Mitochondrial DNA -- New York (State) -- New York.
Y chromosome -- Abnormalities -- New York (State) -- New York.
Human population genetics -- New York (State) -- New York.
Pooled DNA samples have been used in association studies of Mendelian disease genes. This method involves combining equal quantities of DNA from patients and control subjects into separate pools and comparing the pools for distributions of genetic markers. In this study identical quantities of DNA from 300 individuals representing 6 populations were pooled and amplified for 296 loci using the touchdown polymerase chain reaction (PCR) method. The purpose of this study is to test the efficacy of pooled DNA markers in the reconstruction of the genetic structure of human populations. The populations sampled included Chuvash, Buryats, Kizhi, Native Americans, South Africans, and New York City whites. To test the accuracy of the allele-frequency distributions, we genotyped the Buryats and New York samples individually for six microsatellite markers and compared their frequencies to the allele frequencies derived from the electropherogram peak heights for the pooled DNA, producing a correlation of 0.9811 with a variance of less than 0.04. Two-dimensional scaling of genetic distances among the six populations produced clusters that reflected known historical relationships. A distance matrix was created using all 296 loci, and matrices based on individual chromosomes were correlated against the total matrix. As expected, the largest chromosomes had the highest correlations with the total matrix, whereas one of the smallest chromosomes, chromosome 22, had the lowest correlation and differed most from the combined STR distance matrix.
Pooled DNA, Short Tandem Repeats, Genetic Diversity, R Matrix Analysis, Chuvash, Buryats, Kizhi, Native Americans, South Africans, New York City Whites.
Sherwood, Richard J.
Hlusko, Leslea J.
Duren, Dana L.
Emch, Victoria C.
Walker, Alan, 1938-
The hominoid mandibular symphysis has received a great deal of attention from anatomists, human biologists, and paleontologists. Much of this research has focused on functional interpretations of symphyseal shape variation. Here, we examine the two-dimensional cross-sectional shape of the adult mandibular symphysis for 45 humans, 42 chimpanzees, 37 gorillas, and 51 orangutans using eigenshape analysis, an outline-based morphometric approach. Our results demonstrate that a large proportion of the variation described by the first eigenshape correlates with proposed functional adaptations to counteract stresses at the mandibular midline during mastication. Subsequent eigenshapes describe subtle aspects of shape variation in the mandibular symphysis. The morphology associated with these eigenshapes does not conform with functional predictions, nor does it show a relationship with sexual dimorphism. However, eigenshapes provide for considerable taxonomic discrimination between the four taxa studied and may consequently prove useful in the analysis of fossil material. Comparison with elliptical Fourier analysis of the mandibular symphysis identifies eigenshape analysis as providing superior taxonomic discrimination. The results presented here demonstrate that the cross-sectional shape of the mandibular symphysis results from a complex interplay of functional and nonfunctional influences and for the first time identifies and quantifies the specific aspects of variation attributable to these factors.
School children -- Channel Islands -- Jersey -- Growth -- History -- 20th century.
School children -- Great Britain -- Growth -- History -- 20th century.
The 1940–45 German occupation of the Channel Islands was accompanied by a gradual deterioration in food availability and culminated in a nine-month siege with severe food shortages after supplies from France were cut off following the liberation of Normandy in 1944. The aim of this study was to compare the growth rates of schoolchildren resident on one of the Channel Islands (Jersey) with children growing up on mainland Britain. Secondary analyses were conducted on published data describing the growth of approximately 3,500 schoolchildren resident on Jersey throughout the occupation, 10,000–15,000 London schoolchildren, and about 5,000 children evacuated from mainland cities to "residential camp schools" in rural areas. A comparison of age- and sex-adjusted average annual growth rates between 1940 and 1943 confirmed that 8½–12½-year-old children on Jersey gained 28.2–33.1% less weight and 23.6–26.5% less height per year than children on the mainland. Because food shortages on Jersey intensified after 1943 (when the mid-occupation growth measurements had been recorded), growth rates toward the end of the occupation (in 1944 and early 1945) are likely to have been even worse than those observed between 1940 and 1943. As such, these analyses provide a somewhat conservative estimate of the decline in childhood growth rates that occurred on Jersey during the 1940–45 German occupation.
Secular Trend, Growth, Height, Weight, World War II, British Schoolchildren, Channel Islands.
Mosher, M. J.
Martin, L. J.
Cupples, L. A.
Dyer, T. D.
Williams, J. T.
North, K. E.
Low levels of high-density lipoprotein (HDL) are widely documented as a risk factor for cardiovascular disease (CVD). Furthermore, there is marked sexual dimorphism in both HDL levels and the prevalence of CVD. However, the extent to which genetic factors contribute to such dimorphism has been largely unexplored. We examined the evidence for genotype-by-sex effects on HDL in a longitudinal sample of 1,562 participants from 330 families in the Framingham Heart Study at three times points corresponding approximately to 1971–1974, 1980–1983, and 1988–1991. Using a variance component method, we conducted a genome scan of HDL at each time point in males and females, separately and combined, and tested for genotype-by-sex interaction at a quantitative trait locus (QTL) at each time point. Consistent findings were noted only for females on chromosome 2 near marker D2S1328, with adjusted LOD scores of 2.6, 2.2, and 2.1 across the three time points, respectively. In males suggestive linkage was detected on chromosome 16 near marker D16S3396 at the second time point and on chromosome 18 near marker D18S851 at the third time point (adjusted LOD=2.2 and 2.4, respectively). Although the heritability of HDL is similar in males and females, sex appears to exert a substantial effect on the QTL-specific variance of HDL. When genotype-by-sex interactions exist and are not modeled, the power to detect linkage is reduced; thus our results may explain in part the paucity of significant linkage findings for HDL.
Coronary heart disease -- Saudi Arabia -- Genetic aspects.
The substitution of tryptophan (Trp) by arginine (Arg) at position 64 in the β3-adrenoceptor (β3-AR) gene has been associated with obesity, diabetes mellitus, and coronary artery disease (CAD). We have investigated whether the Trp64Arg polymorphism is associated with the manifestation of CAD or one of its important risk factors, such as obesity, diabetes mellitus, elevated cholesterol and triglyceride levels, or hypertension in the Arab population. All participating subjects were genotyped for this polymorphism using the polymerase chain reaction followed by enzymatic digestion and sequencing. In the angiographed normal control subjects (n=495), 90.3% were homozygous Trp/Trp, 9.5% were heterozygous Trp/Arg, and 0.2% were homozygous for the Arg/Arg genotype, compared to 87%, 12.3%, and 0.7%, respectively, among angiographically confirmed CAD patients (n=981). There was no statistical difference in the distribution of genotypes or allele frequencies between the CAD and control groups. We carried out a stepwise logistic regression analysis to study the possible combined effect of the genotypes and other risk factors on CAD. All variables were retained in the model, with p values of 0.014, 0.006, 0.005, <0.001, 0.045, 0.002, <0.001, and 0.016 for genotype, diabetes mellitus, sex, family history of CAD, obesity, myocardial infarction, smoking, and age, respectively. In conclusion, the Trp64Arg polymorphism of the β3-AR gene does not represent an independent risk factor for CAD in Arabs. However, in the presence of other CAD risk factors, this polymorphism may be used as a predictor of CAD.
Microsatellites (Genetics) -- India -- Andhra Pradesh.
Social stratification -- India -- Andhra Pradesh.
DNA samples of 948 individuals belonging to 27 populations from southern Andhra Pradesh were analyzed for nine AmpFlSTR Profiler Plus loci. The nature and extent of genomic diversity within and between these populations have been examined with reference to socioeconomic and geographic affiliations. The results suggest that the average heterozygosity is uniformly high in these populations (>0.80) and that the patterns of allele distributions are similar across the populations. The value of the coefficient of gene differentiation and the AMOVA and structure analysis results suggest that these populations are highly homogeneous. The neighbor-joining tree constructed using either DA or FST distances suggests no intelligible pattern of population clusters based on ethnohistoric or geographic affiliations. All these observations suggest either a common recent origin of these populations or extensive gene flow across the populations that erased the original genetic differences. Given strict endogamy, the latter explanation can hold only if there has been unauthorized or unrecognized gene flow transecting the social boundaries. Nevertheless, the regression plot of average heterozygosity versus distance from the centroid (Rii), based on Harpending and Ward's (1982) model, and the genetic distances computed between different hierarchical groups within Andhra Pradesh tend to support this conjecture. Overall, the results suggest lack of a significant degree of genetic stratification that is consistent with social stratification in Andhra Pradesh. Furthermore, the neighbor-joining tree based on comparative data from other Indian and continental populations brings out a single and compact cluster of all the Andhra populations that is clearly separated from the rest.
Local vs. Global Variation, Microsatellite Diversity, Short Tandem Repeats, D3S1358, D8S1179, D5S818, VWA D21S11, D13S317, FGA, D7S820, D18S5, Endogamy, Gene Flow, Homogenization, India.
Shepard, E. M.
Chow, R. A.
Pérez-Miranda, A. M.
Garcia-Bertrand, R. L.
Herrera, R. J.
Human population characteristics at the genetic level are integral to both forensic biology and population genetics. This study evaluates biparental microsatellite markers in five Austronesian-speaking groups to characterize their intra- and interpopulation differences. Genetic diversity was analyzed using 15 short tandem repeat (STR) loci from 338 unrelated individuals from 5 Pacific islands populations, including the aboriginal Ami and Atayal groups from Taiwan, Bali and Java in Indonesia, and the Polynesian islands of Samoa. Allele frequencies from the STR profiles were determined and compared to other geographically targeted worldwide populations procured from recent literature. Hierarchical AMOVA analysis revealed a large number of loci that exhibit significant correspondence to linguistic partitioning among groups of populations. A pronounced divide exists between Samoa and the East (Formosa) and Southeast Asian (Bali and Java) islands. This is clearly illustrated in the topology of the neighbor-joining tree. Phylogenetic analyses also indicate clear distinctions between the Ami and Atayal and between Java and Bali, which belie the respective geographic proximities of the populations in each set. This differentiation is supported by the higher interpopulation variance components of the Austronesian populations compared to other Asian non-Austronesian groups. Our phylogenetic data indicate that, despite their linguistic commonalities, these five groups are genetically distinct. This degree of genetic differentiation justifies the creation of population-specific databases for human identification.
To contribute to a better understanding of the origin and distribution of CFTR mutations in the Brazilian population, we have investigated the linkage between four polymorphic markers (XV2c, KM19, GATT, and TUB9) within or near the CFTR locus. The distribution of alleles for each polymorphism for both parental and cystic fibrosis (CF) chromosomes from Rio de Janeiro CF families were ascertained using a maximum-likelihood method. This same method was applied to study the distribution of the haplotypes defined by these markers. There was no significant association between the XV2c and KM19 loci on the parental and CF chromosomes. On the other hand, a strong association between GATT and TUB9 loci was observed on both CF and parental chromosomes, and striking linkage disequilibrium between the GATT-TUB9 pair and ΔF508 was observed (Χ2 =26.48, p<0.0001). Remarkable linkage disequilibrium between the GATT-TUB9 marker pair and non-ΔF508 was also found (Χ2 = 17.05, p<0.0001). Our finding of a linkage disequilibrium between GATT-TUB9 and the CFTR locus could suggest that gene flow between different ethnic groups, mainly sub-Saharan and Mediterranean populations, with Brazilian populations could have resulted in some CF mutations originating on chromosomes that carried the GATT-TUB9 marker haplotype 7-2 (OR=1.34<2.83<6.00; p=0.0066).
Human population genetics -- Mexico -- Veracruz-Llave (State)
We report allele frequencies for the most common polymorphism of the APOE gene in Mexican individuals from two regions not previously described: Coras and Huicholes from Nayarit, and Nahuas and mestizos from Veracruz. We also report APOE allele frequencies for inhabitants of Mexico City. These descriptive data underscore the allelic heterogeneity for this particular locus in Mexico.
Apolipoprotein E, Apoe, Coras, Huicholes, Nahuas, Mestizos, Mexico.
Human population genetics -- Uruguay -- Montevideo.
mtDNA Amerindian polymorphisms were studied in 108 inhabitants of Montevideo, Uruguay, using PCR RFLP analysis. Amerindian haplogroups were found in 20.4% of the sample. The frequency of Amerindian polymorphisms in Montevideo differed significantly from that observed in Tacuarembó, a city about 400 km away, indicating the high level of variation within Uruguay. Results for mitochondrial markers indicate that admixture occurred primarily as a result of Amerindian females mating with European males.