The Early Peopling of the Philippines based on mtDNA

Despite the eforts made to reconstruct the history of modern humans, there are still poorly explored regions that are key for understanding the phylogeography of our species. One of them is the Philippines, which is crucial to unravel the colonization of Southeast Asia and Oceania but where little is known about when and how the frst humans arrived. In order to shed light into this settlement, we collected samples from 157 individuals of the Philippines with the four grandparents belonging to the same region and mitochondrial variants older than 20,000 years. Next, we analyzed the hypervariable I mtDNA region by approximate Bayesian computation based on extensive spatially explicit computer simulations to select among several migration routes towards the Philippines and to estimate population genetic parameters of this colonization. We found that the colonization of the Philippines occurred more than 60,000 years ago, with long-distance dispersal and from both north and south migration routes. Our results also suggest an environmental scenario especially optimal for humans, with large carrying capacity and population growth, in comparison to other regions of Asia. In all, our study suggests a rapid expansion of modern humans towards the Philippines that could be associated with the establisment of maritime technologies and favorable environmental conditions

Influence of Genetic Admixture Components on CYP3A5*3 Allele-Associated Hypertension in Amerindian Populations From Northwest Mexico

CYP3A5 metabolizes endogenous substrates and ~30% of prescription drugs. The CYP3A5 gene contains an active CYP3A5*1 allele, and a non-functional version, the CYP3A5*3 (rs776746), with consequences for drug therapeutic responses and side effects. Both CYP3A5*1 and *3 have been associated with hypertension. The frequency of CYP3A5*3 varies between populations of different ancestries, with Europeans having the highest allele frequency (> 90%). Given the importance of CYP3A5*3 in drug response and hypertension development, the aim of the present study was to evaluate the frequency of this polymorphism and its association with hypertension in vulnerable indigenous populations in Mexico. A total of 372 subjects were recruited from eight ethnic groups in Northwest Mexico. Systolic (SBP), diastolic (DBP), and median (MBP) blood pressures as well as body mass index (BMI) were measured. Ancestry was evaluated through STR analysis, and the CYP3A5*1/*3 polymorphisms were identified using real-time PCR with TaqMan® probes. Higher frequencies of CYP3A5*1 and *3 were observed in groups with higher (>90%) and lower (<90%) Amerindian ancestry, respectively. The CYP3A5*3/*3 genotype was more frequent in indigenous women with higher SBP and DBP values. On the other hand, the *1 allele showed a protective effect against both high SBP (OR, 0.38; 95% CI, 0.17–0.83, p = 0.001) and DBP (OR 0.38, 95% CI 0.18–0.81, p = 0.007) in women. This association remained significant after adjusting for BMI and age for diastolic (OR, 0.38; 95% CI, 0.17–0.84, p = 0.011) and systolic BP (OR, 0.33; 95% CI, 0.15–0.76, p = 0.005) BP levels in women. Thus, the frequency of CYP3A5*3 varies between groups and seems to depend on ancestry, and CYP3A5*1 decreases the risk of hypertension in Mexican indigenous women. This population analysis of CYP3A5*1/*3 has profound implications not only for the susceptibility to diseases, such as hypertension, but also for safer drug administration regimens, assuring better therapeutic responses and fewer side effects

Online calculator for individual affiliation to a major population group

Because of their sensitivity and high level of discrimination, short tandem repeat (STR) maker systems are currently the method of choice in routine forensic casework and data banking, usually in multiplexes up to 15–17 loci. Constraints related to sample amount and quality, frequently encountered in forensic casework, will not allow to change this picture in the near future, notwithstanding the technological developments. In this study, we present a free online calculator named PopAffiliator (http://cracs.fc.up.pt/popaffiliator) for individual population affiliation in the three main population groups, Eurasian, East Asian and sub-Saharan African, based on genotype profiles for the common set of STRs used in forensics. This calculator performs affiliation based on a model constructed using machine learning techniques. The model was constructed using a data set of approximately fifteen thousand individuals collected for this work. The accuracy of individual population affiliation is approximately 86%, showing that the common set of STRs routinely used in forensics provide a considerable amount of information for population assignment, in addition to being excellent for individual identification

Association of the 5HTTLPR Polymorphism with Obesity in Mexican Women with High Native American Ancestry

Aims: The 5HTT gene has been associated with obesity; this study aimed to determine the association between L- and S-alleles at the 5HTTLPR polymorphism with obesity in indigenous Mexican populations. Materials and Methods: A total of 362 individuals, 289 belonging to eight Native American (NA) groups; 40 Mexican mestizos; and 33 Caucasian Mennonites were enrolled in a cross-sectional study. High (≥90%) and low (30 kg/m2 was considered as obese. The L- and S-alleles of the 5HTTLPR locus were identified by PCR; the association between alleles and obesity was performed by logistic regression analysis. Results: A significantly lower prevalence of obesity (35%) was observed in participants from communities with high NA ancestry (p < 0.005). Under a dominant heritance model the L-allele was associated with obesity in women with high NA ancestry (odds ratio [OR] 7.27; 95% confidence interval [CI] 1.6–32.5; p = 0.009) but not in women with low NA ancestry (OR 0.83; 95% CI 0.3–2.2; p = 0.71); no association was observed in men. Conclusion:Our results suggest that the 5HTTLPR L-allele is a risk factor for developing obesity in Mexican women with high NA ancestry (≥90%)

Demographic History of Indigenous Populations in Mesoamerica Based on mtDNA Sequence Data

The genetic characterization of Native American groups provides insights into their history and demographic events. We sequenced the mitochondrial D-loop region (control region) of 520 samples from eight Mexican indigenous groups. In addition to an analysis of the genetic diversity, structure and genetic relationship between 28 Native American populations, we applied Bayesian skyline methodology for a deeper insight into the history of Mesoamerica. AMOVA tests applying cultural, linguistic and geographic criteria were performed. MDS plots showed a central cluster of Oaxaca and Maya populations, whereas those from the North and West were located on the periphery. Demographic reconstruction indicates higher values of the effective number of breeding females (Nef) in Central Mesoamerica during the Preclassic period, whereas this pattern moves toward the Classic period for groups in the North and West. Conversely, Nef minimum values are distributed either in the Lithic period (i.e. founder effects) or in recent periods (i.e. population declines). The Mesomerican regions showed differences in population fluctuation as indicated by the maximum Inter-Generational Rate (IGRmax): i) Center-South from the lithic period until the Preclassic; ii) West from the beginning of the Preclassic period until early Classic; iii) North characterized by a wide range of temporal variation from the Lithic to the Preclassic. Our findings are consistent with the genetic variations observed between central, South and Southeast Mesoamerica and the North-West region that are related to differences in genetic drift, structure, and temporal survival strategies (agriculture versus hunter-gathering, respectively). Interestingly, although the European contact had a major negative demographic impact, we detect a previous decline in Mesoamerica that had begun a few hundred years before

Relación del polimorfismo TaqI del gen del receptor de la vitamina D con la lepra lepromatosa en población mexicana Association between the TaqI polymorphism of Vitamin D Receptor gene and lepromatous leprosy in a Mexican population sample

OBJETIVO: Determinar la relación del polimorfismo TaqI del gen del receptor de la vitamina D (RVD) con la lepra lepromatosa (LL) en individuos originarios de Sinaloa, México. MATERIAL Y MÉTODOS: Se amplificó un fragmento de 740 pb del gen RVD en muestras de ADN de 71 pacientes con LL y 144 controles en el Hospital General de Culiacán durante el periodo 2004-2007. El polimorfismo se identificó mediante la endonucleasa TaqI. RESULTADOS: Se observó un aumento de relevancia estadística del genotipo TT en pacientes con LL en comparación con los controles (p= 0.040; RM= 1.82). CONCLUSIÓN: Se demuestra un nexo entre el genotipo TT y la susceptibilidad a la LL.<br>OBJETIVE: To establish the association of the vitamin D receptor gene TaqI polymorphism with lepromatous leprosy (LL) in individuals from Sinaloa, Mexico. MATERIAL AND METHODS: A 740 bp fragment was amplified from the VDR gene in DNA samples of 71 patients with LL and 144 controls in the Hospital General de Culiacán during 2004-2007. Polymorphism was identified through TaqI endonuclease. RESULTS: A significant increase in the genotype TT of the VDR gene was observed in patients when compared to controls (p = 0.040; OR = 1.82). CONCLUSIONS: Our data support the association between the TT genotype and susceptibility to LL in this Mexican population

Forensic parameters and admixture in seven geographical regions of the Guerrero state (South, Mexico) based on STRs of the Globalfiler® kit

Background: New commercial STR kits have emerged with greater numbers of markers, which allows for obtaining stronger conclusions in forensic casework, which has been poorly studied in Mexico. Aim: To obtain forensic parameters and to analyse the genetic relationships, structure and admixture in seven geographic regions of Guerrero state (South, Mexico) based on the Globalfiler® kit. Subjects and methods: A total of 245 unrelated Mexican individuals from seven regions of the state of Guerrero were analysed with the Globalfiler® kit. Forensic parameters, pairwise comparisons, genetic distances, structure analysis and admixture levels were estimated. Results: Allele frequencies and forensic parameters of 22 STRs were estimated in this Mexican population sample. The combined power of exclusion and power of discrimination values were > 99.9999% and >99.99999999%, respectively. The Native American, European and African ancestries estimated in the Guerrero state population were 70.9%, 25.9% and 3.2%, respectively. Conclusion: Forensic validation of the Globalfiler® kit was performed in the Guerrero state population. The geographic isolation level seems to be the principal factor in defining genetic relationships and admixture among the Guerrero sub-populations. Despite the intrinsic limitations of STRs for admixture analysis, these results are very close to previous values based on AIMs and genome-wide SNPs

Exploring the African genetic influence in the first settlement founded by African slaves in America

The present study aims to outline the genetic makeup of the current population of the town of Yanga (Veracruz State, Mexico), the first Latin American settlement founded by African slaves in Mexico. For this purpose, we carried out the genetic characterization of 60 individuals from Yanga, analysing 15 autosomal short tandem repeats (STRs) and interpreting the results in the context of the admixed population known as Mexican mestizos. The genetic contribution from the three most important human groups in the current admixed Yanga population was calculated using Structure software. We detected a high percentage of Amerindian (48%) and European inheritance (44.7%), and a much less important African contribution (7.3%). These results were then compared with 10 other Mexican mestizo populations. The results fit the tri-hybrid model for admixture characterized by a high genetic contribution from Europeans and Africans in the north—though the African influence is lower—and a decreasing contribution from these two populations to the south and southeast. Conversely, the Amerindian component presents maximum values in the south and minimum values in the north. The Amerindian and European genetic traces are related to their ancestral settlements, but the African contribution can be explained by other parameters. To understand the current African genetic traces, we have to assume that there was a redistribution of these population groups and an important admixture phenomenon which led to the dilution of the African ancestral genetic pool. Furthermore, admixture was favoured by conditions that allowed individuals who intermarried to ascend in social status. These reasons would explain why despite the fact that Yanga was founded by black slaves, high levels of African ancestry are not found in the current population