MGEA5-14 polymorphism and type 2 diabetes in Mexico City.

A family-based study has recently reported that a variant located in intron 10 of the gene MGEA5 increases susceptibility to Type 2 Diabetes (T2D). We evaluated the distribution of this SNP in a sample of T2D patients (N = 271) and controls (N = 244) from Mexico City. The frequency of the T allele was higher in the cases (2.6%) than in the controls (1.8%). After adjusting for age, sex, BMI, education, and individual ancestry the odds ratio was 1.60 but the 95% confidence interval was wide and overlapped 1 (0.52-4.86, P-value : 0.404). In order to characterize the distribution of the MGEA5-14 polymorphism in the relevant parental populations, we genotyped this variant in European (and European Americans), West African, and Native American samples. The T-allele was present at a frequency of 2.3% in Spain, 4.2% in European Americans, and 13% in Western Africans, but was absent in two Native American samples from Mexico and Peru. Given the low frequency of the T-allele, further studies using large sample sizes will be required to confirm the role of this variant in T2D.

Correlation between molecular and conventional genealogies in Aicuña: a rural population from Northwestern Argentina.

Aicuña is a village in the northwest of Argentina, located about 300 km south of La Rioja city, in the province of La Rioja. The population of Aicuña derives from a founder couple established in the uninhabited Aicuña valley in the early years of the 17th century. Due to land ownership litigation, the descendants maintained a well-documented genealogy that extends for 12 generations, comprising more than 8,000 individuals. From the historical pedigree of Aicuña, we selected 14 males with direct patrilineal descent from the 2 most ancient male founders, and 23 donors (9 females and 14 males) with direct matrilineal descent from the most ancient female founder. All 3 founders lived in the 17th century. We collected DNA from buccal swabs and characterized the mitochondrial DNA (mtDNA) and Y haplotypes using 14 Y-specific markers, 11 mtDNA polymorphic markers and sequencing of the mt hypervariable regions 1 and 2. We found four different Y haplotypes: Y1 and Y2 haplotypes of European origin corresponding to the founder ancestors Francisco Páez de Espinoza and Apolinario Ormeño, which were shared by 6 and 3 donors, respectively. Three males selected as Ormeño patrilineal descendants showed a different Y haplotype (Y3), probably originated by erroneous paternity registration due to illegitimacy. The remaining case (haplotype Y4), also assumed to belong to the Ormeño lineage, was probably also due to an erroneously registered paternity. Twenty-two donors showed an association of mtDNA markers corresponding to the Amerindian haplotype A2. The founder of this matrilineage could be traced back for more than 14 generations. The haplotype B of one remaining female did not correspond with the historical pedigree and could be due to an error in the genealogy registration. Our results showed an 85% agreement between conventional and molecular genealogies, with mtDNA markers being Amerindian, and Y markers being European. The methodology used in this report is a tool which could potentially be employed as a precedent for land ownership by Aicuña villagers and Amerindian populations.

Origin of YAP+ lineages of the human Y-chromosome.

We screened a total of 841 Y-chromosomes representing 36 human populations of wide geographical distribution for the presence of a Y-specific Alu insert (YAP+ chromosomes). The Alu element was found in 77 cases. We tested 5 biallelic and 8 polyallelic markers in 70 out of the 77 YAP+ chromosomes. We could identify the existence of a hierarchical and chronological structuring of ancestral and derived YAP+ lineages, giving rise to 4 haplogroups, 14 subhaplogroups and 60 haplotypes. Moreover, we propose a monophyletic origin for each one of the YAP+ lineages. Out-of-Africa and out-of-Asia models have been suggested to explain the origin and evolution of ancestral and derived YAP+ elements. We analyze the evidence supporting these two hypotheses, and we conclude that the information available does not allow one to decide between the out-of-Asia or out-of-Africa models.

Characterization of ancestral and derived Y-chromosome haplotypes of New World native populations.

We analyze the allelic polymorphisms in seven Y-specific microsatellite loci and a Y-specific alphoid system with 27 variants (alphah I-XXVII), in a total of 89 Y chromosomes carrying the DYS199T allele and belonging to populations representing Amerindian and Na-Dene linguistic groups. Since there are no indications of recurrence for the DYS199C-->T transition, it is assumed that all DYS199T haplotypes derive from a single individual in whom the C-->T mutation occurred for the first time. We identified both the ancestral founder haplotype, 0A, of the DYS199T lineage and seven derived haplogroups diverging from the ancestral one by one to seven mutational steps. The 0A haplotype (5.7% of Native American chromosomes) had the following constitution: DYS199T, alphah II, DYS19/13, DYS389a/10, DYS389b/27, DYS390/24, DYS391/10, DYS392/14, and DYS393/13 (microsatellite alleles are indicated as number of repeats). We analyzed the Y-specific microsatellite mutation rate in 1,743 father-son transmissions, and we pooled our data with data in the literature, to obtain an average mutation rate of.0012. We estimated that the 0A haplotype has an average age of 22,770 years (minimum 13,500 years, maximum 58,700 years). Since the DYS199T allele is found with high frequency in Native American chromosomes, we propose that 0A is one of the most prevalent founder paternal lineages of New World aborigines.

Paternal directional mating in two Amerindian subpopulations located at different altitudes in northwestern Argentina.

We used mitochondrial DNA (mtDNA) and Y-chromosome DNA polymorphisms to analyze the ethnic origin of maternal and paternal lineages in two Amerindian subpopulations from northwestern Argentina. One of the subpopulations was from San Salvador de Jujuy, located 1200 m above sea level. The second subpopulation inhabits the Quebrada de Humahuaca area at altitudes ranging from 2500 to 3500 m. Both subpopulations have the same ethnic background. All mtDNA haplotypes were identified as Amerindian with a frequency of 64.6% of the B form (9-bp deletion in mtDNA region V). Because all Central Andean Amerindian populations studied so far exhibit high frequencies of the B haplotype, we propose that they probably are derived from a common ancestral population that inhabited the Central Andes 6000-8000 years B.P. The presence of paternal directional mating (asymmetric contribution of one parental lineage to interethnic gene mixtures) was demonstrated by the finding of an average introgression of 40.5% Spanish Y chromosomes into our Amerindian sample. This introgression was more evident at low altitude than at high altitude, with frequencies of 64.3% in San Salvador de Jujuy (low altitude) and 27.6% in Quebrada de Humahuaca (high altitude) (p < 0.05). The San Salvador de Jujuy subpopulation also showed a significantly higher Y-chromosome gene variability than the Quebrada de Humahuaca subpopulation. These findings are in good agreement with historical reports indicating that the colonization of South America was undertaken by men who usually practiced polygamous unions with Amerindian women and that San Salvador de Jujuy was the main northwestern Argentinian region of European to Amerindian gene admixture. We found 16.7% of cases with Spanish Y chromosomes and Amerindian family names, and the same percentage with Amerindian Y chromosomes and Hispanic names. The former group probably is the result of unions between Hispanic men, who transmitted the Y chromosome, and Amerindian women, who transmitted the family name to the progeny. The latter group likely illustrates the practice of changing names from Amerindian to Hispanic during the baptism of native Americans in colonial times.

Characterization of mitochondrial DNA and Y-chromosome haplotypes in a Uruguayan population of African ancestry.

We used a set of informative mtDNA and Y-chromosome-specific markers to determine the origin of maternal and paternal lineages in a sample of 41 Uruguayan black individuals. We found that 20 maternal lineages were African, 13 were Amerindian, and 5 were Caucasian. In three individuals we were unable to determine the ethnic origin of the mtDNA lineages. Of the 22 males analyzed we found 4 Y chromosomes of African origin, 5 of Caucasian origin, and 13 of undetermined ancestry. Our results suggest that mtDNA and Y-chromosome-specific DNA variants may be a useful tool in determining the level of mtDNA and Y chromosome ethnic introgression in a population of a given ethnic origin.

Origin of Amerindian Y-chromosomes as inferred by the analysis of six polymorphic markers.

We analysed the frequency of six Y-specific polymorphisms in 105 Amerindian males from seven different populations, 42 Caucasian males, and a small number of males of African, Chinese, and Melanesian origin. The combination of three of the six polymorphisms studied produced four different Y-haplogroups. The haplogroups A (non-variant) was the most frequent one. Eighty-five percent of Amerindians showing haplogroup A have the alphoid II (alpha hII) and the DYS19A Y-specific markers, an association that is found only in 10% of Caucasians and that has not been detected in Asiatics and Africans. Haplogroups C (YAP+) and D (YAP+ plus an A-->G transmission in the locus DYS271) are of African origin. Four percent of Amerindians and approximately 12% of Caucasians showed haplogroup C; approximately 1% of Amerindians and approximately 2% of Caucasians had haplogroup D. Haplogroup B is characterized by a C-->T transition in nucleotide position 373 of the SRY gene domain; this haplogroup is found in Caucasians (approximately 12%) and Amerindians (approximately 4%). None of the Amerindians exhibiting the haplogroups B, C, or D show the haplotype alpha hII/DYS19A. By haplotyping the the Alu insert and the DNA region surrounding the insert in YAP+ individuals, we could demonstrate that Amerindian Y chromosomes bearing African markers (haplogroups C and D) are due to recent genetic admixture. Most non-alpha hII/DYS19A Amerindian Y-chromosomes in haplogroup A and most cases in haplogroup B are also due to gene flow. We show that haplotype alpha hII/DYS19A is in linkage disequilibrium with a C-->T transition in the locus DYS19A. Our results suggest that most Amerindian Y-chromosomes derive from a single paternal lineage characterized by the alpha hII/DYS19A/DYS199T Amerindian-specific haplotype. The analysis of a larger sample of native American Y-chromosome will be required in order to confirm or correct this hypothesis.