Thursday, May 31, 2007

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."

Wednesday, May 30, 2007

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 typologybut 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.

Tuesday, May 29, 2007

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.

Saturday, May 26, 2007

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."

Thursday, May 24, 2007

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


Molecular Ecology May 2007

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.

Tuesday, May 22, 2007

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 ( 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.

Sunday, May 20, 2007

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.

Wednesday, May 16, 2007

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:

A remarkable female cranium of the early Oligocene anthropoid Aegyptopithecus zeuxis

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

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.

Tuesday, May 15, 2007

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.

Sunday, May 13, 2007

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.

Thursday, May 10, 2007

NYT article on heritability (0.7) of body weight

Genes Take Charge, and Diets Fall by the Wayside


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.”

Wednesday, May 09, 2007

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.

Tuesday, May 08, 2007

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.

Monday, May 07, 2007

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.

Saturday, May 05, 2007

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.

Friday, May 04, 2007

DRD4 and personality in birds

Apparently they selected for two lines of 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.

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.

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.

Thursday, May 03, 2007

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.

Wednesday, May 02, 2007

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 background
s, 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.

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