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.
Friday, June 29, 2007
Tuesday, June 26, 2007
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.
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.
Monday, June 25, 2007
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.
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.
Saturday, June 23, 2007
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.
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.
Thursday, June 21, 2007
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.
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.
Wednesday, June 20, 2007
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.
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.
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.
Monday, June 18, 2007
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.
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.
Sunday, June 17, 2007
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.
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.
Thursday, June 14, 2007
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).
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.
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.
Tuesday, June 12, 2007
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."
"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.
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.
Saturday, June 09, 2007
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.
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.
Wednesday, June 06, 2007
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
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.
Tuesday, June 05, 2007
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.
Sunday, June 03, 2007
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.
Saturday, June 02, 2007
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
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.
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