Tuesday, July 25, 2006

The use of dietary fatty acids by migratory birds

Performance-enhancing role of dietary fatty acids in a long-distance migrant shorebird: the semipalmated sandpiper

Dominique Maillet and Jean-Michel Weber

Journal of Experimental Biology 209, 2686-2695 (2006)

At the end of summer, semipalmated sandpipers (Calidris pusilla) traveling from the Arctic stop in the Bay of Fundy (east coast of Canada) to build large fat reserves before a non-stop flight to South America. During a 2-week stopover, the body mass of this small shorebird is doubled (~20 g to 40 g) by feeding on a burrowing amphipod, Corophium volutator, that contains unusually high levels of n-3 polyunsaturated fatty acids (PUFA). In mammals, high n-3 PUFA content of membrane phospholipids (PL) is linked to improved exercise performance due to increased membrane fluidity that accelerates transmembrane lipid transport. We hypothesized that dietary n-3 PUFA could be used as a natural `performance-enhancing substance' by semipalmated sandpipers to prepare their flight muscles for migration. Also, PUFA stored as fuel in neutral lipids (NL) can be mobilized more quickly than saturated fatty acids, but they contain less energy per unit mass. It is therefore unclear whether dietary fatty acids are modified before storage. Birds were collected at various stages of fat loading to examine changes in the composition of tissue PL (membranes) and NL (fuel stores). Results show that dietary n-3 PUFA are incorporated in tissue lipids in less than 2 weeks. During the stopover, the double bond index of muscle PL increases by 25% and the fatty acid profiles of both muscle PL and adipose NL converge with that of the diet. However, >50% of dietary n-3 PUFA are converted to other fatty acids before storage, mainly to oleate (18:1), possibly because monounsaturates offer a compromise between high energy density and ease of mobilization. This study shows that long-distance migrant birds can (1) use natural diets rich in specific lipids to prime flight muscles for endurance exercise, and (2) modify dietary fatty acids before storing them as fuel.

Monday, July 24, 2006

Review of human pigmentation genetics

A new paper in Trends in Genetics by Richard Sturm that reviews some of the most recent research on human pigmentation genetics, mainly highlighting SLC24A5.

A golden age of human pigmentation genetics

Richard A. Sturm

Trends in Genetics, Epub ahead of print

Abstract: The zebrafish golden mutation is characterized by the production of small and irregular-shaped melanin granules, resulting in a lightening of the pigmented lateral stripes of the animal. The recent positional cloning and localization of the golden gene, combined with genotype-phenotype correlations of alleles of its human orthologue (SLC24A5) in African-American and African-Caribbean populations, provide insights into the genetic and molecular basis of human skin colour. SLC24A5 promotes melanin deposition through maturation of the melanosome, highlighting the importance of ion-exchange in the function of this organelle.

some notes of interest:
- 127 loci in which gene mutations have been linked to changes in mouse coat hair, skin or eye colour.
- importance of getting a phenotype-genotype correlation (functional genetics) for SLC24A5
- SLC24A5 in a genomic region representing the second largest span of diminished heterozygosity in the European genome (according to recent Voight et al. study in PLoS Biology)

I would just also add that we have very little information on the skin pigmentation genetics in Native American populations.

Wednesday, July 19, 2006

SLC24A5 & SLC45A2 in Europe, Asia and Africa

..A new paper reporting on allele frequencies of two skin pigmentation-related genes SLC24A5 and SLC45A2. The cool thing about this paper is the populations they sampled (most notably the central and south Asian populations, Uygurs and Tamils). Their results hint at admixture between Europeans and these Asian populations but not with other more east Asians (Chinese).
I wonder why this was published in International Journal of Legal Medicine.

Population differences of two coding SNPs in pigmentation-related genes SLC24A5 and SLC45A2

Mikko Soejima and Yoshiro Koda

International Journal of Legal Medicine, Online First

Abstract: The two genes SLC24A5 and SLC45A2 were recently identified as major determinants of pigmentation in humans and in other vertebrates. The allele p.A111T in the former gene and the allele p.L374F in the latter gene are both nearly fixed in light-skinned Europeans, and can therefore be considered ancestry informative marker (AIMs). AIMs are becoming useful for forensic identification of the phenotype from a DNA profile sampled, for example, from a crime scene. Here, we generate new allelic data for these two genes from samples of Chinese, Uygurs, Ghanaians, South African Xhosa, South African Europeans, and Sri Lankans (Tamils and Sinhalese). Our data confirm the earlier results and furthermore demonstrate that the SLC45A2 allele is a more specific AIM than the SLC24A5 allele because the former clearly distinguishes the Sri Lankans from the Europeans.

Monday, July 17, 2006

Intergroup contact and prejudice

Here is a short review from the current issue of Science of a new paper in The Journal of Personality and Social Psychology (Pettigrew and Tropp). It reports on a meta analysis of the effect of inter-group contact on prejudice. Here is the review. I didn't put the abstract because I thought this review was more useful. With all the current literature on the role of punishment in human cooperation, it is interesting that they find that "official sanction" (although not sure exactly what this means) is one of the more important features that contribute to the reduction of prejudice.

The effect of contact between groups on prejudice has been a topic of research at least as far back as the middle of the 20th century. Since then, there have been a very large number of studies and many reviews of this literature. Pettigrew and Tropp have conducted a meta-analysis of what has become known as intergroup contact theory. They (and their dedicated research assistants) have combed through published papers and unpublished dissertations, using a methodological (rather than topical) basis for inclusion; the final data set covers 515 studies, containing over 700 independent samples representing a quarter million individuals spread over 38 countries. The summary finding is that intergroup contact reduces prejudice.

Their statistical analyses reveal that this cannot be ascribed to self-selection by the participants, or to a publication bias toward positive results, or to the rigor of the research (methodologically stronger studies yielded larger effect sizes). Roughly half of the studies focused on nonracial and nonethnic groups (as described by sexual orientation or physical or mental disability, for example), and the effect sizes seen within this subset were the same as that for the racial/ethnic targets that stimulated the historical development of intergroup contact theory. Furthermore, it appears that the effects on individual attitudes can generalize to other members of the outgroup and even to other outgroups.

How is this mediated? They find that Allport's four features (common goals, intergroup cooperation, equal status, and official sanction) contribute significantly to the reduction of prejudice but are not essential, and that the last of the four conditions may be the most important one. Greater contact may reduce feelings of uncertainty or discomfort that might otherwise coalesce into anxiety or perceived threat, which might in turn harden into prejudice. Yet these ameliorative shifts may not survive in the absence of normative or authoritarian support, and studies of why contact fails to curb prejudice are needed. -- GJC

J. Pers. Soc. Psychol. 90, 751 (2006).

Saturday, July 15, 2006

Malarial Resistance in Chimps vs. Humans

In this paper, the authors examine whether the variation and LD found in human G6PD is also evident in other primates, and conclude that humans responded to the malarial selection pressure differently than chimpanzees.

Contrasting Histories of G6PD Molecular Evolution and Malarial Resistance in Humans and Chimpanzees

Brian C. Verrelli, Sarah A. Tishkoff, Anne C. Stone and Jeffrey W. Touchman

Molecular Biology and Evolution, 23(8), 1592-1601. 2006

Abstract: Although mutations in the glucose-6-phosphate dehydrogenase (G6PD) gene result in several blood-related diseases in humans, they also confer resistance to malarial infection. This association between G6PD and malaria was supported by population genetic analyses of the G6PD locus, which indicated that these mutations may have recently risen in frequency in certain geographic regions as a result of positive selection. Here we characterize nucleotide sequence variation in a 5.2-kb region of the G6PD locus in a population sample of 56 chimpanzees, as well as among 7 other nonhuman primates, to compare with that in humans in determining whether other primates that are impacted by malaria also exhibit patterns of G6PD polymorphism or divergence consistent with positive selection. We find that chimpanzees have several amino acid variants but that the overall pattern at G6PD in chimpanzees, as well as in Old and New World primates in general, can be explained by recent purifying selection as well as strong functional constraint dating back to at least 30–40 MYA. These comparative analyses suggest that the recent signature of positive selection at G6PD in humans is unique.

Wednesday, July 12, 2006

Group (multilevel) selection: don't call it a comeback

Evolution of cooperation by multilevel selection

Arne Traulsen and Martin A. Nowak

PNAS July 18, 2006, vol 103, 10952-10955

We propose a minimalist stochastic model of multilevel (or group) selection. A population is subdivided into groups. Individuals interact with other members of the group in an evolutionary game that determines their fitness. Individuals reproduce, and offspring are added to the same group. If a group reaches a certain size, it can split into two. Faster reproducing individuals lead to larger groups that split more often. In our model, higher-level selection emerges as a byproduct of individual reproduction and population structure. We derive a fundamental condition for the evolution of cooperation by group selection: if b/c > 1 + n/m, then group selection favors cooperation. The parameters b and c denote the benefit and cost of the altruistic act, whereas n and m denote the maximum group size and the number of groups. The model can be extended to more than two levels of selection and to include migration.

a notable excerpt:
In our opinion, group selection is an important organizing principle that permeates evolutionary processes from the emergence of the first cells to eusociality and the economics of nations.

The authors mention the complications that may arise from the fact that kin selection is also operating in real groups of organisms.

Tuesday, July 11, 2006

Homosexuality and older brothers

It seems that the best predictor of male homosexuality is the number of older brothers. This is confirmed in this study that controls for non-biological factors.

Biological versus nonbiological older brothers and men's sexual orientation

Anthony F. Bogaert

PNAS; July 11, 2006, v. 103, no. 28 10771-10774

Abstract: The most consistent biodemographic correlate of sexual orientation in men is the number of older brothers (fraternal birth order). The mechanism underlying this effect remains unknown. In this article, I provide a direct test pitting prenatal against postnatal (e.g., social/rearing) mechanisms. Four samples of homosexual and heterosexual men (total n = 944), including one sample of men raised in nonbiological and blended families (e.g., raised with half- or step-siblings or as adoptees) were studied. Only biological older brothers, and not any other sibling characteristic, including nonbiological older brothers, predicted men’s sexual orientation, regardless of the amount of time reared with these siblings. These results strongly suggest a prenatal origin to the fraternal birth-order effect.

Sunday, July 09, 2006

Parallel Molecular Evolution in African and Asian Leaf Monkeys

This paper provides evidence for independent parallel evolution at the protein sequence level of RNases in Afican and Asian Colobine monkeys who need extra Rnases to digest bacterial RNA. The author establishes four criteria for demonstrating parallel adaptive evolution:

I propose that four requirements should be fulfilled to demonstrate adaptive parallel evolution at the protein sequence level. First, similar changes in protein function occur in independent evolutionary lineages. Second, parallel amino acid substitutions are observed in these proteins. Third, the parallel substitutions are not attributable to chance alone and therefore must have been driven by a common selective pressure. Fourth, the parallel substitutions are responsible for the parallel functional changes.

I can imagine many other research possibilities, not only for this gene in New World leaf eating monkeys, but also in other systems in humans and other organisms. In humans: parallel evolution for lactose tolerance, high altitude...

Parallel adaptive origins of digestive RNases in Asian and African leaf monkeys

Jianzhi Zhang

Nature Genetics (2006) 38, 819-823

Abstract: Similar morphological or physiological changes occurring in multiple evolutionary lineages are not uncommon. Such parallel changes are believed to be adaptive, because a complex character is unlikely to originate more than once by chance. However, the occurrence of adaptive parallel amino acid substitutions is debated1, 2, 3. Here I propose four requirements for establishing adaptive parallel evolution at the protein sequence level and use these criteria to demonstrate such a case. I report that the gene encoding pancreatic ribonuclease was duplicated independently in Asian and African leaf-eating monkeys. Statistical analyses of DNA sequences, functional assays of reconstructed ancestral proteins and site-directed mutagenesis show that the new genes acquired enhanced digestive efficiencies through parallel amino acid replacements driven by darwinian selection. They also lost a non-digestive function independently, under a relaxed selective constraint. These results demonstrate that despite the overall stochasticity, even molecular evolution has a certain degree of repeatability and predictability under the pressures of natural selection.

Thursday, July 06, 2006

Ethnicity and skin color for dermatologists

There is a series of short commentaries (colloquium) about the use of ethnicity/race in dermatology research.

Journal of the American Academy of Dermatology, June 2006: v54, Issue 6, p.1067-1077

This is what the editors Michael Bigby, MD and Jeffrey Bernhard MD conclude:

What then is the policy at the JAAD regarding the identification of race/ethnicity/skin color in scientific papers? Rather than a policy,
we suggest that authors inclined to include such descriptions in their
manuscripts ask themselves the following questions:

1. Is the identification of the patient's race/ethnicity/skin color
important to the understanding or pedagogical value of the
submitted manuscript?

2. Would the patient identify him/herself in the same way as the
authors have (and how do you know)?

3. Might the descriptor be open to racist intent or interpretation?

4. What is the evidence that the race/ethnicity/color of the patient(s)
plays a role in the entities described?

Tuesday, July 04, 2006

'Economy of the Mind'

Economy of the Mind
Kendall Powell
PLoS Biology v.1 Dec, 2003

Some interesting passages:

McCabe's experiment hints that humans are wired to cooperate. “We're biologically endowed to engage in personal exchange,” he says. “And what makes economies run so well is not personal exchange per se, but our ability to trade with people we don't even know—to buy food at the grocery store from a farmer we've never met.”

Another group, led by Read Montague, director of the Human Neuroimaging Laboratory at Baylor College of Medicine in Houston, Texas, has also looked at brains of cooperators in the Trust Game. Here, an investor decides to trust a trustee with some of her money. The investment is increased by the experimenter and then the trustee decides how much to give back to the investor. This game is played out ten times by two people who meet each other at the beginning and whose brains are scanned simultaneously as they play.

The researchers wanted to see what happens in each player's brain when the trustee's decision is revealed to both on a computer screen. “The trustee's brain shows the visual cortical activity only of seeing the screen,” Montague explains. “But the investor's brain goes haywire, with both emotional and cognitive reactions to what they see.” Presumably, the activity represents the investor trying to assimilate the information into her decision of how much to invest in the next round.

Montague, a physicist by training, says he's found a home in the computational nature of neuroeconomics, which adds a “fresh look at a bunch of problems that were previously only at the margins of behavioral psychology.” But he also sees the advantages that the field brings to economists by shoring up their models with physical evidence: “Let's face it, they don't have good models now or they could tell you what's going to happen [in the stock market] tomorrow. This is starting to give economists a way to loop back into experiments—they realized they've got to crack the head open.”

Montague's collaborator Camerer agrees that knowing how individual humans make decisions could certainly improve our understanding of larger markets. After all, global trade institutions are still run by individuals who draw on their own ability to trade and make decisions. Unraveling the decision-making code would open windows on economic questions ranging from the global (Why do certain countries enjoy economic growth?) to the very personal (What causes compulsive behavior when reward systems go bad?).

Camerer sees neuroeconomics as trying to “make a one-to-one mapping from economic theory to the brain. We have a head start, but it's very difficult to produce clear neuroscience that also has economic significance.” In just a few decades, he envisions that economic theory may look very different, perhaps throwing out utility altogether and instead having a system of mechanisms found in the brain that interact to help a shopper decide, “What's for dinner?”

And the knowledge coming out of the fledgling field—how the brain codes motivation and reward value—could be used to increase work output, promote more effective addictive drug rehab programs, and stabilize economies. Camerer adds, “This work can really go from synapses seen in brain imaging to explaining the most important thing in the world—why is Africa poor and Singapore rich?”

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