Thursday, August 30, 2007

SLC24A5 and population differentiation

Unfortunately, I don't have full text access to this one. SLC24A5 is a gene that was found to account for about 30% (I believe) of skin color variation between Africans and Europeans. It is also used as an AIM (ancestry informative marker) in admixture studies. Here are links to some other posts I have regarding the gene (here, here, here) and the paper in Science that originally described the locus in zebrafish and made the connection to humans.
In this paper, they find that using this locus in addition to Y-SNPs, it becomes feasible to differentiate some population groups.

The golden gene (SLC24A5) differentiates US sub-populations within the ethnically admixed Y-SNP haplogroups.

Sims LM, Ballantyne J.

Leg Med (Tokyo) 2007 Aug 24; [Epub ahead of print]
Abstract: Y-SNPs are currently being investigated for their potential to predict the ethnogeographic origin of the donor of a crime scene sample. Unfortunately, due to the presence of genetically admixed individuals within ethnic sub-populations within a particular haplogroup (hg), it is sometimes difficult to predict the ethnogeographic ancestry of an individual using only Y-SNPs. In the present work we determine the feasibility of using a combination of the golden pigmentation gene (SLC24A5) SNP and recently described high resolution Y-SNP markers to distinguish some of the different ethnic groups within particular Y-SNP hgs. Four hundred twenty-four individuals (128 African, 206 European, 50 Hispanic/Latin, 20 Pakistan, 20 E.Asian/Indian) were typed for a SNP within the golden gene. The Y-SNP hg was determined for all males and it was found that many of the European derived hg possessed a significant amount of ethnic admixture, with R1b3 having the most. We show the use of the golden gene, in combination with more informative Y-SNPs (U152, U106, and M222) and those that define the major hg, can differentiate between most of the African vs. European and African vs. E. Asian members of these heterogeneous populations.

Wednesday, August 29, 2007

Men /Women, Culture, and Group Selection

There's an article in the NYT entitled "Is There Anything Good About Men? And Other Tricky Questions" By John Tierney. It describes a recent speech by Roy Baumeister, a social psychologist. There's a few interesting excerpts from the article in addition to the somewhat obvious differences between men and women. Throughout it, Roy Baumeister invokes an assumption of group selection which I'm ok with to some extent, but which may rub people the wrong way especially with a phrase like "enabled the species to survive"!
“I’m certainly not denying that culture has exploited women,” he said. “But rather than seeing culture as patriarchy, which is to say a conspiracy by men to exploit women, I think it’s more accurate to understand culture (e.g., a country, a religion) as an abstract system that competes against rival systems — and that uses both men and women, often in different ways, to advance its cause.”
and then:
"Culture is not about men against women. By and large, cultural progress emerged from groups of men working with and against other men. While women concentrated on the close relationships that enabled the species to survive, men created the bigger networks of shallow relationships, less necessary for survival but eventually enabling culture to flourish. The gradual creation of wealth, knowledge, and power in the men’s sphere was the source of gender inequality. Men created the big social structures that comprise society, and men still are mainly responsible for this, even though we now see that women can perform perfectly well in these large systems.

What seems to have worked best for cultures is to play off the men against each other, competing for respect and other rewards that end up distributed very unequally. Men have to prove themselves by producing things the society values. They have to prevail over rivals and enemies in cultural competitions, which is probably why they aren’t as lovable as women."

Tuesday, August 28, 2007

Circumpolar populations and biology/health

I too think that there are many interesting research opportunities here. A few months ago AJHB had a special issue on circumpolar people and biology.

Arctic Peoples and Beyond: research opportunities in neuroscience and behaviour.

Duffy L, Bult-Ito A, Castillo M, Drew K, Harris M, Kuhn T, Ma Y, Schulte M, Taylor B, van Muelken M.

Int J Circumpolar Health. 2007 Jun;66(3):264-75.
OBJECTIVES: Arctic and northern peoples are spread across Alaska, Canada, Russia and the Scandinavian countries. Inhabiting a variety of ecosystems, these 4 million residents include Indigenous populations who total about 10% of the population. Although Arctic peoples have very diverse cultural and social systems, they have health issues related to environmental impacts and knowledge/treatment disparities that are common to other minority and Indigenous peoples around the world. Research that explores the neuroscience and behavioural aspects of these health disparities offers challenges and significant opportunities. As the next generation of neuroscientists enter the field, it is imperative that they view their contributions in terms of translational medicine to address health disparities. STUDY DESIGN: A workshop was designed to bring neuroscientists together to report on the current directions of neuroscience research and how it could impact health disparities in the North. This workshop produced research recommendations for the growth of neuroscience in the North. METHODS: On May 31, 2006 the National Institute of Neurological Disorders and Stroke, the Burroughs Wellcome Foundation, the Arctic Division of AAAS and the University of Alaska co-sponsored a workshop entitled "Arctic Peoples and Beyond: Decreasing Health Disparities through Basic and Clinical Research." Also, the role and goals of the International Union for Circumpolar Health (IUCH) were presented at the meeting. RESULTS: A set of recommendations related to research opportunities in neuroscience and behaviour research and ways to facilitate national and international partnerships were developed. CONCLUSIONS: These recommendations should help guide the development of future health research in circumpolar neuroscience and behaviour. They provide ideas about research support and informational exchange that will address health challenges.

Wednesday, August 22, 2007

For all you southpaws

I had to post on this one not only for its behavioral ecology significance, but also because I had my first start in science experimenting with fiddler crab circadian rhythms and pigmentation, back in high school. The advantage of having a left claw, they find, probably has to do with something other than a frequency dependent advantage in fighting ability. I like the straightforward question as posed in the title, although they should have included that they were asking the question in reference to fighting.
This is also interesting in the context of that recent paper on the left-handedness gene. Maybe they could check out that gene in the crab. In that paper they also went through an evolutionary explanation for left-handedness in humans.. sorry, don't have link to that paper. I think it was in Molecular Psychiatry.

What are the consequences of being left-clawed in a predominantly right-clawed fiddler crab?

P.R.Y. Backwell, M. Matsumasa, M. Double, A. Roberts, M. Murai, J.S. Keogh, M.D. Jennions

Proceedings Royal Society, B Online: Tuesday, August 21, 2007
Abstract: Male fiddler crabs (genus Uca) have an enlarged major claw that is used during fights. In most species, 50% of males have a major claw on the left and 50% on the right. In Uca vocans vomeris, however, less than 1.4% of males are left-clawed. Fights between opponents with claws on the same or opposite side result in different physical alignment of claws, which affects fighting tactics. Left-clawed males mainly fight opposite-clawed opponents, so we predicted that they would be better fighters due to their relatively greater experience in fighting opposite-clawed opponents. We found, however, that (i) a left-clawed male retains a burrow for a significantly shorter period than a size-matched right-clawed male, (ii) when experimentally displaced from their burrow, there is no difference in the tactics used by left- and right-clawed males to obtain a new burrow; however, right-clawed males are significantly more likely to initiate fights with resident males, and (iii) right-clawed residents engage in significantly more fights than left-clawed residents. It appears that left-clawed males are actually less likely to fight, and when they do fight they are less likely to win, than right-clawed males. The low-level persistence of left-clawed males is therefore unlikely to involve a frequency-dependent advantage associated with fighting experience.

Tuesday, August 21, 2007

Trivers-Willard tested

Trivers–Willard at birth and one year: evidence from US natality data 1983–2001

Douglas Almond, Lena Edlund

Proceedings of the Royal Society, B Volume 274, Number 1624 / October 07, 2007
Abstract: Trivers & Willard (TW) hypothesized that evolution would favour deviations from the population sex ratio in response to parental condition: parents in good condition would have more sons and parents in poor condition would have more daughters. We analyse the universe of US linked births and infant deaths to white mothers 1983–2001, covering 48 million births and 310000 deaths. We find that (i) married, better educated and younger mothers bore more sons and (ii) infant deaths were more male if the mother was unmarried and young. Our findings highlight the potential role of offspring sex ratio as an indicator of maternal status, and the role of infant mortality in shaping a TW pattern in the breeding population.

Sperm competition in chimps and humans

Functional evidence for differences in sperm competition in humans and chimpanzees

Matthew J. Anderson, Shannon J. Chapman, Elaine N. Videan, Erika Evans, Jo Fritz, Tara S. Stoinski, Alan F. Dixson, Pascal Gagneux

AJPA: published early online
Abstract: Sperm competition occurs when the gametes of or more males compete for opportunities to fertilize a given set of ova. Previous studies have demonstrated that certain morphological characteristics are affected by sperm competition intensity (e.g. relative testes size and sperm midpiece volume). This study examined whether aspects of sperm energetics may also be affected by sexual selection. We compared the membrane potential of mitochondria in live sperm between H. sapiens (single partner mating system) and P. troglodytes (multiple partner mating system). Flow cytometry of sperm stained with the carbocyanine fluorescent dye JC-1 (an assay for mitochondrial membrane potential) revealed marked differences in red fluorescence intensity. P. troglodytes sperm showed significantly higher mitochondrial membrane potential. Mitochondria provide a substantial part of the energy required for sperm motility. A higher mitochondrial loading may therefore be associated with enhanced sperm motility and/or longevity. Additionally, examination of JC-1 red fluorescence levels before and after in vitro capacitation revealed further differences. Whereas chimpanzee sperm showed maintenance of membrane potential after capacitation (in some cases even an increase), sperm from humans consistently showed reduction in membrane potential. These results indicate that the sperm of human beings and chimpanzees exhibit marked differences in mitochondrial function, which are affected by selection pressures relating to sperm competition and that these pressures differ significantly between humans and chimpanzees.

Monday, August 20, 2007

Americans are short and don't live very long

According to this news story in Discovery (via TAMU Anthro. in the News) Americans ranks 42nd in life expectancy. This follows a story a few months ago about Americans being short compared to other "Western" nations. (I assume they controlled for recent immigrants and other obvious confounders). From the Discovery story on life expectancy:

"A baby born in the United States in 2004 will live an average of 77.9 years. That life expectancy ranks 42nd, down from 11th two decades earlier, according to international numbers provided by the Census Bureau and domestic numbers from the National Center for Health Statistics.

Andorra, a tiny country in the Pyrenees mountains between France and Spain, had the longest life expectancy, at 83.5 years, according to the Census Bureau. It was followed by Japan, Macau, San Marino and Singapore."

Thursday, August 16, 2007

The costs and benefits of being fat or skinny

on the trade-off between between being fat & slow & energetically buffered and lean & fast & prone to starvation. There could be several alternative explanations for their finding, but maybe they control for some of these.

Mass-dependent predation risk and lethal dolphin–porpoise interactions

R. MacLeod, C.D. MacLeod, J.A. Learmonth, P.D. Jepson, R.J. Reid, R. Deaville, G.J. Pierce

Proc. Roy. Soc. B Online: Tuesday, August 14, 2007
Abstract: In small birds, mass-dependent predation risk (MDPR) is known to make the trade-off between avoiding starvation and avoiding predation dependent on individual mass. This occurs because carrying increased fat reserves not only reduces starvation risk but also results in a higher predation risk due to reduced escape flight performance and/or the increased foraging exposure needed to maintain a higher body mass. In principle, the theory of MDPR could also apply to any animal capable of storing energy reserves to reduce starvation and whose escape performance decreases with increasing mass. We used a unique situation along certain parts of coastal Britain, where harbour porpoises (Phocoena phocoena) are pursued and killed but crucially not eaten by bottlenose dolphins (Tursiops truncatus), to investigate whether a MDPR effect can occur in non-avian species. We show that where high levels of dolphin ‘predation’ occur, porpoises carry significantly less energy reserves than would otherwise be expected and this equates to reducing by approximately 37% the length of time that a porpoise could survive without feeding. These results provide the first evidence that a mass-dependent starvation–predation risk trade-off may be a general ecological principle that can apply to widely different animal types rather than, as is currently thought, only to birds.

Wednesday, August 15, 2007

Spencer Wells on Colbert Report

I love the Colbert Report: (via Eye on DNA)

The genetics of pigmentation in beach mice

They looked at some mice in Florida, some of which have very light pigmentation, did crosses etc..., examined 11 candidate pigmentation genes (for mice) , did linkage and QTL analysis, and found a strong effect of MC1R and the agouti signaling protein. Most interestingly, they go into how they think the genes interact. (gene expression vs. coding region mutations, and epistasis)

some interesting parts from the conclusion:
Our results also have several implications for understanding the genetic basis of adaptation. First, this subspecific difference in color pattern is produced by a few interacting genes of large effect, supporting the idea that adaptations can involve relatively few genes rather than, as is often believed, many genes of small effect.
These results support the idea that adaptation is not necessarily driven largely by cis-regulatory changes [29,30] or by (semi) dominant alleles. Third, we show that the nature of epistasis between Mc1r and Agouti in wild populations does not mirror that seen in the laboratory, suggesting that one should be cautious not only about extrapolating the genetics of laboratory strains to evolution in nature, but also about inferring the directionality of biochemical pathways from patterns of gene interactions. Finally, most genetic studies of morphological change have concentrated on the loss of phenotypic traits through loss-of-function mutations (e.g., reduced armor in stickleback fish [33,34], absence of wing spots in Drosophila [35], and lack of pigment in cavefish [36]). This study provides a novel example of how adaptation can result from mutations involving a gain of function.
Adaptive Variation in Beach Mice Produced by Two Interacting Pigmentation Genes

Cynthia C. Steiner, Jesse N. Weber, Hopi E. Hoekstra

PLoS Biology early online Aug 14, 2007
Abstract: Little is known about the genetic basis of ecologically important morphological variation such as the diverse color patterns of mammals. Here we identify genetic changes contributing to an adaptive difference in color pattern between two subspecies of oldfield mice (Peromyscus polionotus). One mainland subspecies has a cryptic dark brown dorsal coat, while a younger beach-dwelling subspecies has a lighter coat produced by natural selection for camouflage on pale coastal sand dunes. Using genome-wide linkage mapping, we identified three chromosomal regions (two of major and one of minor effect) associated with differences in pigmentation traits. Two candidate genes, the melanocortin-1 receptor (Mc1r) and its antagonist, the Agouti signaling protein (Agouti), map to independent regions that together are responsible for most of the difference in pigmentation between subspecies. A derived mutation in the coding region of Mc1r, rather than change in its expression level, contributes to light pigmentation. Conversely, beach mice have a derived increase in Agouti mRNA expression but no changes in protein sequence. These two genes also interact epistatically: the phenotypic effects of Mc1r are visible only in genetic backgrounds containing the derived Agouti allele. These results demonstrate that cryptic coloration can be based largely on a few interacting genes of major effect.

Thursday, August 09, 2007

Whites are a minority in 1 in 10 US counties

I wonder what Andrew at Statistical Modeling, Causal Inference, and Social Science would think about this figure. I think they could have done a much better job with it. It's just very hard to look at, especially because the county lines are too bold.

Lactase persistence allele - haplotype diversity

In this paper, the authors look at the 13910C/T allele that is pretty well known to be asociated with lactase persistence (LP) in Europeans and 8 markers in the 30 kb surrounding this particular allele among a set of global populations (1611 samples in 37 populations) - looking for patterns of diversity. They identified 9 haplotypes with the LP (13910-T) allele and 14 haplotypes with the non-LP allele. They were not able to reconcile the fact that the LP allele occured on two different haplotypic backgrounds, hence they assert that the mutation arose independently. Their age estimates of the mutation on the two different haplotypes also supposedly confirm this. I still don't quite get the gist and the methods in this paper. I'd probably have to read it a few more times.
Interestingly, the French have lactase persistence rate of only 58.8% while the neighboring Basques have a rate of 91.7%! ... and southern Italians only 11%! I wonder how much the environmental component of "getting used" to lactose over one's lifespan is that accounts for the ability to use/tolerate lactose... these percentages seem very low.

Evidence of Still-Ongoing Convergence Evolution of the Lactase Persistence T-13910 Alleles in Humans

Nabil Sabri Enattah, Aimee Trudeau et al.

American Journal of Human Genetics Sept 2007

Abstract: A single-nucleotide variant, C/T-13910, located 14 kb upstream of the lactase gene (LCT), has been shown to be completely correlated with lactase persistence (LP) in northern Europeans. Here, we analyzed the background of the alleles carrying the critical variant in 1,611 DNA samples from 37 populations. Our data show that the T-13910 variant is found on two different, highly divergent haplotype backgrounds in the global populations. The first is the most common LP haplotype (LP H98) present in all populations analyzed, whereas the others (LP H8–H12), which originate from the same ancestral allelic haplotype, are found in geographically restricted populations living west of the Urals and north of the Caucasus. The global distribution pattern of LP T-13910 H98 supports the Caucasian origin of this allele. Age estimates based on different mathematical models show that the common LP T-13910 H98 allele (5,000–12,000 years old) is relatively older than the other geographically restricted LP alleles (1,400–3,000 years old). Our data about global allelic haplotypes of the lactose-tolerance variant imply that the T-13910 allele has been independently introduced more than once and that there is a still-ongoing process of convergent evolution of the LP alleles in humans.

Thursday, August 02, 2007

The role of CREs in evolution

first a description of CREs and their role from the paper, and then the abstract below:
"Most loci encoding pattern-regulating proteins were found to include multiple individual cis-regulatory elements (CREs), with each CRE typically comprising binding sites for multiple distinct transcription factors and controlling gene expression within a discrete spatial domain in a developing animal. The realization that the total expression pattern of a gene was the sum of many parts, each directed by distinct CREs, marked a profound change in concepts of gene regulation. The modular arrangement of CREs also had clear implications for evolutionary genetics, because it suggested a mechanism for how selective changes in gene expression and morphology could evolve in one part of the body, independent of other parts. The conservation of the biochemical activity of regulatory proteins, the divergence of their expression patterns across taxa, and the modular organization of CREs provided the basis for the general proposal that gene expression evolution, and therefore morphological evolution, would occur primarily through changes in cis-regulatory sequences controlling gene transcription."

Emerging principles of regulatory evolution

Benjamin Prud'homme, Nicolas Gompel, and Sean B. Carroll

PNAS | May 15, 2007 | vol. 104 | Suppl. 1 | 8605-8612

Understanding the genetic and molecular mechanisms governing the evolution of morphology is a major challenge in biology. Because most animals share a conserved repertoire of body-building and -patterning genes, morphological diversity appears to evolve primarily through changes in the deployment of these genes during development. The complex expression patterns of developmentally regulated genes are typically controlled by numerous independent cis-regulatory elements (CREs). It has been proposed that morphological evolution relies predominantly on changes in the architecture of gene regulatory networks and in particular on functional changes within CREs. Here, we discuss recent experimental studies that support this hypothesis and reveal some unanticipated features of how regulatory evolution occurs. From this growing body of evidence, we identify three key operating principles underlying regulatory evolution, that is, how regulatory evolution: (i) uses available genetic components in the form of preexisting and active transcription factors and CREs to generate novelty; (ii) minimizes the penalty to overall fitness by introducing discrete changes in gene expression; and (iii) allows interactions to arise among any transcription factor and downstream CRE. These principles endow regulatory evolution with a vast creative potential that accounts for both relatively modest morphological differences among closely related species and more profound anatomical divergences among groups at higher taxonomical levels.
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