Tuesday, July 31, 2007

Monogamy associated with larger brain

A paper entitled "The evolution of the social brain: Anthropoid primates contrast with other vertebrates" just came out in Proceedings of the Royal Society, B (a great journal, I would add). The article is open access, so the link will take you directly to the paper. The authors, Susanne Shultz and Robin Dunbar (of “social intelligence” or “social brain” hypothesis fame), examine the relationship between brain size and pairbonding/enduring social bonds. Previous research has attempted to correlate big brains with group size and amount of deception, for example. Basically the theory goes: Animals have large brains to deal with living in groups - it takes a big brain to be social.

The interesting thing that they find in this paper is that, in non-primate taxa, pairbonded species have larger brain sizes than would be predicted for group size. So there’s something about monogamy or related to monogamy that requires more brain power. In primates this effect does not happen. For them, those species that live in the largest groups have the larger brains. The authors give a short explanation as to why the pattern does not hold in primates, namely because in primates “these bonded relationships have been generalized to all social partners”. The authors also do a pretty good job of explaining many of the potential confounders (phylogeny, ecology etc…).

In the case of humans, it is hard to disentangle our ecological niche in terms of food type from our social systems. Some argue that we need large brains to obtain hard-to-get foods (meat, roots, nuts etc…) while others claim is that it’s our social complexity that requires a big brain. The two are not mutually exclusive since you need to be cooperative and have a social network to get food.

There’s got to be some way to separate these two, or some kind of comparative analysis that would separate the two variables (feeding ecology and sociality). And then, let’s not forget the sexual selection hypothesis that says that a large brain, in humans mainly, is the result of sexual selection.

Monday, July 30, 2007

The genetic affinities of click-speaking populations

Dienekes has the abstract to a paper called "History of Click-Speaking Populations of Africa Inferred from mtDNA and Y Chromosome Genetic Variation."

Genetics of human skin pigmentation

OCA2*481Thr , a hypofunctional allele in pigmentation, is characteristic of northeastern Asian populations

Journal of Human Genetics Volume 52, Number 8 / August, 2007

Isao Yuasa, Kazuo Umetsu, Shinji Harihara, Aya Miyoshi, Naruya Saitou, Kyung Sook Park, Bumbein Dashnyam, Feng Jin, Gérard Lucotte, Prasanta K. Chattopadhyay, Lotte Henke and Jürgen Henke

Abstract: Asians as well as Europeans have light skin, for which no genes to date are known to be responsible. A mutation, Ala481Thr (c.G1559A), in the oculocutaneous albinism type II (OCA2) gene has approximately 70% function of the wild type allele in melanogenesis. In this study, the distribution of the mutation was investigated in a total of 2,615 individuals in 20 populations from various areas. OCA2*481Thr prevailed almost exclusively in a northeastern part of Asia. The allele frequency was highest in Buryat (0.24) in Mongolia and showed a north–south downward geographical gradient. These findings suggest that OCA2*481Thr arose in a region of low ultraviolet radiation and thereafter spread to neighboring populations.

Sunday, July 29, 2007

ACE in baboons and humans

genetic polymorphisms, phenotypes and cross species comparisons:

Parallel effects of genetic variation in ACE activity in baboons and humans

Jenny Tung, Johannes Rudolph, Jeanne Altmann, Susan C. Alberts

American Journal of Physical Anthropology 2007, Volume 134, Issue 1,1-8

Abstract: Like humans, savannah baboons (Papio sp.) show heritable interindividual variation in complex physiological phenotypes. One prominent example of such variation involves production of the homeostatic regulator protein angiotensin converting enzyme (ACE), which shows heritable variation in both baboons and humans. In humans, this phenotypic variation is associated with an Alu insertion-deletion polymorphism in the ACE gene, which explains approximately half of the variation in serum ACE activity. We identified a similar Alu insertion-deletion polymorphism in the baboon ACE homologue and measured its frequency in a wild population and a captive population of baboons. We also analyzed the contribution of ACE genotype at this indel to variation in serum ACE activity in the captive population. When conditioned on weight, a known factor affecting ACE activity in humans, age and ACE genotype both accounted for variance in ACE activity; in particular, we identified a significant nonadditive interaction between age and genotype. A model incorporating this interaction effect explained 21.6% of the variation in residual serum ACE activity. Individuals homozygous for the deletion mutation exhibited significantly higher levels of ACE activity than insertion-deletion heterozygotes at younger ages (10-14 years), but showed a trend towards lower levels of ACE activity compared with heterozygotes at older ages (15 years). These results demonstrate an interesting parallel between the genetic architecture underlying ACE variation in humans and baboons, suggesting that further attention should be paid in humans to the relationship between ACE genetic variation and aging.

Friday, July 27, 2007

Where did the Africans in Brazil come from?

I assume that in this paper they give some historical context to the bio-geographical origin of the African lineages found today among Black males in Africa.

The Phylogeography of African Brazilians.

Gonçalves VF, Carvalho CM, Bortolini MC, Bydlowski SP, Pena SD.

Hum Hered. 2008 Jul 25;65(1):23-32

Background/Aims: Approximately four million Africans were taken as slaves to Brazil, where they interbred extensively with Amerindians and Europeans. We have previously shown that while most White Brazilians carry Y chromosomes of European origin, they display high proportions of African and Amerindian mtDNA lineages, because of sex-biased genetic admixture. Methods: We studied the Y chromosome and mtDNA haplogroup structure of 120 Black males from Sao Paulo, Brazil. Results: Only 48% of the Y chromosomes, but 85% of the mtDNA haplogroups were characteristic of sub-Saharan Africa, confirming our previous observation of sexually biased mating. We mined literature data for mtDNA and Y chromosome haplogroup frequencies for African native populations from regions involved in Atlantic Slave Trade. Principal Components Analysis and Bayesian analysis of population structure revealed no genetic differentiation of Y chromosome marker frequencies between the African regions. However, mtDNA examination unraveled considerable genetic structure, with three clusters at Central-West Africa, West Africa and Southeast Africa. A hypothesis is proposed to explain this structure. Conclusion: Using these mtDNA data we could obtain for the first time an estimate of the relative ancestral contribution of Central-West (0.445), West (0.431) and Southeast Africa (0.123) to African Brazilians from Sao Paulo. These estimates are consistent with historical information.

Thursday, July 26, 2007

The Grandfather hypothesis

I'm not sure what to think about this paper, nor do I have time to really think about it ... but I do have time to put pictures.

Selection for long lifespan in men: benefits of grandfathering?

M. Lahdenperä, A.F. Russell, V. Lummaa

Proc. Roy. Soc. B
online before print

Abstract: Life-history theory suggests that individuals should live until their reproductive potential declines, and the lifespan of human men is consistent with this idea. However, because women can live long after menopause and this prolonged post-reproductive life can be explained, in part, by the fitness enhancing effects of grandmothering, an alternative hypothesis is that male lifespan is influenced by the potential to gain fitness through grandfathering. Here we investigate whether men, who could not gain fitness through reproduction after their wife's menopause (i.e. married only once), enhanced their fitness through grandfathering in historical Finns. Father presence was associated with reductions in offspring age at first reproduction and birth intervals, but generally not increases in reproductive tenure lengths. Father presence had little influence on offspring lifetime fecundity and no influence on offspring lifetime reproductive success. Overall, in contrast to our results for women in the same population, men do not gain extra fitness (i.e. more grandchildren) through grandfathering. Our results suggest that if evidence for a ‘grandfather’ hypothesis is lacking in a monogamous society, then its general importance in shaping male lifespan during our more promiscuous evolutionary past is likely to be negligible.

Wednesday, July 25, 2007

Variation, cont.

see smallest horse below largest horse:

Tuesday, July 24, 2007

Chimp vs. human punishment

This study is part of a recent line of research that examines how chimpanzees and humans are different. This one highlights the ultra-sociality of humans who are willing to undergo a net cost so that they can punish someone. ... like the ultimatum game, where an individual could accept an offer of 3 out of $10, but instead refuses to accept free money for the sake of fairness. There are several ways to interpret this. Humans are so extremely social, and punishment is a way of signalling that a person is more concerned about fairness and is willing to undergo a cost to show to others that he values fairness. In this way he gains a good reputation. It is hard to interpret behavior through these games, since it was not in a game-like environment that these behaviors evolved. Alternatively, this research could be used to argue that group selection is operating, since an individual is undergoing a net cost for the good of the group... although the counter-argument is that the individual is not undergoing a net cost - he is gaining a good reputation... bottom line here - humans are ultra-social.

Chimpanzees are vengeful but not spiteful

Keith Jensen, Josep Call, and Michael Tomasello

PNAS online before print July 20, 2007

Abstract: People are willing to punish others at a personal cost, and this apparently antisocial tendency can stabilize cooperation. What motivates humans to punish noncooperators is likely a combination of aversion to both unfair outcomes and unfair intentions. Here we report a pair of studies in which captive chimpanzees (Pan troglodytes) did not inflict costs on conspecifics by knocking food away if the outcome alone was personally disadvantageous but did retaliate against conspecifics who actually stole the food from them. Like humans, chimpanzees retaliate against personally harmful actions, but unlike humans, they are indifferent to simply personally disadvantageous outcomes and are therefore not spiteful.

Saturday, July 21, 2007


It's all about the mutations

this one is probably worth a few reads...

The new mutation theory of phenotypic evolution

Masatoshi Nei

PNAS Published online before print

Abstract: Recent studies of developmental biology have shown that the genes controlling phenotypic characters expressed in the early stage of development are highly conserved and that recent evolutionary changes have occurred primarily in the characters expressed in later stages of development. Even the genes controlling the latter characters are generally conserved, but there is a large component of neutral or nearly neutral genetic variation within and between closely related species. Phenotypic evolution occurs primarily by mutation of genes that interact with one another in the developmental process. The enormous amount of phenotypic diversity among different phyla or classes of organisms is a product of accumulation of novel mutations and their conservation that have facilitated adaptation to different environments. Novel mutations may be incorporated into the genome by natural selection (elimination of preexisting genotypes) or by random processes such as genetic and genomic drift. However, once the mutations are incorporated into the genome, they may generate developmental constraints that will affect the future direction of phenotypic evolution. It appears that the driving force of phenotypic evolution is mutation, and natural selection is of secondary importance.

Thursday, July 19, 2007

LD in African-Americans

making the case for the utility of admixed populations (with greater LD) in genotyping and association studies.

Dissecting Linkage Disequilibrium in African American Genomes: Roles of Markers and Individuals.

Xu S, Huang W, Wang H, He Y, Wang Y, Wang Y, Qian J, Xiong M, Jin L.

Mol Biol Evol. 2007 Jul 13; [Epub ahead of print]

Abstract: Substantial increases of linkage disequilibrium (LD) both in magnitude and in range have been observed in recently admixed populations such as African American (AfA). On the other hand, it has also been shown that LD in African Americans was very similar to that of African. In this study, we attempted to resolve these contradicting observations by conducting a systematic examination of the LD structure in African Americans by genotyping a sample of African American individuals at 24,341 SNPs spanning almost the entire chromosome 21, with an average density of 1.5 kb/SNP. The overall LD in African Americans is similar to that in African populations and much less than that in European populations. Even when the ancestry-informative markers (AIMs) were used, extended LD in AfA was found to be limited to certain magnitude range (0.2

Wednesday, July 18, 2007

Cranial sizes and distance from Africa

I wonder if their test is really able to detect if there was even a tiny bit of a "second origin"... otherwise this looks pretty cool, though haven't gone through the details.

The effect of ancient population bottlenecks on human phenotypic variation

Andrea Manica, William Amos, François Balloux & Tsunehiko Hanihara

Nature 448, 346-348 (19 July 2007)

Abstract: The origin and patterns of dispersal of anatomically modern humans are the focus of considerable debate. Global genetic analyses have argued for one single origin, placed somewhere in Africa. This scenario implies a rapid expansion, with a series of bottlenecks of small amplitude, which would have led to the observed smooth loss of genetic diversity with increasing distance from Africa. Analyses of cranial data, on the other hand, have given mixed results, and have been argued to support multiple origins of modern humans. Using a large data set of skull measurements and an analytical framework equivalent to that used for genetic data, we show that the loss in genetic diversity has been mirrored by a loss in phenotypic variability. We find evidence for an African origin, placed somewhere in the central/southern part of the continent, which harbours the highest intra-population diversity in phenotypic measurements. We failed to find evidence for a second origin, and we confirm these results on a large genetic data set. Distance from Africa accounts for an average 19–25% of heritable variation in craniometric measurements—a remarkably strong effect for phenotypic measurements known to be under selection.


Andrew at the "Statistical Modeling, Causal Inference, and Social Science" blog (that's a long name!) is often talking about how he think that graphs should always be used in favor of tables.
He has created a website called tables2graphs describing how this can be done and has developed some programs to do it.
I agree that tables are not as visually pleasing as graphs and I think that seeing data graphically can illuminate patterns that we might not otherwise see. The only advantage of tables that I can imagine is that with graphs you don't get the exact values, you just get eyeball guesses, but I'm sure they have some way of addressing that.

Monday, July 16, 2007

Lucy comes to Houston

Via TAMU Anthropology in the News, this is a story about how local Ethiopians are irate, for political and other reasons, at the arrival of Lucy to the Houston Museum, the first stop on her US tour. I had to post on this since I grew up in Houston and had some Ethiopian friends.
Ethiopians in Houston decry debut of Lucy fossil

Tuesday, July 10, 2007

Another paper on the evolution of human running

The evolution of human running: Effects of changes in lower-limb length on locomotor economy

Karen L. Steudel-Numbers, Timothy D. Weaver, and Cara M. Wall-Scheffler

Journal of Human Evolution Volume 53, Issue 2, August 2007, Pages 191-196

Abstract: Previous studies have differed in expectations about whether long limbs should increase or decrease the energetic cost of locomotion. It has recently been shown that relatively longer lower limbs (relative to body mass) reduce the energetic cost of human walking. Here we report on whether a relationship exists between limb length and cost of human running. Subjects whose measured lower-limb lengths were relatively long or short for their mass (as judged by deviations from predicted values based on a regression of lower-limb length on body mass) were selected. Eighteen human subjects rested in a seated position and ran on a treadmill at 2.68 m s−1 while their expired gases were collected and analyzed; stride length was determined from videotapes. We found significant negative relationships between relative lower-limb length and two measures of cost. The partial correlation between net cost of transport and lower-limb length controlling for body mass was r = −0.69 (p = 0.002). The partial correlation between the gross cost of locomotion at 2.68 m s−1 and lower-limb length controlling for body mass was r = −0.61 (p = 0.009). Thus, subjects with relatively longer lower limbs tend to have lower locomotor costs than those with relatively shorter lower limbs, similar to the results found for human walking. Contrary to general expectation, a linear relationship between stride length and lower-limb length was not found.

Monday, July 09, 2007

Sexually antagonistic traits maintain genetic variation in populations

This paper looks really interesting. I don't know if I buy it, and don't have time to make that determination now. The maintenance of high levels of genetic variation in populations is a fascinating topic.

Sexually antagonistic genetic variation for fitness in red deer

Katharina Foerster, Tim Coulson, Ben C. Sheldon, Josephine M. Pemberton, Tim H. Clutton-Brock & Loeske E. B. Kruuk

Nature 447, 1107-1110 (28 June 2007) |

Abstract: Evolutionary theory predicts the depletion of genetic variation in natural populations as a result of the effects of selection, but genetic variation is nevertheless abundant for many traits that are under directional or stabilizing selection. Evolutionary geneticists commonly try to explain this paradox with mechanisms that lead to a balance between mutation and selection. However, theoretical predictions of equilibrium genetic variance under mutation–selection balance are usually lower than the observed values, and the reason for this is unknown. The potential role of sexually antagonistic selection in maintaining genetic variation has received little attention in this debate, surprisingly given its potential ubiquity in dioecious organisms. At fitness-related loci, a given genotype may be selected in opposite directions in the two sexes. Such sexually antagonistic selection will reduce the otherwise-expected positive genetic correlation between male and female fitness. Both theory and experimental data suggest that males and females of the same species may have divergent genetic optima, but supporting data from wild populations are still scarce. Here we present evidence for sexually antagonistic fitness variation in a natural population, using data from a long-term study of red deer (Cervus elaphus). We show that male red deer with relatively high fitness fathered, on average, daughters with relatively low fitness. This was due to a negative genetic correlation between estimates of fitness in males and females. In particular, we show that selection favours males that carry low breeding values for female fitness. Our results demonstrate that sexually antagonistic selection can lead to a trade-off between the optimal genotypes for males and females; this mechanism will have profound effects on the operation of selection and the maintenance of genetic variation in natural populations.

Tuesday, July 03, 2007

Generalized reciprocity in rats

I think it was Trivers who first came out with this notion of generalized reciprocity a while back. It never really gained that much attention in the literature, although I was always a fan of this notion for explaining human cooperation - because so many instances of cooperation can not be explained by just reciprocity. In this paper, not only do they discuss generalized reciprocity but they also find that it happens in rats...pretty cool! (the effect that they find doesn't appear to be very big, however)

Generalized Reciprocity in Rats

Claudia Rutte, Michael Taborsky

PLoS Biology, 5(7)

Abstract: The evolution of cooperation among nonrelatives has been explained by direct, indirect, and strong reciprocity. Animals should base the decision to help others on expected future help, which they may judge from past behavior of their partner. Although many examples of cooperative behavior exist in nature where reciprocity may be involved, experimental evidence for strategies predicted by direct reciprocity models remains controversial; and indirect and strong reciprocity have been found only in humans so far. Here we show experimentally that cooperative behavior of female rats is influenced by prior receipt of help, irrespective of the identity of the partner. Rats that were trained in an instrumental cooperative task (pulling a stick in order to produce food for a partner) pulled more often for an unknown partner after they were helped than if they had not received help before. This alternative mechanism, called generalized reciprocity, requires no specific knowledge about the partner and may promote the evolution of cooperation among unfamiliar nonrelatives.

Monday, July 02, 2007

Race-based medical research baseless?

The title is quite straightforward and somewhat shocking at first. When I saw it, the only rationale I could think of that would lead someone to make such a claim is if they say that compared to individual genome based medicine, race-based medicine is a lousy second best option...also maybe given our not-so-good ways of classifying race. The journal name sounded like a pretty legit. journal, and to be fair, I've only read the abstract, but this does seem like uninformed research.

There is no scientific rationale for race-based research.

Hoover EL.

J Natl Med Assoc. 2007 Jun;99(6):690-2.

Abstract: For centuries, the colonial governments used a combination of race and ethnic characteristics to subjugate and control people of color, and scientists of the day provided evidence of the "natural order of things" to support national policies of domination, segregation and control. There have been many examples of events in the past 70 years to suggest that achievements by ethnic peoples are not genetically determined and that race and ethnicity are merely terms to describe external features, language, culture, social mores and folklore. BiDil was the first drug in this country approved by the FDA for use in a single "race" after a clinical trial that enrolled only members of that race. Thus arose the question of the efficacy of doing race-based research in humans. In order for this kind of research to have any scientific basis, each individually defined or self-declared race would have to have a 100% pure gene pool, and the data show that the gene pool among whites, blacks and Hispanics in America is very heterogeneous. This makes for far greater similarities among U.S. citizens than any perceived differences, and genomic science has failed to support the concept of racial categories in medicine. Scientists involved with the first mapping of the human genome have noted that there is no basis in the genetic code for race. That being the case, there appears to be no justification for race-based research among human beings.
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