Geographic patterns of genome admixture in Latin American Mestizos

The large and diverse population of Latin America is potentially a powerful resource for elucidating the genetic basis of complex traits through admixture mapping. However, no genome-wide characterization of admixture across Latin America has yet been attempted. Here, we report an analysis of admixture in thirteen Mestizo populations (i.e. in regions of mainly European and Native settlement) from seven countries in Latin America based on data for 678 autosomal and 29 X-chromosome microsatellites. We found extensive variation in Native American and European ancestry (and generally low levels of African ancestry) among populations and individuals, and evidence that admixture across Latin America has often involved predominantly European men and both Native and African women. An admixture analysis allowing for Native American population subdivision revealed a differentiation of the Native American ancestry amongst Mestizos. This observation is consistent with the genetic structure of pre-Columbian populations and with admixture having involved Natives from the area where the Mestizo examined are located. Our findings agree with available information on the demographic history of Latin America and have a number of implications for the design of association studies in population from the region.     

Linguistic and maternal genetic diversity are not correlated in Native Mexicans

Mesoamerica, defined as the broad linguistic and cultural area from middle southern Mexico to Costa Rica, might have played a pivotal role during the colonization of the American continent. The Mesoamerican isthmus has constituted an important geographic barrier that has severely restricted gene flow between North and South America in pre-historical times. Although the Native American component has been already described in admixed Mexican populations, few studies have been carried out in native Mexican populations. In this study, we present mitochondrial DNA (mtDNA) sequence data for the first hypervariable region (HVR-I) in 477 unrelated individuals belonging to 11 different native populations from Mexico. Almost all of the Native Mexican mtDNAs could be classified into the four pan-Amerindian haplogroups (A2, B2, C1, and D1); only two of them could be allocated to the rare Native American lineage D4h3. Their haplogroup phylogenies are clearly star-like, as expected from relatively young populations that have experienced diverse episodes of genetic drift (e.g., extensive isolation, genetic drift, and founder effects) and posterior population expansions. In agreement with this observation, Native Mexican populations show a high degree of heterogeneity in their patterns of haplogroup frequencies. Haplogroup X2a was absent in our samples, supporting previous observations where this clade was only detected in the American northernmost areas. The search for identical sequences in the American continent shows that, although Native Mexican populations seem to show a closer relationship to North American populations, they cannot be related to a single geographical region within the continent. Finally, we did not find significant population structure in the maternal lineages when considering the four main and distinct linguistic groups represented in our Mexican samples (Oto-Manguean, Uto-Aztecan, Tarascan, and Mayan), suggesting that genetic divergence predates linguistic diversification in Mexico.     

Evaluation of the contribution of D9S1120 to anthropological studies in Native American populations

The D9S1120 locus exhibits a population-specific allele of 9 repeats (9RA) in all Native American and two Siberian populations currently studied, but it is absent in other worldwide populations. Although this feature has been used in anthropological genetic studies, its impact on the evaluation of the structure and genetic relations among Native American populations has been scarcely assessed. Consequently, the aim of this study was to evaluate the anthropological impact of D9S1120 when it was added to STR population datasets in Mexican Native American groups. We analyzed D9S1120 by PCR and capillary electrophoresis (CE) in 1117 unrelated individuals from 13 native groups from the north and west of Mexico. Additional worldwide populations previously studied with D9S1120 and/or 15 autosomal STRs (Identifier kit) were included for interpopulation analyses. We report statistical results of forensic importance for D9S1120. On average, the modal alleles were the Native American-specific allele 9RA (0.3254) and 16 (0.3362). Genetic distances between Native American and worldwide populations were estimated. When D9S1120 was included in the 15 STR population dataset, we observed improvements for admixture estimation in Mestizo populations and for representing congruent genetic relationships in dendrograms. Analysis of molecular variance (AMOVA) based on D9S1120 confirms that most of the genetic variability in the Mexican population is attributable to their Native American backgrounds, and allows the detection of significant intercontinental differentiation attributed to the exclusive presence of 9RA in America. Our findings demonstrate the contribution of D9S1120 to a better understanding of the genetic relationships and structure among Mexican Native groups.     

Genetic characterization of indigenous peoples from Oaxaca, Mexico, and its relation to linguistic and geographic isolation

We used 15 short tandem repeat (STR) loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818, and FGA) to genetically characterize 361 individuals from 11 indigenous populations (Amuzgo, Chinanteco, Chontal, Huave, Mazateco, Mixe, Mixteco, Triqui, Zapoteco del Istmo, Zapoteco del Valle, and Zoque) from Oaxaca, Mexico. We also used previously published data from other Mexican peoples (Maya, Chol, Tepehua, Otomí, and Mestizos from northern and central Mexico) to delineate genetic relations, for a total of 541 individuals. Average heterozygosity (H) was lower in most populations from Oaxaca (range 0.687 in Zoque to 0.756 in Chontal) than values observed in Mestizo populations from Mexico (0.758 and 0.793 in central and northern Mestizo, respectively) but higher than values observed in other Amerindian populations from South America; the same relation was true for the number of alleles (n(a) ). We tested (using the software Structure) whether major geographic or linguistic barriers to gene flow existed among the populations of Oaxaca and found that the populations appeared to constitute one or two genetic groups, suggesting that neither geographic location nor linguistics had an effect on the genetic structure of these culturally and linguistically highly diverse indigenous peoples. Moreover, we found a low but statistically significant between-population differentiation. In addition, the genetic structure of Oaxacan populations did not fit an isolation-by-distance model. Finally, using AMOVA and a Bayesian clustering approach, we did not detect significant geographic or linguistic barriers to gene flow within Oaxaca. These results suggest that the indigenous communities of Oaxaca, although culturally isolated, can be genetically defined as a large, nearly panmictic population in which migration could be a more important population mechanism than genetic drift. Finally, compared with outgroups in Mexico (both indigenous peoples and Mestizos), three groups were apparent. Among them, only the Otomí population from Hidalgo has a different culture and language.     

PNPLA3 I148M polymorphism is associated with elevated alanine transaminase levels in Mexican Indigenous and Mestizo populations

The patatin like phospholipase domain-containing (PNPLA3) I148M variant is the strongest genetic factor associated with elevated alanine transaminase (ALT) levels in different populations, particularly in Hispanics who have the highest 148M risk allele frequency reported to date. It has been suggested that Indigenous ancestry is associated with higher ALT levels in Mexicans. The aim of the present study was to assess the frequency of the PNPLA3 148M risk allele in Mexican indigenous and Mestizo individuals, and to examine its association with serum ALT levels. The study included a total of 1624 Mexican individuals: 919 Indigenous subjects from five different native groups and 705 Mexican Mestizo individuals (141 cases with ALT levels ≥40 U/L and 564 controls with ALT <40 U/L). The I148M polymorphism was genotyped by TaqMan assays. The frequency of elevated ALT levels in Indigenous populations was 18.7 %, and varied according to obesity status: 14.4 % in normal weight, 19.9 % in overweight and 24.5 % in obese individuals. The Mexican indigenous populations showed the highest reported frequency of the PNPLA3 148M risk allele (mean 0.73). The M148M genotype was significantly associated with elevated ALT levels in indigenous individuals (OR = 3.15, 95 % CI 1.91–5.20; P = 7.1 × 10^?6) and this association was confirmed in Mexican Mestizos (OR = 2.24, 95 % CI 1.50–3.33; P = 8.1 × 10^?5). This is the first study reporting the association between M148M genotype and elevated ALT levels in Indigenous Mexican populations. The 148M allele risk may be considered an important risk factor for liver damage in Mexican indigenous and Mestizo populations.     

Reconstructing the population history of Nicaragua by means of mtDNA,Y‐chromosome STRs,and autosomal STR markers

Before the arrival of the Spaniards in Nicaragua, diverse Native American groups inhabited the territory. In colonial times, Native Nicaraguan populations interacted with Europeans and slaves from Africa. To ascertain the extent of this genetic admixture and provide genetic evidence about the origin of the Nicaraguan ancestors, we analyzed the mitochondrial control region (HVSI and HVSII), 17 Y chromosome STRs, and 15 autosomal STRs in 165 Mestizo individuals from Nicaragua. To carry out interpopulation comparisons, HVSI sequences from 29 American populations were compiled from the literature. The results reveal a close relationship between Oto‐manguean, Uto‐Aztecan, Mayan groups from Mexico, and a Chibchan group to Nicaraguan lineages. The Native American contribution to present‐day Nicaraguan Mestizos accounts for most of the maternal lineages, whereas the majority of Nicaraguan Y chromosome haplogroups can be traced back to a West Eurasian origin. Pairwise Fst distances based on Y‐STRs between Nicaragua and European, African and Native American populations show that Nicaragua is much closer to Europeans than the other populations. Additionally, admixture proportions based on autosomal STRs indicate a predominantly Spanish contribution. Our study reveals that the Nicaraguan Mestizo population harbors a high proportion of European male and Native American female substrate. Finally, the amount of African ancestry is also interesting, probably because of the contribution of Spanish conquerors with NorthAfrican genetic traces or that of West African slaves. Am J Phys Anthropol, 2010. © 2010 Wiley‐Liss, Inc.     

Biological races in humans

Races may exist in humans in a cultural sense, but biological concepts of race are needed to access their reality in a non-species-specific manner and to see if cultural categories correspond to biological categories within humans. Modern biological concepts of race can be implemented objectively with molecular genetic data through hypothesis-testing. Genetic data sets are used to see if biological races exist in humans and in our closest evolutionary relative, the chimpanzee. Using the two most commonly used biological concepts of race, chimpanzees are indeed subdivided into races but humans are not. Adaptive traits, such as skin color, have frequently been used to define races in humans, but such adaptive traits reflect the underlying environmental factor to which they are adaptive and not overall genetic differentiation, and different adaptive traits define discordant groups. There are no objective criteria for choosing one adaptive trait over another to define race. As a consequence, adaptive traits do not define races in humans. Much of the recent scientific literature on human evolution portrays human populations as separate branches on an evolutionary tree. A tree-like structure among humans has been falsified whenever tested, so this practice is scientifically indefensible. It is also socially irresponsible as these pictorial representations of human evolution have more impact on the general public than nuanced phrases in the text of a scientific paper. Humans have much genetic diversity, but the vast majority of this diversity reflects individual uniqueness and not race.     

Reconstructing the Population Genetic History of the Caribbean

The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, we investigate the population genetic history of this region by characterizing patterns of genome-wide variation among 330 individuals from three of the Greater Antilles (Cuba, Puerto Rico, Hispaniola), two mainland (Honduras, Colombia), and three Native South American (Yukpa, Bari, and Warao) populations. We combine these data with a unique database of genomic variation in over 3,000 individuals from diverse European, African, and Native American populations. We use local ancestry inference and tract length distributions to test different demographic scenarios for the pre- and post-colonial history of the region. We develop a novel ancestry-specific PCA (ASPCA) method to reconstruct the sub-continental origin of Native American, European, and African haplotypes from admixed genomes. We find that the most likely source of the indigenous ancestry in Caribbean islanders is a Native South American component shared among inland Amazonian tribes, Central America, and the Yucatan peninsula, suggesting extensive gene flow across the Caribbean in pre-Columbian times. We find evidence of two pulses of African migration. The first pulse—which today is reflected by shorter, older ancestry tracts—consists of a genetic component more similar to coastal West African regions involved in early stages of the trans-Atlantic slave trade. The second pulse—reflected by longer, younger tracts—is more similar to present-day West-Central African populations, supporting historical records of later transatlantic deportation. Surprisingly, we also identify a Latino-specific European component that has significantly diverged from its parental Iberian source populations, presumably as a result of small European founder population size. We demonstrate that the ancestral components in admixed genomes can be traced back to distinct sub-continental source populations with far greater resolution than previously thought, even when limited pre-Columbian Caribbean haplotypes have survived.     

QUANTITATIVE GENETICS OF SIZE,SHAPE, LIFE-HISTORY,AND FRUIT CHARACTERISTICS OF THE SEED HETEROMORPHIC COMPOSITE HETEROSPERMA PINNATUM. II. CORRELATION STRUCTURE

We have investigated phenotypic, environmental, within-population broad-sense genetic correlations and among-population genetic correlations for 17 traits in six populations of Heterosperma pinnatum Cav. (Compositae) grown in the greenhouse. The within-population genetic, environmental, and phenotypic correlations were somewhat similar while the among-population genetic correlations showed little correspondence to these. The different correlation matrices were compared to a hypothesis matrix, which predicted higher correlations for groups of functionally and developmentally related traits. The groups were seed and head traits, size and shape traits, and life history traits, with subgroups predicted to have still higher correlations. The phenotypic and environmental matrices corresponded well to the hypothesis matrix, the within-population broad-sense genetic matrix showed weaker, though still significant, correspondence, and the among-population genetic correlations showed no correspondence. Genetic correlations did not differ significantly among populations, though the power of these comparisons was low. Some particular genetic correlations are discussed as possible examples of adaptive correlations (e.g., a negative correlation between dispersal and dormancy) and as examples of developmental or physiological constraints including life-history tradeoffs.     

Genetic admixture of European FRDA genes is the cause of Friedreich ataxia in the Mexican population

Friedreich ataxia accounts for approximately 75% of European recessive ataxia patients. Approximately 98% of pathogenic chromosomes have large expansions of a GAA triplet repeat in the FRDA gene (E alleles), and strong linkage disequilibrium among polymorphisms spanning the FRDA locus indicates a common origin for all European E alleles. In contrast, we found that only 14 of 151 (9.3%) Mexican Mestizo patients with recessive ataxia were homozygous for E alleles. Analysis of polymorphisms spanning the FRDA locus revealed that all Mestizo E alleles had the common European haplotype, indicating that they share a single origin. Genetic admixture levels were determined, which revealed that the relative contributions to the Mestizo FRDA gene pool by Native American and European genes were 76-87% and 13-24%, respectively, commensurate with the observed low prevalence of Friedreich ataxia in Mestizos. This indicates that Friedreich ataxia in Mexican Mestizos is due to genetic admixture of European mutant FRDA genes in the Native American gene pool that existed prior to contact with Europeans.     

Pre-Columbian origins of Native American dog breeds,with only limited replacement by European dogs,confirmed by mtDNA analysis

Dogs were present in pre-Columbian America, presumably brought by early human migrants from Asia. Studies of free-ranging village/street dogs have indicated almost total replacement of these original dogs by European dogs, but the extent to which Arctic, North and South American breeds are descendants of the original population remains to be assessed. Using a comprehensive phylogeographic analysis, we traced the origin of the mitochondrial DNA lineages for Inuit, Eskimo and Greenland dogs, Alaskan Malamute, Chihuahua, xoloitzcuintli and perro sín pelo del Peru, by comparing to extensive samples of East Asian (n = 984) and European dogs (n = 639), and previously published pre-Columbian sequences. Evidence for a pre-Columbian origin was found for all these breeds, except Alaskan Malamute for which results were ambigous. No European influence was indicated for the Arctic breeds Inuit, Eskimo and Greenland dog, and North/South American breeds had at most 30% European female lineages, suggesting marginal replacement by European dogs. Genetic continuity through time was shown by the sharing of a unique haplotype between the Mexican breed Chihuahua and ancient Mexican samples. We also analysed free-ranging dogs, confirming limited pre-Columbian ancestry overall, but also identifying pockets of remaining populations with high proportion of indigenous ancestry, and we provide the first DNA-based evidence that the Carolina dog, a free-ranging population in the USA, may have an ancient Asian origin.     

Tibetan and Andean patterns of adaptation to high-altitude hypoxia

Understanding the workings of the evolutionary process in contemporary humans requires linking the evolutionary history of traits with their current genetics and biology. Unusual environments provide natural experimental settings to investigate evolution and adaptation. The example of high-altitude hypoxia illustrates some of the progress and many of the remaining challenges for studies of evolution in contemporary populations. Current studies exemplify the frequently encountered problem of determining whether large, consistent population differences in mean values of a trait reflect genetic differences. In this review I describe 4 quantitative traits that provide evidence that indigenous populations of the Tibetan and Andean plateaus differ in their phenotypic adaptive responses to high-altitude hypoxia. These 4 traits are resting ventilation, hypoxic ventilatory response, oxygen saturation, and hemoglobin concentration. The Tibetan means of the first 2 traits were more than 0.5 standard deviation higher than the Aymara means, whereas the Tibetan means were more than 1 standard deviation lower than the Aymara means for the last 2 traits. Quantitative genetic analyses of within-population variance revealed significant genetic variance in all 4 traits in the Tibetan population but only in hypoxic ventilatory response and hemoglobin concentration in the Aymara population. A major gene for oxygen saturation was detected among the Tibetans. These findings are interpreted as indirect evidence of population genetic differences. It appears that the biological characteristics of sea-level humans did not constrain high-altitude colonists of the 2 plateaus to a single adaptive response. Instead, microevolutionary processes may have operated differently in the geographically separated Tibetan and Andean populations exposed to the same environmental stress. Knowledge of the genetic bases of these traits will be necessary to evaluate these inferences. Future research will likely be directed toward determining whether the population means reflect differences identified at the chromosomal level. Future research will also likely consider the biological pathways and environmental influences linking genotypes to phenotypes, the costs and benefits of the Tibetan and Andean patterns of adaptation, and the question of whether the observed phenotypes are indeed adaptations that enhance Darwinian fitness.     

Geographic variation in Mexican jays (Aphelocoma ultramarina): local differentiation,polyphyly or hybridization?

Studies of genetic variation within highly variable taxa can provide valuable insight into the factors influencing biological diversification. We examined six microsatellite loci, a nuclear intron and the mitochondrial control region to determine if the Mexican jay subspecies Aphelocoma ultramarina couchii and A. u. potosina have hybridized with western scrub-jays (A. californica). We suspected hybridization because these Mexican Jay populations resemble scrub-jays in several traits. We sampled six Mexican jay (N = 105) and four scrub-jay (N = 78) populations. Suspected hybrid Mexican Jay populations did not share any mitochondrial types or intron alleles with scrub-jays. All microsatellite alleles found in the suspected hybrid Mexican jay populations are also found in the control Mexican jay populations. Genetic distance-based trees from microsatellites supported reciprocal monophyly of Mexican jays and scrub-jays with bootstrap support > 80%. We randomized genotypes among populations to test scenarios consistent with hybridization. In some areas where Mexican jays and scrub-jays occur in sympatry or geographical proximity, randomization tests yield results expected under hybridization (100% support for seven of nine scenarios). However, these populations were not the primary candidates for hybridization based on phenotype. Even if low-level hybridization did occur, hybridization does not appear to be the main reason some Mexican jay populations resemble scrub-jays more than others. The scrub-jay-like traits in these populations may be due to drift, adaptation or plasticity. Alternatively, ancient hybridization, followed by selection for scrub-jay like traits in some Mexican jay populations, might have given rise to the observed variation.     

Conquests of the Imagination: Maya-Mexican Polarity and the Story of Chichén Itzá

For generations scholars have explained the marked difference in the ruins of Chichén Itzá by attributing the southern buildings to indigenous Yucatecan Maya and then telling of central Mexican Toltec invaders who built (or forced the Maya to build) the Tula-like plaza to the north. But evidence now suggests that the infamous "Toltec conquest of the Maya" never happened. The story may actually be the manifestation of a Western tendency to express ambivalent attitudes toward Native Americans in terms of polar opposites, in this case, "gentle Maya priests" versus "brutal Mexican warriors." In the end, the story may reveal more about the Western politics of knowledge than about pre-Columbian Mesoamerican history.     

Dental morphology and ancestry in Albuquerque, New Mexico Hispanics

The term “Hispanic” groups people from Central and South America and the Caribbean, combining disparate cultures, languages, and ancestry, and masking biological differences. Historical and current admixture patterns within these populations and with indigenous and European-, African-, and/or Asian- derived populations complicate the biological picture. Although “Hispanic” has little biological meaning, it is used widely in epidemiology, disease management, and forensics as a biologically significant group. An interdisciplinary approach combining historical, cultural, and biological data can characterize regional and temporal differences between Hispanic populations.We examined biological distances with a population of central New Mexico Hispanics, as a case study of the local specificity of population history. We collected dental morphological trait frequencies from samples of recent Albuquerque-area Hispanic Americans and several ancestral and contemporary groups. To explore regional admixture patterns we calculated biological distances using the modified Mahalanobis D² statistic. Our results indicate that Albuquerque Hispanics are more similar to their European and African ancestral groups than to Native Americans in New Mexico. Additionally, their affinity to Native Americans is greater with prehistoric rather than contemporary samples. We argue that these results reflect a local rather than pan-Hispanic admixture pattern; they underscore that populations are better understood at the local and regional levels. It is undesirable to make sweeping biological generalizations for groups known to be geographically and genetically disparate. This research is part of a growing trend in biological research concerning Hispanics and other groups—an emphasis on local samples, informed by historical, cultural, and biological factors.     

Pre‐Hispanic Mesoamerican demography approximates the present‐day ancestry of Mestizos throughout the territory of Mexico

Over the last 500 years, admixture among Amerindians, Europeans, and Africans, principally, has come to shape the present‐day gene pool of Mexicans, particularly Mestizos, who represent about 93% of the total Mexican population. In this work, we analyze the genetic data of 13 combined DNA index system‐short tandem repeats (CODIS‐STRs) in 1,984 unrelated Mestizos representing 10 population samples from different regions of Mexico, namely North, West, Central, and Southeast. The analysis of molecular variance (AMOVA) test demonstrated low but significant differentiation among Mestizos from different regions (F_ST = 0.34%; P = 0.0000). Although the spatial analysis of molecular variance (SAMOVA) predicted clustering Mestizo populations into four well‐delimited groups, the main differentiation was observed between Northwest when compared with Central and Southeast regions. In addition, we included analysis of individuals of Amerindian (Purepechas), European (Huelva, Spain), and African (Fang) origin. Thus, STRUCTURE analysis was performed identifying three well‐differentiated ancestral populations (k = 3). STRUCTURE results and admixture estimations by means of LEADMIX software in Mestizo populations demonstrated genetic heterogeneity or asymmetric admixture throughout Mexico, displaying an increasing North‐to‐South gradient of Amerindian ancestry, and vice versa regarding the European component. Interestingly, this distribution of Amerindian ancestry roughly reflects pre‐Hispanic Native‐population density, particularly toward the Mesoamerican area. The forensic, epidemiological, and evolutionary implications of these findings are discussed herein. Am J Phys Anthropol 2009. © 2009 Wiley‐Liss, Inc.     

Endothelial nitric oxide synthase gene polymorphism in the Indian and Mestizo populations of Mexico

Endothelium-derived nitric oxide (NO) is an important factor in vasodilation synthesized by endothelial nitric oxide synthase (eNOS). A polymorphism (894 G to T) in exon 7 of the eNOS gene causes the conversion of Glu to Asp in position 298. The Glu298Asp polymorphism has been extensively associated with cardiovascular disease. We determined the Glu298Asp polymorphism frequency in healthy Mexican Mestizo, Huastec, Mayo, and Mayan populations by the endonuclease restriction method. The four populations analyzed were in Hardy-Weinberg equilibrium. Allele frequencies were similar among Mexican populations but different when compared with Caucasians. However, when compared with allele frequencies in Asian populations, Mestizo and Huastec allele frequencies were significantly different. Genotypically, only the Mestizos presented Asp298 homozygosity. The absence of double mutants in Indian populations resembles that in Asians. With these data, we conclude that the low frequency of the eNOS Glu298Asp polymorphism in Indian and Mestizo populations of Mexico is related to the Asian origin of Amerindian groups.     

Ethnic and racial differences on the Standard Progressive Matrices in Mexico

Raven's Standard Progressive Matrices test was administered to a representative sample of 920 white, Mestizo and Native Mexican Indian children aged 7-10 years in Mexico. The mean IQs in relation to a British mean of 100 obtained from the 1979 British standardization sample and adjusted for the estimated subsequent increase were: 98.0 for whites, 94.3 for Mestizos and 83.3 for Native Mexican Indians.     

Quantitative trait, genetic, environmental, and geographical distances among populations of the C4 grass Trachypogon plumosus in Neotropical savannas

Venezuelan savannas are exposed to land‐use changes and biological invasions which compromise their persistence and function. The native C₄ grass Trachypogon plumosus is the most important component of the savannas under diverse combinations of climate and soils, suggesting substantial interpopulation variation. We examined quantitative traits and isozyme variation of nine populations of this grass and related these estimates to geographical and environmental features of sampled locations. Isozyme diversity estimates were based on 10 polymorphic enzyme systems whereas 21 quantitative traits, from field and controlled growth conditions, were evaluated. Distance matrices for quantitative traits, isozyme, geographical and environmental data were subjected to clustering analysis. Correspondence between quantitative trait distance and genetic distance, and their association to geographical and environmental distances were analysed with Mantel tests. All quantitative traits differed significantly among populations. The average Q_ST calculated for eight quantitative traits measured in the greenhouse was 0.157. Isozyme diversity differed significantly among populations. About 28% of total isozyme variation occurred among populations. Significant positive associations were detected between environmental, quantitative field traits, and geographical distance as well as between the later and genetic distances. Genetic distances did not correspond significantly with quantitative traits nor did environmental distances. Ecologically meaningful associations were detected between field quantitative traits, environmental, and geographical data using cluster analysis. Our results support the hypothesis that processes of the neutral type are mainly responsible for the variation patterns observed in T. plumosus populations in Venezuelan savannas. Variation observed for quantitative traits among populations seems to be due to the effect of environmental conditions on phenotypically plastic traits, and not the result of directional selection favouring different phenotypes in different populations.     

Natural selection at genomic regions associated with obesity and type-2 diabetes: East Asians and sub-Saharan Africans exhibit high levels of differentiation at type-2 diabetes regions

Different populations suffer from different rates of obesity and type-2 diabetes (T2D). Little is known about the genetic or adaptive component, if any, that underlies these differences. Given the cultural, geographic, and dietary variation that accumulated among humans over the last 60,000 years, we examined whether loci identified by genome-wide association studies for these traits have been subject to recent selection pressures. Using genome-wide SNP data on 938 individuals in 53 populations from the Human Genome Diversity Panel, we compare population differentiation and haplotype patterns at these loci to the rest of the genome. Using an “expanding window” approach (100–1,600 kb) for the individual loci as well as the loci as ensembles, we find a high degree of differentiation for the ensemble of T2D loci. This differentiation is most pronounced for East Asians and sub-Saharan Africans, suggesting that these groups experienced natural selection at loci associated with T2D. Haplotype analysis suggests an excess of obesity loci with evidence of recent positive selection among South Asians and Europeans, compared to sub-Saharan Africans and Native Americans. We also identify individual loci that may have been subjected to natural selection, such as the T2D locus, HHEX, which displays both elevated differentiation and extended haplotype homozygosity in comparisons of East Asians with other groups. Our findings suggest that there is an evolutionary genetic basis for population differences in these traits, and we have identified potential group-specific genetic risk factors.