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

Abstract

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.

Admixture and population structure in Mexican-Mestizos based on paternal lineages

“…13 Similarly, states with presumable higher African ancestry (that is, Veracruz and Guerrero) have not shown a significant increase; they have only presented the highest interpopulation genetic variance of this ancestry. 5 This also could be Genetic relationships and population structure In general, the significant paternal population structure inferred here was similar to that observed in a previous study based on Y-STRs in Mexican-Mestizos, 15 in which three main regions are distinguished, including the following: (1) north-west, (2) center-south and (3) southeast. Coincidentally, analysis of autosomal STRs has shown a similar structural pattern, 39 and for practical purposes this could be relevant for epidemiological or human identification purposes.…”

“…15 Interestingly, both studies based on Y-chromosome markers displayed similar increasing gradients of European and Native American ancestries toward the north, west, center-south and southeast, respectively. However, in the majority of the aforementioned states (3/5), we found differences in paternal ancestry proportions between Y-STR and Y-SNP admixture estimates (p p0.010480).…”

“…In fact, the paternal ancestry estimates obtained herein are more reliable and include a large number of populations compared to the previous Y-STR report. 15 This information is important for association studies concerning Y-linked diseases, such as infertility, some cancers, alcohol dependence, among others. 31,32 For human identification purposes, our results are relevant for selecting the correct population database for interpretation of Y-linked DNA profiles that generally are obtained with Y-STRs.…”

“…Exact tests were carried out in order to compare paternal admixture estimates (Y-SNPs) with those obtained from Y-STRs. 15 Exact tests were performed to check homogeneity of ancestral components among Mexican-Mestizos using RxC software. 24 Population structure was evaluated by analysis of molecular variance, 25 in addition to spatial analysis of molecular variance, which allows establishing population clusters incorporating genetic and geographical criteria.…”

“…11,12 The study of NRY biallelic variation for defining paternal lineages is particularly limited in Mestizos from Mexico and is even scarcer in Native American groups from this country. 13,14 Although the Y-STRs used in human identification have been employed to estimate paternal admixture in different Mexican-Mestizo populations, 15 these markers do not constitute the ideal tool for this purpose. 16 Available estimates based on Y-SNPs have been generated from a small number of populations, such as that of Mexico City, 17 and those of the states of Guerrero, 18 Jalisco 13 and Nuevo Leó n. 19 Moreover, with the exception of the latter report on Nuevo Leó n, the remaining studies were restricted to two or three Y-linked biallelic markers; thus, the wide diversity of paternal lineages evaluated by Y-SNPs is relatively unknown throughout the Mexican territory.…”