Social class,admixture, and skin color variation in Mexican-Americans and Anglo-Americans living in San Antonio,Texas

Social class may act in different ways as a barrier to gene flow in urban populations, depending on ethnicity. We test the hypothesis that biological variation is affected by social class subdivision using skin reflectance data collected for 393 Anglo-American and 930 Mexican-American adults in the major urban population of San Antonio, Texas. Two socioeconomic groups were sampled for the Anglo-American population: a middle-income transitional group and a high-income suburban group. In addition, we sampled a third socioeconomic group for Mexican-Americans: a low income barrio. Sex and age effects on skin color are minimal. Social class has no effect on skin color variation for Anglo-Americans, whereas there is a highly significant effect on social class subdivision for Mexican-Americans. Admixture estimates were derived from skin reflectance data and show that the proportion of native American ancestry decreases as social class increases.     

Genetic admixture and gallbladder disease in Mexican Americans

Gallbladder disease is a common source of morbidity in the Mexican American population. Genetic heritage has been proposed as a possible contributor, but evidence for this is limited. Because gallbladder disease has been associated with Native American heritage, genetic admixture may serve as a useful proxy for genetic susceptibility to the disease in epidemiologic studies. The objective of our study was to examine the possibility that gallbladder disease is associated with greater Native American admixture in Mexican Americans. This study used data from the Hispanic Health and Nutrition Examination Survey and was based on 1,145 Mexican Americans who underwent gallbladder ultrasonography and provided usable phenotypic information. We used the GM and KM immunoglobulin antigen system to generate estimates of admixture proportions and compared these for individuals with and without gallbladder disease. Overall, the proportionate genetic contributions from European, Native American, and African ancestries in our sample were 0.575, 0.390, and 0.035, respectively. Admixture proportions did not differ between cases and noncases: Estimates of Native American admixture for the two groups were 0.359 and 0.396, respectively, but confidence intervals for estimates overlapped. This study found no evidence for the hypothesis that greater Native American admixture proportion is associated with higher prevalence of gallbladder disease in Mexican Americans. Reasons for the finding that Native American admixture proportions did not differ between cases and noncases are discussed. Improving our understanding of the measurement, use, and limitations of genetic admixture may increase its usefulness as an epidemiologic tool as well as its potential for contributing to our understanding of disease distributions across populations. Am. J. Phys. Anthropol. 106:361–371, 1998. Published 1998 Wiley-Liss, Inc.     

Type 2-diabetes is associated with elevated levels of TNF-alpha, IL-6 and adiponectin and low levels of leptin in a population of Mexican Americans: a cross-sectional study

The goal of the study was to determine the association between diabetes and inflammation in clinically diagnosed diabetes patients. We hypothesized that low-grade inflammation in diabetes is associated with the level of glucose control. Using a cross-sectional design we compared pro- and anti-inflammatory cytokines in a community-recruited cohort of 367 Mexican Americans with type 2-diabetes having a wide range of blood glucose levels. Cytokines (IL-6, TNF-α, IL-1β, IL-8) and adipokines (adiponectin, resistin and leptin) were measured using multiplex ELISA. Our data indicated that diabetes as whole was strongly associated with elevated levels of IL-6, leptin, CRP and TNF-α, whereas worsening of glucose control was positively and linearly associated with high levels of IL-6, and leptin. The associations remained statistically significant even after controlling for BMI and age (p = 0.01). The association between TNF-α, however, was attenuated when comparisons were performed based on glucose control. Strong interaction effects between age and diabetes and BMI and diabetes were observed for IL-8, resistin and CRP. The cytokine/adipokine profiles of Mexican Americans with diabetes suggest an association between low-grade inflammation and quality of glucose control. Unique to in our population is that the chronic inflammation is accompanied by lower levels of leptin.     

The Diabetes Alert study: growth, fatness, and fat patterning, adolescence through adulthood in Mexican Americans

Diabetes Alert is a multidisciplinary genetic and epidemiological study of Type II (non insulin-dependent) diabetes in Texas Mexican Americans. We report the anthropometry of 1,155 individuals 10 to 70 or more years with particular reference to overweight, fatness, and anatomical fat patterning in the sample. Children ages 10-18 of both sexes are growing at the 50th percentile of the reference data (U.S. Health and Nutrition Examination Survey-1) for height, Wt/Ht2, and triceps and subscapular skinfolds. Adults are well below median height but well above median Wt/Ht2 and skinfolds. Prevalence of obesity (Wt/Ht2 greater than or equal to 30) among adults is typically 30% or higher by age 30. Diabetics compared to age/sex-matched non diabetics have shorter sitting heights, have more upper body fat (subscapular skinfold), have less lower body fat (lateral calf skinfold), and were heavier at maximum weight and at age 18. The ratio of lower to upper body fat distribution decreases over the life cycle, being highest at adolescence and lowest at ages 40-50 in both sexes. Our results show a precipitous weight gain after maturity in the sample and an association of diabetes with differences in anatomical fat patterning. The age-related changes in fat patterning need to be explained in terms of their ecological and genetic influences.     

Estimating African American admixture proportions by use of population-specific alleles.

We analyzed the European genetic contribution to 10 populations of African descent in the United States (Maywood, Illinois; Detroit; New York; Philadelphia; Pittsburgh; Baltimore; Charleston, South Carolina; New Orleans; and Houston) and in Jamaica, using nine autosomal DNA markers. These markers either are population-specific or show frequency differences >45% between the parental populations and are thus especially informative for admixture. European genetic ancestry ranged from 6.8% (Jamaica) to 22.5% (New Orleans). The unique utility of these markers is reflected in the low variance associated with these admixture estimates (SEM 1.3%-2.7%). We also estimated the male and female European contribution to African Americans, on the basis of informative mtDNA (haplogroups H and L) and Y Alu polymorphic markers. Results indicate a sex-biased gene flow from Europeans, the male contribution being substantially greater than the female contribution. mtDNA haplogroups analysis shows no evidence of a significant maternal Amerindian contribution to any of the 10 populations. We detected significant nonrandom association between two markers located 22 cM apart (FY-null and AT3), most likely due to admixture linkage disequilibrium created in the interbreeding of the two parental populations. The strength of this association and the substantial genetic distance between FY and AT3 emphasize the importance of admixed populations as a useful resource for mapping traits with different prevalence in two parental populations.     

Associations of serum CRP levels with demographics,health behaviors,and risk of cancer among the Mexican American Mano A Mano Cohort

C-Reactive protein (CRP) is a well-known inflammatory marker, and elevated CRP levels has been reported to be associated with the risk of various cancers. To date, no study has investigated the association between elevated CRP and incidents of cancer among Mexican Americans. In the current prospective cohort study, we measured pre-diagnostic CRP levels in serum samples and evaluated their relationships with demographic characteristics and health behaviors associated with cancer risk among 2753 Mexican Americans selected from the Mano-A-Mano Mexican American Cohort Study. At baseline, median levels of serum CRP significantly differed by demographics (sex, age category, marital status, and education levels) and health behaviors (cigarette smoking status, alcohol drinking status, BMI category, and physical activity levels). In the multivariable analysis, the study participants who were women, older, never drinking alcohol, overweight or obese, and physically inactive had increased likelihood of having high CRP levels (≥ median levels among all study participants) compared to their counterparts. A total of 177 cancer cases were identified during the follow-up with a median follow-up time of 127 months. In the quartile analysis, study participants in the 4^th quartile with highest CRP levels had significantly 1.88 fold increased risk of cancer (hazard ratio (HR) = 1.88, 95%CI: 1.12, 3.13) compared to those in the 1^st quartile with lowest CRP levels. The association was further confirmed in analyses using clinical CRP levels. In summary, our findings suggested that serum CRP levels have potential to serve as a predictive marker of cancer risk in Mexican Americans.     

Cherokee admixture and its estimation by the gene identity method: A critique

A previous application to a Cherokee hybrid population of two methods for measuring admixture proportions by use of gene identity probabilities was examined. The results suggest that neither procedure has been correctly applied, and that underlying statistical difficulties limit their reliability.     

Comparison of Mexican Wolf and Coyote Diets in Arizona and New Mexico

ABSTRACT Interactions between wolves (Canis lupus) and coyotes (C. latrans) can have significant impacts on their distribution and abundance. We compared diets of recently translocated Mexican wolves (C. l. baileyi) with diets of resident coyotes in Arizona and New Mexico, USA. We systematically collected scats during 2000 and 2001. Coyote diet was composed mostly of mammalian species, followed by vegetation and insects. Elk (Cervus elaphus) was the most common item in coyote scats. Mexican wolf diet had a higher proportion of large mammals and fewer small mammals than coyote diet; however, elk was also the most common food item in Mexican wolf scats. Our results suggest that Mexican wolf diet was more similar to coyote diet than previously reported, but coyotes had more seasonal variation. Considering results in other areas, we expect that Mexican wolves will have a negative impact on coyotes through direct mortality and possibly competition. Reintroduction of Mexican wolves may have great impacts on communities by changing relationships among other predators and their prey.     

Effects of English admixture and geographic distance on anthropometric variation and genetic structure in 19th-century Ireland

The analysis of anthropometric data often allows investigation of patterns of genetic structure in historical populations. This paper focuses on interpopulational anthropometric variation in seven populations in Ireland using data collected in the 1890s. The seven populations were located within a 120-km range along the west coast of Ireland and include islands and mainland isolates. Two of the populations (the Aran Islands and Inishbofin) have a known history of English admixture in earlier centuries. Ten anthropometric measures (head length, breadth, and height; nose length and breadth; bizygomatic and bigonial breadth; stature; hand length; and forearm length) on 259 adult Irish males were analyzed following age adjustment. Discriminant and canonical variates analysis were used to determine the degree and pattern of among-group variation. Mahalanobis' distance measure, D2, was computed between each pair of populations and compared to distance measures based on geographic distance and English admixture (a binary measure indicating whether either of a pair of populations had historical indications of admixture). In addition, surname frequencies were used to construct distance measures based on random isonymy. Correlations were computed between distance measures, and their probabilities were derived using the Mantel matrix permutation method. English admixture has the greatest effect on anthropometric variation among these populations, followed by geographic distance. The correlation between anthropometric distance and geographic distance is not significant (r = -0.081, P = .590), but the correlation of admixture and anthropometric distance is significant (r = 0.829, P = .047). When the two admixed populations are removed from the analysis the correlation between geographic and anthropometric distance becomes significant (r = 0.718, P = .025). Isonymy distance shows a significant correlation with geographic distance (r = 0.425, P = .046) but not with admixture distance (r = -0.052, P = .524). The fact that anthropometrics show past patterns of gene flow and surnames do not reflects the greater impact of stochastic processes on surnames, along with the continued extinction of surnames. This study shows that 1) anthropometrics can be extremely useful in assessing population structure and history, 2) differential gene flow into populations can have a major impact on local genetic structure, and 3) microevolutionary processes can have different effects on biological characters and surnames.     

The use of nonmetric variation in estimating human population admixture: a test case with Brazilian blacks, whites, and mulattos

Measurements in populations which serve as valid indicators of biological relationship should be proportional to genetic distance. In order to test the utility of discrete cranial traits for estimating genetic distances among populations, estimates of admixture are obtained for gene frequency data and nonmetric cranial data in São Paulo mulattos (M). The gene frequency data serve as a control that the three populations are related as stated: estimates of admixture are obtained by using São Paulo whites (W) and blacks (B) as parental populations and by estimating the parameter of admixture, m, in the model p_M = (1 ? m) p_W + mp_B (Elston, 1971) where the p's are either gene frequencies or nonmetric trait frequencies. A test of goodness of fit of the model provides a means of ascertaining whether or not the data fit this linear model. While the gene frequency data indicate distances among the three populations which are highly compatible with the linear model of admixture, the nonmetric data show significant deviations from the model. This implies that the frequencies of the nonmetric traits in the populations used in this analysis are not a linear function of genetic distance. This discourages the use of nonmetric traits in making quantitative conclusions about genetic relationships. It also suggests the need for investigation of the use of other skeletal characters for estimating genetic distance, as well as approaches for such investigations through the study of hybrid individuals.     

A deterministic model of admixture and genetic introgression: the case of Neanderthal and Cro-Magnon

There is an ongoing debate in the field of human evolution about the possible contribution of Neanderthals to the modern human gene pool. To study how the Neanderthal private alleles may have spread over the genes of Homo sapiens, we propose a deterministic model based on recursive equations and ordinary differential equations. If the Neanderthal population was large compared to the Homo sapiens population at the beginning of the contact period, we show that genetic introgression should have been fast and complete meaning that most of the Neanderthal private alleles should be found in the modern human gene pool in case of ancient admixture. In order to test/reject ancient admixture from genome-wide data, we incorporate the model of genetic introgression into a statistical hypothesis-testing framework. We show that the power to reject ancient admixture increases as the ratio, at the time of putative admixture, of the population size of Homo sapiens over that of Neanderthal decreases. We find that the power to reject ancient admixture might be particularly low if the population size of Homo sapiens was comparable to the Neanderthal population size.     

Genetic distance and gene diversity among linguistically different tribes of Mexican Indians.

Using gene frequency data for 14 genetic loci, genetic distances between 13 tribes of Mexican Indians belonging to 12 language groups were determined and a dendrogram was constructed. The genetic distance between tribes is correlated more with geographic proximity than with language affinity. The gene diversity (heterozygosity) of the total population was decomposed into the three components, i.e., the gene diversity between three main linguistic groups, the gene diversity between tribes within the main linguistic groups and the gene diversity within tribes. About 95% of the total gene diversity exists within tribes, the intergroup and intertribe components being only about 5%.     

Frequencies of ABO, Rh and Kell phenotypes in couples from Han, Kazak, Uyghur and Hui in Xinjiang: an inheritance simulation model for blood group incompatibility in new-born

The Xinjiang region with residents from more than 13 minorities represents an area of many diverse ethnicities. This ethnic diversity in relation to their blood groups and immune status may have a consequential impact on the clinical status of married couples. To evaluate the risks of haemolytic disease in new-born infants, we investigated the rate of blood-group incompatibility among 487 married couples from four ethnic minorities, namely the Han, Hui, Uyghur and Kazak populations. Han minority married couples showed significantly different ABO, Rh and K phenotype frequencies between marrial relationship, whereas there was no significant difference in ABO, Rh and K phenotypes between the Uyghur, Hui and Kazak .There was a significant difference between ABO blood types in Han married couples, in the Kazak Rh-C phenotype and in the Uyghur Rh-D phenotype. The Hui married couples only demonstrated ABO, Rh and K phenotypes. The Hui minority showed the highest incompatibility rate for Rh-C and Rh-E phenotypes between mothers and their new-born infants. The highest incompatibility rate for the ABO phenotype occurred in the Kazak group. These results particularly demonstrate the clinical issues relating to ABO and Rh incompatibility, in the Kazak and Hui minorities, respectively.     

Gene frequencies and admixture estimates in the state of Puebla, Mexico

Three hundred ninety-three individuals from the Universidad Autónoma de Puebla and its University Hospital were studied to determine the distribution of ABO, MN, Rh-Hr, Duffy, and Diego blood groups; red cell hemoglobin and glucose-6-phosphate dehydrogenase variants; and serum haptoglobins, albumins, and factor Bf types. With the results we estimated that the proportions of black, indian, and white genes are 10.7%, 56.3%, and 33.0%, respectively, in a trihybrid model. Reasons are given as to why the black ancestry may be artifically high, and it is pointed out that independent confirmation with other markers is needed before the figure can be accepted as a true value.     

Disentangling Signatures of Selection Before and After European Colonization in Latin Americans

Throughout human evolutionary history, large-scale migrations have led to intermixing (i.e., admixture) between previously separated human groups. Although classical and recent work have shown that studying admixture can yield novel historical insights, the extent to which this process contributed to adaptation remains underexplored. Here, we introduce a novel statistical model, specific to admixed populations, that identifies loci under selection while determining whether the selection likely occurred post-admixture or prior to admixture in one of the ancestral source populations. Through extensive simulations, we show that this method is able to detect selection, even in recently formed admixed populations, and to accurately differentiate between selection occurring in the ancestral or admixed population. We apply this method to genome-wide SNP data of ∼4,000 individuals in five admixed Latin American cohorts from Brazil, Chile, Colombia, Mexico, and Peru. Our approach replicates previous reports of selection in the human leukocyte antigen region that are consistent with selection post-admixture. We also report novel signals of selection in genomic regions spanning 47 genes, reinforcing many of these signals with an alternative, commonly used local-ancestry-inference approach. These signals include several genes involved in immunity, which may reflect responses to endemic pathogens of the Americas and to the challenge of infectious disease brought by European contact. In addition, some of the strongest signals inferred to be under selection in the Native American ancestral groups of modern Latin Americans overlap with genes implicated in energy metabolism phenotypes, plausibly reflecting adaptations to novel dietary sources available in the Americas.     

Induced resistance to Mexican bean beetles in soybean: variation among genotypes and lack of correlation with constitutive resistance

Fourteen genotypes (varieties) of soybean (Glycine max) were screened for levels of induced resistance to Mexican bean beetle (Epilachna varivestis) damage, and a subset of 6 of those varieties was screened for levels of constitutive resistance to Mexican bean beetles. Experiments were carried out in the greenhouse, with damage imposed by Mexican bean beetle larvae, and levels of resistance measured by a choice test bioassay with adult beetles. We found significant variation among soybean genotypes in levels of both induced and constitutive resistance. We found no significant correlation between levels of induced and constitutive resistance measured in the same genotypes. We compare these results to past work on resistance in the soybean-Mexican bean beetle system, consider the implications of variation in both types of resistance for plant-herbivore interactions in agricultural and natural systems, and discuss the relationship between induced and constitutive resistance. Received: 30 November 1998 / Accepted: 25 June 1999     

Deep learning prediction of attention-deficit hyperactivity disorder in African Americans by copy number variation

Current understanding of the underlying molecular network and mechanism for attention-deficit hyperactivity disorder (ADHD) is lacking and incomplete. Previous studies suggest that genomic structural variations play an important role in the pathogenesis of ADHD. For effective modeling, deep learning approaches have become a method of choice, with ability to predict the impact of genetic variations involving complicated mechanisms. In this study, we examined copy number variation in whole genome sequencing from 116 African Americans ADHD children and 408 African American controls. We divided the human genome into 150 regions, and the variation intensity in each region was applied as feature vectors for deep learning modeling to classify ADHD patients. The accuracy of deep learning for predicting ADHD diagnosis is consistently around 78% in a two-fold shuffle test, compared with ∼50% by traditional k-mean clustering methods. Additional whole genome sequencing data from 351 European Americans children, including 89 ADHD cases and 262 controls, were applied as independent validation using feature vectors obtained from the African American ethnicity analysis. The accuracy of ADHD labeling was lower in this setting (∼70–75%) but still above the results from traditional methods. The regions with highest weight overlapped with the previously reported ADHD-associated copy number variation regions, including genes such as GRM1 and GRM8, key drivers of metabotropic glutamate receptor signaling. A notable discovery is that structural variations in non-coding genomic (intronic/intergenic) regions show prediction weights that can be as high as prediction weight from variations in coding regions, results that were unexpected.     

Uncontrolled admixture and loss of genetic diversity in a local Vietnamese pig breed

The expansion of intensive livestock production systems in developing countries has increased the introduction of highly productive exotic breeds facilitating indiscriminate crossbreeding with local breeds. In this study, we set out to investigate the genetic status of the Vietnamese Black H'mong pig breed by evaluating (1) genetic diversity and (2) introgression from exotic breeds. Two exotic breeds, namely Landrace and Yorkshire used for crossbreeding, and the H'mong pig population from Ha Giang (HG) province were investigated using microsatellite markers. Within the province, three phenotypes were observed: a White, a Spotted and a Black phenotype. Genetic differentiation between phenotypes was low (0.5-6.1%). The White phenotypes showed intermediate admixture values between exotic breeds and the Black HG population (0.53), indicating a crossbreed status. Management practices were used to predict the rate of private diversity loss due to exotic gene introgressions. After 60 generations, 100% of Black private alleles will be lost. This loss is accelerated if the admixture rate is increased but can be slowed down if the mortality rate (e.g., recruitment rate) is decreased. Our study showed that a large number of markers are needed for accurately identifying hybrid classes for closely related populations. While our estimate of admixture still seems underestimated, genetic erosion can occur very fast even through indiscriminate crossbreeding.     

Evaluation of Neurotrophic Tyrosine Receptor Kinase 2 (NTRK2) as a positional candidate gene for variation in estimated Glomerular Filtration Rate (eGFR) in Mexican American participants of San Antonio Family Heart Study

Background

The estimated glomerular filtration rate (eGFR) is a well-known measure of kidney function and is commonly used for the diagnosis and management of patients with chronic kidney disease. The inter-individual variation in eGFR has significant genetic component. However, the identification of underlying genetic susceptibility variants has been challenging. In an attempt to identify and characterize susceptibility genetic variant(s) we previously identified the strongest evidence for linkage of eGFR occurring on chromosome 9q21 in the Mexican American participants of San Antonio Family Heart Study (SAFHS). The objective of the present study was to examine whether the common genetic variants in Neurotrophic Tyrosine Receptor Kinase 2 (NTRK2), a positional candidate gene on 9q21, contribute to variation in eGFR.

Results

Twelve tagging single nucleotide polymorphisms (SNPs) across the NTRK2 gene region were selected (r2 ≥ 0.80, minor allele frequency of ≥ 0.05) from the Hapmap database. SNPs were genotyped by TaqMan assay in the 848 Mexican American subjects participated in the SAFHS. Association analysis between the genotypes and eGFR (estimated by the Modification of Diet in Renal Disease equation) were performed by measured genotype approach as implemented in the program SOLAR. Of the 12 common genetic variants examined, the rs1036915 (located in 3′UTR) and rs1187274 (located in intron-14), present in perfect linkage disequilibrium, exhibited an association (P = 0.017) with eGFR after accounting for the effects of age, sex, diabetes, diabetes duration, systolic blood pressure and blood pressure medication. The carriers of minor allele of rs1036915 (G; 38%) had increased eGFR (104 ± 25 ml/min/1.73 m²) in comparison to the carriers of major allele A (98 ± 25 ml/min/1.73 m²).

Conclusion

Together, our results suggest for the first time that the genetic variants in NTRK2 may regulate eGFR.