Forensic Science International: Genetics
Volume 6, Issue 1 , Pages e58-e60, January 2012

Allele frequencies of 15 STRs in the Calchaqui Valleys population (North-Western Argentina)

Institut Universitari d’Investigació en Ciències de la Salut (IUNICS) i Laboratori de Genètica, Departament de Biologia, Universitat de les Illes Balears, Campus de la UIB, 07122 Palma de Mallorca, Spain

Cátedra de Antropología, Facultad de Humanidades, Universidad Nacional de Salta, Av. Bolivia 5150, 4400 Salta, Argentina

Institut Universitari d’Investigació en Ciències de la Salut (IUNICS) i Laboratori de Genètica, Departament de Biologia, Universitat de les Illes Balears, Campus de la UIB, 07122 Palma de Mallorca, Spain

Received 7 March 2011; received in revised form 5 May 2011; accepted 7 May 2011. published online 06 June 2011.

Article Outline

Abstract 

Allele frequencies for 15 short tandem repeat (STR) loci were obtained from a sample of 110 individuals from the Calchaqui Valleys population (North-Western Argentina). The combined power of exclusion and combined power of discriminating for the 15 tested STR loci were 0.999964 and 0.9999999999999998, respectively. Matching probability was 1 in 4.58×10(15). Therefore, it may be concluded that the set of 15 STRs included in the AmpF STR Identifiler kit, represents a powerful tool for forensic applications, paternity testing and population genetics studies in the Calchaqui Valleys population.

Keywords: STRs, Allelic frequencies, Calchaqui Valleys, North-Western Argentina (NOA)

 

Dear Editor

The Calchaqui Valleys are located in the Andes Mountains, in the North Western Argentina region (NOA), occupying a band of approximately 200km in a North–South direction at an altitude between 1700 and 3000m (provinces of Salta, Tucumán and Catamarca). In the pre-Hispanic era, these valleys were inhabited by the diaguitas whose societies reached the highest socioeconomic and cultural levels. The population dynamics of this area was complex, as a consequence of the invasion of the Incas, subsequent European colonization and, finally, the policy of estrangement of the rebels, from the XVI until the end of the XVII century, which led to the disappearance of an important part of the population. There is little reliable information on the structure of these populations before contact with Europeans in the late XV century. In addition, the lack of historical data for the post-contact period means that the exact origin and/or degree of admixture of the inhabitants of this region are also unknown [1]. The current population (approximately 25,000 inhabitants) has a low density and is unequally distributed; with Cafayate (approx. 9000 inhabitants) and Cachi (6000) as the most populated localities (Fig. 1). The migration rate is considerable among different locations in the Calchaqui Valleys, however the proportion of migrants from neighbour regions is almost nonexistent [2]. Calchaqui Valley inhabitants can be considered as a rural “mestizo” population, a result of intermarriage between Spanish and natives through a long process of conquest and colonization of North Western Argentina.

Blood samples were obtained from 110 unrelated healthy individuals living in different villages of the Calchaqui Valleys after informed consent. DNA was extracted by standard phenol–chloroform method. Multiplex PCR amplification of 15 STR loci was performed using the AmpFℓSTR Identifiler PCR amplification kit (Applied Biosystems, Foster City, CA, USA) according to the manufacturer's instructions. For genetic typing, an ABI Prism 3130 DNA Genetic Analyzer along with GeneMapper ID 3.2.1 software (Applied Biosystems, Foster City, CA) was used.

Allele frequencies were estimated by gene counting and the Hardy–Weinberg equilibrium was tested. Forensic statistic parameters were obtained using PowerStats v. 1.2 software [3]. In order to examine the relationship of the population studied with other neighbouring populations, Reynolds’ genetic distances [4], calculated using PHYLIP v. 3.69 [5], were performed to generate the multi-dimensional scaling (MDS) plot carried out with SPSS v. 15.0 (SPSS, Inc., Chicago, IL, USA).

Table 1 included statistical parameters of forensic interest. Allelic frequencies of the analysis markers and the whole genotype set are presented in Supplementary Tables S1 and S2. All the analyzed loci reached the Hardy–Weinberg equilibrium after Bonferroni's correction. TPOX may be considered the least informative locus. FGA had the highest values in all of parameters, except in PE and TPI, where the highest values were found in D19S433. Different studies in Latin American populations [6], [7] have also found TPOX as the locus with the minimum PD (between 66.3 and 87.7) and D18S51 as the one with the highest values (PD ranging from 87.5 to 97.4). In accordance with these studies, in the Calchaqui Valleys the TPOX value was also the lowest (75.6). D18S51 had a PD value similar to other Latin American populations (95.1), but the highest PD value was found in the FGA locus (95.3). The combined probability of exclusion, power of discrimination and matching probability for the 15 tested STR loci were 0.999964, 0.9999999999999998 and 1 in 4.58×10(15), respectively.

Table 1. Statistical parameters for AmpFℓSTR Identifiler-15 loci in the Calchaqui Valleys population.
D8S1179D21S11D7S820CSF1POD3S1358TH01D13S317D16S539D2S1338D19S433vWATPOXD18S51D5S818FGA
NA81076668711126615913
Ho0.82730.79090.71150.63550.59630.59810.78900.77980.75930.84260.67590.58720.77140.71560.7830
He0.81590.84200.66740.69220.61760.62870.82300.77550.82750.83220.69710.56790.84610.70520.8549
MP0.06380.04990.17840.14300.21450.19140.05560.09130.05760.04870.13910.24370.04910.11720.0470
PD0.93620.95010.82160.85700.78550.80860.94440.90870.94240.95130.86090.75630.95090.88280.9530
PIC0.79130.82260.60460.63970.55430.57830.79950.73930.80840.81210.64560.50860.82850.67200.8399
PE0.65060.58230.44630.33570.28650.28860.57880.56210.52570.68030.39200.27580.54710.45280.5679
TPI2.89472.39131.73331.37181.23861.24422.36962.27082.07693.17651.54291.21112.18751.75812.3043
P0.75630.13800.32190.19340.64350.50370.34510.91250.05610.76890.62650.68050.0285a0.81010.0307a

NA, number of alleles; Ho, observed heterozygosity; He, expected heterozygosity; MP, matching probability; PD, power of discrimination; PIC, polymorphism information content; PE, probability of exclusion; TPI, typical paternity index; P, Hardy–Weinberg equilibrium exact test. Numbers in bold indicate the highest and the lowest value in each forensic parameter.

aNot statistically significant after Bonferroni's correction.

Allele frequencies of Calchaqui Valleys population were compared to available data for the same markers in 42 other populations, mainly Amerindians, South Europeans and other Latin American populations [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31], [32], [33], [34], [35], [36]. Fig. 2 shows a multi-dimensional scaling plot based on Reynold's genetic distances (Supplementary Table S3). Three different groups can be clearly observed along the X-axis, ranging from the one including the European populations to the genetically more heterogeneous group comprised of Amerindian populations. Most Latin American populations show an intermediate position between these two groups, in accordance with the admixture from European and Native American ancestries of these populations. The population of the Salta province is closer to Amerindians, harbouring a higher Native American ancestry component than other Argentinean populations, as previously described for the country's North-Western region e.g., [37], [38].

  • View full-size image.
  • Fig. 2. 

    MDS plot based on Reynolds’ distances (★ Calchaqui Valleys [this study] and ● Amerindian: Conchagua, Pilagá, Toba-Chaco, Toba-Formosa, Wichí-Chaco, Wichí-Formosa; ○ Latin-American: Argentina (Buenos Aires, Neuquén, Misiones, Salta, Formosa, Chaco, Corrientes, Santa Fe, Mendoza, Río Negro, Chubut, Pampa, San Luis, Santa Cruz, Tucumán), Puerto Rico, Mexico, Brazil, Colombia (Antioquia, Caldas), Venezuela (Maracaibo), Peru; ▴ European: Spain, South Spain, Portugal, Macedonia, Poland, Greece, Northern Greece, Sweden, Italy, Portugal; □ Others: India, Mozambique, South Africa, Nepal).

The Calchaqui Valleys population stands in the Amerindian cluster, suggesting that this population has a predominantly Native American origin, despite both a lack of admixture proportions data and their self-recognized European ancestry. This finding based on autosomal STRs is consistent with previous mtDNA studies in our study population, indicating almost exclusive Amerindian maternal heritage [39].

The heterogeneity found in Amerindian populations together with the displaced position of some urban general population samples (Neuquén, Argentina) demonstrate the high level of population substructure existing in most South American countries. This fact is presumably due to different admixture proportions from African, European and Native American ancestries, but in some geographical regions it could also be attributed to founding effects and genetic drift in small, isolated populations. These findings emphasize the need of developing more detailed local databases for both genetic studies and forensic applications, instead of using a common pooled database, given that differences may exist even between urban samples within a country region.

In conclusion, this is the first study for the Calchaqui Valleys region based on the 15 AmpFℓSTR Identifiler loci. These data can contribute to the development of a suitable STR database for forensic sciences and anthropology in the Calchaqui Valleys region.

This study follows the ISFG recommendations [40] and the guidelines for publication of population data proposed by the journal [41].

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Acknowledgement 

This work was partially supported by grant PRDIB-2006-687872 from the Direcció General de R+D+I (Comunitat Autònoma de les Illes Balears).

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Appendix A. Supplementary data 

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PII: S1872-4973(11)00097-4

doi:10.1016/j.fsigen.2011.05.002

Forensic Science International: Genetics
Volume 6, Issue 1 , Pages e58-e60, January 2012

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