Genetic Overview of the Maya Populations: Mitochondrial DNA Haplogroups.

We identified mitochondrial DNA haplogroups A, B, C, and D in 75 present-day Maya individuals, 24 Maya individuals of the colonial period, and 1 pre-Columbian Maya individual from Quintana Roo, Mexico. We examined these data together with those of 21 Maya populations reported in the literature, comprising 647 present-day Maya individuals and 71 ancient Maya individuals. A demographic study based on analysis of fertility and endogamy was carried out in two modern Maya populations to identify cultural factors that influence the mitochondrial haplogroup genetic diversity. Most present-day and ancient Maya populations show a distribution pattern of mitochondrial haplogroup frequencies A, C, B, and D in decreasing order, with haplogroup D absent in several populations. Considering only modern Maya populations with at least 50 individuals analyzed, the present-day Tzotzil and Lacandon populations from Chiapas show the highest and lowest genetic diversity, 0.706 and 0.025, respectively. Our results show small genetic differences between the Maya populations, with the exception of the present-day Tojolabal and Lacandon populations from Chiapas. The present-day Lacandon population from Chiapas differs from other Maya populations in showing almost only haplogroup A. This result suggests a long history of isolation and endogamy as well as a possible founder effect inside the Lacandonian rain forest. The contemporary Tojolabal population is the only one with an unusual mitochondrial haplogroup pattern, exhibiting a frequency of haplogroup B higher than A and the absence of haplogroup C. With a small sample size, the pre-Columbian Copán Maya show a high content of haplogroup C and a low frequency of haplogroup D. The genetic homogeneity of the Maya populations is indicative of a common origin and nearly continuous gene flow in the long term within a general isolation of the whole group, in contrast to the Nahua populations that had different origins. Our demographic study showed high fertility rates and high levels of endogamy in the present-day Maya populations from Quintana Roo that are consistent with their general low genetic diversity. We propose that the genetic similarity among ancient and present-day Maya populations persists due to a strong sense of social cohesion and identity that impacts their marriage practices, keeping this cultural group isolated. These factors have constrained gene flow inside the Maya region and have impeded the differentiation among the Maya. Discernment of genetic differentiation within the peninsula is constrained by the lack of sampling documentation in the literature.

Genetic Diversity and Differentiation in Urban and Indigenous Populations of Mexico: Patterns of Mitochondrial DNA and Y-Chromosome Lineages.

Aside from the admixture between indigenous people and people from overseas, populations in Mexico changed drastically after the Spanish conquest of the sixteenth century, forming an intricate history that has been underutilized in understanding the genetic population structure of Mexicans. To infer historical processes of isolation, dispersal, and assimilation, we examined the phylogeography of mitochondrial (mt) DNA and Y-chromosome lineages in 3,026 individuals from 10 urban and nine indigenous populations by identifying single nucleotide polymorphisms. A geographic array with a predominance of Amerindian lineages was observed for mtDNA, with northern indigenous populations being divergent from the central and southern indigenous populations; urban populations showed low differentiation with isolation by distance. Y-chromosome variation distinguished urban and indigenous populations through the Amerindian haplogroup Q frequency. The MtDNA and the Y-chromosome together primarily distinguished urban and indigenous populations, with different geographic arrays for both. Gene flow across geographical distance and between the urban and indigenous realms appears to have altered the pre-Hispanic phylogeography in central and southern Mexico, mainly by displacement of women, while maintaining the indigenous isolation in the north, southeast, and Zapotec regions. Most Amerindian mtDNA diversity currently occurs in urban populations and appears to be reduced among indigenous people.

Haplotype and nucleotide variation in the exon 3-VNTR of the DRD4 gene from indigenous and urban populations of Mexico.

OBJECTIVE: To describe the population structure of the 48-bp variable number of tandem repeats (VNTR), located in exon 3 of the dopamine receptor D4 gene (DRD4), in 41 Tarahumara from northern Mexico, 20 Mixe from southern Mexico, and 169 people from Mexico City. METHODS: Genotypes for the DRD4-VNTR were determined, from which 15 Tarahumara, eight Mixe, and 37 urban homozygous individuals were sequenced. Repeat-allele frequencies were compared with other world populations. RESULTS: The DRD4-VNTR variation in Mexico City appeared similar to the world mean. For the Mixe and Maya, DRD4-VNTR diversity appeared closer to South American groups whereas the Tarahumara were similar to North American groups. People from Mexico City and the Mixe exhibited attributes of a large and admixed population and an isolated population, respectively. The Tarahumara showed endogamy associated with a substructure as suggested by a preliminary regional differentiation. For the DRD4-VNTR and/or the adjacent 5'-173 bp sequence, the three populations exhibited negative Tajima's D. Two new VNTR haplotypes were discovered: one in Mexico City and another among the Tarahumara. CONCLUSIONS: A differentiation in the DRD4-VNTR of global relevance occurs between northern and southern populations of Mexico suggesting that the Mexican Trans-volcanic Belt has been a major frontier for human dispersion in the Americas. Ancient trespass of this barrier appears thus related to a major change in the population structure of the DRD4-VNTR. Distinctive and independent patterns of DRD4-VNTR diversity occur among the two Mexican indigenous populations by a still undefined combination of drift and selection.

Evolution of the MHC-DQB exon 2 in marine and terrestrial mammals.

On the basis of a general low polymorphism, several studies suggest that balancing selection in the class II major histocompatibility complex (MHC) is weaker in marine mammals as compared with terrestrial mammals. We investigated such differential selection among Cetacea, Artiodactyla, and Primates at exon 2 of MHC-DQB gene by contrasting indicators of molecular evolution such as occurrence of transpecific polymorphisms, patterns of phylogenetic branch lengths by codon position, rates of nonsynonymous and synonymous substitutions as well as accumulation of variable sites on the sampling of alleles. These indicators were compared between the DQB and the mitochondrial cytochrome b gene (cytb) as a reference of neutral expectations and differences between molecular clocks resulting from life history and historical demography. All indicators showed that the influence of balancing selection on the DQB is more variable and overall weaker for cetaceans. In our sampling, ziphiids, the sperm whale, monodontids and the finless porpoise formed a group with lower DQB polymorphism, while mysticetes exhibited a higher DQB variation similar to that of terrestrial mammals as well as higher occurrence of transpecific polymorphisms. Different dolphins appeared in the two groups. Larger variation of selection on the cetacean DQB could be related to greater stochasticity in their historical demography and thus, to a greater complexity of the general ecology and disease processes of these animals.