Genetic population data of three Y-STR genetic systems in Mexican-Mestizos from Monterrey, Nuevo León (Northeast, Mexico)

Accepted Manuscript Title: Genetic population data of three Y-STR genetic systems in Mexican-Mestizos from Monterrey, Nuevo Le´on (Northeast, Mexico) Author: Benito Ramos-Gonz´alez PII: DOI: Reference:

S1872-4973(17)30100-X http://dx.doi.org/doi:10.1016/j.fsigen.2017.04.016 FSIGEN 1712

To appear in:

Forensic Science International: Genetics

Author: Jos´e Alonso Aguilar-Vel´azquez PII: DOI: Reference:

S1872-4973(17)30100-X http://dx.doi.org/doi:10.1016/j.fsigen.2017.04.016 FSIGEN 1712

To appear in:

Forensic Science International: Genetics

Author: Mar´ıa de Lourdes Ch´avez-Briones PII: DOI: Reference:

S1872-4973(17)30100-X http://dx.doi.org/doi:10.1016/j.fsigen.2017.04.016 FSIGEN 1712

To appear in:

Forensic Science International: Genetics

Authors: Mar´ıa del Roc´ıo Escare˜no-Hern´andez, Elizabeth Alfaro-Lopez PII: DOI: Reference:

S1872-4973(17)30100-X http://dx.doi.org/doi:10.1016/j.fsigen.2017.04.016 FSIGEN 1712

To appear in:

Forensic Science International: Genetics

Author: H´ector Rangel-Villalobos PII: DOI:

S1872-4973(17)30100-X http://dx.doi.org/doi:10.1016/j.fsigen.2017.04.016

Reference:

FSIGEN 1712

To appear in:

Forensic Science International: Genetics

Received date: Revised date: Accepted date:

17-6-2016 17-4-2017 21-4-2017

Please cite this article as: H´ector Rangel-Villalobos, Genetic population data of three Y-STR genetic systems in Mexican-Mestizos from Monterrey, Nuevo Le´on (Northeast, Mexico), Forensic Science International: Geneticshttp://dx.doi.org/10.1016/j.fsigen.2017.04.016 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

Forensic population genetics—Letter to the Editor Genetic population data of three Y-STR genetic systems in MexicanMestizos from Monterrey, Nuevo León (Northeast, Mexico)

Benito Ramos-González1*¥, José Alonso Aguilar-Velázquez2¥, María de Lourdes ChávezBriones1,3, María del Rocío Escareño-Hernández1, Elizabeth Alfaro-Lopez1, Héctor RangelVillalobos2* 1

Laboratorio de Genética Forense, Instituto de Criminalística y Servicios Periciales,

Procuraduría General de Justicia, Nuevo León. 2

Instituto de Investigación en Genética Molecular, Universidad de Guadalajara (CUCI-

UdeG), Ocotlán, Jalisco, México. 3

Departamento de Patología, Facultad de Medicina, Universidad Autónoma de Nuevo

León, Monterrey, Nuevo León, México.

¥ These authors contributed equally to this work * Correspondence: Dr. Héctor Rangel Villalobos, Dr. Benito Ramos González Instituto de Investigación en Genética Molecular, Universidad de Guadalajara, Av. Universidad #1115, Ocotlán, Jalisco, México. CP 47810. TEL/FAX: (+52) (392) 9257112. e-mail: [email protected]; [email protected]

1

ABSTRACT We analyzed 1,481 unrelated Mexican–Mestizo (admixed) males from Monterrey City (Northeast, Mexico) using three different Y-STR genetic systems: PowerPlex® Y (n= 267), AmpFlSTR® Yfiler™ (n= 814), and PowerPlex® Y23 (n= 400). The obtained haplotypes were uploaded into the YHRD database (accession number: YA004177). The discriminatory capacity of the haplotypes ranged from 82.4% to 93.75%, and the haplotype diversity ranged from 99.46% to 99.81%. Based on the Y-filer haplotypes, we analyzed the genetic relationships and the genetic structure of previously published Mexican–Mestizo and American populations. Genetic homogeneity was observed between most of the Mexican populations analyzed; the main exception was Monterrey, which can be attributed to its higher European ancestry. Despite the difficulties in establishing geographic limits to define consistent population clusters, it was possible to predict a higher similarity between Mexican–Mestizos populations geographically nearby. Finally, based on the PowerPlex Y23, the population of Monterrey was compared with some worldwide populations (www.yhrd.org) and was found to display a close genetic relationship with Hispanic American populations.

Keywords: Mestizos; Y-STRs; Male identification; Mexico; Haplotypes; Powerplex Y23

2

Dear Editor, Mestizos constitute the largest population in Mexico ( 90%); they arose from roughly 500 years of admixture between Europeans, Amerindians and, to a lesser extent, Africans initially brought to America as slaves [1]. Short tandem repeats of the Y chromosome (Y-STRs) are used to solve special situations in paternity and forensic cases, and they are helpful to disclose the origin, history, and evolution of human populations [2]. The PowerPlex® Y System and AmpFlSTR® Yfiler™ Kit have been used to analyze 12 and 17 Y-STRs, respectively, in Mexican–Mestizo males from different populations of Mexico [3-7]. However, to our knowledge, no Mexican population has been analyzed using the PowerPlex® Y23 System. Consequently, the aim of this study was to analyze the Mexican–Mestizo population of Monterrey located in the Nuevo León state (Northeast, Mexico), which has never been studied for any Y-STR genetic system. For this purpose, 1,481 DNA samples were analyzed using the PowerPlex® Y System (n= 267), AmpFlSTR® Yfiler™ Kit (n= 814), and PowerPlex® Y23 System (n= 400). Before being included in our study, all volunteers signed an informed consent form according to the ethical guidelines of the Helsinki Declaration. This project was approved by the Ethical Research Committee at the Institute of Criminalistics and Forensic Services of the Attorney General of Nuevo León state. The anonymity of the individuals investigated was preserved. Blood and buccal swab samples were spotted on Whatman®FTA cards, and the genomic DNA was extracted using the Chelex 100 protocol. PCR amplifications were carried out following the manufacturer’s recommendations. For the genotyping process, we used GeneMapper® ID-X Software v1.4, and the corresponding allelic ladders included in the kits. Consensus haplotypes after two independent reads were reported in the final Y3

STR database. Our laboratory annually participates in a quality control proficiency test organized by the Latin American Society for Forensic Genetics (http://slagf.org.ar/a2/); successful results were obtained for the Y-STR loci constituting the PowerPlex Y23 System in the last quality control proficiency test (2015). The haplotype frequency was estimated by the gene-counting method. The haplotype diversity (D) was computed according to the Nei’s formula [8]. Using the Y-filer™ haplotypes, we estimated Rst genetic distances and Fst p-values with the Arlequin v3.5 software [9]; the Rst distances were graphically displayed on a multidimensional scaling (MDS) plot using the SPSS v17 software. For this analysis, we included previously published Y-STR haplotypes of Mexican–Mestizo populations from the following states and geographic regions: Chihuahua (North-Center) [3], Jalisco (West), Guanajuato (CenterWest), Yucatán (Southeast), Chiapas (South) [4], Zacatecas (Northwest) [5], and the Central Valley of Mexico represented by the states of Puebla, Guanajuato, and Querétaro [6]. In addition, populations from Chile (South America) [10] and four major ethnic groups from the USA (Caucasian, Hispanic, African, and Asian) were included as reference [11]. Population structure among these populations was evaluated using the analysis of molecular variance (AMOVA). For analyses of the genetic structure and population relationships, the DYS389II allele length was corrected by subtracting the DYS389I allele length, whereas DYS385 was omitted because the alleles cannot be separated by locus, which prevented the computation of size differences. Based on the PowerPlex® Y23 haplotypes, we estimated Rst p-values and Rst distances that were graphically represented on a MDS plot. For this purpose, we used the tools available in the YHRD database (https://yhrd.org/), including Hispanic Americans and Los Angeles Mexicans (USA), as well as haplotype datasets from the following countries: Argentina, Bolivia, Brazil, Costa 4

Rica, Ghana, Panama, Peru, Portugal, and Spain [12, 13]. In the MDS plot, indistinguishable populations were clustered when Rst distance< 0.01; a minimum cluster size of three populations was considered for this purpose. The full list of Y-STR haplotypes from Monterrey City is available as electronic supplementary material (ESM) in Table S1, and was submitted to the YHRD (https://yhrd.org/; accession numberYA004177) [12]. As expected, the largest male discriminatory capacity was offered by the PowerPlex-Y23 System (375/400 = 93.75%), followed by the AmpFlSTR Y-filer kit (708/814 = 86.98%) and the PowerPlex Y System (222/267= 82.4%). In addition, the haplotype diversity (D) for the PowerPlex-Y23 System (D= 99.81%), Y-filer kit (99.77%) and PowerPlexY System (D= 99.46 %) were estimated in the Monterrey population sample. By Y-STR, the genetic diversity was computed as the expected heterozygosity ranging from 0.47471 to 0.91536 for DYS393 and DYS385, respectively (data not shown). These values are similar to those reported in previous studies on Mexican–Mestizo populations [3-7]. The pairwise comparison based on Y-filer haplotypes showed similarities among the Mexican–Mestizo, Chilean, and Hispanic American populations, as indicated by the nonsignificant Fst p-values after Bonferroni correction (Table S2). This observation is perceptible by the position of most of the Mexican populations in the MDS plot, except for the Monterrey population (Figure S1a). The position of Monterrey is probably explained by a higher European ancestry than the rest of Mexican–Mestizo populations, which agrees with the previously reported increasing gradient of European ancestry toward the northern region of the Mexican territory [1,4,14]. Previous ancestry estimates from Monterrey based on single nucleotide polymorphisms of the Y-chromosome (Y-SNPs) are compatible with this interpretation [15]. In fact, additional MDS plots performed online (https://yhrd.org/) 5

verified that Monterrey was closer to the European populations than to the rest of Mexican– Mestizo populations (data not shown). Similarly, although the Rst p-values based on PowerPlexY23 between worldwide populations were significant (Table S3), two population clusters were created, which can be observed in the MDS plot (Figure S1b). The first cluster included Hispanic populations from North America (Monterrey, HispanicAmericans, and Los Angeles Mexicans), while the second cluster incorporated South American populations (Argentina, Brazil, and Costa Rica). In general, the AMOVA tests indicated a large genetic variability within populations (Fit > 99%). In addition, the analysis of the genetic structure based on 15 Y-STRs with the Y-filer kit indicated a low but significant differentiation among the Mexican–Mestizo populations (Fst = 0.056%) (Table S4). We evaluated the genetic structure clustering the Mexican–Mestizo populations under the two following geographic criteria: (i) Two clusters: Northwestern and Southeastern-Central Mexico; and (ii) Four clusters: Northern, Western, Central, and Southeastern Mexico. For both criteria, the variability among population clusters was not significant (Fct; p> 0.05), and the differentiation among populations within clusters had similar values (Fsc= 0.029; p= 0.00489; Fsc= 0.024; p= 0.0235) (Table S4). These Fsc p-values suggest that four clusters can better explain the genetic structure of the Mexican–Mestizo populations. In brief, these findings are compatible with the gradient of European and Amerindian ancestries throughout the Mexican territory [1,4,14], which complicate establishing consistent geographic limits to define specific regions, but allow predicting a higher similarity between nearby populations. In conclusion, we describe the Y-STR haplotypes from the Mestizo population of Monterrey (Northeastern, Mexico) using the most common commercial kits for male 6

identification. We report the first population dataset for the PowerPlex Y23 System in this country. The genetic relationship and structure analyses suggest homogeneity based on the geographic proximity between Mexican–Mestizo populations. This study follows the guidelines for publication of population data requested by the journal [16]. Acknowledgments We are grateful with all the volunteers for generously collaborating in this study, and with all the staff of the Forensic Genetics Laboratory, especially to Porfirio Díaz Torres, General Manager of the Criminalistics and Forensic Services Institute. This project was supported by Procuraduría General de Justicia de Nuevo León. References 1]

R. Rubi-Castellanos, G. Martínez-Cortés, J.F. Muñoz-Valle, A. González-Martín, R.M. Cerda-Flores, M. Anaya-Palafox, et al., Pre-Hispanic Mesoamerican demography approximates the present-day ancestry of Mestizos throughout the territory of Mexico, Am J Phys Anthropol (2009) 284-294.

[2] M.A. Jobling, C. Tyler-Smith: Fathers and sons: the Y-chromosome and human evolution. TIG. 11(1995) 449-456. [3] A.B. Gutiérrez-Alarcón, M. Moguel-Torres, A.K. León-Jiménez, G.E. Cuéllar-Nevárez, H. Rangel-Villalobos:

Allele and haplotype

distribution for 16 Y-STRs

(AmpFlSTRY-filer kit) in the state of Chihuahua at North Center of Mexico. Leg Med (Tokyo) 9 (2007), 154-157. [4] J. Salazar-Flores, R. Dondiego-Aldape, R. Rubi-Castellanos, M. Anaya-Palafox, I. Nuño-Arana, L.M. Canseco-Avila et al., Population structure and paternal admixture 7

landscape on present-day Mexican-Mestizos revealed by Y-STR haplotypes. Am J Hum Biol 22 (2010), 401-409. [5] E.J. Vallín-Reza, F.deM. Trejo-Medinilla, Genética poblacional del cromosoma “Y” en el estado de Zacatecas, México, Arch Med 8 (2012)e1-e14 [6] C. Santana, G. Noris, M.A. Meraz-Ríos, J.J. Magaña, E.S. Calderon-Aranda, M.dL. Muñoz, et al.,GeneticAnalysis of 17 Y-STRs in a Mestizo populationfrom the central Valley of Mexico. HumBiol 86(2014)289-312. [7] A. Luna-Vázquez, G. Vilchis-Dorantes, M.O. Aguilar-Ruiz, A. Bautista-Rivas, A. Perez-Garcia, R. Orea-Ochoa R, et al., Haplotype frequencies of the PowerPlex Y system in a Mexican-Mestizo population simple from Mexico City. Forensic Sci Int Genet 2 (2008) e11-13. [8] M. Nei: Molecular evolutionary genetics (1987) New York: Columbia University Press. [9] L. Excoffier, H. Lischer, Arlequin suite ver3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Res 10(2010) [10] U. Toscanini, F. Brisighelli, F. Moreno, J.A. Pantoja-Astudillo, E.A. Morales, P. Bustos, et al., Analysis of Y-chromosome STRs in Chile confirms an extensive introgression of European male lineages in urban populations, Forensic Sci Int Genet21 (2015) 76-80. [11] M.D. Coble, C.R. Hill, J.M. Butler, Haplotype data for 23 Y-chromosome markers in four U.S. population groups. Forensic Sci Int Genet 7 2013 e66-e68.

8

[12] S. Willuweit, L. Roewer, The new Y chromosome haplotype reference database. Forensic Sci Int Genet 15 (2015) 43-48. [13] J. Purps, S. Siegert, S. Willuweit, M. Nagy, C. Alves, R. Salazar, et al., A global analysis of Y-chromosomal haplotype diversity for 23 STR loci. Forensic Sci Int Genet12(2014) 12-23. [14] G. Martínez-Cortés, J. Salazar-Flores, L.G. Fernández-Rodríguez, R. RubiCastellanos, C. Rodríguez-Loya, J.S. Velarde-Félix, et al., Admixture and population structure in Mexican-Mestizos based on paternal lineages. J Hum Genet 57 (2012) 568-74. [15] M.L. Martinez-Fierro, J. Beuten, R.J. Leach, E.J. Parra, M. Cruz-Lopez, H. RangelVillalobos, et al., Ancestry informative markers and admixture proportions in northeastern Mexico. J Hum Genet 54 (2009) 504-9. [16] A. Carracedo, J.M. Butler, L. Gusmão, A. Linacre, W. Parson, L. Roewer, et al., New guidelines for the publication of genetic population data, Forensic SciInt Genet 7 (2013) 217–220.

9