports, as Iran claims. The U.S. infers, therefore, that Iran's entire nuclear technology program must pertain to weapons development. However, some industry analysts project an Irani oil export decline [e.g., Clark JR (2005) Oil Gas J 103(18):34-39]. If such a decline is occurring, Iran's claim to need nuclear power could be genuine. Because Iran's government relies on monopoly proceeds from oil exports for most revenue, it could become politically vulnerable if exports decline. Here, we survey the political economy of Irani petroleum for evidence of this decline. We define Iran's export decline rate (edr) as its summed rates of depletion and domestic demand growth, which we find equals 10-12%. We estimate marginal cost per barrel for additions to Irani production capacity, from which we derive the "standstill" investment required to offset edr. We then compare the standstill investment to actual investment, which has been inadequate to offset edr. Even if a relatively optimistic schedule of future capacity addition is met, the ratio of 2011 to 2006 exports will be only 0.40-0.52. A more probable scenario is that, absent some change in Irani policy, this ratio will be 0.33-0.46 with exports declining to zero by 2014-2015. Energy subsidies, hostility to foreign investment, and inefficiencies of its state-planned economy underlie Iran's problem, which has no relation to "peak oil."

Saturday, December 23, 2006

Science breakthroughs of the year and areas to watch in 2007

The #1 breakthrough according to Science was the proof of the Poincare conjecture. The runners-up are, in order: (see here for all the relevant pubs)

- Sequencing of Neanderthal autosomal DNA
- The worlds two great ice sheets losing ice to the oceans, at an accelerating pace
- Discovery of a fossil of a fish/amphibian.. "missing link" between water and land dwellers
- Cloaking technology: playing around with optics
- advances in understanding and treating age-related macular degeneration
- genetics of biodiversity and speciation
- new microscopy technology that gives clearer view of cells and proteins.
- the role of long-term potentiation in the formation of memory.
- the discovery of piRNAs, another class of small RNA molecules.

Areas to watch in 2007.

I won't list them all here, but obviously more genetic stuff (including whole genome association studies), and global warming.

Also in this issue of Science is a profile of Bruce Lahn. Check out GNXP on this.

Friday, December 22, 2006

Elevated ethnocentrism in the first trimester of pregnancy

This paper seemed really cool at first glance but then I was disappointed when I read it. It basiacally supports the hypothesis that during the first trimester of pregnancy in-group favoritism is at the most heightened state of the whole pregnancy because this is when the mother's immune system is on its highest alert.
The major thing that I did not like about it was that the title says ethnocentrism but then the research looks at American vs. non-American, so not so much at ethnicity, per se, after all.

Elevated ethnocentrism in the first trimester of pregnancy

Carlos David Navarrete, Daniel M.T. Fessler and Serena J. Eng

Evolution and Human Behavior Volume 28, Issue 1 , January 2007, Pages 60-65

Abstract: Recent research employing a disease-threat model of the psychology of intergroup attitudes has provided preliminary support for a link between subjectively disease-salient emotional states and ethnocentric attitudes. Because the first trimester of pregnancy is a period of particular vulnerability to infection, pregnant women offer an opportunity to further test this association. We explored the expression of intergroup attitudes in a sample of pregnant women from the United States. Consistent with the predictions of the disease-threat model, results from our cross-sectional study indicate that favoritism toward the ingroup peaks during the first trimester of pregnancy and decreases during the second and third trimesters. We discuss this finding in light of the possible contributions of cultural and biological factors affecting ethnocentrism.

Wednesday, December 20, 2006

CNVs and human-chimp differences

Evolgen has covered the recent papers on CNVs and he has another one up about how CNVs might help us explain phenotypic differences between chimpanzees and humans. There is a paper by Hahn that will be coming out soon in PLoS One. This journal has still not published its first issue.

Tuesday, December 19, 2006

Samuel Bowles on group competition and relatedness as important factors in human cooperation

I thought I would go over some more of the details of this paper by Samuel Bowles in Science. I had briefly covered it in a recent post. The paper hasn't gotten as much coverage as I think it deserves so I'll try to spread the meme here.
My understanding of it, in a (long) sentence is that using the Price Equation for the evolution of altruism which takes into account the balance of a within-deme and between deme effect, and some estimates of group competition and within-group relatedness among modern hunter-gatherers, S. Bowles argues that with group competition and group relatedness being high enough (and he provides evidence that it may indeed have been) and with reproductive leveling due to monogamy (thereby reducing the amount of intra-group competition), human large scale cooperation can flourish.

Ok, that was a long sentence. Maybe a shorter way of saying this is that cooperation in humans is largely due to the relatedness of people within groups, along with the fact that conflict between groups was frequent enough and that reproductive leveling (monogamy) offset any possibility that within-group competition would increase too much.

Some questions:

Is it safe to make the assumption that the extent of group warfare we see in today's hunter-gatherers closely approximates what it was for most of our hominin evolution? - not so sure about that. Bowles actually notes that "even very infrequent contests would have been sufficient to spread quite costly forms of altruism. He also thinks that recurrent warfare would explain the frequent catastrophic mortality and very slow growth rates seen in human demographic history.

Is it safe to assume that levels of relatedness among individuals in groups was the same now in hunter-gatherers as it was for most of our hominin evolution? - I'm not very clear on how/where S. Bowles gets his data for relatedness among the hunter-gatherer groups and also why if they are so surprisingly high (just under that for cousins) no one else would have noticed this before.

I have always had a strong intuition that human cooperation is greatly strenthened by relatedness within groups and non-relatedness between groups and by group conflict. I had never thought of the importance of reproductive leveling. Sam Bowles gives these ideas which resemble the arguments of group selection) some empirical and theoretical strength.

These ideas have been passed around before, but it seems that the multilevel-selection approach to understanding human cooperation has gained much more acceptance recently.

Saturday, December 16, 2006

Tradeoffs: UV, Folate, vitamin D, pregnancy loss

gotta love the name of this gene .... mthfr..... anyway, here's a short letter about multiple selective pressures and tradeoffs relating to folate metabolism and UV and the gradient of a particular genotype across northern to southern Europe, and also across N to S Americas.

Ultraviolet radiation represents an evolutionary selective pressure for the south-to-north gradient of the MTHFR 677TT genotype

Loren Cordain, Matthew Hickey

American Journal of Clinical Nutrition, Vol. 84, No. 5, 1243, November 2006

The pubmed link to this paper is not functioning properly and there is no abstract to link to, but here's the full-text below without the references.

In a recent issue of the Journal, Guéant-Rodriguez et al (1) and Devlin et al (2) confirmed prior observations (3) of a nutrient-gene interaction between methylenetetrahydrofolate reductase (MTHFR) and folate status. Homozygosity for the MTHFR 677TT genotype converts an alanine to a valine at position 222 in the amino acid sequence and reduces the enzyme activity, which causes hyperhomocysteinemia (4), which in turn increases the risk for cardiovascular disease, cognitive dysfunction, Alzheimer disease, and osteoporotic fractures (5), as well as recurrent early pregnancy loss (6, 7). These pathophysiologic sequelae likely materialize only when folate status is compromised (1, 2). Hence, it has been suggested that MTHFR 677TT genotype homozygosity may confer survival value in populations with sufficient dietary folate (8, 9), because this polymorphism is protective against colon cancer (10) and acute lymphatic leukemia (11), perhaps by contributing methylenetetrahydrofolate to DNA synthesis and thereby preventing double-strand DNA ruptures (12).

In addition to reduced dietary folate intake and absorption, it is less well appreciated that other environmental factors, including dermal exposure to ultraviolet (UV) radiation, may adversely influence folate status (13, 14). Exposure of human plasma in vitro to simulated strong sunlight causes a 30–50% loss of folate within 60 min, and light-skinned patients chronically exposed to UV radiation for dermal disorders maintain low plasma folate concentrations, which suggests in vivo dermal photolysis of folate (13). In contrast, dark skin (via its greater concentration of melanin) may prevent UV photolysis of folate (13, 14).

In European populations, a simultaneous south-to-north gradient exists for dermal pigmentation (14) and the presence of MTHFR 677TT (15). The prevalence of MTHFR 677TT decreases in a south-to-north manner: 10–12% of light-skinned Northern Europeans maintain the MTHFR 677TT genotype (2), but the highest frequency of this polymorphism occurs in more dark-skinned Southern Europeans, such as Sicilians (1). A similar, simultaneous and latitudinally dependent gradient in the frequency of the MTHFR 677TT allele (16, 17) and dermal pigmentation (14) has been found in the Americas.

As human populations move into more northern latitudes where they are exposed to less annual UV radiation, the evolutionary selection for less pigmented, lighter skin may represent an asset in that it can improve vitamin D status and lessen the risk for rickets and other vitamin D–related disorders (14). However, because lighter skin contains less protective melanin, it represents a liability with respect to folate metabolism, because lighter skin may be more susceptible than darker skin to photolysis of folate (13). Hence, to counter the increased loss of folate in lighter-skinned populations during seasonal exposure to UV sunlight, genes that lower plasma homocysteine concentrations by favoring increased the synthesis of MTHFR would convey selective advantage, perhaps by reducing recurrent early pregnancy loss (6, 7). The risk of recurrent early pregnancy loss in those who are homozygous for the MTHFR 677TT genotype is 2- to 3-fold that in those who maintain the wild or heterozygous genotype (6). In females of reproductive age, recurrent early pregnancy loss caused by impaired folate status represents the most likely environmental pressure favoring the selection of protective genotypes such as MTHFR 677CC, because cardiovascular disease, cognitive dysfunction, Alzheimer disease, and osteoporotic fractures typically occur in the postreproductive years.

Thursday, December 14, 2006

On the need and preference for the costly punishment option

The efficient interaction of indirect reciprocity and costly punishment

Bettina Rockenbach and Manfred Milinski

444, 718-723 (7 December 2006)

Abstract: Human cooperation in social dilemmas challenges researchers from various disciplines. Here we combine advances in experimental economics and evolutionary biology that separately have shown that costly punishment and reputation formation, respectively, induce cooperation in social dilemmas. The mechanisms of punishment and reputation, however, substantially differ in their means for 'disciplining' non-cooperators. Direct punishment incurs salient costs for both the punisher and the punished, whereas reputation mechanisms discipline by withholding action, immediately saving costs for the 'punisher'. Consequently, costly punishment may become extinct in environments in which effective reputation building—for example, through indirect reciprocity—provides a cheaper and powerful way to sustain cooperation. Unexpectedly, as we show here, punishment is maintained when a combination with reputation building is available, however, at a low level. Costly punishment acts are markedly reduced although not simply substituted by appreciating reputation. Indeed, the remaining punishment acts are concentrated on free-riders, who are most severely punished in the combination. When given a choice, subjects even prefer a combination of reputation building with costly punishment. The interaction between punishment and reputation building boosts cooperative efficiency. Because punishment and reputation building are omnipresent interacting forces in human societies, costly punishing should appear less destructive without losing its deterring force.

Tuesday, December 12, 2006

More on CNVs in the human genome

A Comprehensive Analysis of Common Copy-Number Variations in the Human Genome

Kendy K. Wong, Ronald J. deLeeuw, Nirpjit S. Dosanjh, Lindsey R. Kimm, Ze Cheng, Douglas E. Horsman, Calum MacAulay, Raymond T. Ng, Carolyn J. Brown, Evan E. Eichler, and Wan L. Lam

Am. J. Hum. Genet.
, 80:91-104, 2007

Abstract: Segmental copy-number variations (CNVs) in the human genome are associated with developmental disorders and susceptibility to diseases. More importantly, CNVs may represent a major genetic component of our phenotypic diversity. In this study, using a whole-genome array comparative genomic hybridization assay, we identified 3,654 autosomal segmental CNVs, 800 of which appeared at a frequency of at least 3%. Of these frequent CNVs, 77% are novel. In the 95 individuals analyzed, the two most diverse genomes differed by at least 9 Mb in size or varied by at least 266 loci in content. Approximately 68% of the 800 polymorphic regions overlap with genes, which may reflect human diversity in senses (smell, hearing, taste, and sight), rhesus phenotype, metabolism, and disease susceptibility. Intriguingly, 14 polymorphic regions harbor 21 of the known human microRNAs, raising the possibility of the contribution of microRNAs to phenotypic diversity in humans. This in-depth survey of CNVs across the human genome provides a valuable baseline for studies involving human genetics.

Monday, December 11, 2006

Another one on lactose tolerance

This paper is very similar to the recent one in Human Genetics that identified the T/G-13915 SNP in a Sudanes population. Here, Tishkoff et al. identify two other SNPs in a population of Kenyans, Tanzanians and Sudanese. I wonder if there's some sort of rivalry going on between these two groups.

Convergent adaptation of human lactase persistence in Africa and Europe

Sarah A Tishkoff, Floyd A Reed, Alessia Ranciaro, Benjamin F Voight, Courtney C Babbitt, Jesse S Silverman, Kweli Powell, Holly M Mortensen, Jibril B Hirbo, Maha Osman, Muntaser Ibrahim, Sabah A Omar, Godfrey Lema, Thomas B Nyambo, Jilur Ghori, Suzannah Bumpstead, Jonathan K Pritchard, Gregory A Wray & Panos Deloukas

Nature Genetics Published online: 10 December 2006;

A SNP in the gene encoding lactase (LCT) (C/T-13910) is associated with the ability to digest milk as adults (lactase persistence) in Europeans, but the genetic basis of lactase persistence in Africans was previously unknown. We conducted a genotype-phenotype association study in 470 Tanzanians, Kenyans and Sudanese and identified three SNPs (G/C-14010, T/G-13915 and C/G-13907) that are associated with lactase persistence and that have derived alleles that significantly enhance transcription from the LCT promoter in vitro. These SNPs originated on different haplotype backgrounds from the European C/T-13910 SNP and from each other. Genotyping across a 3-Mb region demonstrated haplotype homozygosity extending >2.0 Mb on chromosomes carrying C-14010, consistent with a selective sweep over the past 7,000 years. These data provide a marked example of convergent evolution due to strong selective pressure resulting from shared cultural traits—animal domestication and adult milk consumption.

Friday, December 08, 2006

Group competition, relatedness, and the evolution of human altruism

Science and Nature both seem to love research on human altruism/cooperation. Here is the latest by Sam Bowles from the Santa Fe Institute. The argument that he makes and the empirical and modeling evidence that he uses implies that human cooperation can be partly attributed to genetic relatedness between groups and conflict with other a sort of group/kin selection, the two of which are basically the same. There's a commentary by Rob Boyd and a related paper by Marin Nowak on the five rules for the evolution of cooperation (see below). Sam Bowles uses some relatedness data from modern hunter gatherers where the average degree of relatedness between group members turn out to be almost as high as cousins. I haven't looked too closely yet at how all this was measured, but sounds compelling.

Group Competition, Reproductive Leveling, and the Evolution of Human Altruism

Samuel Bowles

Science 8 December 2006:Vol. 314. no. 5805, pp. 1569 - 1572

Abstract: Humans behave altruistically in natural settings and experiments. A possible explanation—that groups with more altruists survive when groups compete—has long been judged untenable on empirical grounds for most species. But there have been no empirical tests of this explanation for humans. My empirical estimates show that genetic differences between early human groups are likely to have been great enough so that lethal intergroup competition could account for the evolution of altruism. Crucial to this process were distinctive human practices such as sharing food beyond the immediate family, monogamy, and other forms of reproductive leveling. These culturally transmitted practices presuppose advanced cognitive and linguistic capacities, possibly accounting for the distinctive forms of altruism found in our species.

Five Rules for the Evolution of Cooperation

Martin A. Nowak

Science 8 December 2006:Vol. 314. no. 5805, pp. 1560 - 1563

Abstract: Cooperation is needed for evolution to construct new levels of organization. Genomes, cells, multicellular organisms, social insects, and human society are all based on cooperation. Cooperation means that selfish replicators forgo some of their reproductive potential to help one another. But natural selection implies competition and therefore opposes cooperation unless a specific mechanism is at work. Here I discuss five mechanisms for the evolution of cooperation: kin selection, direct reciprocity, indirect reciprocity, network reciprocity, and group selection. For each mechanism, a simple rule is derived that specifies whether natural selection can lead to cooperation.

Wednesday, December 06, 2006

Four Stone Hearth Anthropology Blog Carnival - 4th Edition

Welcome to the fourth edition of the Four Stone Hearth Anthropology Blog Carnival. The excitement that was generated from all the Neanderthal DNA papers will be a hard act to follow, but it looks like we have many excellent, thought provoking submissions. We’ll go field by field and due to my bias, we'll begin with Biological Anthropology.

Biological Anthropology

Afarensis starts us off with a great review of a recent paper describing the results of an experiment where one species of baboon was mated (willingly or not, I don't know) with another species of baboons mainly to see if good (heterosis) or bad things (dysgenesis) resulted. The authors note that this is a good model with which to examine the likelihood of hybridization between homo species. One thing I remember from this paper was that the matings were always the male of one species with the female of the other species, or some sort of analogous asymmetry.

In light of all the exciting things happening in Molecular Anthropology these days, I'm happy that Kambiz from submitted his piece on copy number variation (CNV in the human genome. Kambiz does a really thorough job of introducing the basic concepts and the major findings from the study. As we continue to study the genomes (and continue to develop better ways to look at it) we are finding more and more sources of complexity. If I remember correctly, the researchers were able to assess a small fraction of these CNVs (only the big ones) as most of them are small repeats. Kambiz reviews the health implications these CNVs might have and how they cluster human population-wise.

Cultural Anthropology

Martin Rundkvist's submission called Leave the Ghetto from his blog Saltos Sobrius is very thought provoking and throws up the question of whether distinct minority cultures and ethnicities should be maintained or encouraged under a nation-state system. He makes the argument that to reduce inequalities, the minority cultures/ethnicities must "assume places inside majority society through education and employment". Even with programs like affirmative action in the US, progress in this area is very slow, highlighting the extent to which the generational cycle of economic class is very hard to break. This goes hand in hand with the fact that when times are tough, humans tend to rely even more on their groups (ethnic or otherwise) as buffering and support systems. This provides me with the perfect segue to the next submission about how disconnected our modern lives may be.

William Klinger at Nomadic Thoughts has submitted his post entitled Social (dis)connections. He discusses a New York Times op-ed piece which talks about how our social lives have been transformed from many face to face interactions to interactions through text and voice. I have heard stories about how the circle of friends of average Americans has been getting smaller as we lead more individualistic lives. The author of this piece presents a balanced description of what may be going on. As Will Klinger puts it: "The reason Johnson’s post satisfies me is because it strikes a happy medium between a hypersensitivity to the effects of technology in our lives on the one hand and the unbridled technophilia that so many of my generation have succumbed to"

Over at Wanna be an Anthropologist, Paul Wren has submitted a post about Anthropology on the Moon. In it, he discusses how NASA plans to install a permanent base on the moon where people will be stationed. He then discusses all the things that anthropologists might like to study in this type of a living situation (development of culture, social dynamics, marriage and kinship) I've often wondered myself if there are anthropologists out there taking down data from TV shows like Survivor.

Lexis2Praxis has a post at that examines the anthropology of the modern office space. Like any living environment of humans, each place develops its own set of cultural norms. These are discussed in the post. It reminds me of the movie Office Space. There is also a post on our networked culture and who gets to participate and who doesn't.

Lucy Jr. at The Second Sight has this entry which is a commentary on paleoanthropologists behaving badly over the Hobbit find in Flores Island, Indonesia. According to Lucy Jr., actions taken and the interpretation of the find was not so much of scientists interpreting a discovery, as a drama of passion, jealousy and old rivalries. Please click on the links of the characters in this story, as I was pleasantly surprised to see links to websites of actual researchers who, I assume, are working in Flores.

Stolen and Looted: Cultural History Lost and Destroyed for a Buck is the title of a post by Carl Feagans at Hot Cup of Joe. Here, we learn that many archaeological sites in Peru, Iraq, South East Asia and the American Southwest are under the threat of looting for archaeological treasures that can be sold for profit. Some quite stunning photos of looted sites are shown in the post...pretty surreal!! Also, check out his other post: Stolen and Looted: Who Does the Past Belong To? for related information.

K. Kris Hirst at has submitted an interesting piece on Damascus Steel. Apparently this is a type of steel used to make blades around the 11 or 12th century AD that seems to be very sophisticated and must have required a high level of technology to make, thus mystifying archaeologists.

Last but not least, Johan Normark at Archaeolog has submitted a post on Polyagentive Archaeology. "The polyagentive approach primarily differs from the humanocentric archaeology in that it tries to decentralize the human, to give an account of active tangible archaeological materialities and intangibilities (anything that can be perceived but which is not solid or palpable). This approach also aims to initially de-culturalize and de-socialize the past by emphasizing what lasts, differentiates and repeats."

Well, there we are. I hope that everyone enjoys this. I think we had a good turnout from the Cultural Anthropologists and the Archaeologits. It would have been nice to have a few more bio submissions (I'll take some blame for that, given my lack of a submission) and some linguistic submissions.

Tuesday, December 05, 2006

Requesting submissions for Four Stone Hearth Anthropology Blog Carnival

If any of you bloggers out there have any submissions for the latest edition of the Four Stone Hearth Anthro. Blog Carnival, please email them as soon as possible to These can be any posts related in any way to Anthropology. I will then put all the submissions together in a sort of highlights post of all the submissions, meant to reflect what is being blogged about at this time in the area of Anthropology.

Monday, December 04, 2006

New book about Omega-3 fatty acids

Here's a review in Nature of a new book on Omega-3 fatty acids:

The Queen of Fats: Why Omega-3s Were Removed from the Western Diet and What We Can Do to Replace Them
by Susan Allport
University of California Press: 2006. 232 pp. $22.50, £14.95

Thursday, November 30, 2006

Malfunctioning links

I just realized that a lot of the links to abstracts or journal papers on my posts don't work. I'll pay more attention to making sure the links work in future posts.

The genetics of lactase persistence in different populations

adaptation by whatever means available, like skin color and adaptation to high altitude.

A novel polymorphism associated with lactose tolerance in Africa: multiple causes for lactase persistence?

Catherine J. E. Ingram, Mohamed F. Elamin, Charlotte A. Mulcare, Michael E. Weale, Ayele Tarekegn, Tamiru Oljira Raga, Endashaw Bekele, Farouk M. Elamin, Mark G. Thomas, Neil Bradman and Dallas M. Swallow

Human Genetics Published online: 21 November 2006

Abstract: Persistence or non-persistence of lactase expression into adult life is a polymorphic trait that has been attributed to a single nucleotide polymorphism (C-13910T) in an enhancer element 13.9 kb upstream of the lactase gene (LCT). The -13910*T allele occurs at very high frequency in northern Europeans as part of a very long haplotype (known as A), and promotes binding of the transcription factor Oct-1. However, -13910*T is at very low frequency in many African milk drinking pastoralist groups where lactase persistence phenotype has been reported at high frequency. We report here for the first time, a cohort study of lactose digester and non-digester Sudanese volunteers and show there is no association of -13910*T or the A haplotype with lactase persistence. We support this finding with new genotype/phenotype frequency comparisons in pastoralist groups of eastern African and Middle Eastern origin. Resequencing revealed three new SNPs in close proximity to -13910*T, two of which are within the Oct-1 binding site. The most frequent of these (-13915*G) is associated with lactose tolerance in the cohort study, providing evidence for a cis-acting effect. Despite its location, -13915*G abolishes, rather than enhances Oct-1 binding, indicating that this particular interaction is unlikely to be involved in lactase persistence. This study reveals the complexity of this phenotypic polymorphism and highlights the limitations of C-13910T as a diagnostic test for lactase persistence status, at least for people with non-European ancestry.

Tuesday, November 28, 2006

Tying testosterone, immune function, and sexual signaling.

From what I can glean, testosterone increases coloration, but is also immunosuppressant, and it seems like extra carotenoids are first diverted to immune function, then to coloration thus providing an honest signal.

Testosterone increases bioavailability of carotenoids: Insights into the honesty of sexual signaling

J. Blas, L. Pérez-Rodríguez, G. R. Bortolotti, J. Viñuela , and T. A. Marchant

PNAS Published online before print November 22, 2006

Abstract: Androgens and carotenoids play a fundamental role in the expression of secondary sex traits in animals that communicate information on individual quality. In birds, androgens regulate song, aggression, and a variety of sexual ornaments and displays, whereas carotenoids are responsible for the red, yellow, and orange colors of the integument. Parallel, but independent, research lines suggest that the evolutionary stability of each signaling system stems from tradeoffs with immune function: androgens can be immunosuppressive, and carotenoids diverted to coloration prevent their use as immunostimulants. Despite strong similarities in the patterns of sex, age and seasonal variation, social function, and proximate control, there has been little success at integrating potential links between the two signaling systems. These parallel patterns led us to hypothesize that testosterone increases the bioavailability of circulating carotenoids. To test this hypothesis, we manipulated testosterone levels of red-legged partridges Alectoris rufa while monitoring carotenoids, color, and immune function. Testosterone treatment increased the concentration of carotenoids in plasma and liver by >20%. Plasma carotenoids were in turn responsible for individual differences in coloration and immune response. Our results provide experimental evidence for a link between testosterone levels and immunoenhancing carotenoids that (i) reconciles conflicting evidence for the immunosuppressive nature of androgens, (ii) provides physiological grounds for a connection between two of the main signaling systems in animals, (iii) explains how these signaling systems can be evolutionary stable and honest, and (iv) may explain the high prevalence of sexual dimorphism in carotenoid-based coloration in animals.

Monday, November 27, 2006

Religion, Geography, and Genes in India

The abstract of this paper is long, but fairly interesting in itself. According to their study, "Islamization in India did not involve large-scale replacement of Hindu Y chromosomes".

A shared Y-chromosomal heritage between Muslims and Hindus in India

Ramana Gutala, Denise R. Carvalho-Silva, Li Jin, Bryndis Yngvadottir, Vasanthi Avadhanula, Khaja Nanne, Lalji Singh, Ranajit Chakraborty and Chris Tyler-Smith

Human Genetics Volume 120, Number 4 / November, 2006

Abstract: Arab forces conquered the Indus Delta region in 711 AD and, although a Muslim state was established there, their influence was barely felt in the rest of South Asia at that time. By the end of the tenth century, Central Asian Muslims moved into India from the northwest and expanded throughout the subcontinent. Muslim communities are now the largest minority religion in India, comprising more than 138 million people in a predominantly Hindu population of over one billion. It is unclear whether the Muslim expansion in India was a purely cultural phenomenon or had a genetic impact on the local population. To address this question from a male perspective, we typed eight microsatellite loci and 16 binary markers from the Y chromosome in 246 Muslims from Andhra Pradesh, and compared them to published data on 4,204 males from East Asia, Central Asia, other parts of India, Sri Lanka, Pakistan, Iran, the Middle East, Turkey, Egypt and Morocco. We find that the Muslim populations in general are genetically closer to their non-Muslim geographical neighbors than to other Muslims in India, and that there is a highly significant correlation between genetics and geography (but not religion). Our findings indicate that, despite the documented practice of marriage between Muslim men and Hindu women, Islamization in India did not involve large-scale replacement of Hindu Y chromosomes. The Muslim expansion in India was predominantly a cultural change and was not accompanied by significant gene flow, as seen in other places, such as China and Central Asia.

Friday, November 24, 2006

Ten rules to get the right postdoc

A paper appearing in the November 2006 issue PLoS Computational Biology (see link below) lists ten rules for selecting a postdoctoral position:

Rule 1: Select a Position that Excites You
Rule 2: Select a Laboratory That Suits Your Work and Lifestyle
Rule 3: Select a Laboratory and a Project That Develop New Skills
Rule 4: Have a Backup Plan
Rule 5: Choose a Project with Tangible Outcomes That Match Your Career Goals
Rule 6: Negotiate First Authorship before You Start
Rule 7: The Time in a Postdoctoral Fellowship Should Be Finite
Rule 8: Evaluate the Growth Path
Rule 9: Strive to Get Your Own Money
Rule 10: Learn to Recognize Opportunities

see the full text at:
Ten Simple Rules for Selecting a Postdoctoral Position by Philip E. Bourne, Iddo Friedberg

Tuesday, November 21, 2006

Food and Anthropology

For the latest edition of the Four Stone Hearth, there will be a food theme, so I thought I'd post some issues/questions that I have regarding food and anthropology:
  • To what extent did our ancestors eat a diet high in carbohydrates and sugar?
  • What is the significance of this regarding the prevalence of diabetes today? and how does this relate to the population differences in diabetes?
  • To what extent did marine foods contribute to our increase in brain size?
  • What's the deal with mannose and other sugars that degrade once vegatables and fruits are ripped from their plants or from their roots, but are supposedly vitally important, and lacking in our diet?
  • Does calorie restriction extend lifespan in humans? I don't think we'll know this "for sure" for several years.
  • Is a high protein diet healthy for humans? Did our ancestors consume a high protein diet?
  • What does the "optimal foraging strategy" consist of in today's modern environments? How might this differ between different SES levels and between different cultures?

Friday, November 17, 2006

Eye Color determined by a three SNP haplotype

Check out Dienekes' post on this new paper in AJHG. They find that eye color can be explained by a three SNP haplotype in OCA2, a gene that has been implicated in other pigmentary phenotypes as well.

Color and Ancestry in Brazil

From what I can understand, this study divides Brazilians into three "color" groups and then sees if their genomic ancestry as measured by 12 forensic markers predicts which color group they should fall in. They found a lot of overlap between the middle and extremes, but not between extremes. The number of markers is small. I'd like to see how they did their "physical evaluation" to determine who is white, intermediate, or black.

Color and Genomic Ancestry in Brazilians: A Study with Forensic Microsatellites.

Pimenta JR, Zuccherato LW, Debes AA, Maselli L, Soares RP, Moura-Neto RS, Rocha J, Bydlowski SP, Pena SD.

Hum Hered. 2006 Nov 10;62(4):190-195 [Epub ahead of print.]

The population of Brazil, formed by extensive admixture between Amerindians, Europeans and Africans, is one of the most variable in the world. We have recently published a study that used ancestry-informative markers to conclude that in Brazil, at an individual level, color, as determined by physical evaluation, was a poor predictor of genomic ancestry, estimated by molecular markers. To corroborate these findings we undertook the present investigation based on data from 12 commercially available forensic microsatellites that were utilized to estimate the personal genomic origin for each of 752 individuals from the city of Sao Paulo, belonging to different Brazilian color categories (275 Whites, 192 Intermediates and 285 Blacks). The genotypes permitted the calculation of a personal likelihood-ratio estimator of African or European ancestry. Although the 12 marker set proved capable of discriminating between European and African individuals, we observed very significant overlaps among the three color categories of Brazilians. This was confirmed quantitatively using a Bayesian analysis of population structure that did not demonstrate significant genetic differentiation between the three color groups. These results corroborate and validate our previous conclusions using ancestry-informative markers that in Brazil at the individual level there is significant dissociation of color and genomic ancestry.

Thursday, November 16, 2006

Neanderthal hoopla

I've been staying away from posting anything on the recent Neanderthal stuff, but I thought I'd give some props to the many posts at Gene Expression and Razib's Gene Expression.
In particular I like this post where Razib discusses the idea of "Ecotype persistence", then Chet Snicker's post showing an example of an ecotype in bears.
Check all these out, as well as John Hawks weblog.

Tuesday, November 14, 2006

Epigenetic modification through diet

Germ cells carry the epigenetic benefits of grandmother's diet

Craig Cooney

PNAS published online November 13, 2006

This is a commentary of a paper in PNAS about how mice fed differently (with methyl) during pregnancy can have offspring and grandoffspring with different coat color. "They find that this effect is inherited by the next generation, presumably through germ-line modifications during grandmaternal supplementation."
Then, from the last paragraph:
"In humans, the possibility even the likelihood, that grandmaternal diets contributed to the incidence of obesity and diabetes in the current generation and that today's dietary habits will have effects for generations to come make the work of Cropley et al. especially important."

Cropley JE, Suter CM, Beckman KB, Martin DIK (2006) PNAS USA 103:17308-17312

Monday, November 13, 2006

Genes underlying adaptation to hypoxia

Finding the genes underlying adaptation to hypoxia using genomic scans for genetic adaptation and admixture mapping.

Shriver MD, Mei R, Bigham A, Mao X, Brutsaert TD, Parra EJ, Moore LG.

Adv Exp Med Biol. 2006;588:89-100.

Abstract: The complete sequencing the human genome and recent analytical advances have provided the opportunity to perform genome-wide studies of human variation. There is substantial potential for such population-genomic approaches to assist efforts to uncover the historical and demographic histories of human populations. Additionally, these genome-wide datasets allow for investigations of variability among genomic regions. Although all genomic regions in a population have experienced the same demographic events, they have not been affected by these events in precisely the same way. Much of the variability among genomic regions is simply the result of genetic drift (i.e., gene frequency changes resulting from the effects of small breeding-population size), but some is also the result of genetic adaptation, which will only affect the gene under selection and nearby regions. We have used a new DNA typing assay that allows for the genotyping of thousands of SNPs on hundreds of samples to identify regions most likely to have been affected by genetic adaptation. Populations that have inhabited different niches (e.g., high-altitude regions) can be used to identify genes underlying the physiological differences. We have used two methods (admixture mapping and genome scans for genetic adaptation) founded on the population-genomic paradigms to search for genes underlying population differences in response to chronic hypoxia. There is great promise that together these methods will facilitate the discovery of genes influencing hypoxic response.

Friday, November 10, 2006

Human Gene Map for Performance and Health Related Phenotypes

This is always an interesting yearly paper to look at. It is a review of studies that have found associations between genetic variants and phenotypes such as endurance, muscle strength, training response, hemodynamic traits, insulin and glucose metabolism, fat distribution, blood lipid, exercise intolerance, Vo2max, and more ...

The Human Gene Map for Performance and Health-Related Fitness Phenotypes: The 2005 Update


Medicine and Science in Sports & Exercise Volume 38, Number 11 (November 2006)

Abstract: The current review presents the 2005 update of the human gene map for physical performance and health-related fitness phenotypes. It is based on peer-reviewed papers published by the end of 2005. The genes and markers with evidence of association or linkage with a performance or fitness phenotype in sedentary or active people, in adaptation to acute exercise, or for training-induced changes are positioned on the genetic map of all autosomes and the X chromosome. Negative studies are reviewed, but a gene or locus must be supported by at least one positive study before being inserted on the map. By the end of 2000, in the early version of the gene map, 29 loci were depicted. In contrast, the 2005 human gene map for physical performance and health-related phenotypes includes 165 autosomal gene entries and QTL, plus five others on the X chromosome. Moreover, there are 17 mitochondrial genes in which sequence variants have been shown to influence relevant fitness and performance phenotypes. Thus, the map is growing in complexity. Unfortunately, progress is slow in the field of genetics of fitness and performance, primarily because the number of laboratories and scientists focused on the role of genes and sequence variations in exercise-related traits continues to be quite limited.

Thursday, November 09, 2006

Why do humans have white sclera?

Here is a post from John Hawks about a paper that is coming out soon on how white sclera in humans may be an adaptation for communicating gaze direction. There is some experimental stuff here, comparing humans to other primates, so looks good.

Monday, November 06, 2006

Genes vs. environment in Afican American kidney function

Unfortunately, I don't have access to the full text, but this looks like an interesting study that attempts to disentangle the effects of genes and environment on physiology. Here, they seem to find that socioeconomic status plays a stronger role than genetics (as determined through genetic ancestry).

African Ancestry, Socioeconomic Status, and Kidney Function in Elderly African Americans: A Genetic Admixture Analysis.
Peralta CA, Ziv E, Katz R, Reiner A, Burchard EG, Fried L, Kwok PY, Psaty B, Shlipak M.

J Am Soc Nephrol. 2006 Nov 2; [Epub ahead of print]

Abstract: Kidney disease is a major public health problem in the United States that affects African Americans disproportionately. The relative contribution of environmental and genetic factors to the increased burden of kidney disease among African Americans is unknown. The associations of genetic African ancestry and socioeconomic status with kidney function were studied cross-sectionally and longitudinally among 736 community-dwelling African Americans who were aged >65 yr and participating in the Cardiovascular Health Study. Genetic African ancestry was determined by genotyping 24 biallelic ancestry-informative markers and combining this information statistically to generate an estimate of ancestry for each individual. Kidney function was evaluated by cystatin C and estimated GFR (eGFR) using the Modification of Diet in Renal Disease equation. Longitudinal changes in serum creatinine and eGFR were estimated using baseline and follow-up values. In cross-sectional analyses, there was no association between genetic African ancestry and either measure of kidney function (P = 0.36 for cystatin C and 0.68 for eGFR). African ancestry was not associated with change in serum creatinine >/=0.05 mg/dl per yr (odds ratio [OR] 0.94; 95% confidence interval [CI] 0.83 to 1.06) or with change in eGFR >/=3 ml/min per 1.73 m(2) per yr (OR 1.02; 95% CI 0.92 to 1.13). In contrast, self reported African-American race was strongly associated with increased risk for kidney disease progression compared with white individuals for change in creatinine (OR 1.77; 95% CI 1.33 to 2.36) and for change in eGFR (OR 3.21; 95% CI 2.54 to 4.06). Among self-identified African Americans, low income (<$8000/yr) was strongly associated with prevalent kidney dysfunction by cystatin C >1.29 g/dl (adjusted OR 2.7; 95% CI 1.0 to 7.5) or by eGFR <60>$35,000/yr. Alleles that are known to be present more frequently in the African ancestral group were not associated with kidney dysfunction or kidney disease progression. Rather, kidney dysfunction in elderly African Americans seems more attributable to differences in environmental and social factors.

Friday, November 03, 2006

Noncoding sequences and fast brain evolution in humans

Accelerated Evolution of Conserved Noncoding Sequences in Humans

Shyam Prabhakar, James P. Noonan, Svante Pääbo, Edward M. Rubin

Science: 3 November 2006:Vol. 314. no. 5800, p. 786

Abstract: Changes in gene regulation likely influenced the profound phenotypic divergence of humans from other mammals, but the extent of adaptive substitution in human regulatory sequences remains unknown. We identified 992 conserved noncoding sequences (CNSs) with a significant excess of human-specific substitutions. These accelerated elements were disproportionately found near genes involved in neuronal cell adhesion. To assess the uniqueness of human noncoding evolution, we examined CNSs accelerated in chimpanzee and mouse. Although we observed a similar enrichment near neuronal adhesion genes in chimpanzee, the accelerated CNSs themselves exhibited almost no overlap with those in human, suggesting independent evolution toward different neuronal phenotypes in each species. CNSs accelerated in mouse showed no bias toward neuronal cell adhesion. Our results indicate that widespread cis-regulatory changes in human evolution may have contributed to uniquely human features of brain development and function.

Wednesday, November 01, 2006

Do "good gene" dads make "good gene" offspring

Good genes sexual selection in nature

John A. Byers, and Lisette Waits

October 31, 2006 vol. 103 no. 44 16343-16345

Whether the mate sampling and choice performed by females in nature influences offspring performance is a controversial issue in theory and an open empirical question. Pronghorn (Antilocapra americana) females engage in an obvious and energetically expensive mate sampling process to identify vigorous males. Although individual females sample independently, their choices converge on a small proportion of males that sire most young. Offspring of attractive males were more likely to survive to weaning and to age classes as late as 5 years, resulting in a selection differential, calculated by expected differences in lifetime number of offspring weaned, of 0.32 against random mating. Enhanced survival to weaning appeared to be accomplished by faster growth rates. Females compensated for matings with a less attractive mate by elevating rates of milk delivery to their young. Because pronghorn males do not have costly ornaments, we conclude that female choice for good genes can exist in the absence of ornaments. Furthermore, female choice may be important and unrecognized as a force that can lower population genetic load.

Directional, then stabilizing selection on brain size

Nothing too surprising here, I don't think:

The dynamics of Machiavellian intelligence

Sergey Gavrilets and Aaron Vose

PNAS Published online before print October 30, 2006

Abstract: The "Machiavellian intelligence" hypothesis (or the "social brain" hypothesis) posits that large brains and distinctive cognitive abilities of humans have evolved via intense social competition in which social competitors developed increasingly sophisticated "Machiavellian" strategies as a means to achieve higher social and reproductive success. Here we build a mathematical model aiming to explore this hypothesis. In the model, genes control brains which invent and learn strategies (memes) which are used by males to gain advantage in competition for mates. We show that the dynamics of intelligence has three distinct phases. During the dormant phase only newly invented memes are present in the population. During the cognitive explosion phase the population’s meme count and the learning ability, cerebral capacity (controlling the number of different memes that the brain can learn and use), and Machiavellian fitness of individuals increase in a runaway fashion. During the saturation phase natural selection resulting from the costs of having large brains checks further increases in cognitive abilities. Overall, our results suggest that the mechanisms underlying the "Machiavellian intelligence" hypothesis can indeed result in the evolution of significant cognitive abilities on the time scale of 10 to 20 thousand generations. We show that cerebral capacity evolves faster and to a larger degree than learning ability. Our model suggests that there may be a tendency toward a reduction in cognitive abilities (driven by the costs of having a large brain) as the reproductive advantage of having a large brain decreases and the exposure to memes increases in modern societies.

Tuesday, October 31, 2006

HapMap of three population groups not too shabby

A worldwide survey of haplotype variation and linkage disequilibrium in the human genome

Donald F Conrad, Mattias Jakobsson, Graham Coop, Xiaoquan Wen, Jeffrey D Wall, Noah A Rosenberg & Jonathan K Pritchard

Nature Genetics 38, 1251 - 1260 (2006)

Abstract: Recent genomic surveys have produced high-resolution haplotype information, but only in a small number of human populations. We report haplotype structure across 12 Mb of DNA sequence in 927 individuals representing 52 populations. The geographic distribution of haplotypes reflects human history, with a loss of haplotype diversity as distance increases from Africa. Although the extent of linkage disequilibrium (LD) varies markedly across populations, considerable sharing of haplotype structure exists, and inferred recombination hotspot locations generally match across groups. The four samples in the International HapMap Project contain the majority of common haplotypes found in most populations: averaging across populations, 83% of common 20-kb haplotypes in a population are also common in the most similar HapMap sample. Consequently, although the portability of tag SNPs based on the HapMap is reduced in low-LD Africans, the HapMap will be helpful for the design of genome-wide association mapping studies in nearly all human populations.

Monday, October 30, 2006

Admixture in Mexico City: implications for admixture mapping of Type 2 diabetes genetic risk factors.
Martinez-Marignac VL, Valladares A, Cameron E, Chan A, Perera A, Globus-Goldberg R, Wacher N, Kumate J, McKeigue P, O'donnell D, Shriver MD, Cruz M, Parra EJ.

Hum Genet. 2006 Oct 26; [Epub ahead of print]

Abstract: Admixture mapping is a recently developed method for identifying genetic risk factors involved in complex traits or diseases showing prevalence differences between major continental groups. Type 2 diabetes (T2D) is at least twice as prevalent in Native American populations as in populations of European ancestry, so admixture mapping is well suited to study the genetic basis of this complex disease. We have characterized the admixture proportions in a sample of 286 unrelated T2D patients and 275 controls from Mexico City and we discuss the implications of the results for admixture mapping studies. Admixture proportions were estimated using 69 autosomal ancestry-informative markers (AIMs). Maternal and paternal contributions were estimated from geographically informative mtDNA and Y-specific polymorphisms. The average proportions of Native American, European and, West African admixture were estimated as 65, 30, and 5%, respectively. The contributions of Native American ancestors to maternal and paternal lineages were estimated as 90 and 40%, respectively. In a logistic model with higher educational status as dependent variable, the odds ratio for higher educational status associated with an increase from 0 to 1 in European admixture proportions was 9.4 (95%, credible interval 3.8-22.6). This association of socioeconomic status with individual admixture proportion shows that genetic stratification in this population is paralleled, and possibly maintained, by socioeconomic stratification. The effective number of generations back to unadmixed ancestors was 6.7 (95% CI 5.7-8.0), from which we can estimate that genome-wide admixture mapping will require typing about 1,400 evenly distributed AIMs to localize genes underlying disease risk between populations of European and Native American ancestry. Sample sizes of about 2,000 cases will be required to detect any locus that contributes an ancestry risk ratio of at least 1.5.

Saturday, October 28, 2006

Smithsonian makes a statement

Check out for a story on how the Smithsonian is refusing to display the Lucy skeleton that will be making a US tour over the next several years. Basically, the risk involved in moving this skeleton is deemed too high.

Friday, October 27, 2006

Cooperation model allows for adjustment of social ties

Cooperation Prevails When Individuals Adjust Their Social Ties

Francisco C. Santos, Jorge M. Pacheco, Tom Lenaerts

PLoS Computuational Biology Volume 2 | Issue 10 | OCTOBER 2006

Abstract: Conventional evolutionary game theory predicts that natural selection favours the selfish and strong even though cooperative interactions thrive at all levels of organization in living systems. Recent investigations demonstrated that a limiting factor for the evolution of cooperative interactions is the way in which they are organized, cooperators becoming evolutionarily competitive whenever individuals are constrained to interact with few others along the edges of networks with low average connectivity. Despite this insight, the conundrum of cooperation remains since recent empirical data shows that real networks exhibit typically high average connectivity and associated single-to-broad–scale heterogeneity. Here, a computational model is constructed in which individuals are able to self-organize both their strategy and their social ties throughout evolution, based exclusively on their self-interest. We show that the entangled evolution of individual strategy and network structure constitutes a key mechanism for the sustainability of cooperation in social networks. For a given average connectivity of the population, there is a critical value for the ratio W between the time scales associated with the evolution of strategy and of structure above which cooperators wipe out defectors. Moreover, the emerging social networks exhibit an overall heterogeneity that accounts very well for the diversity of patterns recently found in acquired data on social networks. Finally, heterogeneity is found to become maximal when W reaches its critical value. These results show that simple topological dynamics reflecting the individual capacity for self-organization of social ties can produce realistic networks of high average connectivity with associated single-to-broad–scale heterogeneity. On the other hand, they show that cooperation cannot evolve as a result of “social viscosity” alone in heterogeneous networks with high average connectivity, requiring the additional mechanism of topological co-evolution to ensure the survival of cooperative behaviour.

Thursday, October 26, 2006

Brain size and diet in orangutans

This is a paper in press in the Journal of Human Evolution. They found that individuals in one well fed group of orangs had larger brain sizes than in another not so well fed group. They say that this lends some support to the expensive tissue hypothesis. The sample sizes are small and, if I'm not mistaken, the differences are only significant for females. From the abstract (the link to H. floresiensis is interesting):

Our results, therefore, provide conditional support for the hypothesis that decreased brain size is related to prolonged episodes of food scarcity, and suggest a correlation between brain size, diet quality, and life history at the lowest macroevolutionary level. The association of a relatively small brain and poor diet quality in Pongo further suggests that ecological factors may plausibly account for such a reduction in brain size as observed in the recently recovered Homo floresiensis from Indonesia.

here's a press release from EurekAlert

Variation in brain size and ecology in Pongo

Andrea B. Taylor, and Carel P. van Schaik

Journal of Human Evolution Arcticle in Press

Abstract: Numerous hypotheses have been advanced to explain relative increases in brain size in primates and other mammals. However, notably less attention has been directed towards addressing the biological limits to increasing brain size. Here we explore variation in brain size in orangutans. We evaluated both raw and size-adjusted cranial capacity (CC) in adult Pongo pygmaeus pygmaeus (n = 147), P. p. wurmbii (n = 24), P. p. morio (n = 14), and P. abelii (n = 36). Results demonstrate significant variation in CC among orangutan taxa. Population differences in raw CC are significant for females (p = 0.014) but not males. Post-hoc pairwise comparisons among females further reveal that raw CC is significantly smaller in P. p. morio compared to both P. abelii and P. p. pygmaeus. When evaluated for proportionality, geometric equivalence in CC is not maintained in orangutans, as P. p. morio has a significantly smaller CC when compared to one or more other orangutan groups. Even after statistically partitioning size and size-correlated shape, P. p. morio has a significantly smaller CC compared to most other orangutan groups. These observed differences in relative brain size are consistent with known variation in resource quality and life history amongst orangutan populations. Specifically, P. p. morio is characterized by the least productive habitat, the lowest energy intake during extended lean periods, and the shortest interbirth intervals. Our results, therefore, provide conditional support for the hypothesis that decreased brain size is related to prolonged episodes of food scarcity, and suggest a correlation between brain size, diet quality, and life history at the lowest macroevolutionary level. The association of a relatively small brain and poor diet quality in Pongo further suggests that ecological factors may plausibly account for such a reduction in brain size as observed in the recently recovered Homo floresiensis from Indonesia.

Four Stone Hearth- Anthropology Blog Carnival

Check out the first edition of the Four Stone Hearth ... the first of a biweekly/bimonthly (whichever one means twice a month) Anthropology Blog Carnival...a sort of coming together of various Anthro-related blogs.

Tuesday, October 24, 2006

The uniqueness of Andaman Islanders

The authors use 9 autosomal STR markers to examine the affinities between The Andaman Islanders and Indians and Africans. I am unsure as to why they didn't examine other neighboring populations (Thailand, Indonesia, Burma), but maybe because in their previous study on Y-chromosome and mt-DNA they find the closest affinity with Indians. Anyway, they find/confirm that the Andaman Islanders are genetically very unique and may trace their ancestry to a first wave of humans out of Africa.

Unique origin of Andaman Islanders: insight from autosomal loci

K. Thangaraj, G. Chaubey, A. G. Reddy, V. K. Sing and L. Singh

Journal of Human Genetics Volume 51, Number 9 / September, 2006

Abstract: Our mtDNA and Y chromosome studies lead to the conclusion that the Andamanese “Negrito” mtDNA lineages have survived in the Andaman Islands in complete genetic isolation from other South and Southeast Asian populations since the initial settlement of the region by the out-of-Africa migration. In order to obtain a robust reconstruction of the evolutionary history of the Andamanese, we carried out a study on the three aboriginal populations, namely, the Great Andamanese, Onge and Nicobarese, using autosomal microsatellite markers. The range of alleles (7–31.2) observed in the studied population and heterozygosity values (0.392–0.857) indicate that the selected STR markers are highly polymorphic in all the three populations, and genetic variability within the populations is significantly high, with a mean gene diversity of 77%. The Andaman “Negrito” populations do not show particular affinities either with the African populations or with the Indian populations, confirming their unique origin. In contrast, Nicobarese show close affinities with the Southeast Asian populations, suggesting their recent entry in the Islands.

Monday, October 23, 2006

ACTN3 and muscle function

Variants of the ACTN3 gene show pretty large population differences (also not present in chimps) and have been associated with ability in sprint sports vs. endurance. This is thought to be due to the function of ACTN3 in determining the slow twitch vs. fast twitch muscle fiber proportions. In this paper they look at some Greek people (not a self-selected group, because unlike previous studies, these are not professional or even amateur athletes and they are young) to see if they can reproduce that association and they only find an association for the 40 meter sprint in the predicted direction. They cite a paper that I had also missed that fails to support the hypothesized association among Kenyan marathon runners.

Association analysis of the ACTN3 R577X polymorphism and complex quantitative body composition and performance phenotypes in adolescent Greeks

European Journal of Human Genetics

advance online publication 11 October 2006

Colin N Mora, Nan Yang, Mark E S Bailey, Athanasios Tsiokanos, Athanasios Jamurtas, Daniel G MacArthur, Kathryn North, Yannis P Pitsiladis and Richard H Wilson

Abstract: The functional allele (577R) of ACTN3, which encodes human -actinin-3, has been reported to be associated with elite athletic status and with response to resistance training, while the nonfunctional allele (577X) has been proposed as a candidate metabolically thrifty allele. In a study of 992 adolescent Greeks, we show that there is a significant association (P=0.003) between the ACTN3 R577X polymorphism and 40 m sprint time in males that accounts for 2.3% of phenotypic variance, with the 577R allele contributing to faster times in an additive manner. The R577X polymorphism is not associated with other power phenotypes related to 40 m sprint, nor with an endurance phenotype. Furthermore, the polymorphism is not associated with obesity-related phenotypes in our population, suggesting that the 577X allele is not a thrifty allele, and thus the persistence of this null allele must be explained in other terms.

Genetic relatedness in chimp groups

Check out John Hawks' entry on Patrilocality and genetic relatedness in chimpanzees. They fail to support the hypothesis that interactions in large groups are driven strongly by kin selection, because the relatedness between males of the same group is only a bit higher than relatedness between groups.
In the paper, the authors assume that humans are universally patrilocal, but this still seems to be under considerable debate. (once I'm organized, I'll start giving references for this sort of thing)

Friday, October 20, 2006

What it takes to become a good hunter

To be fair, I haven't read the paper, but it seems like body size and skills/knowledge are not the only hypotheses that predict hunting competence. Another might just be motivation, mainly mediated by number of dependents. In addition, Kaplan et al. have found that hunting return rates tend to peak at 4o years old or so, long after human males have reached their peak body size, so I'm unclear as to why they would even consider something like body size.

How long does it take to become a proficient hunter? Implications for the evolution of extended development and long life span

Michael Gurven, Hillard Kaplan and Maguin Gutierrez
Journal of Human Evolution Volume 51, Issue 5 , November 2006, Pages 454-470
Abstract: Human hunting is arguably one of the most difficult activities common to foraging peoples now and in the past. Children and teenagers have usually been described as incompetent hunters in ethnographies of hunter-gatherers. This paper explores the extent to which adult-level competence is limited more by the constraints of physical capital, or body size, and brain-based capital, or skills and learning. The grandmother hypothesis requires that production is an increasing function of size alone, while the embodied capital model stipulates that production is a function of both size and delayed learning. Tests based on observational, interview, and experimental data collected among Tsimane Amerindians of the Bolivian Amazon suggest that size alone cannot explain the long delay until peak hunting productivity. Indirect encounters (e.g., smells, sounds, tracks, and scat) and shooting of stationary targets are two components of hunting ability limited primarily by physical size alone, but the more difficult components of hunting—direct encounters with important prey items and successful capture—require substantial skill. Those skills can take an additional ten to twenty years to develop after achieving adult body size.

Wednesday, October 18, 2006

Characteristics of HARs (human accelerated regions)

...they are:
- A/T to G/C changes (weak to strong)
- located in high recombination areas
- next to genes that are enriched for transcription factors
- located in high G/C content areas near telomeres

Forces Shaping the Fastest Evolving Regions in the Human Genome

Katherine S. Pollard, Sofie R. Salama, Bryan King, Andrew D. Kern, Tim Dreszer, Sol Katzman1, Adam Siepel, Jakob S. Pedersen, Gill Bejerano, Robert Baertsch, Kate R. Rosenbloom, Jim Kent, David Haussler

PLoS Genetics vol. 2 issue 10; October 2006

Abstract: Comparative genomics allow us to search the human genome for segments that were extensively changed in the last ~5 million years since divergence from our common ancestor with chimpanzee, but are highly conserved in other species and thus are likely to be functional. We found 202 genomic elements that are highly conserved in vertebrates but show evidence of significantly accelerated substitution rates in human. These are mostly in non-coding DNA, often near genes associated with transcription and DNA binding. Resequencing confirmed that the five most accelerated elements are dramatically changed in human but not in other primates, with seven times more substitutions in human than in chimp. The accelerated elements, and in particular the top five, show a strong bias for adenine and thymine to guanine and cytosine nucleotide changes and are disproportionately located in high recombination and high guanine and cytosine content environments near telomeres, suggesting either biased gene conversion or isochore selection. In addition, there is some evidence of directional selection in the regions containing the two most accelerated regions. A combination of evolutionary forces has contributed to accelerated evolution of the fastest evolving elements in the human genome.

Tuesday, October 17, 2006

Back to blogging soon

I'm back from a short vacation and ready to get back to blogging... looking forward to the neanderthal sequence report coming out soon, supposedly

Monday, October 09, 2006

Bruce Lahn interview

Check out JP's post at Gene Expression where they have 10 questions for Bruce Lahn...some interesting tidbits, including his take on brain size difference among hominid species, how to test for signatures of selection, and about the future of research in human genetics with respect to niches for data miners vs. researhers who generate their own data.

Another way to estimate admixture

This looks like a STRUCTURE-type program.

Bayesian identification of admixture events using multilocus molecular markers.

Corander J, Marttinen P.

Molecular Ecology 2006 Sep;15(10):2833-43

Abstract: Bayesian statistical methods for the estimation of hidden genetic structure of populations have gained considerable popularity in the recent years. Utilizing molecular marker data, Bayesian mixture models attempt to identify a hidden population structure by clustering individuals into genetically divergent groups, whereas admixture models target at separating the ancestral sources of the alleles observed in different individuals. We discuss the difficulties involved in the simultaneous estimation of the number of ancestral populations and the levels of admixture in studied individuals' genomes. To resolve this issue, we introduce a computationally efficient method for the identification of admixture events in the population history. Our approach is illustrated by analyses of several challenging real and simulated data sets. The software (baps), implementing the methods introduced here, is freely available at

Thursday, October 05, 2006

Do we know all the ways that humans got to the Americas?

A paper in Current Anthropology from a few months back that, using data on presence of hookworm the pre-Columbian hookworms and "paleoclimate modelling simulations" implies that there were other colonizers of the Americas, other than the Clovis ones who came through the Bering Strait. From the last paragraph:

The Americas might very well have been originally inhabited by humans moving along an interior land route across Beringia at around 13,000 years BP; however, our research indicates that the Clovis people were unlikely carriers of the hookworm, and this suggests that the parasites were introduced by some alternative mechanism. Alternative mechanisms include the possibility that the parasite entered the Americas by an interior route via Beringia during a period of lower sea level but with regional temperatures significantly higher than at 13,000 years BP. The archaeological literature offers a number of possible nonterrestrial routes, including transoceanic contacts between Japan and Central America (Meggers 1975) and coastal routes along the North Pacific (Heusser 1960; Fladmark 1979; Hetherington et al. 2003) and the North Atlantic (Bradley and Stanford 2004). Pointing to paleoparasitological findings, Araujo, Ferreira, and Confalonieri (1981; Araujo et al. 1988) have discussed the possibility of a trans-Pacific introduction.

Parasites, Paleoclimate, and the Peopling of the Americas
Using the Hookworm to Time the Clovis Migration

Alvaro Montenegro, Adauto Araujo, Michael Eby, Luiz Fernando Ferreira, Renée Hetherington, and Andrew J. Weaver

CURRENT ANTHROPOLOGY Volume 47, Number 1, February 2006

Abstract: Paleoparasitological findings and paleoclimate modelling simulations indicate that early peoples migrating via the "Clovis first" route across Beringia into North America could not have traversed the required distance in time to provide a reasonable explanation for the presence of the hookworm in the pre-Columbian Americas. The introduction of the hookworm into the Americas by a land migration at around 13,000 years BP could have happened only under extraordinary circumstances and even then would have required displacement rates that appear to have no parallel in the archaeology of the continent. This implies that while the Clovis people may have been the first migrants to the Americas, they were almost certainly not the only such migrants.

Tuesday, October 03, 2006

A(nother) "muscle gene" shows population differences

Dienekes reports on this in-press AJHG paper, by Matthew A. Saunders, Jeffrey M. Good, Elizabeth C. Lawrence, Robert E. Ferrell, Wen-Hsiung Li and Michael W. Nachman, entitled Human adaptive evolution at Myostatin, a regulator of muscle growth

The authors find strong evidence of (maybe diversifying) selection in humans on some variants of the Myostatin gene (GDF8), which encodes a negative regulator of skeletal muscle growth. They also find somewhat large differences in frequency of these mutations between sub-Saharan Africans (up to 31%) and rare in others.

The authors don't mention much about the implications of this in terms of adaptation, except for a passing mention that "one of the many possible adaptive implications of such an effect could be protection from muscle-wasting in times of famine, a potentially recurrent phenomenon for early agricultural societies."

This gene falls in a line of other muscle related genes found to have population differences, the main one being ACTN3.

Monday, October 02, 2006

Review of programs for population genetics data analysis

This looks like a great paper. It is the first in a four paper focus on statistical genetics in the latest Nature Review Genetics. It describes and compares 20 or so programs based on what they can be used for, how they can be used, what type of data they can work with, their assumptions, gives links to their online resources, how the same data files can be used with several programs, computation time, etc... can make for great reference material.

Computer programs for population genetics data analysis: a survival guide

Laurent Excoffier and Gerald Heckel

Nature Reviews Genetics 7, 745-758 (October 2006)
Focus on: Statistical Analysis

Abstract: The analysis of genetic diversity within species is vital for understanding evolutionary processes at the population level and at the genomic level. A large quantity of data can now be produced at an unprecedented rate, requiring the use of dedicated computer programs to extract all embedded information. Several statistical packages have been recently developed, which offer a panel of standard and more sophisticated analyses. We describe here the functionalities, special features and assumptions of more than 20 such programs, indicate how they can interoperate, and discuss new directions that could lead to improved software and analyses.

Friday, September 29, 2006

Male vs. Female genetic histories among Native Americans

Asymmetric Male and Female Genetic Histories among Native Americans from Eastern North America

Deborah A. Bolnick, Daniel I. Bolnick and David Glenn Smith

Molecular Biology and Evolution 2006 23(11):2161-2174

Previous studies have investigated the human population history of eastern North America by examining mitochondrial DNA (mtDNA) variation among Native Americans, but these studies could only reconstruct maternal population history. To evaluate similarities and differences in the maternal and paternal population histories of this region, we obtained DNA samples from 605 individuals, representing 16 indigenous populations. After amplifying the amelogenin locus to identify males, we genotyped 8 binary polymorphisms and 10 microsatellites in the male-specific region of the Y chromosome. This analysis identified 6 haplogroups and 175 haplotypes. We found that sociocultural factors have played a more important role than language or geography in shaping the patterns of Y chromosome variation in eastern North America. Comparisons with previous mtDNA studies of the same samples demonstrate that male and female demographic histories differ substantially in this region. Postmarital residence patterns have strongly influenced genetic structure, with patrilocal and matrilocal populations showing different patterns of male and female gene flow. European contact also had a significant but sex-specific impact due to a high level of male-mediated European admixture. Finally, this study addresses long-standing questions about the history of Iroquoian populations by suggesting that the ancestral Iroquoian population lived in southeastern North America.

Thursday, September 28, 2006

The eight Americas of mortality

I thought the most interesting thing from this paper is how much Asians (America 1, top black line in figure below) stood out compared to the other groups as the Americans with the lowest mortality:
Eight Americas: Investigating Mortality Disparities across Races, Counties, and Race-Counties in the United States

Christopher J. L. Murray Sandeep C. Kulkarni, Catherine Michaud, Niels Tomijima, Maria T. Bulzacchelli, Terrell J. Iandiorio, Majid Ezzati

PLoS Medicine September 2006, vol. 3 Issue 9: 1513-1524

Editor's Summary
It has been recognized for a long time that the number of years that people in the United States can expect to live (“life expectancy”) varies enormously. For example, white Americans tend to live longer than black Americans, and life expectancy is much greater in some of the roughly 3,000 counties of the US than it is in others. However, there is a lack of information and understanding on how big a part is played in “health inequalities” by specific diseases and injuries, by risk factors (such as tobacco, alcohol, and obesity), and by variations in access to effective health care.

Why Was This Study Done?
The researchers wanted to find a way of dividing the people of the US into groups based on a small number of characteristics—such as location of county of residence, race, and income—that would help demonstrate the most important factors accounting for differences in life expectancy.

What Did the Researchers Do and Find?
The researchers used figures from the US Census Bureau and the National Center for Health Statistics to calculate mortality (death) rates for the years 1982–2001. They took note of the county of residence and of the race of all the people who died during that period of time. This enabled them to calculate the mortality rates for all 8,221 “race-county units” (all of the individuals of a given race in a given county). They experimented with different ways of combining the race-counties into a small and manageable number of groups. They eventually settled on the idea of there being “eight Americas,” defined on the basis of race-county, population density, income, and homicide rate. Each group contains millions or tens of millions of people. For each of the eight groups the researchers estimated life expectancy, the risk of mortality from specific diseases, the proportion of people who had health insurance, and people's routine encounters with health-care services. (The researchers also created maps of life expectancies for the US counties.) They describe their eight Americas as follows: Asians, northland low-income rural whites, Middle America, low-income whites in Appalachia and the Mississippi Valley, western Native Americans, black Middle America, low-income southern rural blacks, and high-risk urban blacks.

Many striking differences in life expectancy were found between the eight groups. For example, in 2001, the life expectancy gap between the 3.4 million high-risk urban black males and the 5.6 million Asian females was nearly 21 years. Within the sexes, the life expectancy gap between the best-off and the worst-off groups was 15.4 years for males (Asians versus high-risk urban blacks) and 12.8 years for females (Asians versus low-income rural blacks in the South). The causes of death that were mainly responsible for these variations were various chronic diseases and injury. The gaps between best-off and worst-off were similar in 2001 to what they were in 1987.

What Do These Findings Mean?
Health inequalities in the US are large and are showing no sign of reducing. Social and economic reforms would certainly help change the situation. At the same time, the public health system should also improve the way in which it deals with risk factors for chronic diseases and injuries so that groups with the highest death rates receive larger benefits.

Wednesday, September 27, 2006

Did several homo species live together at the same time?

This is a new paper in the Journal of Human Evolution. It makes the argument that Pleistocene Homo could not have speciated into several species because we are like canids in many ways and canids have not speciated very much:

In this paper, I use an analogy to the wolf-like canids (Canis lupus, C. rufus, and C. latrans) to ask the question, How many Homo species should there be, given their likely behavioral profile(s)? (cf. Foley, 1991). The wolf-like canids are behaviorally similar to Pleistocene hominids in three key ways: (1) they are adapted for endurance locomotion, (2) they have a diverse diet, and (3) they are socially flexible. These characteristics lead to high habitat tolerance, which appears to have made the wolf-like canids resistant to allopatric speciation. I argue that analogous habitat tolerance would have likewise made isolation and allopatric speciation among Pleistocene Homo unlikely, especially in Africa. In contrast to an earlier single-species hypothesis which posited competitive exclusion between sympatric hominid species (Wolpoff, 1971), this paper explores behavioral constraints on the process of speciation itself under conditions of temporary allopatry.

This paper cites the endurance running model of humans (D.M. Bramble and D.E. Lieberman, Endurance running and the evolution of Homo, Nature 432 (2004), pp. 345–352). I'm surprised how often that paper gets cited.

I think the paper is an important contribution, and I personally have always liked the comparison between humans and canines (cooperative hunting, highly social, cooperative child care, fission-fusion groups, etc...), and I think the issue of whether several Homo species lived together at the same time is important and fascinating, but there are still many questions that remain, as discussed by the authors in the conclusion. Here is the last paragraph:

Finally, a “species resilience” perspective on Pleistocene Homo evolution offers the potential for new comparative analyses of modern species to explore constraints on the speciation process. It has long been recognized that eurytopic mammals tend to be more widely distributed and less speciose than stenotopic ones. However, detailed quantitative analyses of mobility, dietary breadth, and genetic variation within and between eurytopic species, in conjunction with fossil evidence, are needed to resolve more precisely the determinants of relative species resilience. Especially interesting would be comparative analyses of intercontinentally distributed carnivores such as ursids, felids, and canids, as well as of widely distributed primates. Coyne and Orr (2004: 425) note that relatively little research has been devoted to factors that prevent speciation. Comparative analyses of species resilience in Homo and other eurytopes, therefore, offer the possibility of contributing both to debates about hominid taxonomy and to our understanding of mammalian speciation in general (cf. Vrba, 1992).

Species resilience in Pleistocene hominids that traveled far and ate widely: An analogy to the wolf-like canids
A. Clark Arcadia

Journal of Human Evolution Vo. 51, Issue 4 October, 2006: 383-394

Abstract: Morphological and genetic analyses have yet to resolve the question of whether more than one species of Homo existed contemporaneously in the Pleistocene. In an effort to contribute a process-related perspective to hominid phylogenetic reconstruction, this paper uses an analogy to the northern wolf-like canids (the wolves and coyotes) to ask the question, How many Homo species should there be, given their likely behavioral profile(s)? In contrast to earlier comparisons to social carnivores which sought to illuminate specific aspects of hominid behavioral ecology, this paper explores behavioral constraints on the process of speciation itself. The analogy suggests that because Pleistocene Homo probably exhibited high habitat tolerance, they would not have had the opportunity to speciate, especially in Africa. In contrast to an earlier single-species hypothesis based on competitive exclusion between sympatric hominid species, this paper explores constraints on the process of speciation under conditions of temporary allopatry.
Locations of visitors to this page