Monday, April 30, 2007

Cooperation in chimps: kin selection, reciprocity?

This paper makes the case that reciprocity may be a strong force in chimpanzee society: "the majority of highly affiliative and cooperative dyads are actually unrelated or distantly related."
I think they make a pretty convincing case except that I wish they would have resolved kinship more than either r=. 5 or r=0. It would have been nice to see .25 and .125. I wonder if that would have at least nuanced the results a bit more? They were using a decent number of markers, but have no idea if they could have gotten .25 and .125.
Update: I think that the main significance of this paper is to show that chimps, like humans, have an appreciable degree of machiavelian intelligence.

The limited impact of kinship on cooperation in wild chimpanzees

Kevin E. Langergraber, John C. Mitani, and Linda Vigilant

PNAS Online before print

Abstract: The complex cooperative behavior exhibited by wild chimpanzees generates considerable theoretical and empirical interest, yet we know very little about the mechanisms responsible for its evolution. Here, we investigate the influence of kinship on the cooperative behavior of male chimpanzees living in an unusually large community at Ngogo in Kibale National Park, Uganda. Using long-term field observations and molecular genetic techniques to identify kin relations between individuals, we show that male chimpanzees clearly prefer to affiliate and cooperate with their maternal brothers in several behavioral contexts. Despite these results, additional analyses reveal that the impact of kinship is limited; paternal brothers do not selectively affiliate and cooperate, probably because they cannot be reliably recognized, and the majority of highly affiliative and cooperative dyads are actually unrelated or distantly related. These findings add to a growing body of research that indicates that animals cooperate with each other to obtain both direct and indirect fitness benefits and that complex cooperation can occur between kin and nonkin alike.

Monday Map - Google Maps blog

Check out this blog: Google Maps Mania: "An unofficial Google Maps blog tracking the websites, mashups and tools being influenced by Google Maps."

I could spend a whole afternoon looking at this blog, but I better not. I'll just leave it at that.

Sunday, April 29, 2007

Dog is an outgroup to mouse and human

Apparently whether dog or mouse is the outgroup was under debate...pretty interesting question when you think about it. Some thought that mouse should be an outgroup to human and dog, but this person doesn't think the phylogeny (dog, (mouse, human)) needs to be reconsidered.

Dog as an Outgroup to Human and Mouse

Gerton Lunter

PLoS Comput Biol 3(4): e74

Abstract: In a recent contribution to PLoS Computational Biology, Cannarozzi, Schneider, and Gonnet published evidence that rodents form an outgroup to human and dog [1], in disagreement with several recent studies suggesting that the dog is an outgroup to the primate–rodent clade [2,3]. The authors' arguments rest on a variety of analyses of human, mouse, and dog genes, using opossum to root the phylogeny. Here I argue that despite the large number of characters used in this study, their results may well be erroneous. I then provide new and, I believe, conclusive evidence in favour of the current consensus phylogeny, and I briefly review other recent studies that support this conclusion.

Saturday, April 28, 2007

Combining gene expression and genotype data

more rich data requires smaller sample sizes is the seemingly obvious point here. I'm surprised this is a new concept (combining gene expression and genotype data, that is), especially in the gene expression literature, given that it's probably easier to get genotype data if you're getting gene expression data, than the other way around.

Increasing the Power to Detect Causal Associations by Combining Genotypic and Expression Data in Segregating Populations

Jun Zhu, Matthew C. Wiener, Chunsheng Zhang, Arthur Fridman, Eric Minch, Pek Y. Lum, Jeffrey R. Sachs, Eric E. Schadt

PLoS Computational Biology 3(4): e69

Summary: Complex phenotypes such as common human diseases are caused by variations in DNA in many genes that interact in complex ways with a number of environmental factors. These multifactorial gene and environmental perturbations induce changes in molecular networks that in turn lead to phenotypic changes in the organism under study. The comprehensive monitoring of transcript abundances using gene expression microarrays in different tissues over a large number of individuals in a population can be used to reconstruct molecular networks that underlie higher-order phenotypes such as disease. The cost to generate these large-scale gene activity measurements over large numbers of individuals can be extreme. However, by integrating DNA variation and gene activity data monitored in each individual in a given population of interest, we demonstrate that the power to elucidate molecular networks that drive complex phenotypes can be significantly enhanced, without increasing the sample size. Using a biologically realistic simulation framework, we demonstrate that molecular networks reconstructed using the combined DNA variation and gene activity data are more accurate than molecular networks reconstructed from gene activity data alone, implying that adding DNA variation data might allow us to use fewer subjects to produce molecular networks that better explain complex phenotypes such as disease.

How to make a good presentation

For anyone in academia or research, check out "Ten simple rules for making a good oral presentation" in PLoS Comp. Biology - nothing really new, but always good to remind yourself.

Thursday, April 26, 2007

Modeling Mess-opotamia

There's a story in the new issue of Science called "Pentagon Asks Academics for Help in Understanding Its Enemies" by Yudhijit Bhattacharjee about how "a new program at the U.S. Department of Defense would support research on how local populations behave in a war zone"

I like the reaction of one critic:

The plan has drawn mixed reactions from defense experts. "They are smoking something they shouldn't be," says Paul Van Riper, a retired lieutenant general who served as director of intelligence for the U.S. Army in the mid-1990s. Human systems are far too complex to be modeled, he says: "Only those who don't know how the real world works will be suckers for this stuff."

I tend to agree with this general... and his not so subtle stereotyping of 'academic types' is funny... but then again any (non violent) thing that will help the situation even a little bit should be considered. I just share the general's skepticism of modeling.

at the end of the story:

Accomplishing those goals is a tall order, Page admits. "Despite tons and tons of data from U.S. elections," he says, "we are still not very good at predicting how people will vote."

Building comprehensive and realistic models of societies is a challenge that will require enormous amounts of empirical data, says GMU's Levis, a former chief scientist of the U.S. Air Force. But it is doable, he says, adding that the field will benefit greatly from linking social science researchers and computer scientists. "The goal here is to win popular support in the conflict zone," he says.

Wednesday, April 25, 2007

Reproductive ecology of men

... from the mighty, hallowed halls of UNM Anthropology!

Why do men marry and why do they stray?

Jeffrey Winking, Hillard Kaplan, Michael Gurven, Stacey Rucas

Proceedings of the Royal Society B: Biological Sciences Early Online Publishing

Abstract: Humans are quite unusual compared to other great apes in that reproduction typically takes place within long-term, iteroparous pairings—social arrangements that have been culturally reified as the institution of marriage. With respect to male behaviour, explanations of marriage fall into two major schools of thought. One holds that marriage facilitates a sexual division of labour and paternal investment, both important to the rearing of offspring that are born helpless and remain dependent for remarkably long periods (provisioning model). And the other suggests that the main benefits which men receive from entering into marriage derive from monopolizing access to women's fertility (mating effort model). In this paper, we explore extramarital sexual relationships and the conditions under which they occur as a means of testing predictions derived from these two models. Using data on men's extramarital sexual relationships among Tsimane forager–horticulturists in lowland Bolivia, we tested whether infidelity was more common when men had less of an opportunity to invest in their children or when they risked losing less fertility. We found that Tsimane men appear to be biasing the timing of their affairs to when they are younger and have fewer children, supporting the provisioning model.

Tuesday, April 24, 2007

Mom's early menarche predicts kid's obesity

"A mother with larger energy reserves or a history of rapid development could somehow signal to her offspring to set up a rapid postnatal growth trajectory, possibly through programming or epigenetic modulation of genes relating to appetite and growth, and thereby steer her offspring toward earlier maturation."

There are so many possible confounding variables and different ways this can happen. They seem to address these somewhat in the paper. (see below)

Earlier Mother's Age at Menarche Predicts Rapid Infancy Growth and Childhood Obesity


Early menarche tends to be preceded by rapid infancy weight gain and is associated with increased childhood and adult obesity risk. As age at menarche is a heritable trait, we hypothesised that age at menarche in the mother may in turn predict her children's early growth and obesity risk.

Methods and Findings

We tested associations between mother's age at menarche, mother's adult body size and obesity risk, and her children's growth and obesity risk in 6,009 children from the UK population-based Avon Longitudinal Study of Parents and Children (ALSPAC) birth cohort who had growth and fat mass at age 9 y measured by dual-energy X-ray absorptiometry. A subgroup of 914 children also had detailed infancy and childhood growth data. In the mothers, earlier menarche was associated with shorter adult height (by 0.64 cm/y), increased weight (0.92 kg/y), and body mass index (BMI, 0.51 kg/m2/y; all p <>2/y), and fat mass index (0.22 kg/m2/year; all p <0.001). Children in the earliest mother's menarche quintile (≤11 y) were more obese than the oldest quintile (≥15 y) (OR, 2.15, 95% CI 1.46 to 3.17; p < 0.001, adjusted for mother's education and BMI). In the subgroup, children in the earliest quintile showed faster gains in weight (p < 0.001) and height (p < 0.001) only from birth to 2 y, but not from 2 to 9 y (p = 0.3–0.8).


Earlier age at menarche may be a transgenerational marker of a faster growth tempo, characterised by rapid weight gain and growth, particularly during infancy, and leading to taller childhood stature, but likely earlier maturation and therefore shorter adult stature. This growth pattern confers increased childhood and adult obesity risks.

Monday, April 23, 2007

"Modest levels of assimilation of Neandertals into early modern human(s)"

Modest, but not rare seems to be the main point here.

European early modern humans and the fate of the Neandertals

Erik Trinkaus

PNAS Published online before print April 23, 2007

Abstract: A consideration of the morphological aspects of the earliest modern humans in Europe (more than 33,000 B.P.) and the subsequent Gravettian human remains indicates that they possess an anatomical pattern congruent with the autapomorphic (derived) morphology of the earliest (Middle Paleolithic) African modern humans. However, they exhibit a variable suite of features that are either distinctive Neandertal traits and/or plesiomorphic (ancestral) aspects that had been lost among the African Middle Paleolithic modern humans. These features include aspects of neurocranial shape, basicranial external morphology, mandibular ramal and symphyseal form, dental morphology and size, and anteroposterior dental proportions, as well as aspects of the clavicles, scapulae, metacarpals, and appendicular proportions. The ubiquitous and variable presence of these morphological features in the European earlier modern human samples can only be parsimoniously explained as a product of modest levels of assimilation of Neandertals into early modern human populations as the latter dispersed across Europe. This interpretation is in agreement with current analyses of recent and past human molecular data.

Hyenas and canids

Hyenas are more closely related to felines than they are to canids! ...somewhat surprising.

Sunday, April 22, 2007

Brain size correlates

Sexual Selection and the Evolution of Brain Size in Primates

Michael A. Schillaci

PLoS ONE 1(1): e62

Abstract: Reproductive competition among males has long been considered a powerful force in the evolution of primates. The evolution of brain size and complexity in the Order Primates has been widely regarded as the hallmark of primate evolutionary history. Despite their importance to our understanding of primate evolution, the relationship between sexual selection and the evolutionary development of brain size is not well studied. The present research examines the evolutionary relationship between brain size and two components of primate sexual selection, sperm competition and male competition for mates. Results indicate that there is not a significant relationship between relative brain size and sperm competition as measured by relative testis size in primates, suggesting sperm competition has not played an important role in the evolution of brain size in the primate order. There is, however, a significant negative evolutionary relationship between relative brain size and the level of male competition for mates. The present study shows that the largest relative brain sizes among primate species are associated with monogamous mating systems, suggesting primate monogamy may require greater social acuity and abilities of deception.

Saturday, April 21, 2007

Endurance/Persistence running

Razib has a post on a story about a recent talk by Daniel Lieberman. Also see: here, here.


"Specifically, we developed long, springy tendons in our legs and feet that function like large elastics, storing energy and releasing it with each running stride, reducing the amount of energy it takes to take another step. There are also several adaptations to help keep our bodies stable as we run, such as the way we counterbalance each step with an arm swing, our large butt muscles that hold our upper bodies upright, and an elastic ligament in our neck to help keep our head steady.

Even the human waist, thinner and more flexible than that of our primate relatives allows us to twist our upper bodies as we run to counterbalance the slightly-off-center forces exerted as we stride with each leg.

Once humans start running, it only takes a bit more energy for us to run faster, Lieberman said. Other animals, on the other hand, expend a lot more energy as they speed up, particularly when they switch from a trot to a gallop, which most animals cannot maintain over long distances.

While animals get rid of excess heat by panting, they can’t pant when they gallop, Lieberman said. That means that to run a prey animal into the ground, ancient humans didn’t have to run further than the animal could trot and didn’t have to run faster than the animal could gallop. All they had to do is to run faster, for longer periods of time, than the slowest speed at which the animal started to gallop.

All together, Lieberman said, these adaptations allowed us to relentlessly pursue game in the hottest part of the day when most animals rest. Lieberman said humans likely practiced persistence hunting, chasing a game animal during the heat of the day, making it run faster than it could maintain, tracking and flushing it if it tried to rest, and repeating the process until the animal literally overheated and collapsed.

Lieberman said he envisions an evolutionary scenario where humans began eating meat as scavengers. Over time, evolution favored scavenging humans who could run faster to the site of a kill and eventually allowed us to evolve into persistence hunters. Evolution likely continued to favor better runners until projectile weapons made running less important relatively recently in our history. "

Friday, April 20, 2007

Light skin color in Europeans is recent

News Focus
European Skin Turned Pale Only Recently, Gene Suggests

Ann Gibbons

20 April 2007 Vol. 316, p. 364

This is a news feature regarding a recent talk at the AAPA meetings. I don't quite know what to make of it. On the one hand it reminds me of the absence of the lactose tolerance allele 7,000 ya in Europe, but this seems a bit more implausible since it kinda suggests that Europeans developed lighter skin only 6,000 to 12,000 ya, as opposed to when they first entered the area. (possible reasons given below)

First of all, can we spare these cheesy kinds of opening sentences?: "Researchers have disagreed for decades about an issue that is only skin-deep"

The research was conducted by Heather Norton. Some of the interesting parts:

Regarding the fact that this (SLC24A5) is only one of several genes that is responsible for lighter skin:

"She added that other, unknown, genes probably also cause paling in Europeans" ...

"Either way, the implication is that our European ancestors were brown-skinned for tens of thousands of years--a suggestion made 30 years ago by Stanford University geneticist L. Luca Cavalli-Sforza. He argued that the early immigrants to Europe, who were hunter-gatherers, herders, and fishers, survived on ready-made sources of vitamin D in their diet. But when farming spread in the past 6000 years, he argued, Europeans had fewer sources of vitamin D in their food and needed to absorb more sunlight to produce the vitamin in their skin. Cultural factors such as heavier clothing might also have favored increased absorption of sunlight on the few exposed areas of skin, such as hands and faces, says paleoanthropologist Nina Jablonski of PSU in State College."

This is all really cool. I prefer the Cavalli-Sforza hypothesis, however. It would be great to look at some of the other candidate alleles and to look at them in Neanderthals!! ... looking forward to the publication and what SLC24A5 looks like in the Native American sample they looked at.

Wednesday, April 18, 2007

Genetics, race, health, and social perceptions

Very interesting...on the differences in perceptions surrounding race, health and genetics. I'm getting the full text from inter-library loan now, so maybe more on this later. The main thing that I would note from the abstract is that Whites are maybe less likely to acknowledge Environment in the Gene X Environment interaction contributing to disease, something not missed by Blacks. I may be over-interpreting here, but that's what I think.

Applications and implications of advances in human genetics: perspectives from a group of Black Americans.

Sheldon JP, Epstein Jayaratne T, Feldbaum MB, DiNardo CD, Petty EM.
Community Genet. 2007;10(2):82-92
OBJECTIVES: We explored the opinions of 40 Black Americans regarding: (1) what they thought most Blacks and Whites believe about genetic causes for perceived race differences in human traits, and (2) the impact of genetic science on them, their families, and Black people. METHODS: We conducted in-depth telephone interviews with 40 self-identified Black men and women. Transcripts of the interviews were recorded and examined for common themes. RESULTS: The majority of our respondents felt that most Whites, unlike most Blacks, attribute differences between these groups to genetic factors. Many in our sample felt that genetic advances may provide benefits in the area of health care, but many also recognized potential harm. CONCLUSIONS: Our results provide a glimpse as to what some Blacks believe about genetic science in the context of racial issues.

Biased gene flow over the Himalayas

"...the Himalayas have been permeable to dispersals from the east. These genetic patterns suggest that this cordillera has been a biased bidirectional barrier."

The Himalayas as a directional barrier to gene flow.

Gayden T, Cadenas AM, Regueiro M, Singh NB, Zhivotovsky LA, Underhill PA, Cavalli-Sforza LL, Herrera RJ.

Am J Hum Genet. 2007 May;80(5):884-94.

Abstract: High-resolution Y-chromosome haplogroup analyses coupled with Y-short tandem repeat (STR) haplotypes were used to (1) investigate the genetic affinities of three populations from Nepal--including Newar, Tamang, and people from cosmopolitan Kathmandu (referred to as "Kathmandu" subsequently)--as well as a collection from Tibet and (2) evaluate whether the Himalayan mountain range represents a geographic barrier for gene flow between the Tibetan plateau and the South Asian subcontinent. The results suggest that the Tibetans and Nepalese are in part descendants of Tibeto-Burman-speaking groups originating from Northeast Asia. All four populations are represented predominantly by haplogroup O3a5-M134-derived chromosomes, whose Y-STR-based age (+/-SE) was estimated at 8.1+/-2.9 thousand years ago (KYA), more recent than its Southeast Asian counterpart. The most pronounced difference between the two regions is reflected in the opposing high-frequency distributions of haplogroups D in Tibet and R in Nepal. With the exception of Tamang, both Newar and Kathmandu exhibit considerable similarities to the Indian Y-haplogroup distribution, particularly in their haplogroup R and H composition. These results indicate gene flow from the Indian subcontinent and, in the case of haplogroup R, from Eurasia as well, a conclusion that is also supported by the admixture analysis. In contrast, whereas haplogroup D is completely absent in Nepal, it accounts for 50.6% of the Tibetan Y-chromosome gene pool. Coalescent analyses suggest that the expansion of haplogroup D derivatives--namely, D1-M15 and D3-P47 in Tibet--involved two different demographic events (5.1+/-1.8 and 11.3+/-3.7 KYA, respectively) that are more recent than those of D2-M55 representatives common in Japan. Low frequencies, relative to Nepal, of haplogroup J and R lineages in Tibet are also consistent with restricted gene flow from the subcontinent. Yet the presence of haplogroup O3a5-M134 representatives in Nepal indicates that the Himalayas have been permeable to dispersals from the east. These genetic patterns suggest that this cordillera has been a biased bidirectional barrier.

Tuesday, April 17, 2007

Evolutionary reasoning in medicine

An editorial in the latest issue of PLoS Biology speaks of the need for evolutionary based reasoning in medical education .

Does Medicine without Evolution Make Sense?
Catriona J. MacCallum

The title is a take from Dobzhansky's quote "Nothing in biology makes sense except in the light of evolution"

The interesting thing from this editorial was some of the reasons why evolutionary reasoning is not taught in medical schools. For example:

"One reason that evolution doesn't figure prominently in the medical community is that although it makes sense to have evolution taught as part of medicine, that doesn't make it essential. As explained at a meeting on evolution and medicine I recently attended in York, United Kingdom (the Society for the Study of Human Biology and the Biosocial Society's 2006 symposium, “Medicine and Evolution”), medicine is primarily focused on problem-solving and proximate causation, and ultimate explanations can seem irrelevant to clinical practice. Crudely put, does a mechanic need to understand the origins, history, and technological advances that have gone into the modern motor vehicle in order to fix it?"

I do not understand the reasoning behind the last sentence in this paragraph at all:

"Many diet-related conditions that typify industrialized populations—e.g., obesity, hypertension, and tooth decay—have been explained as resulting from an evolutionary mismatch between our over-refined, fat-filled contemporary diet and the environment to which humans were once ideally adapted. Sarah Elton (Hull York Medical School, UK) cautioned that while this analogy (the “environment of evolutionary adaptedness”) has been useful as a research tool and has led to public health campaigns for better diets (more seeds, nuts, fish oil, etc.), recreating such a typical “Stone Age diet” as a benchmark can be misleading.
Human ecology in the past was at least as variable as human (and other primate) ecology is today."

...what does "variable" have to do with it?

Monday, April 16, 2007

Calorie restriction in dogs

Check out this article in The Economist about an experiment testing whether calorie restriction in dogs extends their lifespan. They also look at metabolites in urine to get an idea of the mechanism behind the effect.

Monday Map - cool website

Iwka posted on this at GNXP. This website does visualizations of data, including maps with data by country.
Many eyes
here's the world birth rate map

Friday, April 13, 2007

Density dependent, group level benefits of ADHD types

Highly speculative, but interesting. Of course, as luck has it, I can't get access to the full text. I'd much appreciate the pdf if anyone has access to it. They invoke a group selection type mechanism favoring ADHD types of personalities. Groups with these kinds of people are more successful than groups without them: "Simulations of the Changing Food group task show that unpredictable behaviour by a minority optimizes results for the group" -- kind of a division of labor scenario, but within the group (i.e point guard, center, forward in basketball)

The evolution of hyperactivity, impulsivity and cognitive diversity

Jonathan Williams and Eric Taylor

Journal of The Royal Society Interface
Volume 3, Number 8 / June 22, 2006: 399 - 413

Abstract: The evolutionary status of attention deficit/hyperactivity disorder (ADHD) is central to assessments of whether modern society has created it, either physically or socially; and is potentially useful in understanding its neurobiological basis and treatment. The high prevalence of ADHD (5–10%) and its association with the seven-repeat allele of DRD4, which is positively selected in evolution, raise the possibility that ADHD increases the reproductive fitness of the individual, and/or the group. However, previous suggestions of evolutionary roles for ADHD have not accounted for its confinement to a substantial minority. Because one of the key features of ADHD is its diversity, and many benefits of population diversity are well recognized (as in immunity), we study the impact of groups' behavioural diversity on their fitness. Diversity occurs along many dimensions, and for simplicity we choose unpredictability (or variability), excess of which is a well-established characteristic of ADHD.Simulations of the Changing Food group task show that unpredictable behaviour by a minority optimizes results for the group. Characteristics of such group exploration tasks are risk-taking, in which costs are borne mainly by the individual; and information-sharing, in which benefits accrue to the entire group. Hence, this work is closely linked to previous studies of evolved altruism.We conclude that even individually impairing combinations of genes, such as ADHD, can carry specific benefits for society, which can be selected for at that level, rather than being merely genetic coincidences with effects confined to the individual. The social benefits conferred by diversity occur both inside and outside the ‘normal’ range, and these may be distinct. This view has the additional merit of offering explanations for the prevalence, sex and age distribution, severity distribution and heterogeneity of ADHD.

Female stem cells work better

Check out the story at Science Blog

In this study, Dr. Huard’s team injected female and male muscle-derived stem cells into dystrophic mice and then measured the cells’ ability to regenerate dystrophin-expressing muscle fibers.

They then calculated the regeneration index (RI) – the ratio of dystrophin-positive fibers per 100,000 donor cells. Only one of the 10 male populations of implanted stem cells had an RI over 200. In contrast, 40 percent of the female stem cell populations had an RI higher than 200, and 60 percent of the female populations of stem cells had an RI higher than the mean RI of the male cells (95).

This difference may arise from innate sex-related differences in the cells’ stress responses, according to Dr. Deasy, an assistant professor in the Departments of Orthopaedic Surgery and Bioengineering at the University of Pittsburgh School of Medicine and School of Engineering, respectively.

Tuesday, April 10, 2007

New issue of AJHB

The American Journal of Human Biology may not be the most prestigious journal of 'em all, but it covers the most interesting topics of any other journal. It is edited by Peter Ellison. There's a new issue out. Unfortunately, my university does not subscribe to it in any way, making it a bit harder, but of course, not impossible to get the papers.
here are the titles and abstracts of some of the more interesting papers from this issue:

HLA genes and surnames show a similar genetic structure in Lombardy: Does this reflect part of the history of the region? (p 311-318)

Antonella Lisa, Annalisa De Silvestri, Luca Mascaretti, Alberto Degiuli, Carmela R. Guglielmino

Abstract Lombardy, in northern Italy, is the most populated and industrialized Italian region. We attempt to study its genetic structure with two independent sets of data: HLA allele frequencies and surnames. According to our results, it is plausible to deduce that ancient history, more than genetic isolation and drift, may have contributed to the present genetic structure of Lombardy. The hypothesis seems to be confirmed by the results of the cluster analysis of the 11 provinces of the region, which was performed using two different types of markers. Both genes and surnames show approximately the same structure. Not only Celts but also ancient Ligurians (and Etruscans) probably shaped the region into the present three clusters in which the 11 provinces appear to be genetically structured. In particular, an ancient historic, archaeological, and linguistic boundary, along the Adda River, seems to be preserved in present-day Lombardy's population structure.

Nikki L. Rogers , Shelley A. Cole , Hao-Chang Lan , Aldo Crossa, Ellen W. Demerath

Abstract: Epidemiological studies may require noninvasive methods for off-site DNA collection. We compared the DNA yield and quality obtained using a whole-saliva collection device (OrageneTM DNA collection kit) to those from three established noninvasive methods (cytobrush, foam swab, and oral rinse). Each method was tested on 17 adult volunteers from our center, using a random crossover collection design and analyzed using repeated-measures statistics. DNA yield and quality were assessed via gel electrophoresis, spectophotometry, and polymerase chain reaction (PCR) amplification rate. The whole-saliva method provided a significantly greater DNA yield (mean ± SD = 154.9 ± 103.05 g, median = 181.88) than the other methods (oral rinse = 54.74 ± 41.72 g, 36.56; swab = 11.44 ± 7.39 g, 10.72; cytobrush = 12.66 ± 6.19, 13.22 g) (all pairwise P <>260/OD280 and OD260/OD230 ratios. We conclude that both a 10-ml oral-rinse sample and 2-ml whole-saliva sample provide sufficient DNA quantity and better quality DNA for genetic epidemiological studies than do the commonly used buccal swab and brush techniques.

Linda S. Adair

Abstract: Few studies in developing countries follow growth trajectories from birth to adulthood. Such studies are important because size at birth and postnatal growth affect risk of chronic disease in adulthood. This study examines the inter-relationships of maternal factors during pregnancy, infant birth weight and length, early postnatal growth, and young adult height, weight, BMI, and skinfold thicknesses, with particular attention to patterns of growth associated with increased chronic disease risk. Women were recruited in pregnancy, and offspring were followed from birth to age 21 in the community-based Cebu (Philippines) Longitudinal Health and Nutrition Survey. Birth weight and length are independently, positively associated with height, BMI and sum of skinfolds in young adult males and females, and inversely associated with the subscapular to triceps ratio in males only. The effects of size at birth on adult size were modified by birth order, and remained significant after adjusting for maternal nutritional status, socioeconomic status at birth and throughout the growth period, and maturation. Early postnatal growth was strongly influenced by BMI at birth, with rapid early infant weight gain associated with thinness. The growth pattern of the at-risk group most often associated with increased risk of chronic disease (small at birth, relatively heavy as an adult), was characterized by more rapid growth in the first 4 postnatal months. The high level of inter-relatedness of maternal nutrition in pregnancy, prenatal growth, and postnatal growth emphasizes the need to consider the full growth trajectory in studies of developmental origins of adult disease.

V. R. Rao , L. V. K. S. Bhaskar , C. Annapurna , A. G. Reddy , K. Thangaraj , A. Papa Rao , Lalji Singh

Abstract: Seven ADH genes, identified until now, located in the long arm of human chromosome 4, produce seven different isozymes involved in the metabolism of ethanol to acetaldehyde. Of the more than 500 SNPs reported in the coding and non-coding regions of these genes in the world databases, 11 are more extensively studied. Three SNPs, ADH1B Arg47His (Exon3), ADH1B Arg369Cys (Exon9) and ADH1C Val349Ile (Exon8), are functionally validated in terms of phenotype-genotype correlations and are in specific linkage disequilibrium (LD) with non-coding SNPs. However, the frequency of each SNP and configuration of LD varies among populations. The Indian populations studied were conspicuous by the complete absence of African specific allele ADH1B*369Cys, the negligible frequency of East Asian specific ADH1B*47His allele and the presence of a novel SNP ADH1B A3529G (Intron3). The ADH1C*349Ile was the only functional allele polymorphic with a strong LD block in all the populations studied and the high Fst value observed for the non-coding ADH1B Rsa1 variant was in conformity with world populations.

John T. Manning , Laura Morris, Noreen Caswell

Abstract: There is anatomical and physiological evidence that endurance running (ER), i.e., running one or more kilometers using aerobic metabolism, originated early in the evolution of Homo, and the consequences of early selection for ER may be important in modern Homo. Here we examine ER performance in competitive ER. ER is sex dependent such that men tend to run faster than women, and the influence of sex on ER suggests that it may be modified by testosterone (T). It is shown that a putative proxy for prenatal T, the ratio of the length of the 2nd and 4th digits (2D:4D), is correlated with ER. Thus performance in training for ER was associated with high prenatal T, as measured by low 2D:4D, in both men and women. In cross-country races from 1 to 4 miles, 2D:4D explained about 25% of the variance in both male and female ER. Therefore, speed in ER was dependent on a proxy for prenatal T. 2D:4D correlates with performance in sport and exercises, which test a mix of strength and fitness, but the associations are in general quite weak with 2D:4D accounting for less than 10% of the variance in performance. Our finding that 2D:4D explains about 25% of the variance in ER suggests that prenatal T is important in determining efficiency in aerobic exercise. Early populations of Homo may have been strongly selected for ER and high prenatal T. The implications of this for patterns of predisposition to cardiovascular disease in modern Homo are discussed.

....and several more interesting ones. Check out the table of contents.

Monday, April 09, 2007

Monday Map: weird looking neck twister

I kept on seeing this map, not knowing what the hell it was. It looks kinda like a deformed Mexico, but not really. Then, I took a longer, harder look at it in a larger format, (it turns out it's from Wikipedia) and figured it out.. have a look:

Sunday, April 08, 2007

"Group selection and kin selection: Two concepts but one process"

Razib discusses the paper by Traulsen and Nowak about how group selection can occur.
I've covered this topic in several other posts, most notably here and here regardng a paper by Sam Bowles in Science where he shows that multilevel selection could occur in humans due to high relatedness within groups, high levels of inter-group conflict, and reproductive leveling. He notes that it is hard to distinguish group selection from kin selection.

Now comes this new paper in PNAS (see below) that argues that group selection is synonymous with kin selection. I think this probably applies to humans as we tend to extend kinship terms and emotions to everyone in the group, thus facilitating very extended kin selection that would be otherwise limited within other primate groups.
I did not get into the mathematical modeling of this paper. I'd be interested to hear what Razib has to say about it.

Group selection and kin selection: Two concepts but one process

Laurent Lehmann, Laurent Keller, Stuart West, and Denis Roze

PNAS Published online before print April 6, 2007

Absract: In a recent paper, Traulsen and Nowak use a multilevel selection model to show that cooperation can be favored by group selection in finite populations [Traulsen A, Nowak M (2006) Proc Natl Acad Sci USA 103:10952-10955]. The authors challenge the view that kin selection may be an appropriate interpretation of their results and state that group selection is a distinctive process "that permeates evolutionary processes from the emergence of the first cells to eusociality and the economics of nations." In this paper, we start by addressing Traulsen and Nowak's challenge and demonstrate that all their results can be obtained by an application of kin selection theory. We then extend Traulsen and Nowak's model to life history conditions that have been previously studied. This allows us to highlight the differences and similarities between Traulsen and Nowak's model and typical kin selection models and also to broaden the scope of their results. Our retrospective analyses of Traulsen and Nowak's model illustrate that it is possible to convert group selection models to kin selection models without disturbing the mathematics describing the net effect of selection on cooperation.

Saturday, April 07, 2007

Sun, vitamin D, population differences

There's a short news feature in the latest issue of Nature Medicine about the benefits of sunlight.

Essentially, the sun is good (vs. TB, MS, cancer, diabetes...) because we get a lot of vitamin D from it..., for example for MS:

"The strongest evidence available is perhaps for the vitamin's protective role in MS. Several studies have documented a dramatic 'sunshine belt' across the center of the globe: MS is rarer near the equator and more common in northern regions, where ultraviolet light from the sun is less intense.

"There's a very, very strong latitude ingredient," says Alberto Ascherio, associate professor of nutrition and epidemiology at Harvard University. In the US, for example, the incidence of MS is up to four-fold higher in the northwest than in the southeast, he notes."

and cancer:

Latitude also seems to play a role in the incidence of hormone-dependent cancers. "There is a fair bit of epidemiological data showing that places with less sunshine have higher rates of cancer," says David Feldman, professor of medicine at Stanford University and the editor of a 1,300-page treatise on the substance.

The effect is almost certainly because of vitamin D, Feldman says. "People tend to think it can't do all these things when it's a vitamin," notes Feldman. "It's not a vitamin, it's a hormone."

I was really struck by this statement:

"How do you write a paper when everybody says race doesn't matter and here you have a subject where blacks have more TB and it has to do with the color of the skin and nothing else?" asks Bloom. "I thought that was pretty challenging." Bloom says scientists are planning to test vitamin D supplements in TB trials in Africa.

"...everybody says race doesn't matter"???... Either this person is over dramatizing, or hasn't been keeping up with "everybody".

By the way, very dark is good too (via melatonin)... so a lot of sun and a lot of good dark time seems to be the way to go.

News feature: The sunshine cure

Apoorva Mandavilli

Nature Medicine - 13, 396 - 397 (2007)

Could ten minutes of sunlight a day be all that's needed to fight multiple sclerosis, cancer and tuberculosis? Apoorva Mandavilli discovers the growing interest in vitamin D's many virtues.

Friday, April 06, 2007

'Human Evolution and Disease' workshop

I love these meeting/workshop reports. This one looked especially good... see abstract and reference below.

Regarding modern human origins, Paul Mellars asks:

"Why, if AMH originated in Africa 150–200 KYA (thousand years ago) did they only disperse out of Africa 50–60 KYA? To answer this, he pointed to the archaeological signature revealing major technological, economic and social developments in southern Africa roughly 60–80 KYA, which could have been crucial driving forces for AMH to expand their range successfully throughout the world. "

Regarding the unique Andamanese:

"Lalji Singh (CCMB, India) gave evidence from mtDNA sequences that two ancient maternal lineages, M31 and M32, in the Onge and Great Andamanese do not match any other populations in the world, indicating that the Andaman Islanders have survived in complete genetic isolation from other South and Southeast Asian populations, as the migration of AMH out of Africa."

and regarding the relationship between language and genetics:

"As George van Driem (Leiden, The Netherlands) reminded us, although linguistics, archaeology and genetics have often been used in combination to provide support for human origins, the evidence from the three disciplines does not always tell the same story. Languages, in particular, may be better seen as leaves that have fallen to the ground and lost ancient information about their relationships, rather than as branches on an informative evolutionary tree."

He then goes into a discussion on disease related genetic studies, with some interesting insights about where and how we should be looking.

Insights into modern disease from our distant evolutionary past

European Journal of Human Genetics advance online publication 14 March 2007

Bryndis Yngvadottir

Abstract: An EMBO workshop entitled 'Human Evolution and Disease' was held recently (6–9 December 2006, Hyderabad, India) where 141 scientists from many disciplines came together to discuss recent studies of human variation, origins and dispersal, natural selection and disease susceptibility. The meeting tackled the subject of human evolution and disease from the different perspectives of archaeology, linguistics, genetics and genomics based on both new and publicly available data sets. In this report, we highlight the latest fashion crazes in the discipline, in particular, the use of large public data sets and new methods to analyse modern human variation and the links between human evolution and disease susceptibility.

Great Science cover photo

Why is it that the cover photos for Science are usually much better than Nature's? This most recent one is great. They find an IGF1 haplotype that is common to all small dog breeds and not large dog breeds.

Here's the link to the abstract.

Wednesday, April 04, 2007

Statistics Blog

Via p-ter at GNXP, a blog called Statistical Modeling, Causal Inference, and Social Science, on various statisitics related topics. I liked the post on whether the iPod shuffle function is really random - I will probably be checking this blog regularly to improve my understanding of stats in an applied, interesting way.

Monday, April 02, 2007

Genetic basis of adaptation to hypoxia

Let's do this in humans and compare different high altitude populations (E. Africa, Andes, Himalayas). There is some evidence that different populations adapted to hypoxia in different ways. Here they find five amino acid mutations responsible for the effect.

The Molecular Basis of High-Altitude Adaptation in Deer Mice

Jay F. Storz, Stephen J. Sabatino, Federico G. Hoffmann, Eben J. Gering, Hideaki Moriyama, Nuno Ferrand, Bruno Monteiro, Michael W. Nachman

PLoS Genet 3(3): e45

Abstract: Elucidating genetic mechanisms of adaptation is a goal of central importance in evolutionary biology, yet few empirical studies have succeeded in documenting causal links between molecular variation and organismal fitness in natural populations. Here we report a population genetic analysis of a two-locus α-globin polymorphism that underlies physiological adaptation to high-altitude hypoxia in natural populations of deer mice, Peromyscus maniculatus. This system provides a rare opportunity to examine the molecular underpinnings of fitness-related variation in protein function that can be related to a well-defined selection pressure. We surveyed DNA sequence variation in the duplicated α-globin genes of P. maniculatus from high- and low-altitude localities (i) to identify the specific mutations that may be responsible for the divergent fine-tuning of hemoglobin function and (ii) to test whether the genes exhibit the expected signature of diversifying selection between populations that inhabit different elevational zones. Results demonstrate that functionally distinct protein alleles are maintained as a long-term balanced polymorphism and that adaptive modifications of hemoglobin function are produced by the independent or joint effects of five amino acid mutations that modulate oxygen-binding affinity.

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