Genetic Characterization of Indigenous Peoples from Oaxaca, Mexico, and Its Relation to Linguistic and Geographic Isolation

Zellweger's Syndrome With PEX6 Gene Mutation in Mixteco Neonates Due to Possible Founder Effect

Zellweger spectrum disorder (ZSD) is a group of autosomal recessive peroxisomal disorders caused by PEX gene mutations that commonly present with symptoms of severe hypotonia, epileptic seizures, failure to thrive, hepatomegaly, craniofacial dysmorphisms, and sensorineural hearing loss. This article highlights three patients born with ZSD in Central California. All three patients were born to Mixteco mothers. Patients were genetically analyzed, which revealed mutations that correspond to ZSD. They presented with hypotonia at birth, abnormal hepatic panels, and increased fatty acid levels, findings consistent with Zellweger syndrome (ZS). However, only two of three patients displayed sensorineural hearing loss. Two of the patients failed to survive more than one year of age, which reflects the average life expectancy of an infant presenting with ZS. Observed and recorded cases of ZS in the Mixteco population have been postulated to be related to consanguinity and/or a founder effect. Studies have shown that autosomal recessive diseases are more prevalent in consanguineous populations. Consanguinity has been denied by patient 1 and is unknown for patients 2 and 3. Founder mutations have been implicated in areas with high rates of autosomal recessive diseases. All three of our Mixteco patients share a distinct lineage as well as a mutation at PEX6, leading us to believe that they suffered from an inherited founder mutation. The Mixteco population is not studied well enough to come to a definitive conclusion; however, the recognition of the relationship between ZS and Mixteco background is important, as it allows parents to plan accordingly and increases awareness in the community.

Fanconi Anemia Patients from an Indigenous Community in Mexico Carry a New Founder Pathogenic Variant in FANCG

Fanconi anemia (FA) is a rare genetic disorder caused by pathogenic variants (PV) in at least 22 genes, which cooperate in the Fanconi anemia/Breast Cancer (FA/BRCA) pathway to maintain genome stability. PV in FANCA, FANCC, and FANCG account for most cases (~90%). This study evaluated the chromosomal, molecular, and physical phenotypic findings of a novel founder FANCG PV, identified in three patients with FA from the Mixe community of Oaxaca, Mexico. All patients presented chromosomal instability and a homozygous PV, FANCG: c.511-3_511-2delCA, identified by next-generation sequencing analysis. Bioinformatic predictions suggest that this deletion disrupts a splice acceptor site promoting the exon 5 skipping. Analysis of Cytoscan 750 K arrays for haplotyping and global ancestry supported the Mexican origin and founder effect of the variant, reaffirming the high frequency of founder PV in FANCG. The degree of bone marrow failure and physical findings (described through the acronyms VACTERL-H and PHENOS) were used to depict the phenotype of the patients. Despite having a similar frequency of chromosomal aberrations and genetic constitution, the phenotype showed a wide spectrum of severity. The identification of a founder PV could help for a systematic and accurate genetic screening of patients with FA suspicion in this population.

Genetic diversity, structure, and admixture in Mayans from Guatemala and Mexico based on 15 short tandem repeats

OBJECTIVE

To analyze the genetic origin, relationships, structure, and admixture in Mayan Native American groups from Guatemala and Mexico based on 15 autosomal short tandem repeats (STRs) loci commonly used in human identification (HID).

METHODS

We genotyped 513 unrelated Mayan samples from Guatemala based on 15 STR loci (AmpFlSTR® Identifiler kit). Moreover, we included 4408 genotypes previously reported, as following: Mayas from Guatemala and Mexico (n = 1666) and from Latin American, European, and African (n = 2742) populations. Forensic parameters, genetic distances, admixture, and population structure were assessed.

RESULTS

Forensic parameters of the 15 STRs in different Mayan groups from Guatemala were reported. Low (Fst = 0.78%; p = 0.000) and non-significant differentiation (Fst = 1.8%; p = 0.108) were observed in Mayas from Guatemala and Mexico, respectively. The relative homogeneity observed among Mayan groups supported theories of extensive pre-Columbian gene flow and trade throughout the Mayan Empire. The distribution of the three Native American ancestries among these Mayan groups did not support the presumable Guatemalan origin of Tojolabal and Lacandon people (South, Mexico). The nonsignificant differentiation between Ladinos and Mayas suggests a relative panmixia in Guatemala. Mestizos from southeastern Mexico and Guatemala constitute a core of Native American ancestry in Latin America related to the Mayan Empire in Central America.

CONCLUSIONS

The higher European admixture and homogeneity in Mexican Mayas of the Yucatan Peninsula suggest more intensive post-Columbian gene flow in this region than in Guatemalan Mayas.

Importance of the geographic barriers to promote gene drift and avoid pre- and post-Columbian gene flow in Mexican native groups: Evidence from forensic STR Loci

OBJECTIVE

To analyze the origin, structure, relationships, and recent admixture in Mexican Native groups based on 15 STRs commonly used in human identification.

METHODS

We analyzed 39 Mexican Native population samples using STR databases based on the AmpFlSTR® Identifiler kit (n = 3,135), including Mexican-Mestizos (admixed), European and African populations, as reference.

RESULTS

Based upon effective population size (Ne) differences, Native groups were clustered into three regions: i) Center-Southeast groups, characterized by larger Ne, migration rate (Nm), genetic diversity (He), and relative homogeneity principally in the Yucatan Peninsula; ii) Isolated southern groups from Chiapas and Oaxaca, characterized by lower Ne, Nm, and He (i.e. higher isolation and genetic differentiation); iii) North-Northwest groups, which are similar to the previous group but are characterized by generating the widest gene flow barrier in the Pre-Hispanic Mexican territory, and currently by elevated admixture in some northern Native groups. Despite the relative congruence between genetic relationships with cultural, linguistic, geographic criteria, these factors do not explain the present-day population structure of Native groups, excepting in those linguistically related to the Mayan that show higher homogeneity. The Isolation by distance model was demonstrated at long distances (>1,500 km), whereas geographic isolation stands as a determining factor to avoid both non-indigenous admixture and bottleneck processes.

CONCLUSIONS

Different dynamics of gene flow and drift were observed among Mexican Native groups, highlighting the geographic barriers (mountains, canyons and jungle regions) as the main factor differentiating Pre-Hispanic populations, and eventually helping to avoid Post-European contact admixture and population bottleneck. Am J Phys Anthropol 160:298-316, 2016. © 2016 Wiley Periodicals, Inc.

Cytochrome P450 genetic polymorphisms of Mexican indigenous populations

This review focuses on the genetic polymorphisms of the cytochrome P450 (CYP) genes in Mexican indigenous populations, who are a part of the wide ethnic diversity of this country. These native groups have a particular historical trajectory that is different from the Mexican Mestizos. This variability may be reflected in the frequency distribution of polymorphisms in the CYP genes that encode enzymes involved in the metabolism of drugs and other xenobiotics. Therefore, these polymorphisms may affect drug efficacy and safety in indigenous populations in Mexico. The present study aimed to analyze the prevalence of CYP polymorphisms in indigenous Mexicans and to compare the results with studies in Mexican Mestizos. Because the extrapolation of pharmacogenetic data from Mestizos is not applicable to the majority of indigenous groups, pharmacogenetic studies directed at indigenous populations need to be developed. The Amerindians analyzed in this study showed a low phenotypic (CYP2D6) and genotypic (CYP2D6, CYP2C9) diversity, unlike Mexican Mestizos. The frequency of polymorphisms in the CYP1A1, CYP2C19, CYP2E1, and CYP3A4 genes was more similar among the Amerindians and Mexican Mestizos, with the exception of the CYP1A2 gene, whose *1F variant frequency in Mexican Amerindians was the highest described to date.

Altitude effects on growth of indigenous children in Oaxaca, Southern Mexico

The effect of altitude of residence on the growth status of 11,454 indigenous school children 6-14 years of age in Oaxaca, southern Mexico, was examined. Indicators of living conditions (human development index [HDI], index of community nutritional risk [INR], index of marginalization [IM], index of relative isolation [II]) were regressed on z-scores for height, weight and BMI, and the residuals were regressed on altitude of residence (km). Independent of other environmental conditions, altitude negatively affected height by approximately -0.07 z-scores per kilometer altitude above sea level. The estimated average decrease in stature was 0.92 cm per kilometer elevation. BMI was significantly increased, 1.2 units per kilometer elevation, consistent with earlier studies of growth status and altitude. In contrast, weight was not affected by altitude of residence. Approximately 36% of the reduction in height and 54% of the increase in BMI were due to altitude effects; the remaining changes in height and BMI were associated with environmental factors reflected in the indices of community well-being considered.