Int J Legal Med DOI 10.1007/s00414-015-1148-8
POPULATION DATA
Genetic polymorphism of 15 STR loci in El Salvador Pablo Muñoz & Eugenia Leticia Pinto de Erazo & Carlos Baeza & Eduardo Arroyo-Pardo & Ana Maria López-Parra
Received: 30 June 2014 / Accepted: 8 September 2014 # Springer-Verlag Berlin Heidelberg 2015
Abstract The aim of this study was to estimate the allelic frequencies of the 15 short tandem repeat (STR) loci included in AmpFlSTR®Identifiler® PCR Amplification Kit. Biological samples were obtained from 109 unrelated individuals from El Salvador. Allelic frequencies and forensic parameters were calculated. All loci showed no departure from Hardy– Weinberg equilibrium after Bonferroni correction. The obtained frequencies were compared with other previously reported population data. The multidimensional scaling plot and the neighbor-joining phylogeny supported a high native Mesoamerican contribution. Keywords El Salvador . STRs . Population Data . AmpFlSTR® Identifiler® PCR Amplification Kit
The Republic of El Salvador is the smallest and the most densely populated country in Central America. El Salvador borders the Pacific Ocean on the south, Guatemala to the west, and Honduras to the north and east. El Salvador has a population of approximately 6,297,394 people (2012), composed of Mestizos, Caucasian, and indigenous peoples. In the Mestizo population (86 %), Salvadoreans are of predominantly Spanish-European descent and Native Americans. In pre-Columbian times, the territory was inhabited by various Native American peoples, including the Pipil, a NahuatlElectronic supplementary material The online version of this article (doi:10.1007/s00414-015-1148-8) contains supplementary material, which is available to authorized users. P. Muñoz : E. L. Pinto de Erazo : C. Baeza : E. Arroyo-Pardo : A. M. López-Parra (*) Laboratory of Forensic Genetics and Population Genetics, Department of Toxicology and Health Sanitary, Faculty of Medicine, Complutense University of Madrid, Madrid, Spain e-mail: [email protected]
speaking population that occupied the central and western regions of the territory, and the Lenca, who settled in the east of the country. However, since El Salvador occupies the eastern edge of the Mayan civilization, the origins of many of El Salvador people’s is controversial. In this sense, a study of general sample of El Salvador population will provide new information about the genetic composition of this country area and will help to understand the biological relationships established among different regions of Mesoamerica. In the case of Spain, the existence of a significant community of Salvadorean residents makes helpful the availability of database of forensic genetic polymorphisms. A total of 109 blood samples of unrelated individuals from different departments of El Salvador, all of them resident in Spain, was analyzed. The samples were collected with personal informed consent from volunteer donors according to the principles outlined in the Helsinki Declaration. Genomic DNA was obtained from Whatman FTA® cards [1]. DNA concentration was determined using a NanoDrop® ND-1000. Amplification of 15 short tandem repeats (STRs) plus the Amelogenin gender determining marker was performed using AmpFlSTR® Identifiler® PCR Amplification Kit (Applied Biosystems, Foster City, CA, USA). Separation of PCR products was carried out on an ABI3730 DNA Analyzer (Applied Biosystems, Foster City, CA, USA). Allele designations were determined using the GeneMapper software 4.0 (Applied Biosystems, Foster City, CA). The laboratory has participated in proficiency testing of the GHEP-ISFG (Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics) Working Group. The study followed the guidelines and recommendations suggested by Carracedo et al. [2], Poetsch et al. [3], and the International Society of Forensic Genetics (http://www.isfg.org). Allele frequencies, heterozygosities, and exact test for Hardy– Weinberg (HW) equilibrium (100,000 steps in Markov chain
Int J Legal Med
with 1000 of dememorization steps), linkage disequilibrium (LD) between each pair of loci and inbreeding coefficient (FIS) were performed with Arlequin v 3.5.1.2 [4] (http://cmpg.unibe. ch/software/arlequin35/) for the 15 autosomal STR markers (Supplemental Table 1). After Bonferroni’s correction, the original 0.05 significance threshold was reduced to a 0.0033 value for the Hardy–Weinberg equilibrium test [5]. Forensic statistic parameters such as observed heterozygosity (Ho), expected heterozygosity (He), power of discrimination (PD), matching probability (PM), power of exclusion (PE), polymorphism information content (PIC) were computed using PowerStats v.1.2 software (http://promega.com). POPTREE2 software [6] was used to construct a phylogenetic tree using Fst distances with 1000 bootstrap replications and neighbor-joining method [7]. The output of POPTREE was visualized with program TREEVIEW version 1.6.6 [8]. Multidimensional scaling (MDS) plot was performed based on the Fst distances matrix using the ALSCAL procedure in SPSS v. 19.0 (SPSS Inc.). Available published populations included in the present study for comparisons appear in Supplemental Table 2. Allelic frequencies of 15 STR and parameters of forensic interest are shown in Supplemental Table 1. In Hardy–Weinberg equilibrium exact test, a single p value was found below 0.05 in D21S11 locus (p=0.03245). However, after applying the Bonferroni’s correction (p
POPULATION DATA
Genetic polymorphism of 15 STR loci in El Salvador Pablo Muñoz & Eugenia Leticia Pinto de Erazo & Carlos Baeza & Eduardo Arroyo-Pardo & Ana Maria López-Parra
Received: 30 June 2014 / Accepted: 8 September 2014 # Springer-Verlag Berlin Heidelberg 2015
Abstract The aim of this study was to estimate the allelic frequencies of the 15 short tandem repeat (STR) loci included in AmpFlSTR®Identifiler® PCR Amplification Kit. Biological samples were obtained from 109 unrelated individuals from El Salvador. Allelic frequencies and forensic parameters were calculated. All loci showed no departure from Hardy– Weinberg equilibrium after Bonferroni correction. The obtained frequencies were compared with other previously reported population data. The multidimensional scaling plot and the neighbor-joining phylogeny supported a high native Mesoamerican contribution. Keywords El Salvador . STRs . Population Data . AmpFlSTR® Identifiler® PCR Amplification Kit
The Republic of El Salvador is the smallest and the most densely populated country in Central America. El Salvador borders the Pacific Ocean on the south, Guatemala to the west, and Honduras to the north and east. El Salvador has a population of approximately 6,297,394 people (2012), composed of Mestizos, Caucasian, and indigenous peoples. In the Mestizo population (86 %), Salvadoreans are of predominantly Spanish-European descent and Native Americans. In pre-Columbian times, the territory was inhabited by various Native American peoples, including the Pipil, a NahuatlElectronic supplementary material The online version of this article (doi:10.1007/s00414-015-1148-8) contains supplementary material, which is available to authorized users. P. Muñoz : E. L. Pinto de Erazo : C. Baeza : E. Arroyo-Pardo : A. M. López-Parra (*) Laboratory of Forensic Genetics and Population Genetics, Department of Toxicology and Health Sanitary, Faculty of Medicine, Complutense University of Madrid, Madrid, Spain e-mail: [email protected]
speaking population that occupied the central and western regions of the territory, and the Lenca, who settled in the east of the country. However, since El Salvador occupies the eastern edge of the Mayan civilization, the origins of many of El Salvador people’s is controversial. In this sense, a study of general sample of El Salvador population will provide new information about the genetic composition of this country area and will help to understand the biological relationships established among different regions of Mesoamerica. In the case of Spain, the existence of a significant community of Salvadorean residents makes helpful the availability of database of forensic genetic polymorphisms. A total of 109 blood samples of unrelated individuals from different departments of El Salvador, all of them resident in Spain, was analyzed. The samples were collected with personal informed consent from volunteer donors according to the principles outlined in the Helsinki Declaration. Genomic DNA was obtained from Whatman FTA® cards [1]. DNA concentration was determined using a NanoDrop® ND-1000. Amplification of 15 short tandem repeats (STRs) plus the Amelogenin gender determining marker was performed using AmpFlSTR® Identifiler® PCR Amplification Kit (Applied Biosystems, Foster City, CA, USA). Separation of PCR products was carried out on an ABI3730 DNA Analyzer (Applied Biosystems, Foster City, CA, USA). Allele designations were determined using the GeneMapper software 4.0 (Applied Biosystems, Foster City, CA). The laboratory has participated in proficiency testing of the GHEP-ISFG (Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics) Working Group. The study followed the guidelines and recommendations suggested by Carracedo et al. [2], Poetsch et al. [3], and the International Society of Forensic Genetics (http://www.isfg.org). Allele frequencies, heterozygosities, and exact test for Hardy– Weinberg (HW) equilibrium (100,000 steps in Markov chain
Int J Legal Med
with 1000 of dememorization steps), linkage disequilibrium (LD) between each pair of loci and inbreeding coefficient (FIS) were performed with Arlequin v 3.5.1.2 [4] (http://cmpg.unibe. ch/software/arlequin35/) for the 15 autosomal STR markers (Supplemental Table 1). After Bonferroni’s correction, the original 0.05 significance threshold was reduced to a 0.0033 value for the Hardy–Weinberg equilibrium test [5]. Forensic statistic parameters such as observed heterozygosity (Ho), expected heterozygosity (He), power of discrimination (PD), matching probability (PM), power of exclusion (PE), polymorphism information content (PIC) were computed using PowerStats v.1.2 software (http://promega.com). POPTREE2 software [6] was used to construct a phylogenetic tree using Fst distances with 1000 bootstrap replications and neighbor-joining method [7]. The output of POPTREE was visualized with program TREEVIEW version 1.6.6 [8]. Multidimensional scaling (MDS) plot was performed based on the Fst distances matrix using the ALSCAL procedure in SPSS v. 19.0 (SPSS Inc.). Available published populations included in the present study for comparisons appear in Supplemental Table 2. Allelic frequencies of 15 STR and parameters of forensic interest are shown in Supplemental Table 1. In Hardy–Weinberg equilibrium exact test, a single p value was found below 0.05 in D21S11 locus (p=0.03245). However, after applying the Bonferroni’s correction (p
