Population History and Gene Divergence in Native Mexicans Inferred from 76 Human Exomes.

Native American genetic variation remains underrepresented in most catalogs of human genome sequencing data. Previous genotyping efforts have revealed that Mexico's Indigenous population is highly differentiated and substructured, thus potentially harboring higher proportions of private genetic variants of functional and biomedical relevance. Here we have targeted the coding fraction of the genome and characterized its full site frequency spectrum by sequencing 76 exomes from five Indigenous populations across Mexico. Using diffusion approximations, we modeled the demographic history of Indigenous populations from Mexico with northern and southern ethnic groups splitting 7.2 KYA and subsequently diverging locally 6.5 and 5.7 KYA, respectively. Selection scans for positive selection revealed BCL2L13 and KBTBD8 genes as potential candidates for adaptive evolution in Rarámuris and Triquis, respectively. BCL2L13 is highly expressed in skeletal muscle and could be related to physical endurance, a well-known phenotype of the northern Mexico Rarámuri. The KBTBD8 gene has been associated with idiopathic short stature and we found it to be highly differentiated in Triqui, a southern Indigenous group from Oaxaca whose height is extremely low compared to other Native populations.

Latin Americans show wide-spread Converso ancestry and imprint of local Native ancestry on physical appearance.

Historical records and genetic analyses indicate that Latin Americans trace their ancestry mainly to the intermixing (admixture) of Native Americans, Europeans and Sub-Saharan Africans. Using novel haplotype-based methods, here we infer sub-continental ancestry in over 6,500 Latin Americans and evaluate the impact of regional ancestry variation on physical appearance. We find that Native American ancestry components in Latin Americans correspond geographically to the present-day genetic structure of Native groups, and that sources of non-Native ancestry, and admixture timings, match documented migratory flows. We also detect South/East Mediterranean ancestry across Latin America, probably stemming mostly from the clandestine colonial migration of Christian converts of non-European origin (Conversos). Furthermore, we find that ancestry related to highland (Central Andean) versus lowland (Mapuche) Natives is associated with variation in facial features, particularly nose morphology, and detect significant differences in allele frequencies between these groups at loci previously associated with nose morphology in this sample.

The RANKL rs12585014 polymorphism is associated with age at menarche in postmenopausal women with hip fracture.

The RANK/RANKL/OPG signaling is important in the regulation of bone turnover. The aim of the present work was to analyze the rs3018362 and rs12585014 polymorphisms in the RANK and RANKL genes, as well as risk factors in postmenopausal women. Women with hip fracture, with femoral neck osteoporosis and controls (n = 646) were recruited. From these, 303 women who fulfill the inclusion criteria were genotyped using real-time PCR with TaqMan probes. There were no associations of the rs3018362 and rs12585014 with osteoporosis or fracture. When women were divided by age at menarche, the rs12585014 GG genotype was strongly associated with age at menarche >13 years [p = .00774, OR = 6.429 (1.907-21.103)] in women with hip fracture. Significant differences in risk factors such as body mass index, age at menopause, use of estrogens, the presence of hypertension, and diabetes mellitus were found. Carrying the GG genotype of rs12585014 entails a higher risk of having menarche later (>13 years), which could involves a greater risk of fractures. The rs3018362 and rs12585014 do not seem to be associated with hip osteoporosis or hip fracture in Mexican women.

Susceptibility background for type 2 diabetes in eleven Mexican Indigenous populations: HNF4A gene analysis.

The genetic risk of developing type 2 diabetes (T2D) increases in parallel with the proportion of Native American ancestry. Mestizo Mexicans have a 70% Native Amerindian genetic background. The T130I polymorphism in the HNF4A gene has been associated with early-onset T2D in mestizo Mexicans. Thus, the aim of the present study was to evaluate the frequency and relationship of the T130I variant in the HNF4A gene with risk factors for developing T2D in eleven indigenous groups from Mexico. In two groups, all exons of the HNF4A gene were directly sequenced; in the remaining the T130I polymorphism was analyzed by restriction fragment length polymorphism. Ancestry informative markers were assessed to confirm the Amerindian component. An additional analysis of EHH was carried out. Interestingly, HNF4A gene screening revealed only the presence of the T130I polymorphism. The range frequency of the risk allele (T) in the indigenous groups was from 2.7 to 16%. Genotypic frequencies (T130I/I130I) were higher and significantly different from those of all of the populations included in the HapMap Project (P < 0.005). EHH scores suggest a positive selection for T130I polymorphism. Metabolic traits indicate a relationship between the T130I/I130I genotypes with high triglyceride concentrations in the indigenous groups (P < 0.005). These results strongly suggest that the high frequency of the T130I polymorphism and its biological relationship with dysfunction in lipid metabolism in Mexican indigenous groups is a risk factor for the developing of T2D in Mexicans.

Factors associated with degree of atopy in Latino children in a nationwide pediatric sample: the Genes-environments and Admixture in Latino Asthmatics (GALA II) study.

BACKGROUND: Atopy varies by ethnicity, even within Latino groups. This variation might be due to environmental, sociocultural, or genetic factors. OBJECTIVE: We sought to examine risk factors for atopy within a nationwide study of US Latino children with and without asthma. METHODS: Aeroallergen skin test responses were analyzed in 1830 US Latino subjects. Key determinants of atopy included country/region of origin, generation in the United States, acculturation, genetic ancestry, and site to which subjects migrated. Serial multivariate zero-inflated negative binomial regressions stratified by asthma status examined the association of each key determinant variable with the number of positive skin test responses. In addition, the independent effect of each key variable was determined by including all key variables in the final models. RESULTS: In baseline analyses African ancestry was associated with 3 times (95% CI, 1.62-5.57) as many positive skin test responses in asthmatic participants and 3.26 times (95% CI, 1.02-10.39) as many positive skin test responses in control participants. Generation and recruitment site were also associated with atopy in crude models. In final models adjusted for key variables, asthmatic patients of Puerto Rican (exp[ß] [95% CI], 1.31 [1.02-1.69]) and mixed (exp[ß] [95% CI], 1.27 [1.03-1.56]) ethnicity had a greater probability of positive skin test responses compared with Mexican asthmatic patients. Ancestry associations were abrogated by recruitment site but not region of origin. CONCLUSIONS: Puerto Rican ethnicity and mixed origin were associated with degree of atopy within US Latino children with asthma. African ancestry was not associated with degree of atopy after adjusting for recruitment site. Local environment variation, represented by site, was associated with degree of sensitization.

Genetic structure of three Native Mexican communities based on mtDNA haplogroups, and ABO and Rh blood group systems.

OBJECTIVE: The goals of this population genetics study were to describe mtDNA haplogroups and ABO and Rh blood group systems of 3 Native Mexican populations, to determine their genetic variability, and to compare their haplogroups with those of 13 Native Mexican populations previously reported. MATERIAL AND METHODS: The three communities under analysis were a Tepehua-speaking community from Huehuetla (Hidalgo state), an Otomi-speaking community from San Antonio el Grande (Hidalgo state), and a Zapotec-speaking community from Juchitán (Oaxaca state). Every subject studied in each community had four grandparents who were born in the same community and spoke the same language. The four Amerindian mtDNA haplogroups (A, B, C and D) were studied by restriction analysis and gel electrophoresis. RESULTS: Regarding the blood groups, the O group was the most frequent in the three populations (97.2, 94.7, and 86.2%, respectively), as well as the Rh+ group (100, 100, 84%). The three populations analyzed were in Hardy-Weinberg equilibrium. In respect to the mtDNA haplogroups, A, B, C and D, their percentage was 33.3, 36.1, 13.9 and 5.6 % in Huehuetla; 39.5, 13.2, 39.5 and 2.6 % in San Antonio el Grande, and 55.3, 21.0, 7.9 and 5.2 % in Juchitán. Between 5 and 11% of the haplogroups were of non-Amerindian origin, probably due to admixture with Caucasian and African populations, as has been reported in the past. No statistically-significant differences were found among the three populations studied or between them and 13 previously reported Native Mexican populations.

Evaluating the Farming/Language Dispersal Hypothesis with genetic variation exhibited by populations in the Southwest and Mesoamerica.

The Farming/Language Dispersal Hypothesis posits that prehistoric population expansions, precipitated by the innovation or early adoption of agriculture, played an important role in the uneven distribution of language families recorded across the world. In this case, the most widely spread language families today came to be distributed at the expense of those that have more restricted distributions. In the Americas, Uto-Aztecan is one such language family that may have been spread across Mesoamerica and the American Southwest by ancient farmers. We evaluated this hypothesis with a large-scale study of mitochondrial DNA (mtDNA) and Y-chromosomal DNA variation in indigenous populations from these regions. Partial correlation coefficients, determined with Mantel tests, show that Y-chromosome variation in indigenous populations from the American Southwest and Mesoamerica correlates significantly with linguistic distances (r = 0.33-0.384; P < 0.02), whereas mtDNA diversity correlates significantly with only geographic distance (r = 0.619; P = 0.002). The lack of correlation between mtDNA and Y-chromosome diversity is consistent with differing population histories of males and females in these regions. Although unlikely, if groups of Uto-Aztecan speakers were responsible for the northward spread of agriculture and their languages from Mesoamerica to the Southwest, this migration was possibly biased to males. However, a recent in situ population expansion within the American Southwest (2,105 years before present; 99.5% confidence interval = 1,273-3,773 YBP), one that probably followed the introduction and intensification of maize agriculture in the region, may have blurred ancient mtDNA patterns, which might otherwise have revealed a closer genetic relationship between females in the Southwest and Mesoamerica.

Genetic admixture of eight Mexican indigenous populations: based on five polymarker, HLA-DQA1, ABO, and RH loci.

This study explores the genetic admixture of eight Mexican indigenous populations (Otomi-Ixmiquilpan, Otomi-Actopan, Tzeltales, Nahua-Milpa-Alta, Nahua-Xochimilco, Nahua-Zitlala, Nahua-Ixhuatlancillo, and Nahua-Coyolillo) on the basis of five PCR-based polymorphic DNA loci (LDLR, GYPA, HBGG, D7S8, GC), HLA_DQA1, and the blood groups ABO and Rh (CcDEe). Among the indigenous populations, the highest gene frequencies for O and D were 0.9703 and 1.000 for Zitlala (State of Guerrero) and 0.9955 and 0.9414 for Tzeltales (State of Chiapas), respectively. Maximum likelihood estimates of admixture components yield a trihybrid model with Amerindian (assuming that Nahua-Zitlala is the most representative indigenous population), Spanish, and African ancestry with the admixture proportions: 93.03, 6.03, and 0.94 for Tzeltales, and 28.99, 44.03, and 26.98 for Coyolillo. A contribution of the ancestral populations of Ixhuatlancillo, Actopan, Ixmiquilpan, Milpa-Alta, and Xochimilco were found with the following average of admixture proportions: 75.84, 22.50, and 1.66. The findings herein demonstrate that the genetic admixture of the Mexican indigenous populations who at present speak the same Amer-Indian language can be differentiated and that the majority of them have less ancestral indigenous contribution than those considered as Mestizo populations.

[Hemoglobin S frequency in five Mexican populations and its importance in public health]. / Frecuencia de la hemoglobina S en cinco poblaciones mexicanas y su importancia en la salud pública.

OBJECTIVE: To provide information regarding the heterozygote frequency for hemoglobin S (HbS) in five Mexican populations, the Haplotype in five S chromosomes, and underscore its importance for public health. MATERIAL AND METHODS: A total of 162 samples from three Nahua populations (Atocpan and Tlacotenco, DF, and Ixhuatlancillo, Veracruz) and 131 from mestizo populations (Coyolillo and Poza Rica, Veracruz) were studied after obtaining informed consent. The hemoglobin type was determined by electrophoresis, and DNA in leucocytes was obtained from five HbS samples. The haplotype was determined by PCR and cut with restrictases, according to literature. RESULTS: We found one heterozygote for hemoglobin S (0.6%) among Nahua and 18 among Mestizo groups (13.7%). Four haplotypes were Bantu and one was Benin. CONCLUSIONS: These findings are important to public health for populations with a high frequency of HbS, to inform and provide genetic counseling for carriers and medical attention to patients.

Frecuencia de la hemoglobina S en cinco poblaciones mexicanas y su importancia en la salud pública / Hemoglobin S frequency in five Mexican populations and its importance in public health

OBJETIVO: Informar la frecuencia de heterocigotos para la hemoglobina S (HbS) en cinco poblaciones mexicanas y el haplotipo en cinco muestras con HbS y subrayar su relevancia en la salud pública. MATERIAL Y MÉTODOS: Se tomó una muestra de sangre periférica en 162 individuos no relacionados provenientes de tres poblaciones nahuas (Atocpan y Tlacotenco, DF, e Ixhuatlancillo, Veracruz), y en 131 mestizos (Coyolillo y Poza Rica, Veracruz), previo consentimiento informado. Se determinó el tipo de hemoglobina por electroforesis y se extrajo el DNA de leucocitos de cinco muestras en las que se determinó el haplotipo por PCR y corte con restrictasas. RESULTADOS: Entre los nahuas se reconoció un heterocigoto HbAS (0.6 por ciento) y 18 en mestizos (13.7 por ciento). Se identificaron cuatro haplotipos Bantu y uno Benin. CONCLUSIONES: Estos hallazgos son importantes en términos de la salud pública en poblaciones con alta frecuencia de HbS, para dar información y consejo genético a los portadores y la atención médica oportuna y adecuada a los pacientes.

OBJECTIVE: To provide information regarding the heterozygote frequency for hemoglobin S (HbS) in five Mexican populations, the Haplotype in five S chromosomes, and underscore its importance for public health. MATERIAL AND METHODS: A total of 162 samples from three Nahua populations (Atocpan and Tlacotenco, DF, and Ixhuatlancillo, Veracruz) and 131 from mestizo populations (Coyolillo and Poza Rica, Veracruz) were studied after obtaining informed consent. The hemoglobin type was determined by electrophoresis, and DNA in leucocytes was obtained from five HbS samples. The haplotype was determined by PCR and cut with restrictases, according to literature. RESULTS:We found one heterozygote for hemoglobin S (0.6 percent) among Nahua and 18 among Mestizo groups (13.7 percent). Four haplotypes were Bantu and one was Benin. CONCLUSIONS: These findings are important to public health for populations with a high frequency of HbS, to inform and provide genetic counseling for carriers and medical attention to patients.

Genetic structure of Mexican Mestizo women with breast cancer based on three STR loci.

The aim of this population genetics study was to compare the genetic structure of Mexican women with breast cancer (BrCa) with previously reported data of four random populations (Nuevo León, Hispanics, Chihuahua, and Central Region of Mexico). A sample of 115 unrelated women with BrCa and whose four grandparents were born in five zones of Mexico were interviewed at a reference hospital in Northeastern Mexico. Noncodifying STRs D7S820, D13S317, and D16S39 were analyzed; genotype distribution was in agreement with Hardy-Weinberg expectations for all three markers. Similar allele frequencies among four random populations and this selected population were found. According with this and previous studies using molecular and nonmolecular nuclear DNA markers not associated with any disease, Mexican Mestizo population is genetically homogeneous and therefore, genetic causes of BrCa are less heterogeneous, simplifying genetic epidemiologic studies.

Characterization of mtDNA haplogroups in 14 Mexican indigenous populations.

In this descriptive study we investigated the genetic structure of 513 Mexican indigenous subjects grouped in 14 populations (Mixteca-Alta, Mixteca-Baja, Otomi, Purépecha, Tzeltal, Tarahumara, Huichol, Nahua-Atocpan, Nahua-Xochimilco, Nahua-Zitlala, Nahua-Chilacachapa, Nahua-Ixhuatlancillo, Nahua-Necoxtla, and Nahua-Coyolillo) based on mtDNA haplogroups. These communities are geographically and culturally isolated; parents and grandparents were born in the community. Our data show that 98.6% of the mtDNA was distributed in haplogroups A1, A2, B1, B2, C1, C2, D1, and D2. Haplotype X6 was present in the Tarahumara (1/53) and Huichol (3/15), and haplotype L was present in the Nahua-Coyolillo (3/38). The first two principal components accounted for 95.9% of the total variation in the sample. The mtDNA haplogroup frequencies in the Purépecha and Zitlala were intermediate to cluster 1 (Otomi, Nahua-Ixhuatlancillo, Nahua-Xochimilco, Mixteca-Baja, and Tzeltal) and cluster 2 (Nahua-Necoxtla, Nahua-Atocpan, and Nahua-Chilacachapa). The Huichol, Tarahumara, Mixteca-Alta, and Nahua-Coyolillo were separated from the rest of the populations. According to these findings, the distribution of mtDNA haplogroups found in Mexican indigenous groups is similar to other Amerindian haplogroups, except for the African haplogroup found in one population.

Genetic structure of seven Mexican indigenous populations based on five polymarker loci.

This descriptive study investigates the genetic structure of seven Mexican indigenous populations (Mixteca Alta, Mixteca Baja, Otomies, Purepecha, Nahuas-Guerrero, Nahuas-Xochimilco, and Tzeltales) on the basis of five PCR-based polymorphic DNA loci: LDLR, GYPA, HBGG, D7S8, and GC. Genetic distance and diversity analyses indicate that these Mexican indigenous are similar and that more than 96% of the total gene diversity (H(T)) can be attributed to individual variation within populations. Mixteca-Alta, Mixteca-Baja, and Nahuas-Xochimilco show indications of higher admixture with European-derived persons. The demonstration of a relative genetic homogeneity of Mexican Indians for the markers studied suggests that this population is suitable for studying disease-marker associations in the search for candidate genes of complex diseases.