Elsevier

HOMO

Volume 66, Issue 1, February 2015, Pages 44-59
HOMO

Admixture and genetic relationships of Mexican Mestizos regarding Latin American and Caribbean populations based on 13 CODIS-STRs

https://doi.org/10.1016/j.jchb.2014.08.005Get rights and content

Abstract

Short tandem repeats (STRs) of the combined DNA index system (CODIS) are probably the most employed markers for human identification purposes. STR databases generated to interpret DNA profiles are also helpful for anthropological purposes. In this work, we report admixture, population structure, and genetic relationships of Mexican Mestizos with respect to Latin American and Caribbean populations based on 13 CODIS-STRs. In addition, new STR population data were included from Tijuana, Baja California (Northwest, Mexico), which represents an interesting case of elevated genetic flow as a bordering city with the USA. Inter-population analyses included CODIS-STR data from 11 Mexican Mestizo, 12 Latin American and four Caribbean populations, in addition to European, Amerindian, and African genetic pools as ancestral references. We report allele frequencies and statistical parameters of forensic interest (PD, PE, Het, PIC, typical PI), for 15 STRs in Tijuana, Baja California. This Mexican border city was peculiar by the increase of African ancestry, and by presenting three STRs in Hardy–Weinberg disequilibrium, probably explained by recurrent gene flow. The Amerindian ancestry in Central and Southeast of Mexico was the greatest in Latin America (50.9–68.6%), only comparable with the North of Central America and Ecuador (48.8–56.4%), whereas the European ancestry was prevalent in South America (66.7–75%). The African ancestry in Mexico was the smallest (2.2–6.3%) in Latin America (≥2.6%), particularly regarding Brazil (21%), Honduras (62%), and the Caribbean (43.2–65.2%). CODIS-STRs allowed detecting significant population structure in Latin America based on greater presence of European, Amerindian, and African ancestries in Central/South America, Mexican Mestizos, and the Caribbean, respectively.

Introduction

The microsatellites or short tandem repeats (STRs) have demonstrated to be useful for linkage and segregation analyses, and human and non-human (e.g. dogs and cattle) identification. This is due to their elevated heterozygosity, genome abundance, high mutation rate, and simple analysis based on the polymerase chain reaction (PCR) (Butler, 2006). For anthropological purposes, their high mutation rate allows approaching historical questions such as admixture, structure, and migratory events, among others (Wang et al., 2008). Probably, STRs used in forensic and paternity testing are the most commonly employed markers, specifically the core of 13 STRs that comprise the combined DNA index system (CODIS). The inclusion of CODIS-STRs in commercial human identification kits has increased the number of population databases that can be used in molecular anthropology studies (Butler, 2006).

The admixture process presupposes the contact of ancestral populations that have been previously in relative isolation from each other and generated hybrid populations, whereas the population structure implies differences between individuals of one or more populations. This knowledge is essential in tasks such as association mapping, forensic casework, disease susceptibility prediction, wildlife management, and evolutionary studies (Sans, 2000). In Latin-America, hybrid populations have emerged since the European contact with the New World in 1492, and currently reflect a complex genetic structure from old and recent admixture processes (Bryc et al., 2010, Wang et al., 2008). In Mexico, the European colonization began in 1519, when Spaniards arrived to the Southeast; they crossed the current state of Tabasco and settled in Veracruz. After the conquest, about 85% of the Spaniards remained in conquered territory. Based on historical records, their origins are described as follows: 33% from Andalusia, 51% from Leon, Extremadura, the Old and New Castile, 14% from other regions of Spain, and some foreigners (6.2%) mainly from Portugal and Genoa, Italy (Grunberg, 2004). In Mexico, in addition to the European component, African ancestry was incorporated subsequently by means of slave trading from various African countries, such as Cabo Verde, Guinea, and Congo (Aguirre-Beltrán, 1989). In fact, studies of mitochondrial DNA (mtDNA) suggest that West and West-Central Africa regions are the most important providers of African ancestry in Central America and North America (Salas et al., 2004). Nevertheless, African genes could have also arrived in Mexico by Spanish migrants with Moorish ancestry, which in turn, was a result of the Islamic occupation of Iberian Peninsula (Gerard et al., 2006).

Currently, most of the Mexican population speaks Spanish and is the result of admixture between Spaniards, Native Americans and African populations through approx. 500 years. They are called Mestizos and predominantly disclose the European and Native American components, with low levels of African ancestry (<5%) (Bryc et al., 2010, Silva-Zolezzi et al., 2009). However, a Mexican Mestizo is defined as a person born in the country, having a Spanish-derived last name, with family antecedents of Mexican ancestors, at least back to the third generation (Sánchez-Serrano, 1996). A tri-hybrid model has been used to explain the biological diversity of Mexican-Mestizos, where specific ancestral components increase in different geographical areas: European in the North, Amerindian in the Center and Southeast, and the African in the coast. This model has been illustrated in a tripolar diagram where the edges are very narrow, indicating a negligible number of individuals “genetically pure” of any of the three ancestries (Gorodezky et al., 2001).

The admixture analysis in Latin America shows a complex genetic structure and high variation of the Amerindian and European components, principally. These studies have included genome-wide SNPs (Silva-Zolezzi et al., 2009, Bryc et al., 2010) and autosomal STRs in different Latin American populations (Godinho et al., 2008, Marino et al., 2006 Wang et al., 2008), and particularly CODIS-STRs in Mexican populations (Rubi-Castellanos et al., 2009a). However, during the last years further STR datasets used in forensic casework have been reported in Mexican-Mestizo populations (Table 1), and the current inter-populational analyses have not included the continental context. In this study, we analyzed the ancestry, structure, and genetic relationship of Mexican Mestizos with respect to Latin America and the Caribbean, based on 13 CODIS-STRs population datasets. For that purpose, we included reference genetic pools representing the European, Amerindian, and African ancestries. In addition, we included new STR genotype data of Tijuana, Baja California (BC), the border city located in the North of Mexico where thousands of migrants pass to the United States of America. Interestingly, this human mobility comes from various countries, principally Mexico but also Salvador, Guatemala, Honduras, Nicaragua, Panama, Costa Rica, and Belize, respectively (Brick et al., 2011). Therefore, Tijuana border city represents an interesting case to analyze gene flow effects in human populations (INEGI, 2010).

Section snippets

DNA extraction and genotyping

DNA was extracted from buccal swabs or peripheral blood by standard phenol-chloroform method from 409 unrelated Mestizos resident of the Tijuana City, Mexico. The individuals signed a written informed consent according to the Helsinki Declaration. We amplified 15 STRs markers (D3S1358, TH01, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, CSF1PO, vWA, D8S1179, TPOX, FGA, D2S1338 and D19S433) as recommended in the PCR AmpFlSTR Identifiler kit (Applied Biosystems, Foster City, CA). The

Genetic relationships

Genetic distances and pairwise comparisons were estimated between all Mexican-Mestizo, Central American, South American, and Caribbean populations (Suplementary Table 1). Nei and FST distances were represented in a NJ tree and a MDS plot, respectively (Fig. 2A and B). In Mexico, the almost perfect similarity (p > 0.0019; after Bonferroni correction) between populations from the same region is noticeable when they are separated into Northwest and Central-Southeast regions, and differentiation

Discussion

In this work, we analyzed the genetic structure, relationships and admixture components of Mexican-Mestizos based on published CODIS-STR databases from a continental point of view, integrating Latin American and Caribbean populations. When ancestral components are analyzed in hybrid populations, ancestral gene pool references are challenging to obtain because they are part of the past; thus, population geneticists take one or more current populations inhabiting the region that presumably

Acknowledgments

We thank to CONACyT-Mexico the financial support to H. R-V (grant No. 129693) and the post-doctoral fellowship to J. S-F. We thank to Daniel Piñero and Quinto-Cortés et al. (2010) for the STR dataset of Amerindian groups from Oaxaca provided for admixture analysis. The authors report no conflicts of interest.

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