Generalized reciprocity in rats

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

Generalized Reciprocity in Rats

Claudia Rutte, Michael Taborsky

PLoS Biology, 5(7)

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

Race-based medical research baseless?

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

There is no scientific rationale for race-based research.

Hoover EL.

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

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

Caribbean genetic structure

Mitochondrial and Y Chromosome Diversity in the English-Speaking Caribbean.

Torres JB, Kittles RA, Stone AC

Annals of Human Genetics: 2007. Epub ahead of print

Abstract: The transatlantic slave trade lasted over three centuries and represents one of the largest forced migrations in human history. The biological repercussions are not well understood especially in African-Caribbean populations. This paper explores the effects of the forced migration, isolation, and admixture on genetic diversity using mitochondrial and Y chromosome markers for 501 individuals from Dominica, Grenada, Jamaica, St. Kitts, St. Lucia, St. Thomas, St. Vincent, and Trinidad. Genetic diversity and population genetic structure analyses of mitochondrial data and Y chromosome data indicate that there was no post-migration loss in genetic diversity in the African derived lineages. Genetic structure was observed between the islands for both genetic systems. This may be due to isolation, differences in the number and source of Africans imported, depopulation of indigenous populations, and/or differences in colonization history. Nearly 10% of the individuals belonged to a non-African mitochondrial haplogroup. In contrast, Y chromosome admixture estimates showed that there was nearly 30% European contribution to these Caribbean populations. This study sheds light on the history of Africans in the Americas as well as contributing to our understanding of the nature and extent of diversity within the African Diaspora.

Evolutionary Perspective on Iron Deficiency

This is very interesting, although I'm not sure why they refer to "a long evolutionary persistence of iron deficiency" in the last sentence of the abstract when they seem to be arguing for a relatively recent origin of this problem (since the advent of agriculture).
The infectious disease connection to iron deficiency is quite compelling.
I used to be slightly anemic myself, so I can totally relate (haha).

Nutritional iron deficiency: an evolutionary perspective.

Denic S, Agarwal MM

Nutrition 2007 Jun 19; [Epub ahead of print]

Abstract: Iron deficiency, with or without iron-deficiency anemia, is so ubiquitous that it affects all populations of the world irrespective of race, culture, or ethnic background. Despite all the latest advances in modern medicine, improved nutrition, and the ready availability of cheap oral iron, there is still no good explanation for the widespread persistence of iron deficiency. It is possible that the iron deficiency phenotype is very prevalent because of many factors other than the commonly cited causes such as a decreased availability or an increased utilization of iron. Several thousand years ago, human culture changed profoundly with the agrarian revolution, when humans turned to agriculture. Their diet became iron deficient and new epidemic infections emerged due to crowding and lifestyle changes. There is convincing evidence that iron deficiency protects against many infectious diseases such as malaria, plague, and tuberculosis as shown by diverse medical, historical, and anthropologic studies. Thus, this change of diet increased the frequency of iron deficiency, and epidemic infections exerted a selection pressure under which the iron deficiency phenotype survived better. Multiple evolutionary factors have contributed in making iron deficiency a successful phenotype. We analyze some of the recent findings of iron metabolism, the theories explaining excessive menstruation in human primates, the unexplained relative paucity of hemochromatosis genes, the former medical practice of "blood-letting," and other relevant historical data to fully understand the phenomenon of iron deficiency. We suggest that, due to a long evolutionary persistence of iron deficiency, efforts at its prevention will take a long time to be effective.

Human vs. Chimp Cooperation

Via Razib at GNXP, a new paper has come out in PLoS Biology that compares helping ("altruistic") behavior in chimpanzees to altruistic behavior in humans. A paper that came out in Science last year by the same authors showed that human infants were more likely to help out a human who needed help than chimpanzees (that had been reared by and around humans). The purpose of this research is to demonstrate how the extensive cooperation seen in humans (only rivaled by social insects and maybe a few others) is hard-wired. The previous paper in Science shows that human infants were quite a bit more helping than chimpanzees. This new one shows that chimps actually are as helpful as young children. It seems like the difference between this and the previous study is that they changed the experiment around and, this time, they found that chimps were as helpful as humans, and not less.
I think that this is an interesting line of research, mostly because it is done with very young humans - to try to demonstrate the more hard-wired nature of human cooperation. I wonder what the results would look like if the chimps and humans were matched in age.

Spontaneous Altruism by Chimpanzees and Young Children

Felix Warneken, Brian Hare, Alicia P. Melis, Daniel Hanus, Michael Tomasello

PLoS Biology, online before print

Abstract: People often act on behalf of others. They do so without immediate personal gain, at cost to themselves, and even toward unfamiliar individuals. Many researchers have claimed that such altruism emanates from a species-unique psychology not found in humans' closest living evolutionary relatives, such as the chimpanzee. In favor of this view, the few experimental studies on altruism in chimpanzees have produced mostly negative results. In contrast, we report experimental evidence that chimpanzees perform basic forms of helping in the absence of rewards spontaneously and repeatedly toward humans and conspecifics. In two comparative studies, semi–free ranging chimpanzees helped an unfamiliar human to the same degree as did human infants, irrespective of being rewarded (experiment 1) or whether the helping was costly (experiment 2). In a third study, chimpanzees helped an unrelated conspecific gain access to food in a novel situation that required subjects to use a newly acquired skill on behalf of another individual. These results indicate that chimpanzees share crucial aspects of altruism with humans, suggesting that the roots of human altruism may go deeper than previous experimental evidence suggested.

MC1R variants across populations

Comprehensive evaluation of allele frequency differences of MC1R variants across populations.

Gerstenblith MR, Goldstein AM, Fargnoli MC, Peris K, Landi MT.

Human Mutation 2007 May;28(5):495-505.

Abstract: The melanocortin 1 receptor (MC1R), a member of the G protein-coupled receptors superfamily, mediates the response to melanocortins and is currently the best-described contributor to normal pigment variation in humans. A remarkably large number of natural polymorphisms, or variants, of the MC1R gene have been identified in different populations. Some of these variants have been associated with specific hair and skin color phenotypes, the presence of freckling, and melanoma and nonmelanoma skin cancer risk. Interestingly, some MC1R variants have been associated with skin cancer beyond their effects on pigmentation. Although the red hair color variants (RHC variants) have been associated with skin cancer risk in the Celtic population, studies in darkly-pigmented Caucasian populations have demonstrated the importance of non-RHC MC1R variants on skin cancer risk as well. We have reviewed and compared allele frequency differences of MC1R variants across geographic regions. We observed large differences in the distribution of variants across populations, with a prominent difference between lightly and darkly-pigmented individuals. Moreover, among Caucasian groups, there were seven variants (p.V60L, p.V92M, p.D84E, p.R151C, p.R160W, p.R163Q, and p.D294H) with significantly different allele frequencies. Exploring differences in allele frequencies of MC1R variants across populations with varying pigmentation and differing skin cancer risk may improve our understanding of the complex relationship between MC1R, pigmentation, and carcinogenesis.

A Chinese population descended from Romans?

Gotta love these straightforward studies that test a highly testable and simple hypothesis. This one reminds of me of the hypothesis that Kalash people in Northern Pakistan are a population partly derived of the ancestors of Alexander the Great's army. It turns out that these people do cluster out pretty strongly in at least one study. The evidence of a genetic contribution from Greeks however is mixed.
This study fails to support a similar hypothesis, that Romans contributed to the gene pool of a specific Chinese group. Here's a related news story. The Lemba, on the other hand are an example of this sort of story that has been supported by genetic evidence.

Testing the hypothesis of an ancient Roman soldier origin of the Liqian people in northwest China: a Y-chromosome perspective.

Zhou R, An L, Wang X, Shao W, Lin G, Yu W, Yi L, Xu S, Xu J, Xie X.

J Hum Genet. 2007 Jun 20; [Epub ahead of print]

Abstract: To test this hypothesis, 227 male individuals representing four Chinese populations were analyzed at 12 short tandem repeat (STR) loci and 12 single nucleotide polymorphisms (SNP). At the haplogroup levels, 77% Liqian Y chromosomes were restricted to East Asia. Principal component (PC) and multidimensional scaling (MDS) analysis suggests that the Liqians are closely related to Chinese populations, especially Han Chinese populations, whereas they greatly deviate from Central Asian and Western Eurasian populations. Further phylogenetic and admixture analysis confirmed that the Han Chinese contributed greatly to the Liqian gene pool. The Liqian and the Yugur people, regarded as kindred populations with common origins, present an underlying genetic difference in a median-joining network. Overall, a Roman mercenary origin could not be accepted as true according to paternal genetic variation, and the current Liqian population is more likely to be a subgroup of the Chinese majority Han.

Positive selection in human CNS related genes and its' associated costs

Humans are special for their large brains. This paper discusses the genetic record of this, and the deleterious effects of antagonistic pleiotropy due to strong selection on some CNS variants.

Enrichment of HapMap recombination hotspot predictions around human nervous system genes: evidence for positive selection?

Jan Freudenberg, Ying-Hui Fu and Louis J Ptáek

European Journal of Human Genetics Published online 13 June 2007.

Abstract: Channels and developmental genes belong to the molecular key players in the human central nervous system (CNS). Mutations in these genes often cause monogenic neurological disease and interspecies comparisons had shown reduced divergence. On the other hand, accelerated evolution of genes with roles in neurotransmission and development had indicated widespread positive selection in hominids. In the present study, we hypothesized that recombination hotspots could be enriched at genes with particularly important role in the CNS, because at those loci beneficial mutations may occur on a highly constrained background and consequently increased recombination could promote their fixation. To test this hypothesis, we retrieved CNS genes based on keyword search, expression data and expert knowledge. Consistent with our hypothesis, we find an enrichment of hotspot predictions around genes that are retrieved by all three strategies. Moreover, when comparing human genes based on their Gene Ontology annotations, we find hotspot predictions preferentially located around channels and neurodevelopmental genes. Taken together with the distinct sequence evolution that was reported by comparative genomic studies, this finding indicates continued positive selection at many CNS gene loci. In support of this interpretation, we also find an enrichment of recombination hotspot predictions around conserved noncoding regions that were reported to display a signature of accelerated evolution in the human lineage. Widespread positive selection acting on CNS gene loci could relate to the high prevalence of human nervous system disorders with genetically complex inheritance, potentially under an ancestral susceptibility allele model.

Americans are the shortest of all industrialized nations?

This is a story I found via Yahoo! on ABC News. I find it hard to believe. I wonder what other countries they included in the survey. Reasons given were: worse health care for children in the US, and too much junk food which give too much growth hormones too early on. Neither of these is particularly compelling to me. I remain somewhat skeptical about whether they included all that many countries in the survey, and whether the reasons offered up are the correct ones. Here's the link to the video. The kid's reaction at 1min54 seconds is hilarious.

Update: A reader alerted me to the actual paper where this information is published. This seems to be a much more complicated story than what the news story describes.

New look

I thought I would try out the white background. I think the black background with white font isn't very easy to read, especially since most things that we read on the internet or on paper are black on white. So, I fear it might have been a bit hard for readers to have to change their usual visual/cognitive machinery in order to read this blog. Anyway, I hope this makes it easier to read the contents.

Why do humans have big brains?

There are several explanations for this: meat and sociality among them. These are of course not mutually exclusive, by the way. There are a couple of papers by Ann Gibbons (here, here) in the latest Science issue that discuss new evidence and the controversies surrounding the role of cooking meat in allowing for increased energy allocation to brain size.

some excerpts:
To find support for his ideas, Wrangham went to the lab to quantify the nutritional impact of cooking. He found almost nothing in food science literature and began to collaborate with physiologist Stephen Secor of the University of Alabama, Tuscaloosa, who studies digestive physiology and metabolism in amphibians and reptiles. Secor's team fed 24 Burmese pythons one of four diets consisting of the same number of calories of beef: cooked ground beef, cooked intact beef, raw ground beef, or raw intact beef. Then they estimated the energy the snakes consumed before, during, and after they digested the meat, by measuring the declining oxygen content in their metabolic chambers. Pythons fed cooked beef spent 12.7% less energy digesting it and 23.4% less energy if the meat was both cooked and ground. "By eating cooked meat, less energy is expended on digestion; therefore, more energy can be used for other activities and growth," says Secor. Secor also helped Wrangham and graduate student Rachel Carmody design a pilot study in which they found that mice raised on cooked meat gained 29% more weight than mice fed raw meat over 5 weeks. The mice eating cooked food were also 4% longer on average, according to preliminary results. Mice that ate raw chow weighed less even though they consumed more calories than those fed cooked food. "The energetic consequences of eating cooked meat are very high," says Wrangham.

But, there is the issue of when hominins (H. erectus) were first able to use fire. The best evidence for human use of fire happens quite long after the burst in brain size that happened about 2 million years ago.the last paragraph:
Others, such as Carel van Schaik of the University of Zurich, think that cooking may have played an important role early on, along with other adaptations to expand human brainpower. As Aiello observes, the big brain was apparently the lucky accident of several converging factors that accentuate each other in a feedback loop. Critical sources of energy to fuel the brain came from several sources--more meat, reduced guts, cooking, and perhaps more efficient upright walking and running. The order in which our ancestors adopted these energy-saving adaptations is under hot debate, with the timing for cooking hardest to test. Regardless, "it's all beginning to come together," says Aiello.

Cognitive/Behavioral ecology of human altruism

This news story I got to through the TAMU Anthropology in the News is in the same line as research that shows that helping others is one of top contributors to "happiness".

If It Feels Good to Be Good, It Might Be Only Natural

"The results were showing that when the volunteers placed the interests of others before their own, the generosity activated a primitive part of the brain that usually lights up in response to food or sex. Altruism, the experiment suggested, was not a superior moral faculty that suppresses basic selfish urges but rather was basic to the brain, hard-wired and pleasurable."

Regarding the somewhat laughable potential reactions to this finding:
"Even more important, some wonder whether the very idea of morality is somehow degraded if it turns out to be just another evolutionary tool that nature uses to help species survive and propagate."

I wonder how economists would interpret these types of findings. This hard-wired altruism was probably due to selection for those individuals who engaged in strong, generalized reciprocity, or generous tit-for-tat like behavior. The benefit of being nice in leading to reducing risk/variation in food acquisition is the likely ecological factor selecting for this.

Group differences in psychology - Yao Ming style

I guess this paper is still not out yet, but there's a news story about it in Science. Some might think that this line of research is fraught with danger, just as some people think that human genetic diversity research is dangerous; socially dangerous, that is. A few years ago I would have been all for it, but I must say I have become a bit more conservative regarding this issue. Anyway, this paper looks pretty cool. It concludes that "cultures with greater emphasis on interdependence" (i.e. Chinese as opposed to Americans) "induce a greater readiness to adopt or acknowledge the perspective of the other."

PSYCHOLOGY: Thinking Unselfishly

Problems that appear fiendishly challenging at first glance can seem childishly simple if viewed from the perspective of another. The capacity to infer the mental states of others--theory of mind--is known to develop at approximately the same age in children raised in different cultures, but the ease with which adults access these mind-reading abilities has been suggested to vary across countries, from the collectivism of East Asia to the individualism of the United States. Wu and Keysar use a two-player game based on a 4-by-4 array of pigeonholes containing mundane objects, some of which are visible to both players and some only to the second. Directions (to move an object) that are completely unambiguous from the vantage point of the first player can, in fact, cause the second player to hesitate in choosing between two identical objects (only one of which is visible to the first player). They find, by tracking visual gaze and reaching movements, that Chinese reacted more quickly than Americans (non-Asians) and were almost never distracted by the second object that they could see but that their playing partner could not. These results favor the proposal that cultures with greater emphasis on interdependence induce a greater readiness to adopt or acknowledge the perspective of the other. -- GJC Psychol. Sci. 18, 600 (2007).

The genetic nuts and bolts of sexual selection (no pun intended)

this is pretty cool:

Evolution of an avian pigmentation gene correlates with a measure of sexual selection

Nicola J. Nadeau, Terry Burke, Nicholas I. Mundy

Proc. Royal Society B v.274 August 07, 2007

Abstract The extravagant plumage traits of male birds are a favourite example of sexual selection. However, to date the units that selection is acting upon, the genes themselves have been a ‘black box’. Here, we report evidence of change driven by sexual selection at a pigmentation gene locus in the galliform birds. Across species, we find a correlation between the rate of amino acid change (dN/dS) at this locus (MC1R) and the degree of sexual dichromatism, which we use as a measure of the strength of sexual selection. There is no evidence for a similar pattern in any of five other loci (four candidate and one control locus). This is consistent with previous work on colour polymorphisms and suggests that MC1R may be a key target for selection acting on plumage colour. The pattern of selection at MC1R seems to be consistent with the continuous or cyclical evolution of traits and preferences that is the outcome of several Fisherian and good-genes models of sexual selection. In contrast, we found no support for models of sexual selection that predict an increase in purifying selection as a result of purging of deleterious mutations or for models that predict an increased rate of mutation in association with stronger sexual selection.

Edward Tufte

I didn't know about this guy until I saw p-ter's post at GNXP. He has some books that look like great coffee table books (no offense). They're books about graphical displays of data or information, and he also wrote a book about the use and misuse of Powerpoint

What's happening to honey bees in the US?

In case you were wondering why the bee population in the US is suddenly in decline, check out this PLoS Biology paper that describes the problem and lists a bunch of possible reasons. It seems that the specific issue is a drastic reduction in adult workers, called CCD (colony collapse disorder):

"The syndrome is mysterious in that the main symptom is simply a low number of adult bees in the hive. (This is a bit like going to a previously well-populated hen house and finding hardly any hens.) There are no bodies, and although there are often many disease organisms present, no outward signs of disease, pests, or parasites exist. Often there is still food in the hive, and immature bees (brood) are present. The cause of the loss of bees seems to be the sudden early death, in the field, of large numbers of adult workers [2]. Curiously, the dead colonies tend to be left alone by the two cleptoparasites that normally infest dead honey bee colonies: the wax moth Gallaria mellonella and the small hive beetle Aethina tumida. Could this be due to some toxic residue in the dead colonies? Perhaps this was a contributing factor, but more likely the time of year meant that there were few cleptoparasites about—their abundance is seasonal."

Fetal growth at high altitude

Maternal oxygen delivery is not related to altitude- and ancestry- associated differences in human fetal growth.

Zamudio S, Postigo L, Illsley NP, Rodriquez C, Heredia G, Brimacombe M, Echalar L, Torricos T, Tellez W, Maldonado I, Balanza E, Alvarez T, Ameller J, Vargas E.

J Physiol. 2007 May 17

Fetal growth is reduced at high altitude, but the decrease is less among long-resident populations. We hypothesized that greater maternal uteroplacental O2 delivery would explain increased fetal growth in Andean natives versus European migrants to high altitude. O2 delivery was measured with ultrasound, Doppler and haematological techniques. Participants (n=180) were pregnant women of self-professed European or Andean ancestry living at 3600 m or 400 m in Bolivia. Ancestry was quantified using ancestry-informative single nucleotide polymorphims. The altitude-associated decrement in birth weight was 418 g in European versus 236 g in Andean women (p<.005). Altitude was associated with decreased uterine artery diameter, volumetric blood flow and O2 delivery regardless of ancestry. But the hypothesis was rejected as O2 delivery was similar between ancestry groups at their respective altitudes of residence. Instead, Andean neonates were larger and heavier per unit of O2 delivery, regardless of altitude (p<.001). European admixture among Andeans was negatively correlated with birth weight at both altitudes (p<0.01), style="font-weight: bold;">greater placental efficiency in O2 and nutrient transport, and/or greater fetal efficiency in substrate utilization may contribute to ancestry- and altitude-related differences in fetal growth. Uterine artery O2 delivery in these pregnancies was 99+/-3 ml/min, ~5-fold greater than near-term fetal O2 consumption. We concluded that deficits in maternal O2 transport in near-term normal pregnancy are unlikely to be causally associated with variation in fetal growth.

Anthropoid bottleneck

This paper does not look like what I expected. From the abstract, it seems like they're making some inference about human genome architecture from the apparent bottleneck that occured in the Anthropoids (monkeys and apes) after their split from Prosimians. They're focusing on "exogenous DNA" (numts). That's about all I can glean/understand from this abstract.

Population Bottlenecks as a Potential Major Shaping Force of Human Genome Architecture

Adrian Gherman, Peter E. Chen, Tanya Teslovich, Pawel Stankiewicz, Marjorie Withers, Carl S Kashuk, Aravinda Chakravarti, James R. Lupski, David J. Cutler, Nicholas Katsanis

PLoS Genetics: Early online release

Abstract: The modern synthetic view of human evolution proposes that the fixation of novel mutations is driven by the balance between selective advantage, selective disadvantage and genetic drift. When considering the global architecture of the human genome, the same model can be applied to understanding the rapid acquisition and proliferation of exogenous DNA. To explore the evolutionary forces that might have morphed human genome architecture, we investigated the origin, composition, and functional potential of numts (nuclear mitochondrial pseudogenes), partial copies of the mitochondrial genome found abundantly in chromosomal DNA. Our data indicate that these elements are unlikely to be advantageous, since they possess no gross positional, transcriptional, or translational features that might indicate beneficial functionality subsequent to integration. Using sequence analysis and fossil dating, we also show a probable burst of integration of numts in the primate lineage that centers on the prosimian-anthropoid split, mimics closely the temporal distribution of Alu and processed pseudogene acquisition, and coincides with the major climatic change at the Paleocene-Eocene boundary. We therefore propose a model according to which the gross architecture and repeat distribution of the human genome can be largely accounted for by a population bottleneck early in the anthropoid lineage and subsequent effectively neutral fixation of repetitive DNA, rather than positive selection or unusual insertion pressures.

Muslims in India: Spread of people or spread of religion?

This paper in AJPA confirms an earlier study on Indian Muslims using Y-chromosomes, in that, for the most part, Muslims in India are not there because of movement of people from western Asian populations as much as it is due to the movement of ideas, beliefs. This one examines mtDNA and finds pretty much the same thing.

North Indian Muslims: Enclaves of foreign DNA or Hindu converts?

Maria C. Terreros, Diane Rowold, Javier R. Luis, Faisal Khan, Suraksha Agrawal, Rene J. Herrera

American Journal of Physical Anthropology; Volume 133, Issue 3 , Pages 1004 - 1012

Abstract: The mtDNA composition of two Muslim sects from the northern Indian province of Uttar Pradesh, the Sunni and Shia, have been delineated using sequence information from hypervariable regions 1 and 2 (HVI and HVII, respectively) as well as coding region polymorphisms. A comparison of this data to that from Middle Eastern, Central Asian, North East African, and other Indian groups reveals that, at the mtDNA haplogroup level, both of these Indo-Sunni and Indo-Shia populations are more similar to each other and other Indian groups than to those from the other regions. In addition, these two Muslim sects exhibit a conspicuous absence of West Asian mtDNA haplogroups suggesting that their maternal lineages are of Indian origin. Furthermore, it is noteworthy that the maternal lineage data indicates differences between the Sunni and Shia collections of Uttar Pradesh with respect to the relative distributions of Indian-specific M sub-haplogroups (Indo Shia > Indo Sunni) and the R haplogroup (Indo Sunni > Indo Shia), a disparity that does not appear to be related to social status or geographic regions within India. Finally, the mtDNA data integrated with the Y-chromosome results from an earlier study, which indicated a major Indian genetic (Y-chromosomal) contribution as well, suggests a scenario of Hindu to Islamic conversion in these two populations. However, given the substantial level of the African/Middle Eastern YAP lineage in the Indo-Shia versus its absence in the Indo-Sunni, it is likely that this conversion was somewhat gender biased in favor of females in the Indo-Shia.

Polynesian derived chickens in South America

John Hawks and Razib have posts on this. Apparently, genetic analysis of buried chickens in Chile before European contact shows that they are closely related to Polynesian chickens. There's also a story in New York Times, and I guess the paper will be out in PNAS soon. I wonder if anyone has done an in depth analysis of genetic affinities between Native Americans in Chile and Polynesians (humans, that is). There are of course several ways to explain such a finding, and I'd be interested to see if the authors propose several possible interpretations. This story conjures up in my mind Chick-Fil-A nuggets covered in gooey Polynesian sauce.

l'ADN des Francais

Dienekes has a post on a new study on French mtDNA. I agree with Dienekes that a large scale study on French genetic diversity has been a long time coming. This one has a good diverse sample size: 868 people from 12 regions. I don't have access to the full text, but it looks like they also further compare the Basques and the Britons (1/4 of my ancestry is Breton, partly explaining my first name). They don't seem to find anything too surprising, except maybe for: "the French Basques exhibit a number of distinct features, most notably expressed in the prevalence of haplogroups linked with the Neolithic diffusion in Europe", which is somewhat expected, but good to further confirm.

Aquatic ape, continued

back and forth, we go. I don't have time to read the argument here, but this new issue of AJHB has two other (here, here) papers that discuss the issue, the second look like a rebuttal to this rebuttal.

Docosahexaenoic acid and shore-based diets in hominin encephalization: A rebuttal

Stephen C. Cunnane, Mélanie Plourde, Kathy Stewart, Michael A. Crawford

American Journal of Human Biology, Volume 19, Issue 4 , Pages 578 - 581

Abstract: Carlson and Kingston ([2007]: Am J Hum Biol 19:132-141) propose that preformed dietary docosahexaenoic acid (an omega-3 fatty acid in fish) did not have a significant role in hominin encephalization. Their position hinges on claiming that humans are able to make sufficient docosahexaenoic acid from the plant-based parent omega-3 fatty acid - -linolenic acid. They also suggest that hominin fish consumption occurred too late to have materially influenced encephalization. The authors quantify here a summary of the published data showing that humans cannot make sufficient docosahexaenoic acid to maintain normal infant brain development. The authors also provide evidence that the fossil record shows that some of the earliest hominins were regularly consuming fish. Hence, we reject Carlson and Kingston's position and reiterate support for the concept that access to shore-based diets containing docosahexaenoic acid was necessary for hominin encephalization beyond the level seen in the great apes.

James Watson's DNA sequenced

It took two months and cost "less than a million" (which I guess means close to a million) according to this NY Times article. He agreed to have the whole thing made public except for his apolipoprotein E gene that could give information about his susceptibility to Alzheimer's.

some interesting excerpts, including stuff about Dr. Venter's also recently completed genome:

"Both are diploid genomes, meaning that they include the DNA sequence in the chromosomes inherited from both parents, whereas the reference genome completed by the Human Genome Project did not capture these differences.

Some 3.5 percent of Dr. Watson’s genome could not be matched to the reference genome. One reason may be that the project scientists had to amplify human DNA by growing it in bacteria and may have lost many regions of human DNA that are toxic to bacteria, said Michael Egholm, 454’s vice president for research. The 454 sequencer skips the bacteria stage entirely and is free of this source of bias.

Dr. Venter said 454 would have assembled Dr. Watson’s genome by comparing short lengths of analyzed DNA to the reference sequence, so the company might not have detected any structural errors present in the reference assembly.

Dr. Venter said his new genome has been assembled from scratch. There were many more differences than he had expected, including in single units of DNA that were extra or absent. “It’s clear we have grossly underestimated the extent of human variation,” Dr. Venter said."

"Some scientists believe that it will be medically useful to sequence patients’ genomes when the cost of sequencing falls to around $10,000 or less. Dr. Egholm said that with improvements already under way, the 454 sequencing machine will soon be able to sequence a human genome for $100,000. The cost of sequencing has been dropping so fast in the hands of groups like 454 Life Sciences and Solexa Inc. that some technologists predict the $10,000 genome will be attained in a few years."

Mathematical models can explain it all?

Over at the Statistical Modeling, Causal Inference, and Social Science blog, there is a discussion about the over-reliance on mathematical models to explain natural phenomena.
I like this passage by Stan Salthe, the author of "Why Mathematical Models Just Don't Add Up"

"In spite of the fact that qualitative models produce better results, our society as a whole remains overconfident about quantitative modeling. [...] We suggest applying the embarrassment test. If it would be embarrassing to state out loud a simplified version of a model's parameters or processes, then the model cannot accurately portray the process. [...] A scientist who stated those assumptions in a public lecture would be hooted off the podium. But buried deep within a model, such absurdities are considered valid."

Tone languages and ASPM, Microcephalin

This is a new paper in PNAS that finds, after controlling for the obvious underlying population genetic relationships, an association between allele frequencies of both ASPM and Microcephalin alleles and populations with tonal vs. non-tonal language. They also figure out that non-tonal languages are recently derived. The idea that the ancestral human languages were tonal and then many languages became non-tonal (in Europe) reminds me of the idea that the !Kung clicks are an ancestral form of human language (i.e. older hominin species or early H. sapiens communicated that way)

Razib has also got some commentary on this at GNXP. The authors have a website where they go through their argument, and they have some good world maps, like this one that shows locations of people that have tonal languages (grey) and non-tonal (yellow):

and here's the "money passage" from the authors' website:
"By comparing nearly 1000 genetic markers and 26 linguistic features, we were able to show that, as most people would expect, there is generally no correlation between population genetics and language typology – but the relation between tone and the two genes under study emerged as especially strong in all our analyses. It’s because there generally isn’t a correlation between population genetics and language typology that the correlation we’ve found may be interesting. This relationship remains important and statistically highly significant even when we consider the correlation between tone and ASPM and Microcephalinsimultaneously, after we take into account the fact that neighbouring populations tend to share both genes and languages, plus some more tests."

Linguistic tone is related to the population frequency of the adaptive haplogroups of two brain size genes, ASPM and Microcephalin

Dan Dediu and D. Robert Ladd

PNAS, Early Edition May 30

Abstract: The correlations between interpopulation genetic and linguistic diversities are mostly noncausal (spurious), being due to historical processes and geographical factors that shape them in similar ways. Studies of such correlations usually consider allele frequencies and linguistic groupings (dialects, languages, linguistic families or phyla), sometimes controlling for geographic, topographic, or ecological factors. Here, we consider the relation between allele frequencies and linguistic typological features. Specifically, we focus on the derived haplogroups of the brain growth and development-related genes ASPM and Microcephalin, which show signs of natural selection and a marked geographic structure, and on linguistic tone, the use of voice pitch to convey lexical or grammatical distinctions. We hypothesize that there is a relationship between the population frequency of these two alleles and the presence of linguistic tone and test this hypothesis relative to a large database (983 alleles and 26 linguistic features in 49 populations), showing that it is not due to the usual explanatory factors represented by geography and history. The relationship between genetic and linguistic diversity in this case may be causal: certain alleles can bias language acquisition or processing and thereby influence the trajectory of language change through iterated cultural transmission.

Siberian reindeer herders - patrilocal?

The authors here find less Y-chromosome similarities between groups than mtDNA similarities between groups indicating that males are staying put in groups more so than women. This was once thought to be the predominant pattern in all human groups although genetic and ethnogrpahic data shows much diversity in marriage customs accross cultures.

Mating patterns amongst Siberian reindeer herders: Inferences from mtDNA and Y-chromosomal analyses

Brigitte Pakendorf, Innokentij N. Novgorodov, Vladimir L. Osakovskij, Mark Stoneking

American Journal of Physical Anthropology

Abstract: The Evenks and Evens, who speak closely related languages belonging to the Northern Tungusic branch of the Tungusic family, are nomadic reindeer herders and hunters. They are spread over an immense territory in northeastern Siberia, and consequently different subgroups are in contact with diverse peoples speaking Samoyedic, Turkic, Mongolic, Chukotka-Kamchatkan, and Yukaghir languages. Nevertheless, the languages and culture of the Evenks and Evens are similar enough for them to have been classified as a single ethnic group in the past. This linguistic and cultural similarity indicates that they may have spread over their current area of habitation relatively recently, and thus may be closely related genetically. On the other hand, the great distances that separate individual groups of Evens and Evenks from each other might have led to preferential mating with geographic neighbors rather than with linguistically related peoples. In this study, we assess the correlation between linguistic and genetic relationship in three different subgroups of Evenks and Evens, respectively, via mtDNA and Y-chromosomal analyses. The results show that there is some evidence of a common origin based on shared mtDNA lineages and relatively similar Y-haplogroup frequencies amongst most of the Evenk and Even subgroups. However, there is little sharing of Y-chromosomal STR haplotypes, indicating that males within Evenk and Even subgroups have remained relatively isolated. There is further evidence of some female admixture in different Even subgroups with their respective geographic neighbors. However, the Tungusic groups, and especially the Evenks, show signs of genetic drift, making inferences about their prehistory difficult.

Superorganism through intergroup competition

These kinds of papers are interesting for their relevance to human behavioral ecology.

The emergence of a superorganism through intergroup competition

H. Kern Reeve and Bert Hölldobler

PNAS, Published online before print May 21, 2007

Abstract: Surveys of insect societies have revealed four key, recurring organizational trends: (i) The most elaborated cooperation occurs in groups of relatives. (ii) Cooperation is typically more elaborate in species with large colony sizes than in species with small colony sizes, the latter exhibiting greater internal reproductive conflict and lesser morphological and behavioral specialization. (iii) Within a species, per capita brood output typically declines as colony size increases. (iv). The ecological factors of resource patchiness and intergroup competition are associated with the most elaborated cooperation. Predictions of all four patterns emerge elegantly from a game-theoretic model in which within-group tug-of-wars are nested within a between-group tug-of-war. In this individual selection model, individuals are faced with the problem of how to partition their energy between investment in intercolony competition versus investment in intracolony competition, i.e., internal tugs-of-war over shares of the resources gained through intergroup competition. An individual's evolutionarily stable investment in between-group competition (i.e., within-group cooperation) versus within-group competition is shown to increase as within-group relatedness increases, to decrease as group size increases (for a fixed number of competing groups), to increase as the number of competing groups in a patch increases, and to decrease as between-group relatedness increases. Moreover, if increasing patch richness increases both the number of individuals within a group and the number of competing groups, greater overall cooperation within larger groups will be observed. The model presents a simple way of determining quantitatively how intergroup conflict will propel a society forward along a "superorganism continuum."

Saccharomyces cerevisiae genetic diversity

As one would expect, this is research by a French group.

Bread, beer and wine: Saccharomyces cerevisiae diversity reflects human history

JEAN-LUC LEGRAS DIDIER MERDINOGLU JEAN-MARIE CORNUET and FRANCIS KARST

Molecular Ecology May 2007

Abstract Fermented beverages and foods have played a significant role in most societies worldwide for millennia. To better understand how the yeast species Saccharomyces cerevisiae, the main fermenting agent, evolved along this historical and expansion process, we analysed the genetic diversity among 651 strains from 56 different geographical origins, worldwide. Their genotyping at 12 microsatellite loci revealed 575 distinct genotypes organized in subgroups of yeast types, i.e. bread, beer, wine, sake. Some of these groups presented unexpected relatedness: Bread strains displayed a combination of alleles intermediate between beer and wine strains, and strains used for rice wine and sake were most closely related to beer and bread strains. However, up to 28% of genetic diversity between these technological groups was associated with geographical differences which suggests local domestications. Focusing on wine yeasts, a group of Lebanese strains were basal in an FST tree, suggesting a Mesopotamia-based origin of most wine strains. In Europe, migration of wine strains occurred through the Danube Valley, and around the Mediterranean Sea. An approximate Bayesian computation approach suggested a postglacial divergence (most probable period 10 000–12 000 bp). As our results suggest intimate association between man and wine yeast across centuries, we hypothesize that yeast followed man and vine migrations as a commensal member of grapevine flora.

How to explain the demographic transition?

The demographic transition is one of the most interesting puzzles in human evolutionary biology, in my opinion. Several hypothese have been put forward, but in this new paper the authors suggest one that I had never heard or thought of: that in modern societies, interactions with kin are less frequent, and therefore there is less pressure from kin encouraging you to have kids, given that kin have an interest in you having kids... I guess I buy it, to a certain extent. There's got to be several good and easy ways to test this, other than their "role play studies" - whatever that is (...to be fair, I didn't read the paper).

Influences on communication about reproduction: the cultural evolution of low fertility

Lesley Newson, Tom Postmes, S.E.G. Lea, Paul Webley, Peter J. Richerson, Richard Mcelreath

Evolution and Human Behavior Volume 28, Issue 3, Pages 199-210 (May 2007)

Abstract: The cultural norms of traditional societies encourage behavior that is consistent with maximizing reproductive success but those of modern post-demographic transition societies do not. Newson et al (2005) proposed that this might be because interaction between kin is relatively less frequent in modern social networks. Assuming that people's evaluations of reproductive decisions are influenced by a desire to increase their inclusive fitness, they will be inclined to prefer their kin to make fitness-enhancing choices. Such a preference will encourage the emergence of pronatal cultural norms if social networks are dense with kin. Less pronatal norms will emerge if contact between kin makes up a small proportion of social interactions. This article reports evidence based on role-play studies that supports the assumption of the kin influence hypothesis that evaluations of reproductive decisions are influenced by a desire to increase inclusive fitness. It also presents a cultural evolutionary model demonstrating the long-term effect of declining kin interaction if people are more likely to encourage fitness-enhancing choices when interacting with their kin than with nonrelatives.

Neandertal interbreeding with moderns?

John Hawks has a post about a recent story on Neandertals in Science suggesting no interbreeding... haven't looked closely at the particulars yet.

30 mya - a really small primate skull

This skull was well preserved so they were able to infer things about the brain. It has a large visual cortex and pretty considerable sexual dimorphism, which can be interpreted as large brains are not needed for good vision or for living in social groups...a bit of a hasty conclusion in my opinion. This time period corresponds to a time when Asia was not connected to Africa, so there were fewer competitors, another reason given for them not needing bigger brains.
As I was browsing , I found this blog that has great photos in the banner (that change when you reload the page), and pretty regular and good (not silly) posts: Primatology.org

A remarkable female cranium of the early Oligocene anthropoid Aegyptopithecus zeuxis

Elwyn L. Simons, Erik R. Seiffert , Timothy M. Ryan , and Yousry Attia

PNAS early online May 15

Abstract: The most complete and best-preserved cranium of a Paleogene anthropoid ever found, that of a small female of the early Oligocene (29-30 Ma) stem catarrhine species Aegyptopithecus zeuxis, was recovered from the Jebel Qatrani Formation (Fayum Depression, Egypt) in 2004. The specimen is that of a subadult and, in craniodental dimensions, is the smallest Aegyptopithecus individual known. High-resolution computed tomographic (microCT) scanning of the specimen's well preserved cranial vault confirms that Aegyptopithecus had relatively unexpanded frontal lobes and a brain-to-body mass ratio lower than those of living anthropoids. MicroCT scans of a male cranium recovered in 1966 [Egyptian Geological Museum, Cairo (CGM) 40237] reveal that previous estimates of its endocranial volume were too large. Thus, some amount of encephalization evolved independently in platyrrhine and catarrhine anthropoids, and the relative brain size of the last common ancestor of crown Anthropoidea was probably strepsirrhine-like or smaller. A. zeuxis shows extreme sexual dimorphism in craniodental morphology (apparently to a degree otherwise seen only in some highly dimorphic Miocene catarrhines), and the crania of female Aegyptopithecus lack a number of morphological features seen in larger males that have been accorded phylogenetic significance in catarrhine systematics (e.g., a well developed rostrum, elongate sagittal crest, and frontal trigon). Although a unique pattern of craniofacial sexual dimorphism may have characterized advanced stem and basal crown catarrhines, expression of various allegedly "discrete" craniofacial features may have been intraspecifically variable in early catarrhine species due to high levels of dimorphism and so should be treated with caution in phylogenetic analyses.

Insect societies: it's all about the kin

This paper (open access) is from a special issue of PNAS on a colloquium about Adaptation and Complex Design. It emphasizes the importance of kin selection in explaining how insect societies function. I'd have to say that the same applies to humans, but in humans, it is probably so ingrained to think of others in the group as kin and then function on a group selection mode along with some reciprocity thrown in, that even in our groups in these novel times where individuals are more distantly related (large ethnic groups, nation states) we function in what appears to be a group selected way. Reciprocity of course largely figures in there also. Their mention of non-reproducing individuals reminds me of reproductive leveling in humans (monogamy) as mentioned by Sam Bowles in his Science paper (here, here, here)

Insect societies as divided organisms: The complexities of purpose and cross-purpose

Joan E. Strassmann, and David C. Queller

PNAS May 15, 2007 vol. 104 Suppl. 1 8619-8626

Abstract: Individual organisms are complex in a special way. The organization and function of their parts seem directed toward a purpose: the survival and reproduction of that individual. Groups of organisms are different. They may also be complex, but that is usually because their parts, the individual organisms, are working at cross-purposes. The most obvious exception to this rule is the social insects. Here, the individuals cooperate in complex ways toward the common goal of the success of the colony, even if it means that most of them do not reproduce. Kin selection theory explains how this can evolve. Nonreproductive individuals help in the reproduction of their kin, who share and transmit their genes. Such help is most favored when individuals can give more to their kin than they give up by not reproducing directly. For example, they can remain at their natal site and help defend a valuable resource ("fortress defenders"), or they can ensure that at least one adult survives to care for helpless young ("life insurers"). Although kin selection explains the extensive cooperation and common purpose of social insect colonies, it also predicts a certain amount of cross-purpose and conflict behavior. Kin selection has predicted how workers and queens disagree over sex ratios, how potential queens struggle to be the colony's head, how workers try to produce sons, and how other workers often prevent them. Kin selection analysis of cooperation and conflict in social insects is one of the outstanding achievements of evolutionary theory.

Convergent adaptation to hypoxia among Tibetans and Andeans

This is a review type paper. It discusses how these two high altitude populations independently adapted to hypoxia, as indicated by differences in the physiological processes that comprise the adaptation...

Two routes to functional adaptation: Tibetan and Andean high-altitude natives

Cynthia M. Beall

PNAS: early online

Abstract: Populations native to the Tibetan and Andean Plateaus are descended from colonizers who arrived perhaps 25,000 and 11,000 years ago, respectively. Both have been exposed to the opportunity for natural selection for traits that offset the unavoidable environmental stress of severe lifelong high-altitude hypoxia. This paper presents evidence that Tibetan and Andean high-altitude natives have adapted differently, as indicated by large quantitative differences in numerous physiological traits comprising the oxygen delivery process. These findings suggest the hypothesis that evolutionary processes have tinkered differently on the two founding populations and their descendents, with the result that the two followed different routes to the same functional outcome of successful oxygen delivery, long-term persistence and high function. Assessed on the basis of basal and maximal oxygen consumption, both populations avail themselves of essentially the full range of oxygen-using metabolism as populations at sea level, in contrast with the curtailed range available to visitors at high altitudes. Efforts to identify the genetic bases of these traits have included quantitative genetics, genetic admixture, and candidate gene approaches. These reveal generally more genetic variance in the Tibetan population and more potential for natural selection. There is evidence that natural selection is ongoing in the Tibetan population, where women estimated to have genotypes for high oxygen saturation of hemoglobin (and less physiological stress) have higher offspring survival. Identifying the genetic bases of these traits is crucial to discovering the steps along the Tibetan and Andean routes to functional adaptation.

Levant Corridor vs. Horn of Africa

In this paper, they analyze mtDNA of "739 individuals representing ten African and Middle Eastern populations" and "uncover genetic evidence for the preferential use of the Levantine Corridor in the Upper Paleolithic to Neolithic dispersals of haplogroups H, J*, N1b, and T1, in contrast to an overwhelming preference in favor of the Horn of Africa for the intercontinental expansion of M1 during the Middle to Upper Paleolithic mtDNA."
... so this might suggest that the group of Homo sapiens that supposedly went to Australia early on went through the Horn of Africa, and then later on we started using the Levant Corridor as we went into Eurasia. I wonder about Neanderthals and H. erectus.

Mitochondrial DNA geneflow indicates preferred usage of the Levant Corridor over the Horn of Africa passageway

D. J. Rowold, J. R. Luis, M. C. Terreros and Rene J. Herrera

Human Genetics, Volume 52, Number 5 / May, 2007

Abstract: Both the Levantine Corridor and the Horn of Africa route have figured prominently in early hominid migrations from Africa to Eurasia. To gauge the importance of these two African–Asian thoroughfares in the demic movements of modern man, we surveyed the mtDNA control region variation and coding polymorphisms of 739 individuals representing ten African and Middle Eastern populations. Two of these collections, Egypt and Yemen, are geographically close to the Levant and Horn of Africa, respectively. In this analysis, we uncover genetic evidence for the preferential use of the Levantine Corridor in the Upper Paleolithic to Neolithic dispersals of haplogroups H, J*, N1b, and T1, in contrast to an overwhelming preference in favor of the Horn of Africa for the intercontinental expansion of M1 during the Middle to Upper Paleolithic. Furthermore, we also observed a higher frequency of sub-Saharan mtDNA compared to NRY lineages in the Middle Eastern collections, a pattern also seen in previous studies. In short, the results of this study suggest that several migratory episodes of maternal lineages occurred across the African–Asian corridors since the first African exodus of modern Homo sapiens sapiens.

NYT article on heritability (0.7) of body weight

Genes Take Charge, and Diets Fall by the Wayside

by GINA KOLATA

The take home message here is that we all have set points or ranges as to what our bodies like our weights to be, and these differ by individual, and that this set range is under pretty strict genetic control.

some excerpts:
The researchers concluded that 70 percent of the variation in peoples’ weights may be accounted for by inheritance, a figure that means that weight is more strongly inherited than nearly any other condition, including mental illness, breast cancer or heart disease.

The message is so at odds with the popular conception of weight loss — the mantra that all a person has to do is eat less and exercise more — that Dr. Jeffrey Friedman, an obesity researcher at the Rockefeller University, tried to come up with an analogy that would convey what science has found about the powerful biological controls over body weight.

He published it in the journal Science in 2000 and still cites it:

“Those who doubt the power of basic drives, however, might note that although one can hold one’s breath, this conscious act is soon overcome by the compulsion to breathe,” Dr. Friedman wrote. “The feeling of hunger is intense and, if not as potent as the drive to breathe, is probably no less powerful than the drive to drink when one is thirsty. This is the feeling the obese must resist after they have lost a significant amount of weight.”

The American Naturalist

Razib has a link to a list of the most cited paper, by decade, published in The American Naturalist on that journal's 140th Birthday - they include papers by Sewall Wright, Masatoshi Nei and Joseph Felsenstein.

Human Microbiome Project

There's a story in the Economist about the beginning of this project that aims to examine the diversity of bacteria that live in "the intestines (which are home to most of them), the skin, the nose, the mouth, the throat, the respiratory tract, the stomach and the vagina."

"Besides the 10 trillion human cells in a body, there are another 100 trillion bacterial cells"

There are obvious applications to health, as well as to human population genetics.

Genetics of speed in dogs

I've posted on the population differences in GDF8 in humans. Here is a new study that examines the association between a polymorphism in MSTN (myostatin gene which is apparently the same as GDF8) and how fast individual dogs are. The ones who have two copies have a double muscling phenotype and the heterozygotes are faster than either homozygote.

A Mutation in the Myostatin Gene Increases Muscle Mass and Enhances Racing Performance in Heterozygote Dogs

Dana S. Mosher, Pascale Quignon, Carlos D. Bustamante, Nathan B. Sutter, Cathryn S. Mellersh, Heidi G. Parker, Elaine A. Ostrander

PLoS Genetics

Provisional Abstract: Double muscling is a trait previously described in several mammalian species including cattle and sheep and is caused by mutations in the myostatin (MSTN) gene (previously referred to as GDF8). Here we describe a new mutation in MSTN found in the whippet dog breed that results in a double-muscled phenotype known as the "bully" whippet. Individuals with this phenotype carry two copies of a two-base-pair deletion in the third exon of MSTN leading to a premature stop codon at amino acid 313. Individuals carrying only one copy of the mutation are, on average, more muscular than wild-type individuals (p = 7.43 × 10-6; Kruskal-Wallis Test) and are significantly faster than individuals carrying the wild-type genotype in competitive racing events (Kendall's nonparametric measure, τ = 0.3619; p ≈ 0.00028). These results highlight the utility of performance-enhancing polymorphisms, marking the first time a mutation in MSTN has been quantitatively linked to increased athletic performance.

Admixture maps for Hispanics

The latest issue of AJHG has three papers on admixture maps for Hispanics. Admixture mapping has previously been found to be effective in African Americans (here). For Hispanics, the most obvious application would be in mapping diabetes related genes. I wonder how many markers overlap between the three papers. The number of markers they end up using in their maps ranges from about 1,600 to 5,200 SNPs. The second paper distinguishes itself in that its' markers show large frequency differences between Native American and other ancestries, not just between Native Americans and Europeans. The third one has resolution of Native Americans from North vs. South America.

A Genomewide Single-Nucleotide–Polymorphism Panel for Mexican American Admixture Mapping

Chao Tian, David A. Hinds, Russell Shigeta, Sharon G. Adler, Annette Lee, Madeleine V. Pahl, Gabriel Silva, John W. Belmont, Robert L. Hanson, William C. Knowler, Peter K. Gregersen, Dennis G. Ballinger, and Michael F. Seldin

Am. J. Hum. Genet., 80:1014-1023, 2007

Abstract: For admixture mapping studies in Mexican Americans (MAM), we define a genomewide single-nucleotide–polymorphism (SNP) panel that can distinguish between chromosomal segments of Amerindian (AMI) or European (EUR) ancestry. These studies used genotypes for >400,000 SNPs, defined in EUR and both Pima and Mayan AMI, to define a set of ancestry-informative markers (AIMs). The use of two AMI populations was necessary to remove a subset of SNPs that distinguished genotypes of only one AMI subgroup from EUR genotypes. The AIMs set contained 8,144 SNPs separated by a minimum of 50 kb with only three intermarker intervals >1 Mb and had EUR/AMI FST values >0.30 (mean FST = 0.48) and Mayan/Pima FST values <0.05>

A Genomewide Admixture Map for Latino Populations

Alkes L. Price, Nick Patterson, Fuli Yu, David R. Cox, Alicja Waliszewska, Gavin J. McDonald, Arti Tandon, Christine Schirmer, Julie Neubauer, Gabriel Bedoya, Constanza Duque, Alberto Villegas, Maria Catira Bortolini, Francisco M. Salzano, Carla Gallo, Guido Mazzotti, Marcela Tello-Ruiz, Laura Riba, Carlos A. Aguilar-Salinas, Samuel Canizales-Quinteros, Marta Menjivar, William Klitz, Brian Henderson, Christopher A. Haiman, Cheryl Winkler, Teresa Tusie-Luna, Andrés Ruiz-Linares, and David Reich

Am. J. Hum. Genet., 80:1024-1036, 2007

Admixture mapping is an economical and powerful approach for localizing disease genes in populations of recently mixed ancestry and has proven successful in African Americans. The method holds equal promise for Latinos, who typically inherit a mix of European, Native American, and African ancestry. However, admixture mapping in Latinos has not been practical because of the lack of a map of ancestry-informative markers validated in Native American and other populations. To address this, we screened multiple databases, containing millions of markers, to identify 4,186 markers that were putatively informative for determining the ancestry of chromosomal segments in Latino populations. We experimentally validated each of these markers in at least 232 new Latino, European, Native American, and African samples, and we selected a subset of 1,649 markers to form an admixture map. An advantage of our strategy is that we focused our map on markers distinguishing Native American from other ancestries and restricted it to markers with very similar frequencies in Europeans and Africans, which decreased the number of markers needed and minimized the possibility of false disease associations. We evaluated the effectiveness of our map for localizing disease genes in four Latino populations from both North and South America.

A Genomewide Admixture Mapping Panel for Hispanic/Latino Populations

Xianyun Mao, Abigail W. Bigham, Rui Mei, Gerardo Gutierrez, Ken M. Weiss, Tom D. Brutsaert, Fabiola Leon-Velarde, Lorna G. Moore, Enrique Vargas, Paul M. McKeigue, Mark D. Shriver, and Esteban J. Parra

Am. J. Hum. Genet., 80:1171-1178, 2007

Abstract: Admixture mapping (AM) is a promising method for the identification of genetic risk factors for complex traits and diseases showing prevalence differences among populations. Efficient application of this method requires the use of a genomewide panel of ancestry-informative markers (AIMs) to infer the population of origin of chromosomal regions in admixed individuals. Genomewide AM panels with markers showing high frequency differences between West African and European populations are already available for disease-gene discovery in African Americans. However, no such a map is yet available for Hispanic/Latino populations, which are the result of two-way admixture between Native American and European populations or of three-way admixture of Native American, European, and West African populations. Here, we report a genomewide AM panel with 2,120 AIMs showing high frequency differences between Native American and European populations. The average intermarker genetic distance is 1.7 cM. The panel was identified by genotyping, with the Affymetrix GeneChip Human Mapping 500K array, a population sample with European ancestry, a Mesoamerican sample comprising Maya and Nahua from Mexico, and a South American sample comprising Aymara/Quechua from Bolivia and Quechua from Peru. The main criteria for marker selection were both high information content for Native American/European ancestry (measured as the standardized variance of the allele frequencies, also known as "f value") and small frequency differences between the Mesoamerican and South American samples. This genomewide AM panel will make it possible to apply AM approaches in many admixed populations throughout the Americas.

DRD4 and personality in birds

Apparently they selected for two lines of birds...one that had "exploratory" behavior and one that didn't, and found differences in DRD4 and they also found the same associations in free-living birds.

Update: For those who don't know, DRD4 is a pretty well known gene implicated in various behavioral phenotypes (ADHD) in humans, so the fact that they found it in birds is not so surprising, but good to know nonetheless.
They/we shoud look at DRD4 in the various domestic dogs and other canids.

Drd4 gene polymorphisms are associated with personality variation in a passerine bird

Andrew E. Fidler, Kees van Oers, Piet J. Drent, Sylvia Kuhn, Jakob C. Mueller, Bart Kempenaers

Proceedings of the Royal Society London, B online before print

Abstract: Polymorphisms in several neurotransmitter-associated genes have been associated with variation in human personality traits. Among the more promising of such associations is that between the human dopamine receptor D4 gene (Drd4) variants and novelty-seeking behaviour. However, genetic epistasis, genotype–environment interactions and confounding environmental factors all act to obscure genotype–personality relationships. Such problems can be addressed by measuring personality under standardized conditions and by selection experiments, with both approaches only feasible with non-human animals. Looking for similar Drd4 genotype–personality associations in a free-living bird, the great tit (Parus major), we detected 73 polymorphisms (66 SNPs, 7 indels) in the P. major Drd4 orthologue. Two of the P. major Drd4 gene polymorphisms were investigated for evidence of association with novelty-seeking behaviour: a coding region synonymous single nucleotide polymorphism (SNP830) and a 15bp indel (ID15) located 5′ to the putative transcription initiation site. Frequencies of the three Drd4 SNP830 genotypes, but not the ID15 genotypes, differed significantly between two P. major lines selected over four generations for divergent levels of ‘early exploratory behaviour’ (EEB). Strong corroborating evidence for the significance of this finding comes from the analysis of free-living, unselected birds where we found a significant association between SNP830 genotypes and differing mean EEB levels. These findings suggest that an association between Drd4 gene polymorphisms and animal personality variation predates the divergence of the avian and mammalian lineages. Furthermore, this work heralds the possibility of following microevolutionary changes in frequencies of behaviourally relevant Drd4 polymorphisms within populations where natural selection acts differentially on different personality types.

USOs in hominin diet

The isotopic ecology of African mole rats informs hypotheses on the evolution of human diet

Justin D. Yeakel, Nigel C. Bennett, Paul L. Koch, Nathaniel J. Dominy

Proceedings of the Royal Society of London, B; Online before press

Abstract The diets of Australopithecus africanus and Paranthropus robustus are hypothesized to have included C4 plants, such as tropical grasses and sedges, or the tissues of animals which themselves consumed C4 plants. Yet inferences based on the craniodental morphology of A. africanus and P. robustus indicate a seasonal diet governed by hard, brittle foods. Such mechanical characteristics are incompatible with a diet of grasses or uncooked meat, which are too tough for efficient mastication by flat, low-cusped molars. This discrepancy, termed the C4 conundrum, has led to the speculation that C4 plant underground storage organs (USOs) were a source of nutrition for hominin species. We test this hypothesis by examining the isotopic ecology of African mole rats, which consume USOs extensively. We measured δ18O and δ13C of enamel and bone apatite from fossil and modern species distributed across a range of habitats. We show that δ18O values vary little and that δ13C values vary along the C3 to C4/CAM-vegetative axis. Relatively high δ13C values exist in modern Cryptomys hottentotus natalensis and Cryptomys spp. recovered from hominin-bearing deposits. These values overlap those reported for A. africanus and P. robustus and we conclude that the USO hypothesis for hominin diets retains certain plausibility.

Racial bias in basketball foul calling

Black refs supposedly call more fouls on white guys and vice versa...Check out this blog post where there is also a link to the NYT article.

Mediterranean population structure using X-chromosome Alu insertions

Here's a new paper from a group of French, Greek, Spanish and Tunisian scientists (see abstract below).

From the discussion:

"In fact, the Tunisian genetic distances to European samples are smaller than those to North African groups. "
"This could be explained by the history of the Tunisian population, reflecting the influence of the ancient Phoenician settlers of Carthage followed, among others, by Roman, Byzantine, Arab and French occupations, according to historical records. Notwithstanding, other explanations cannot be discarded, such as the relative heterogeneity within current Tunisian populations, and/or the limited sub-Saharan genetic influence in this region as compared with other North African areas, without excluding the possibility of the genetic drift, whose effect might be particularly amplified on the X chromosome."

on the Basque and Crete population:

"An interesting aspect comes from the evidenced relationships between the Basque Country and Crete Island. These two populations have distinct historical, anthropological and cultural backgrounds, and yet no significant differences were found between them when a locus-by-locus 2 comparison was carried out. As for the remaining analyzed populations, Siwa Oasis seems to be the most differentiated (see Table 2 and Figure 1). The differentiation shown by Siwa Oasis, and also by High Atlas, could be related to higher foreign genetic contributions, from West Sahara into High Atlas and Nile groups into the Siwa Oasis. Esteban et al described a similar pattern of GGC allele frequencies of the androgen receptor (located in chromosome X) for the Ivory Coast and Siwa Oasis samples, giving evidence of sub-Saharan genetic influence in this Berber group."

The X chromosome Alu insertions as a tool for human population genetics: data from European and African human groups

Georgios Athanasiadis, Esther Esteban, Marc Via, Jean-Michel Dugoujon, Nicholas Moschonas, Hassen Chaabani and Pedro Moral

European Journal of Human Genetics (2007) 15, 578–583.

Abstract: Alu elements are the most abundant mobile elements in the human genome (1 100 000 copies). Polymorphic Alu elements have been proved to be useful in studies of human origins and relationships owing to two important advantages: identity by descent and absence of the Alu element known to be the ancestral state. Alu variation in the X chromosome has been described previously in human populations but, as far as we know, these elements have not been used in population relationship studies. Here, we describe the allele frequencies of 13 'young' Alu elements of the X chromosome (Ya5DP62, Ya5DP57, Yb8DP49, Ya5a2DP1, Yb8DP2, Ya5DP3, Ya5NBC37, Yd3JX437, Ya5DP77, Ya5NBC491, Yb8NBC578, Ya5DP4 and Ya5DP13) in six human populations from sub-Saharan Africa (the Ivory Coast), North Africa (Moroccan High Atlas, Siwa oasis in Egypt, Tunisia), Greece (Crete Island) and Spain (Basque Country). Eight out of 13 Alu elements have shown remarkably high gene diversity values in all groups (average heterozygosities: 0.342 in the Ivory Coast, 0.250 in North Africa, 0.209 in Europe). Genetic relationships agree with a geographical pattern of differentiation among populations, with some peculiar features observed in North Africans. Crete Island and the Basque Country show the lowest genetic distance (0.0163) meanwhile Tunisia, in spite of its geographical location, lies far from the other two North African samples. The results of our work demonstrate that X chromosome Alu elements comprise a reliable set of genetic markers useful to describe human population relationships for fine-scale geographical studies.