Forensic Science International: Genetics 21 (2016) 76–80

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Forensic Science International: Genetics

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

Short communication

Analysis of Y-chromosome STRs in Chile confirms an extensive

introgression of European male lineages in urban populations
Ulises Toscaninia,b,d,1, Francesca Brisighellib,e,1, Fabián Morenob,c,
Jaime A. Pantoja-Astudilloc, Eugenia Aguirre Moralesc,d, Patricio Bustosc ,
Jacobo Pardo-Secob,d, Antonio Salasb,d,1,*
a
Pricai-Fundación Favaloro, Buenos Aires, Argentina
b
Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX),
Facultade de Medicina, Universidade de Santiago de Compostela, 15872 Galicia, Spain
c
Servicio Medico Legal, Ministerio de Justicia, Santiago, Chile
d
Infectious Diseases and Vaccines Unit, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
e
Sezione di Medicina Legale-Istituto di Sanità Pubblica, Università Cattolica del Sacro Cuore, Roma, Italy

A R T I C L E I N F O A B S T R A C T

Article history: We analyzed the Y chromosome haplotypes (Yfiler) of 978 non-related Chilean males grouped in five
Received 12 May 2015 sampling regions (Iquique, Santiago de Chile, Concepción, Temuco and Punta Arenas) covering main geo-
Received in revised form 5 December 2015 political regions. Overall, 803 different haplotypes and 688 singletons were observed. Molecular diversity
Accepted 9 December 2015
was moderately lower than in other neighboring countries (e.g. Argentina); and AMOVA analysis on Y-
Available online 11 December 2015
STR haplotypes showed that among variation within Chile accounted for only 0.25% of the total variation.
Punta Arenas, in the southern cone, showed the lowest haplotype diversity, and discrimination capacity,
Keywords:
and also the highest matching probability of the five Chilean samples, probably reflecting its more
Y-filer
Y-STR
marked geographic isolation compared to the other regions. Multidimensional scaling (MDS) analysis
Chile based on RST genetic distances suggested a close proximity of Chilean Y-chromosome profiles to European
Forensic genetics ones. Consistently, haplogroups inferred from Y-STR profiles revealed that the Native American
YHRD component constituted only 8% of all the haplotypes, and this component ranged from 5% in the Centre of
the country to 9–10% in the South and 13% in the North, which is in good agreement with the distribution
of Native American communities in these regions. AMOVA computed on inferred haplogroups confirmed
the very low among variation observed in Chilean populations. The present project provides the first
Chilean dataset to the international Y-chromosome STR Haplotype Reference Database (YHRD) and it is
also the first reference database for Y-chromosome forensic casework of the country.
ã 2015 Elsevier Ireland Ltd. All rights reserved.

1. Introduction The national census (INE; http://www.ine.cl) carried out in

Chile has an unusual ribbon-like shape, with more than
4300 km long and on average 175 km wide. Climatic conditions
varied from the world’s driest desert in the Atacama region (North)
to a Mediterranean-like climate in the centre. Chile has a multi-
ethnic society that was mainly originated by the admixture
between local Native populations and Europeans. The main
proportion of Europeans were Spaniards that arrived in the
country in the latter part of the XVI century, most of them males
[1]. Other minor European groups arrived to Chile in more recent
times such as Croatians and Germans.
* Corresponding author.
E-mail address: antonio.salas@usc.es (A. Salas).
1
These authors contributed equally to this work.
1992 aimed to characterize the indigenous population of the
country by recording self-reported ancestry of Chileans. The
1992 census considered only three indigenous populations
(Mapuche, Aymara, and Rapanui; Ley N 19.523; “Ley Indígena”),
but the posterior modification of this law in 1993 adopted the
allocation of each person to one of the following eight population
groups: Alacalufe (Kawaskar), Atacameño, Aymara, Colla, Mapu-
che, Quechua, Rapanui, and Yámana (Yagán). The last official
census from 2002 indicated that only 4.6% of the Chileans
(n = 692.192 persons in a total population of about 15 million)
declared to belong to one of these eight ethnic groups; most of
them belonging to the Mapuche (87.3%), and being the Aymara the
second most important group (7%).
In contrast to other South American countries where Y-
chromosome genetic studies have been very popular on different

http://dx.doi.org/10.1016/j.fsigen.2015.12.005
1872-4973/ ã 2015 Elsevier Ireland Ltd. All rights reserved.
 U. Toscanini et al. / Forensic Science International: Genetics 21 (2016) 76–80 77

anthropological and forensic contexts, there are only a few studies

carried out on the Y-chromosome variation in Chile, all of them
related to small-scale sampling or the genotyping of a few Y-STRs.
The pioneering study by Cifuentes et al. [2] based on autosomal STR
markers, suggested that admixed Chileans had and aboriginal
admixture of around 40%, but this percentage depended on the
socioeconomic stratum, with less than 10% in their social upper
strata and greater in social lower strata. Later, Cifuentes et al. [3]
analyzed the DYS19 and DYS199 markers in two Chilean
population samples of mixed ancestry and inferred admixture
proportions from them. By comparing these results on the Y-
chromosome with autosomal data the authors claimed an
asymmetric pattern of genome admixture between the European
and Native American components, a pattern that is also observed
in many other regions of South America [4–6]. According to these
authors the autosomal Native component was around 40%, while
the Native Y-chromosome component was below 20%. More
recently, Lardone et al. [7] analyzed the prevalence of Amerindian
Y-chromosomes in Chilean patients with spermatogeneic failure
and their association with classical and/or AZFc-partial Y-
chromosome deletions; this study showed the presence of
haplogroup Q1a3a in 9% of their main control group, but
frequencies ranged from 8.2% to 11.8% in their various sub-control
groups.
Chile is one of the very few larger unsampled countries
(together with i.e. Canada and New Zealand) in the Y-Chromosome
STR Haplotype Reference Database (YHRD), the international
reference forensic database that currently contains Y-chromosome
haplotypes sampled worldwide (e.g. 129 countries represented in a
collection of >154,000 minimal haplotypes [MHT]; Release 49,
2015/Feb/27). The present study is therefore the first attempt in
characterizing the Y-chromosome variation of Chile by way of
genotyping one of the forensic Y-STR reference panel (namely, the
Yfiler; see below). This project was prompted by the need of having
population haplotype frequencies from randomly drawn samples
of individuals in Chile for the purpose of human identification
casework being done in the context of Human Rights Program of
the Medico Legal Services of the country. In addition, the Fig. 1. Map of Chile showing the sampled regions in the present study. The pie
populations analyzed in the present project represent a large charts indicate the frequency of the Native American haplogroup frequencies vs. the
sampling effort that has a wide geographic coverage, representing rest of the haplogroups merged in a single category.
the main regions from northern to southernmost Chile.
Yunnan (n = 101), and (iv) Africa (n = 136): Ibadan from Nigeria and
2. Material and methods Zimbabwe.
In addition, further data from the neighboring populations of
2.1. Sampling Argentina (bordering at the East of Chile in all its extension from
North to South) analyzed in Toscanini et al. [10,11], were also added
Buccal swab from 978 unrelated males from urban populations because its geographic proximity and comparable past and recent
were collected after written informed consent at five sample demographic history.
collection sites of Chile, namely, Iquique (n = 196; YHRD accession
number: YA004059), Santiago de Chile (n = 196; YA004061), 2.2. DNA extraction and genotyping
Concepción (n = 198; YA004058), Temuco (n = 194; YA004062)
and Punta Arenas (n = 194; YA004060) (Fig. 1). Sampling was DNA was extracted from buccal swabs using the DNA IQTM
carried out at random without taking social strata into consider- System (Promega Corporation, Madison, USA) on the Tecan
ation; therefore, there is no evidence indicating that social strata Freedom EVO1 100 (Tecan Group Ltd., Männedorf, Switzerland).
were differently represented at the five recruitment sites. The seventeen Y-STR markers included in the AmpF/STR1
The samples analyzed in the present study represent a subset of YfilerTM kit (Life Technologies, USA; DYS19, DYS385a/b, DYS389I,
the samples genotyped for a panel of autosomal STRs in Toscanini DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438,
et al. [8]. DYS439, DYS448, DYS456, DYS458, DYS635, Y-GATA-H4), were
Beside the Chilean samples, various datasets from Purps et al. analyzed following manufacturer instructions. All samples were
[9] were used for population comparisons, representing popula- subjected to electrophoresis on the ABI PRISM1 3130xl Genetic
tions from (i) South America (n = 487): Bolivia (‘Mestizo’ and Native Analyzer (Applied Biosystems, USA). DNA extraction and Y-STR
American), Peru, Brazil (‘Admixed’ from São Paulo and Río de genotyping were carried out in the Laboratory of Human
Janeiro, São Gabriel de Cachoeira, Native Americans), (ii) Europe Identification of the University of North Texas (UNT) Health
(n = 2168): Aragón, Asturias, Barcelona, Galicia, Madrid (all from Science Center.
Spain), Brescia, Calabria, Liguria, Marche, Milano, northeastern Amplified products were subsequently analyzed with the
Italy, Puglia, Ravenna, Sicily, Tuscany (all from Italy), (iii) Asia: GeneMapper v3.2 software (Applied Biosystems). Only
78 U. Toscanini et al. / Forensic Science International: Genetics 21 (2016) 76–80

Table 1
Molecular diversity indices on Y-chromosome profiles from Chile and other reference populations. Values in brackets refer to standard errors. Diversity values from Argentina
were included in this table for reference; the data was obtained from Toscanini et al. [10].

N K UH HD M DC MP

Population MHT Yfiler MHT Yfiler MHT Yfiler MHT Yfiler MHT Yfiler MHT Yfiler
Chile 978 54% 82% 39% 70% 0.9939 (0.0008) 0.9994 (0.0001) 4.89 (2.39) 10.16 (4.64) 0.540 0.821 0.007126 0.0015933
Iquique 196 73% 95% 63% 91% 0.9901 (0.0029) 0.9995 (0.0006) 4.75 (2.33) 9.98 (4.58) 0.735 0.954 0.0149417 0.0056227
Santiago 196 75% 96% 65% 93% 0.9931 (0.0020) 0.9996 (0.0006) 4.93 (2.41) 10.23 (4.70) 0.750 0.964 0.0119221 0.0054665
Concepción 198 74% 92% 62% 84% 0.9942 (0.0015) 0.9991 (0.0006) 4.96 (2.42) 10.21 (4.68) 0.742 0.919 0.0108152 0.0059178
Temuco 194 80% 97% 68% 94% 0.9963 (0.0012) 0.9997 (0.0006) 4.98 (2.43) 10.32 (4.73) 0.799 0.969 0.0088213 0.0054735
Punta Arenas 194 65% 81% 50% 70% 0.9904 (0.0023) 0.9967 (0.0011) 4.84 (2.37) 10.04 (4.61) 0.649 0.809 0.0147199 0.0083962
Argentina 621 73% 95% 60% 90% 0.9972 (0.0006) 0.9998 (0.0001) 5.10 (2.48) 10.51 (4.80) 0.729 0.947 0.0044420 0.0018022
Argentina-North 180 84% 94% 69% 88% 0.9980 (0.0009) 0.9993 (0.0007) 5.35 (2.59) 10.86 (4.96) 0.839 0.939 0.0075926 0.0062963
Argentina-Centre 311 79% 96% 69% 92% 0.9971 (0.0008) 0.9997 (0.0003) 4.99 (2.43) 10.43 (4.77) 0.794 0.958 0.0061517 0.0035256
Argentina-South 130 86% 98% 78% 97% 0.9951 (0.0026) 0.9998 (0.0010) 4.94 (2.42) 10.13 (4.66) 0.862 0.985 0.0125444 0.0079290
Europe 2168 58% 94% 45% 89% 0.9956 (0.0005) 0.9999 (0.0000) 4.98 (2.43) 10.36 (4.73) 0.579 0.938 0.0048789 0.0005408
South America 1108 69% 94% 56% 89% 0.9974 (0.0004) 0.9999 (0.0001) 5.21 (2.52) 10.62 (4.84) 0.693 0.938 0.0034716 0.0010475

MHT: minimal haplotype; K = number of different haplotypes; UH = singletons; HD = haplotype diversity; M = mean number of pairwise differences; DC = discrimination
capacity; MP = match probability.

preliminary results were announced in the Forensic Genetics
13 Proceedings of the 23rd International ISFG Congress [12],
and the data were neither released to public resources nor to the
YHRD.
2.3. Statistical analyses
Molecular diversity indices (Haplotype Diversity [HD], number
of different [K] and unique haplotypes [UH]) and parameters of
forensic interest (Discrimination Capacity [DC] and Matching
Probability [MP]), were estimated as described in Purps et al. [9].
The Arlequin software v3.5.1.2 [13] was used for most of the
analyses. All the indices were calculated for both, the full Yfiler
haplotypes and their corresponding 9-Y-STR MHT.
Computation of Mean Number of Pairwise Differences, Analysis
of Molecular Variance (AMOVA) and estimation of RST genetic
distances (as implemented in Arlequin software v3.5.1.2) were
performed in order to assess the genetic structure and variation
among the different samples. Issues regarding DYS385ab marker
were considered as in Purps et al. [9] for these analyses.
RST genetic distances were also computed between sample sets
from Chile (present study), Argentina [10], Europe, and Africa [9].
The Toba from Argentina [11] was also added to the analysis in order
to attract the Native American component of the Chileans and other
reference populations; the Toba was selected because it has only a
minor proportion of non Native American Y-chromosome ancestry
[11] compare to other Native American populations in South
America. A Kruskal’s Non-metric Multidimensional Scaling analysis
(MDS) analysis based on the RST distances was built using the
isomds function as implemented in MASS package (https://stat.
ethz.ch/R-manual/R-devel/library/MASS/html/isoMDS.html).
2.4. Haplogroup inference
The full Yfiler haplotypes excluding DYS385ab were used to
allocate them to their most likely haplogroup using the Athey’s

Fig. 2. MDS plot on RST distances. The inset is a zoom-in of the European pole of the main MDS plot. The European pole is represented by various Spanish populations; while
the African and the Native American poles are represented by people from Ibadan (Nigeria and Zimbabwe) and the Toba (Argentina), respectively. See Section 2 for more
information.
 U. Toscanini et al. / Forensic Science International: Genetics 21 (2016) 76–80 79

Table 2 related to Europeans and urban Argentineans (see also Ref. [10]),
Haplogroup frequencies inferred from Y-STR in the different regions sampled in
then suggesting a high European Y-chromosome ancestry in Chile.
Chile.
The MDS analysis did not suggest the presence of a sub-Saharan
Chile Iquique Santiago Concepción Temuco Punta Arenas African component in Chileans, as it was clearly observed in other
E1b1a 0.002 0.005 0.005 South American populations i.e. [5,15,16].
E1b1b 0.101 0.071 0.082 0.152 0.119 0.082
G2a 0.044 0.036 0.071 0.051 0.026 0.036
3.3. Haplogroup frequency patterns
H 0.002 0.005 0.005
I1 0.020 0.005 0.005 0.030 0.041 0.021
I2a (xI2a1) 0.011 0.010 0.010 0.010 0.026 Haplogroups were inferred from Y-STR profiles (Table 2). These
I2a1 0.021 0.015 0.020 0.025 0.031 0.015 analyses showed that the Native American lineages (i.e. P + Q
I2b (xI2b1) 0.003 0.010 0.005 haplogroups) fairly represent an 8.3% of the genetic profiles of the
I2b1 0.011 0.005 0.020 0.015 0.005 0.010
global Chilean database; 93% of this indigenous component
J1 0.041 0.046 0.046 0.030 0.036 0.046
J2a1 x J2a1- 0.015 0.015 0.020 0.030 0.005 0.005 belonged to haplogroup Q (the remaining was accounted by
bh haplogroup P). The Native American component was lower in the
J2a1b 0.042 0.036 0.056 0.051 0.036 0.031 Centre of the country (5% in Santiago and Concepción), reached 9%
J2a1h 0.008 0.010 0.005 0.015 0.010
in the South (Temuco: 10%) and in the southernmost region of Chile
J2b 0.022 0.031 0.036 0.005 0.010 0.031
L 0.007 0.005 0.010 0.010 0.010
(Punta Arenas; 9%), and a maximum peak in the North (Iquique:
N 0.001 0.005 13%).
Q 0.083 0.128 0.061 0.051 0.098 0.077 The rest of the haplogroups in Chile (91.7%) were most likely of
R1a 0.016 0.010 0.010 0.015 0.015 0.031 Eurasian origin (Table 2). Their frequencies were relatively
R1b 0.525 0.556 0.515 0.485 0.510 0.557
homogeneous across the country. The most prevalent haplogroup
T 0.022 0.005 0.020 0.040 0.031 0.015
was R1b, which accounted for 51% in Chile; its frequency varied
slightly from 49% in Concepción to 54% in Punta Arenas. The second
most frequent haplogroup was E (10% on average), and it showed a
Haplogroup Predictor tool (http://www.hprg.com/hapest5/ more variable distribution: it reached 7.1% in Iquique and reached a
hapest5a/hapest5.htm?order=num). Petrej9 cíková et al. [14] maximum in Concepción (15.7%).
showed that this tool predicts correctly the haplogroup in
98.19% of the cases using only 12 Y-STRs. In addition, we inferred 4. Discussion
the haplogroup status using the Urasin’s Predictor software v.1.5.0
(http://predictor.ydna.ru). Both haplogroup predictors yielded As previously proven in other populations, Yfiler haplotypes
virtually the same frequency results for the root haplogroups showed a significantly higher molecular diversity and discrimina-
(the phylogenetic resolution used in the present study). tion power than MHT from the same individuals in Chile,
strengthening the convenience of using this Y-STR set in forensic
3. Results genetic instead of the MHT panel.
Various analyses were carried out using Argentina as a
3.1. Molecular diversity reference population given its similar demography to Chile,
historically and contemporarily. Effectively, the data showed some
The full Yfiler haplotypes for the 978 individuals sampled are parallelism in term of molecular diversity and haplogroup
reported in Supplementary Table S1. Neither null alleles nor composition between these two countries. In general, Chile has
duplications were observed. Intermediate alleles were observed in slightly lower values of molecular diversity (reflected on summary
50 individuals, of which 47 were found in DYS458. statistical indices). This is somehow expected if we take into
Diversity and forensic indices are shown in Table 1. HD was account that the impact of European immigrants arriving to South
always higher than 0.999 except for Punta Arenas (0.9967), America was much higher in the countries facing the Atlantic
indicating a decrease in the variation at the southernmost region of shores of the continent than in those countries exposed exclusively
the country. Compared to other populations, the global HD for to the Pacific Ocean (like Chile). Thus, Chile was traditionally a
Chile appeared to be slightly lower than that observed in provinces remote place for migrants because it was far from Europe and quite
from Argentina, Europe (Spain and Italy) and pooled populations inaccessible historically; this fact was already recorded in the
from South America; in part, this is mainly due to the low value census of 1907 indicating that the highest percentage of citizens
observed in Punta Arenas. A similar situation was observed for the born in Europe versus the total population of Chile was 2.2% (INE).
proportion of different haplotypes and of unique haplotypes when Although the arrival of Europeans into Chilean territories was
comparing the whole Chilean sample with those populations probably lower than in Argentina in historical times, the results of
mentioned above (Table 1). the present study indicate a massive introgression of European Y-
Finally, AMOVA, when carried out on the five Chilean regions chromosome haplotypes (about 92%) into the present-day Chilean
analyzed, shows that most of the variation (99.75%) occurred urban population. MDS analysis based on RST distances corrobo-
within populations. rated the presence of this component by allocating all the Chilean
sub-samples very closely related to Europeans.
3.2. Multidimensional scaling analysis The results from AMOVA indicated a very low proportion of
among population Y-chromosome variation in the country.
MDS analysis was performed based on RST distances in order to AMOVA however not always mirrors population differences that
visualize population sample relationships (Fig. 2). A set of could be relevant in forensic genetics [17–20]. Instead, phyloge-
neighboring Argentinean populations was also added for compari- netic analysis can sometimes show patterns of population sub-
son, including the Native American Toba as a reference population structure that could pass unnoticed when using FST-based
of Native American ancestry [11]. The MDS plot displays the three measures. In our study, however, analysis of inferred haplogroups
reference populations in the vertex of a quasi-equilateral triangle; does not reveal the existence of pronounce population stratifica-
each vertex indicating the European, the African, and the Native tion either. Thus, the European haplogroup frequencies observed in
American poles. Genetic distances showed Chileans to be closely Chile were relatively homogeneous all over the country, while the
80 U. Toscanini et al. / Forensic Science International: Genetics 21 (2016) 76–80
scenario was difference in Argentina, where different provinces
showed differential impact of Eurasian source populations. In
addition, the Native American component in Chile, although lower
than in Argentina (and much lower than other South American
populations [5,16]), showed only discrete variation in different
regions from Chile. The highest value of this Native component was
found in the North. Not surprisingly, this is the region that hosts
one of the highest Native American communities of the country
(i.e. Aymara). The southern region of the country showed also a
higher proportion of Native American Y-chromosomes than the
centre; and this is also in good agreement with the presence of the
most important Native American community at this latitude (i.e.
Mapuches).
In summary, the present study is one of the very few population
genetic studies carried out in Chile; and the results provide new
insights into the Y-chromosome genetic characteristics of the
country. Last but not least, the data generated in the present
project represents the first Y-STR database that is available in the
literature for use in forensic casework carried out in Chile, and it is
the first dataset from this country that is included in the YHRD.
This study is also of special value in prosecuting human rights
violations occurring during the military government of the
dictatorship suffered in Chile since 1973 until 1990.
Conflict of interest
None
Acknowledgements
The authors declare no conflicts of interest. AS received funding
from the “Ministerio de Ciencia e Innovación” (SAF2011-26983),
the Plan Galego IDT (EM 2012/045) and the grant from the Sistema
Universitario Gallego- Modalidad REDES (2012-PG226) from the
Xunta de Galicia (A.S.).
Appendix A. Supplementary data
Supplementary data associated with this article can be
found, in the online version, at http://dx.doi.org/10.1016/j.
fsigen.2015.12.005.
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