Thursday, August 31, 2006

More on the potential importance of structural and copy number variants

The actual paper is in the newest Science but this is a link to a story about the paper in Nature:

Multiple copies of a mystery gene may make us human

the gist: humans have a lot more copies than chimps, monkeys or mice of a gene that codes for a protein that is found in the brain/neurons. they found this by sequencing.

Wednesday, August 30, 2006

Discrimination and skin color

Skin tone more important that educational background for African Americans seeking jobs

Hybrid vigor - Isn't it all relative?

It seems that we need some way to quantitate the degree of outbreeding, because there is probably some optimum degree of outbreeding that may differ between organisms and between traits.

Unraveling the genetic basis of hybrid vigor

James A. Birchler, Hong Sao, Sivanandan Chudalayandi

PNAS 103, 12957-12958 (August 29, 2006)

Abstract: The study of hybrid vigor and inbreeding depression traces back to Charles Darwin, who was the first scientist to examine the phenomenon in a systematic manner (1). Hybrid vigor, or heterosis, is the increase in stature, biomass, and fertility that characterizes the progeny of crosses between diverse parents such that the F1 is superior to the better of the two parents. In plants, this is basically achieved by a greater proliferation of cells in some but not all tissues (2). Inbreeding depression refers to the decline in the quantitative measure of these characters upon self-fertilization or other forms of homozygosis of alleles (inbreeding). The genetic basis of heterosis has been debated for nearly a hundred years without an emerging consensus (3–5) (Fig. 1). An early view was that the combination of different alleles in an organism resulted in a superior state for growth and vigor compared with the presence of identical alleles (3). As genetic knowledge increased, the concept that inferior alleles of different genes in the two parents were complemented in the hybrid (6), thus leading to the superior characteristics, gained favor. Although the latter explanation is simple and easily envisioned, results that seemed to favor interactions of diverse alleles have been repeatedly found. In this issue of PNAS, the work of Semel et al. (7) examined an extensive set of quantitative traits in partial hybrids of domesticated tomato and a wild relative. They conclude that most traits that exhibit heterosis do so as a result of heterozygosity of the controlling genomic regions to produce traits superior to the better parent. They also suggest that heterosis was selected over evolutionary time for characteristics that impact reproductive success.

Tuesday, August 29, 2006

Violent fruit flies

This paper uses relatively straightforward methods and produced interesting, and unexpected results. Too bad it would be unethical and would take forever to do this type of study in humans.

Molecular analysis of flies selected for aggressive behavior

Herman A Dierick, Ralph J. Greenspan

Nature Genetics- 38, 1023-1031 (2006)

Abstract: Aggressive behavior is pervasive throughout the animal kingdom, and yet very little is known about its molecular underpinnings. To address this problem, we have developed a population-based selection procedure to increase aggression in Drosophila melanogaster. We measured changes in aggressive behavior in the selected subpopulations with a new two-male arena assay. In only ten generations of selection, the aggressive lines became markedly more aggressive than the neutral lines. After 21 generations, the fighting index increased more than 30-fold. Using microarray analysis, we identified genes with differing expression levels in the aggressive and neutral lines as candidates for this strong behavioral selection response. We tested a small set of these genes through mutant analysis and found that one significantly increased fighting frequency. These results suggest that selection for increases in aggression can be used to molecularly dissect this behavior.

a passage from the conclusion:

The one gene that produced a direct effect on aggression encodes a cytochrome P450 (ref. 32). These enzymes are involved in a variety of fundamental physiological functions as varied as growth, development, reproduction, detoxification and pheromone recognition37. Some members of the CYP6 family have been shown to be enriched in olfactory tissues in D. melanogaster and Phyllopertha diversa38, 39, in which they might be involved in pheromone signaling. If the Cyp6a20 mutant is defective in pheromone degradation, its increased fighting frequency might be explained by abnormal sensitivity to male pheromones eliciting an aggressive response. Cyp6a20 has been shown to undergo circadian fluctuation40. Our results, however, suggest that the Cyp6a20 effect is not due to a phase shift in circadian behavior but rather to an effect of this mutant on aggression.

Another notable change in the list of significant expression differences is the downregulation of Obp56a in the aggressive lines (Table 2), which represents one of the strongest responders in this selection experiment. Odor-binding proteins have also been implicated in pheromone signaling between flies and have been shown to affect complex behavior41. In this regard, in our population cage, we noticed a previously undescribed behavior in which males drag their genital area on the food surface while walking as if making a territorial mark (Supplementary Video 5). This abdomen dipping has been previously reported in other dipterans, in which it has been shown to be associated with territorial attraction of females25, 26. Although premature, it is tempting to speculate that this marking might also act as a repellant to other males and that a decrease in gustatory detection of this repellant might make aggressive males less sensitive to it, eliminating one inhibitory component towards an eventual territorial collision.

Monday, August 28, 2006

Ingroup/Outgroup Altruisitic Punishment

Parochial Altruism in Humans

Helen Bernhard, Urs Fischbacher, Ernst Fehr

Nature 442, 912-915

Abstract:Social norms and the associated altruistic behaviours are decisive for the evolution of human cooperation and the maintenance of social order, and they affect family life, politics and economic interactions. However, as altruistic norm compliance and norm enforcement often emerge in the context of inter-group conflicts, they are likely to be shaped by parochialism—a preference for favouring the members of one's ethnic, racial or language group. We have conducted punishment experiments, which allow 'impartial' observers to punish norm violators, with indigenous groups in Papua New Guinea. Here we show that these experiments confirm the prediction of parochialism. We found that punishers protect ingroup victims—who suffer from a norm violation—much more than they do outgroup victims, regardless of the norm violator's group affiliation. Norm violators also expect that punishers will be lenient if the latter belong to their social group. As a consequence, norm violations occur more often if the punisher and the norm violator belong to the same group. Our results are puzzling for evolutionary multi-level selection theories based on selective group extinction as well as for theories of individual selection; they also indicate the need to explicitly examine the interactions between individuals stemming from different groups in evolutionary models.

This is an interesting paper all in all, although I am somewhat skeptical of economic games, especially among people who might not have a good grasp of math (i.e. every unit spent on punishment reduces A's income by 3).
I agree with the authors' point that it is hard to disentangle progroup behavior when being nice to the other group could constitute progroup behavior in itself:

First, these models focus on norm enforcement within groups for the purpose of winning inter-group conflicts while neglecting the potential benefits from cooperative inter-group interactions. This approach makes it difficult to understand when hostility characterizes inter-group reactions and when cooperative norms govern them.

Monday, August 21, 2006

Costs of big brains

Costs of encephalization: the energy trade-off hypothesis tested in birds

Karen Isler & Carel van Schaik

Journal of Human Evolution v.51, iss 3, 2006

Abstract: Costs and benefits of encephalization are a major topic of debate in the study of primate and human evolution. Comparative studies provide an opportunity to test the validity of a hypothesis as a general principle, rather than it being a special case in primate or hominid evolution. If a population evolves a larger brain, the metabolic costs of doing so must be paid for by either an increased energy turnover (direct metabolic constraint) or by a trade-off with other energetically expensive costs of body maintenance, locomotion, or reproduction, here referred to as the energy trade-off hypothesis, an extension of the influential Expensive Tissue Hypothesis of Aiello and Wheeler (1995, Curr. Anthropol. 36, 199–221). In the present paper, we tested these hypotheses on birds using raw species values, family means, and independent contrasts analysis to account for phylogenetic influences. First, we tested whether basal metabolic rates are correlated with brain mass or any other variable of interest. This not being the case, we examined various trade-offs between brain mass and the mass of other expensive tissues such as gut mass, which is approximated by gut length or diet quality. Only weak support was found for this original Expensive Tissue Hypothesis in birds. However, other energy allocations such as locomotor mode and reproductive strategy may also be reduced to shunt energy to an enlarged brain. We found a significantly negative correlation between brain mass and pectoral muscle mass, which averages 18% of body mass in birds and is indicative of their relative costs of flight. Reproductive costs, on the other hand, are positively correlated with brain mass in birds. An increase in brain mass may allow birds to devote more energy to reproduction, although not through an increase in their own energy budget as in mammals, but through direct provisioning of their offspring. The trade-off between locomotor costs and brain mass in birds lets us conclude that an analogous effect could have played a role in the evolution of a larger brain in human evolution.

Saturday, August 12, 2006

Hypomanic Americans

This is something that surprisingly escaped me in the past year. Apparently two guys wrote abook about how Americans (a self selected group of "crazy" people who actually packed up and left their homeland) are likely to exhibit hypomania - sort of like ADHD, but different. They wrote a book called the Hypomanic Edge.
I found out about this from the New York Times Magazine issue that had the "Year's best ideas".
Here is the link
...and the first paragraph of the short article by Emily Bazelon:

For centuries, scholars have tried to explain the American character: is it the product of the frontier experience, or of the heritage of dissenting Protestantism, or of the absence of feudalism? This year, two professors of psychiatry each published books attributing American exceptionalism to a new and hitherto unsuspected source: American DNA. They argue that the United States is full of energetic risk-takers because it's full of immigrants, who as a group may carry a genetic marker that expresses itself as restless curiosity, exuberance and competitive self-promotion - a combination known as hypomania.

link to Boston Globe article

Anyway this caught my attention because of the link to some previous work done on the association between some variants at the DRD4 locus associated with novelty seeking behavior and linked to migration behavior in humans (Human Nature paper by Chen). There was also a paper about this in PNAS a few years back (I don't have the author of paper with me) and a paper in the same issue by Henry Harpending and Greg Cochran called "In our genes" where they talk about the worldwide population differences in this allele and some behavioral associations with "novelty seeking behavior", migration, and cad vs. dad societies.

This book, "Hypomanic Edge" might be an interesting read.

Monday, August 07, 2006

The "new" variation in our genome

Strategies for the detection of copy number and other structural variants in the human genome

Carson, Andrew R.; Feuk, Lars; Mohammed, Mansoor; Scherer, Stephen W.

Human Genomics, Volume 2, Number 6, June 2006, pp. 403-414(12)

Abstract: Advances in genome scanning technologies are revealing that copy number variants (CNVs) and polymorphisms, ranging from a few kilobases to several megabases in size, are present in genomes at frequencies much greater than previously known. Discoveries of additional forms of genomic variation, including inversions, insertions, deletions and complex rearrangements, are also occurring at an increased rate. Along with CNVs, these sequence alterations are collectively known as structural variants, and their discovery has had an immediate impact on the interpretation of basic research and clinical diagnostic data. This paper discusses different methods, experimental strategies and technologies that are currently available to study copy number variation and other structural variants in the human genome.

Wellcome Trust Sanger Institute CNV project

Friday, August 04, 2006

Positive selection on skin pigmentation loci

A new paper in MBE that uses publicly available SNP and other sequence data to examine which of the candidate skin pigmentation loci are under positive selection. I guess that the main finding here is that both dark and light skin have adaptive value (not just relaxation of selection pressures). Among the African populations, since they find two loci that show positive selection, the authors suggest that dark skin has an adaptive value, possibly as protection against sun-induced damage. In addition:

"The mechanisms by which light skin confers a selective advantage cannot be inferred with these data alone. However, the relevance of mechanisms like vitamin D synthesis, which have been claimed to have a role in the evolution of light pigmentation (Robins 1991 and references therein), could be minimized as neither of the representative loci of this pathway (Omdahl et al. 2002) that have been analyzed, VDR (Vitamin D receptor) and VDRIP (Vitamin D3 receptor-interacting protein), CYP27B1 (P450C1), CYP24A1 (P450C24), and RXRA (Retinoid X receptor), showed clear evidence of positive selection."

A Scan for Signatures of Positive Selection in Candidate Loci for Skin Pigmentation in Humans

Neskuts Izagirre, Iker Garcia, Corina Junquera, Concepcion de la Rua, Santos Alonso

Molecular Biology and Evolution (2006); 23(9) 1697-1706

Abstract: Although the combination of pale skin and intense sun exposure results in an important health risk for the individual, it is less clear if at the population level this risk has possessed an evolutionary meaning. In this sense, a number of adaptive hypotheses have been put forward to explain the evolution of human skin pigmentation, such as photoprotection against sun-induced cancer, sexual selection, vitamin D synthesis or photoprotection of photolabile compounds, among others. It is expected that if skin pigmentation is adaptive, we might be able to see the signature of positive selection on some of the genes involved. In order to detect this signature, we analyze a battery of 81 candidate loci by means of phylogenetic and population genetic tests. Our results indicate that both light and dark skin may possess adaptive value. Of the main loci presenting this signature, TP53BP1 shows clear evidence of adaptive selection in Africans, whereas TYRP1 and SLC24A5 show evidence of adaptive selection in Caucasians. Although we cannot offer a mechanism that based on these genes explains the advantage of light skin, if TP53BP1, and perhaps RAD50, have truly conferred an adaptive value to the African population analyzed, photoprotection against sun-induced skin damage/cancer might be proposed as a mechanism that has driven the evolution of human skin pigmentation.
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