Admixture and genetic relationships of Mexican Mestizos regarding Latin American and Caribbean populations based on 13 CODIS-STRs.

Short tandem repeats (STRs) of the combined DNA index system (CODIS) are probably the most employed markers for human identification purposes. STR databases generated to interpret DNA profiles are also helpful for anthropological purposes. In this work, we report admixture, population structure, and genetic relationships of Mexican Mestizos with respect to Latin American and Caribbean populations based on 13 CODIS-STRs. In addition, new STR population data were included from Tijuana, Baja California (Northwest, Mexico), which represents an interesting case of elevated genetic flow as a bordering city with the USA. Inter-population analyses included CODIS-STR data from 11 Mexican Mestizo, 12 Latin American and four Caribbean populations, in addition to European, Amerindian, and African genetic pools as ancestral references. We report allele frequencies and statistical parameters of forensic interest (PD, PE, Het, PIC, typical PI), for 15 STRs in Tijuana, Baja California. This Mexican border city was peculiar by the increase of African ancestry, and by presenting three STRs in Hardy-Weinberg disequilibrium, probably explained by recurrent gene flow. The Amerindian ancestry in Central and Southeast of Mexico was the greatest in Latin America (50.9-68.6%), only comparable with the North of Central America and Ecuador (48.8-56.4%), whereas the European ancestry was prevalent in South America (66.7-75%). The African ancestry in Mexico was the smallest (2.2-6.3%) in Latin America (≥ 2.6%), particularly regarding Brazil (21%), Honduras (62%), and the Caribbean (43.2-65.2%). CODIS-STRs allowed detecting significant population structure in Latin America based on greater presence of European, Amerindian, and African ancestries in Central/South America, Mexican Mestizos, and the Caribbean, respectively.

Forensic parameters for 15 STRs in eight Amerindian populations from the north and west of Mexico.

Allele frequency distributions for 15 STR loci (AmpFlSTR Identifiler kit) were estimated in 825 volunteers of the following eight Mexican-Amerindian populations from two geographical regions: (1) North: Tarahumara (204), Mayo (45), Seri (28), and Guarijío (17); (2) Northwest: Tepehuano (123), Mexicanero (84), Cora (85), and Huichol (239). Genotype frequency distribution was in agreement with Hardy-Weinberg expectations for all 15 STRs, excepting for two loci (D13S317 and FGA) in the Huichol population. The power of discrimination and power of exclusion values were both larger than 0.99999. These STR databases will support the correct interpreting of DNA profiles in paternity testing and forensic cases in Mexican-Amerindian groups from these regions, until know poorly studied. Genetic distances and pairwise comparisons were estimated between populations. A significant genetic differentiation was observed between these Mexican-Amerindian groups (F(ST)=3.43%; p=0.0000) that was 10 times larger than the observed between Mestizos (F(ST)=0.34%), which represent most of the Mexican population (~90%). This result was in agreement with the incapability to cluster these Native American populations by geographic criteria. Pre-Colombian descriptions of Aridoamerica, including the North region of Mexico, suggest genetic drift effects to explain this noticeable population differentiation of Mexican-Amerindian groups.

Influence of admixture components on CYP2C9*2 allele frequency in eight indigenous populations from Northwest Mexico.

We previously documented the lowest frequency of CYP2C9*2 in Mexican indigenous Tepehuanos followed by Mestizos and Mexican-Americans populations, suggesting a negative correlation between the CYP2C9*2 frequency and the degree of Asian ancestry in indigenous Americans. We determined the influence of ethnic admixture components on the CYP2C9 allele distribution in 505 Amerindian from eight indigenous populations through genotyping CYP2C9*2, *3 and *6 alleles by real-time PCR and molecular evaluation of ancestry. The frequencies for CYP2C9*2 were 0.026 in Seris and 0.057 in Mayos, being higher than in Asians (P<0.001). CYP2C9*3 was found in Tarahumaras (0.104), Mayos (0.091), Tepehuanos (0.075), Guarijíos (0.067), Huicholes (0.033) and Coras (0.037), with East Asians having lower frequencies than the former three groups (P<0.001). CYP2C9*6 was not found. The frequency of CYP2C9*2 was lower in Amerindians than in European populations, and higher than their Asian ancestors. The presence of this allele in ethnic groups in Mexico can be explained by European admixture.

Deletion mapping and paternal origin of a Mexican AMELY negative male.

The amelogenin represents the gender marker most widely used for human identification and biomedical purposes. However, some failures in sex-typing have been observed globally. In this study, we could approximate the population frequency of AMELY negative males in 1230 individuals from five states of Mexico (0.081%). For the sole AMELY negative male detected, we constructed a deletion map by means of 10 markers (7 STS and 3 Y-STRs). This allowed classifying the case into the most common category (Class I deletion), according to the nomenclature proposed by Jobling et al. (2007). Interestingly, the Mexican sample was R1a1(∗), a Y-chromosome haplogroup non-previously reported for AMELY negative cases. The geographic distribution of R1a1(∗), and the Y-STR haplotype similarity with a reported case from Slovenia, suggests an Eastern-Europe paternal origin for this case from Mexico. To our knowledge, this is the first report in Latin America that implies a low population frequency and European paternal origin of AMELY negative cases.

Origin and genetic differentiation of three Native Mexican groups (Purépechas, Triquis and Mayas): contribution of CODIS-STRs to the history of human populations of Mesoamerica.

BACKGROUND: CODIS-STRs in Native Mexican groups have rarely been analysed for human identification and anthropological purposes. AIM: To analyse the genetic relationships and population structure among three Native Mexican groups from Mesoamerica. SUBJECTS AND METHODS: 531 unrelated Native individuals from Mexico were PCR-typed for 15 and 9 autosomal STRs (Identifiler™ and Profiler™ kits, respectively), including five population samples: Purépechas (Mountain, Valley and Lake), Triquis and Yucatec Mayas. Previously published STR data were included in the analyses. RESULTS: Allele frequencies and statistical parameters of forensic importance were estimated by population. The majority of Native groups were not differentiated pairwise, excepting Triquis and Purépechas, which was attributable to their relative geographic and cultural isolation. Although Mayas, Triquis and Purépechas-Mountain presented the highest number of private alleles, suggesting recurrent gene flow, the elevated differentiation of Triquis indicates a different origin of this gene flow. Interestingly, Huastecos and Mayas were not differentiated, which is in agreement with the archaeological hypothesis that Huastecos represent an ancestral Maya group. Interpopulation variability was greater in Natives than in Mestizos, both significant. CONCLUSION: Although results suggest that European admixture has increased the similarity between Native Mexican groups, the differentiation and inconsistent clustering by language or geography stresses the importance of serial founder effect and/or genetic drift in showing their present genetic relationships.

Population structure and paternal admixture landscape on present-day Mexican-Mestizos revealed by Y-STR haplotypes.

Mestizos currently represent most of the Mexican population (>90%); they are defined as individuals born in the country having a Spanish-derived last name, with family antecedents of Mexican ancestors back at least to the third generation. Mestizos are result of 500 years of admixture mainly among Spaniards, Amerindians, and African slaves. Consequently, a complex genetic pattern has been generated throughout the country that has been scarcely studied from the paternal point of view. This fact is important, taking into account that gene flow toward the New World comprised largely males. We analyzed the population structure and paternal admixture of present-day Mexican-Mestizo populations based on Y-STRs. We genotyped at least 12 Y-STRs in DNA samples of 986 males from five states: Aguascalientes (n = 293); Jalisco (n = 185); Guanajuato (n = 168); Chiapas (n = 170); and Yucatán (n = 170). AmpFlSTR Y-filer and Powerplex-Y(R) kits were used. Inclusion of North and Central Y-STR databases in the analyses allowed obtaining a Y-STR variability landscape from Mexico. Results confirmed the population differentiation gradient previously noted in Mestizos with SNPs and autosomal STRs throughout the Mexican territory: European ancestry increments to the Northwest and, correspondingly, Amerindian ancestry increments to the Center and Southeast. In addition, SAMOVA test and Autocorrelation Index for DNA Analysis autocorrelogram plot suggested preferential gene flow of males with neighboring populations in agreement with the isolation-by-distance model. Results are important for disease-risk studies (principally male-related) and for human identification purposes, because Y-STR databases are not available on the majority of Mexican-Mestizo populations.