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FSIGEN-748; No. of Pages 3

Forensic Science International: Genetics xxx (2011) xxx–xxx

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Forensic Science International: Genetics

journal homepage: www.elsevier.com/locate/fsig

Letter to the Editor

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

A B S T R A C T

Keywords: Allele frequencies for 15 short tandem repeat (STR) loci were obtained from a sample of 110 individuals
STRs
from the Calchaqui Valleys population (North-Western Argentina). The combined power of exclusion and
Allelic frequencies
combined power of discriminating for the 15 tested STR loci were 0.999964 and 0.9999999999999998,
Calchaqui Valleys
North-Western Argentina (NOA) 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.
ß 2011 Elsevier Ireland Ltd. All rights reserved.

Dear Editor
The Calchaqui Valleys are located in the Andes Mountains, in
the North Western Argentina region (NOA), occupying a band of
approximately 200 km in a North–South direction at an altitude
between 1700 and 3000 m (provinces of Salta, Tucumán and
Catamarca). In the pre-Hispanic era, these valleys were inhabited
by the diaguitas whose societies reached the highest socioeco-
nomic 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 propor-
tion 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 AmpF‘STR 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 Gene-
Mapper 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.
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 [8–36]. 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 Amerin-
dian 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

1872-4973/$ – see front matter ß 2011 Elsevier Ireland Ltd. All rights reserved.
doi:10.1016/j.fsigen.2011.05.002

Please cite this article in press as: A. Muñoz, Allele frequencies of 15 STRs in the Calchaqui Valleys population (North-Western
Argentina), Forensic Sci. Int. Genet. (2011), doi:10.1016/j.fsigen.2011.05.002
G Model
FSIGEN-748; No. of Pages 3

2 Letter to the Editor / Forensic Science International: Genetics xxx (2011) xxx–xxx

Fig. 1. Map of the situation of the most populated localities in the Calchaqui Valleys
(Argentina).
Fig. 2. MDS plot based on Reynolds’ distances ($ Calchaqui Valleys [this study] and
* Amerindian: Conchagua, Pilagá, Toba-Chaco, Toba-Formosa, Wichı́-Chaco,
Wichı́-Formosa; * Latin-American: Argentina (Buenos Aires, Neuquén, Misiones,
Salta, Formosa, Chaco, Corrientes, Santa Fe, Mendoza, Rı́o 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).

Table 1
Statistical parameters for AmpF‘STR Identifiler-15 loci in the Calchaqui Valleys population.

D8S1179 D21S11 D7S820 CSF1PO D3S1358 TH01 D13S317 D16S539 D2S1338 D19S433 vWA TPOX D18S51 D5S818 FGA

NA 8 10 7 6 6 6 8 7 11 12 6 6 15 9 13
Ho 0.8273 0.7909 0.7115 0.6355 0.5963 0.5981 0.7890 0.7798 0.7593 0.8426 0.6759 0.5872 0.7714 0.7156 0.7830
He 0.8159 0.8420 0.6674 0.6922 0.6176 0.6287 0.8230 0.7755 0.8275 0.8322 0.6971 0.5679 0.8461 0.7052 0.8549
MP 0.0638 0.0499 0.1784 0.1430 0.2145 0.1914 0.0556 0.0913 0.0576 0.0487 0.1391 0.2437 0.0491 0.1172 0.0470
PD 0.9362 0.9501 0.8216 0.8570 0.7855 0.8086 0.9444 0.9087 0.9424 0.9513 0.8609 0.7563 0.9509 0.8828 0.9530
PIC 0.7913 0.8226 0.6046 0.6397 0.5543 0.5783 0.7995 0.7393 0.8084 0.8121 0.6456 0.5086 0.8285 0.6720 0.8399
PE 0.6506 0.5823 0.4463 0.3357 0.2865 0.2886 0.5788 0.5621 0.5257 0.6803 0.3920 0.2758 0.5471 0.4528 0.5679
TPI 2.8947 2.3913 1.7333 1.3718 1.2386 1.2442 2.3696 2.2708 2.0769 3.1765 1.5429 1.2111 2.1875 1.7581 2.3043
P 0.7563 0.1380 0.3219 0.1934 0.6435 0.5037 0.3451 0.9125 0.0561 0.7689 0.6265 0.6805 0.0285a 0.8101 0.0307a

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.
a
Not statistically significant after Bonferroni’s correction.

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].
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 coun-
tries. This fact is presumably due to different admixture propor-
tions 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 AmpF‘STR 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].
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).
Appendix A. Supplementary data
Supplementary data associated with this article can be found, in
the online version, at doi:10.1016/j.fsigen.2011.05.002.
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A. Muñoz
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
M.V. Albeza
N. Acreche
Cátedra de Antropologı´a, Facultad de Humanidades,
Universidad Nacional de Salta, Av. Bolivia 5150,
4400 Salta, Argentina
J.A. Castro
M.M. Ramon
A. Picornell*
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
*Corresponding author. Tel.: +34 971 172050;
fax: +34 971 173184
E-mail address: apicornell@uib.es (A. Picornell).
7 March 2011