Admixture and genetic relationships of Mexican Mestizos regarding Latin American and Caribbean populations based on 13 CODIS-STRs
Summary (4 min read)
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.
- 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).
- 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.
- 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).
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.
- The amplicons and reference allelic ladders were analyzed by capillary electrophoresis in the genetic analyzer ABI-PRISM 310.
- Results were interpreted using the software GeneMapper 3.2.
Statistical analysis
- In the population sample from Tijuana, the authors estimated the following forensic parameters with the software PowerStats (Tereba, 2001): allele frequencies, heterozygosity (Het), power of discrimination (PD), power of exclusion (PE), polymorphic information content (PIC), typical paternity index (TPI), and minimum allele frequencies (MAF).
- Furthermore, for each STR the authors tested the Hardy–Weinberg equilibrium (HWE) and linkage disequilibrium (LD) to check associations between pairs of loci.
- Fisher exact tests based on 3200 simulations were carried out with the program Genetic Data Analysis (GDA 1.1) for these purposes (Lewis and Zaykin, 2001).
African
- Six Central-American populations, 1026 persons from six South-American populations, and 628 individuals from four Caribbean populations (Table 1, Fig. 1).
- In addition, the authors included into the analysis genetic datasets representing the three main ancestral components in Latin American populations: Amerindian, European and African (Table 1).
- The software Arlequin 3.5.1.3 (Excoffier and Lischer, 2010) and the aforementioned population databases were employed to perform pairwise comparisons, Analysis Molecular of Variance , and FST genetic distances were plotted by multidimensional scaling (MDS) with optimum stress of 0.01 using the program SPSS 10.0 for Windows.
- In addition, genetic distances of Nei (1978) were estimated with the software GDA 1.1, and were represented in a neighbor joining (NJ) tree by means of TreeView 3.2 (Page, 1996).
- The coordinates (longitude and latitude) were obtained in Google earth (http://www.google.com/intl/es/earth/index.html).
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 between populations from the opposite region is visible, supporting the existence of two consistent population clusters of Mexican-Mestizos (Fig. 2A).
Population structure
- Analysis molecular of variance showed a low but significant inter-population variability (p ≤ 0.0009).
- In Mexican Mestizos, the inclusion of genetic and geographic criteria to cluster populations sequentially by means of the SAMOVA tests, showed in the first clusters the separation of southeastern populations (data not shown).
- The most congruent population structure, characterized by significant differences between populations of different groups, but not between populations of the same group, indicated the existence of two main clusters: (1) North and West: Chihuahua, Nuevo León, and Nayarit; and (2) West and Center: Jalisco, Guanajuato, Mexico City and Veracruz.
- The rest of Mexican Mestizo populations – principally from the Southeast – remained isolated (Tijuana, Puebla, Chiapas, and Yucatán) (Table 2).
Admixture components
- In Mexican Mestizos, the European ancestry increases to the Northwest, and vice versa the Amerindian counterpart increases to the Southeast, whereas the African ancestry is low and constant throughout the Mexican territory (2.2–6.3%) (Fig. 3A).
- Honduras2 and Nicaragua were the two major exceptions from the aforementioned pattern due to the sudden increment of African ancestry (13.6–62%).
- In order to observe the admixture components variation, the authors plotted the standard deviation of individual ancestry for each population studied here (Fig. 4).
- For most of the Latin American populations, the standard deviations of Amerindian and European ancestries were relatively homogeneous, about two to three times greater than the standard deviation of the African ancestry, except in Honduras2, Brazil, and Caribbean populations, where the African dispersion was higher (range 0.286–0.375), always at the expense of the Amerindian ancestry (Fig. 4).
- Interestingly, the population of Tijuana, characterized by elevated gene flow, showed the highest African standard deviation (0.157) among the Mexican-Mestizo populations (range 0.04–0.094).
Forensic parameters for the 15 STRs in Tijuana
- Allele frequencies and statistical parameters of forensic importance are presented in Table 3.
- Five STRs were in Hardy–Weinberg disequilibrium (p < 0.05), but after applying the Bonferroni correction (p < 0.0033) only three loci remained in disequilibrium: TH01, D21S11, and FGA.
- These cases implied the aforementioned loci in Hardy–Weinberg disequilibrium, which partially explain this finding and does not deserve further discussion (data not shown).
Discussion
- The authors 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.
- A larger ancestral gene pool was obtained (Table 1), which theoretically improved the admixture component estimation regarding the previous study with CODIS-STRs (Rubi-Castellanos et al., 2009a).
- Another essential issue is the forensic origin of a large number of population samples, because these commonly include both resident and native individuals from the populations that they represent.
- Therefore, the authors can predict that Mestizo or Latin American populations with similar ancestral proportions will have similar prevalence of certain diseases; if this is not observed, they can imply environmental factors, which should be confirmed in each case.
Mexican Mestizo populations
- In Mexico, CODIS-STRs allowed inferring a significant genetic structure similar to that described in the previous study of Rubi-Castellanos et al. (2009a).
- The clearest picture of this structure was obtained from pairwise comparisons and genetic distances graphically represented (Fig. 2A), which allow suggesting two principal population clusters: Northwest (Tijuana, Chihuahua, Nuevo Leon, Jalisco, Nayarit and Guanajuato) and Center-Southeast (Mexico City, Puebla, Veracruz, Chiapas and Yucatan).
- Supporting this interpretation, their results indicate that some Central American populations show greater African ancestry than that observed in Mexico, such as those observed in Honduras, El Salvador, Nicaragua and Costa Rica (Fig. 3).
- The admixture component pattern obtained in Mexican Mestizo populations is similar to the previously described by genome-wide SNPs and CODIS-STRs (Rubi-Castellanos et al., 2009a; Silva-Zolezzi et al., 2009).
- This is explained by software Leadmix employed before for that purpose (Wang, 2003), whereas in this study the program Structure was used (Falush et al., 2003).
Central America and the Caribbean
- Interestingly, Mexico shows similarity between populations with elevated Amerindian ancestry (Guatemala, El Salvador and Honduras1), but this gradually decreases to the South (56.4–36.2%).
- In addition, Honduras2 (Black Garifuna), Costa Rica, and Caribbean populations were characterized by greater differentiation (Fig. 2A), attributable to greater African component (Fig. 3A).
- For the Caribbean, their results detect the elevated African genetic legacy received by the populations studied herein, and show a significant differentiation between some of them (Fig. 2, Table 2).
- The prevalence of African component is attributable to the trans-Atlantic slave trade that entered the Bahamas from West Africa (Duncan et al., 1996).
South America
- In South America, pairwise comparisons and genetic distances showed larger population structure than in Mexican Mestizos (Fst = 0.72%, Fig. 2A and B).
- In most of the Latin American populations, standard deviations of Amerindian and European ancestries were two to three times larger than the African ancestry, except for Brazil, Honduras2 and Caribbean populations (Fig. 4).
- The authors report allele frequencies and statistical parameters of forensic interest in Tijuana,. (3) The immigration of: (i) medical professionals, surgeons, and nurses to care for USA patients; (ii) tourists traveling for business; (iii) USA retired persons (∼250,000) living in the Tijuana-Ensenada coastal corridor (Ramírez de Arellano, 2006; Vargas-Hernández, 2011).
- In brief, the effects here detected in Tijuana that could be attributed to elevated gene flow include Hardy–Weinberg disequilibrium in three of 15 STRs (20%), increment of the allele diversity and African ancestry.
Acknowledgments
- The authors 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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13,581 citations
"Admixture and genetic relationships..." refers methods in this paper
...3 (Excoffier and Lischer, 2010) and the aforementioned population databases were employed to perform pairwise comparisons, Analysis Molecular of Variance (AMOVA), and FST genetic distances were plotted by multidimensional scaling (MDS) with optimum stress of 0....
[...]
...The software Arlequin 3.5.1.3 (Excoffier and Lischer, 2010) and the aforementioned population databases were employed to perform pairwise comparisons, Analysis Molecular of Variance (AMOVA), and FST genetic distances were plotted by multidimensional scaling (MDS) with optimum stress of 0.01 using…...
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7,615 citations
"Admixture and genetic relationships..." refers methods in this paper
...This is explained by software Leadmix employed before for that purpose (Wang, 2003), whereas in this study the program Structure was used (Falush et al., 2003)....
[...]
...3 (Falush et al., 2003), with a burn-in-period of 10,000 iterations in each parameter and 25 repetitions for each run (K), using the mixture model, allele frequency correlation, and -value separated for populations, with three populations groups identified as the ancestral references (supervised analysis)....
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...components of admixture were estimated in individuals and populations with the software Structure 2.3.3 (Falush et al., 2003), with a burn-in-period of 10,000 iterations in each parameter and 25 repetitions for each run (K), using the mixture model, allele frequency correlation, and -value…...
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1,831 citations
"Admixture and genetic relationships..." refers methods in this paper
...3 (Excoffier and Lischer, 2010) and the aforementioned population databases were employed to perform pairwise comparisons, Analysis Molecular of Variance (AMOVA), and FST genetic distances were plotted by multidimensional scaling (MDS) with optimum stress of 0.01 using the program SPSS 10.0 for Windows. In addition, genetic distances of Nei (1978) were estimated with the software GDA 1....
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...Different population groups were established considering genetic and geographical criteria using the software SAMOVA 1.0 (Dupanloup et al., 2002)....
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...0 (Dupanloup et al., 2002)....
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"Admixture and genetic relationships..." refers background in this paper
...However, our preliminary admixture estimates could be helpful in the biomedical area for complex disease analysis (i.e. case–control studies) where population genetic composition and dynamics of the admixture processes should be clearly understood (Parra et al., 1998)....
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625 citations
"Admixture and genetic relationships..." refers background or methods in this paper
...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)....
[...]
...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)....
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...This is due to their elevated heterozygosity, genome abundance, high mutation rate, and simple analysis based on the polymerase chain reaction (PCR) (Butler, 2006)....
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