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DYS19 and DYS199 loci in a Chilean population of mixed ancestry.

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AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 125:85– 89 (2004)
DYS19 and DYS199 Loci in a Chilean Population of
Mixed Ancestry
L. Cifuentes,1* R. Morales,2 D. Sepúlveda,3 H. Jorquera,2 and M. Acuña1
1
Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago 7, Chile
Laboratorio de Biologı́a Molecular, Departamento de Laboratorios, Servicio Médico Legal,
Ministerio de Justicia, Santiago, Chile
3
Genética y Tecnologı́a Ltda., Santiago, Chile
2
KEY WORDS
DYS19; Y microsatellite; DYS199; Y-chromosome haplotype; Chilean
population; genetic admixture; asymmetric mating system
ABSTRACT
The current Chilean population originated from admixture between aboriginal populations
(Amerindians) and Spanish conquerors of European origin. Consequently, the unions that gave rise to the Chilean population were chiefly between Spanish males and
aboriginal females, and not the converse. To test the hypothesis that the Y chromosome of the Chilean population
is mainly of Spanish origin, while the other chromosomes
are from mixed (European and aboriginal) origin, we studied the DYS19 and DYS199 loci in two samples. One
sample was obtained from a high socioeconomic stratum,
while a second sample was from a low stratum. We studied male blood donors (N ⫽ 187) from Santiago, the capital
of the country. Subjects were typed for the autosomal ABO
and Rh (locus D) blood groups, and for the Y-linked DYS19
and the DYS199 loci, reported as Y-chromosome haplotypes. The aboriginal admixture was estimated for each
genetic marker. The percentage of aboriginal admixture
The Chilean population was generated by the admixture between aboriginal populations (Amerindians) and Spanish conquerors of European origin
who arrived in the country in the latter part of the
sixteenth century (Encina, 1983). The Spanish conquerors who arrived in the Chilean territory in the
early years of the colonization (roughly from the late
1500s to late 1600s) were mainly males. Some Spanish females arrived later (at the end of the sixteenth
century), but they only accounted for a small fraction of the Spanish population (Thayer-Ojeda, 1919).
Adult male mortality was probably higher during
the period of conquest than adult female mortality
due to a variety of factors, including warfare with
Europeans. This demographic background predicts
that the unions that gave rise to the Chilean population were chiefly between Spanish males and aboriginal females, and not the converse. While a few
Spanish females accompanied the males arriving in
South America, unions between aboriginal males
and Spanish females would have been rare. Fairly
small groups of other immigrants settled later in the
country. For example, Croatians settled in the
©
2004 WILEY-LISS, INC.
was 38.17% for the ABO system and 31.28% for the Rh
system in the low socioeconomic stratum and 19.22% and
22.5%, respectively, in the high stratum. Y-chromosome
haplotype frequencies constructed from the DYS19 and
DYS199 loci demonstrated that the main haplotypes were
DYS19*14/DYS199 C, as is often the case with many
European populations, and DYS19*13/DYS199 C. The aboriginal admixture from Y-haplotype frequencies was estimated to be 15.83% in the low socioeconomic stratum
and 6.91% in the high stratum. These values are lower
than the values found using autosomal genetic markers,
and are consistent with the historical background of the
population studied. This study highlights the population
genetic consequences of the asymmetric pattern of genome
admixture between two ancestral populations (European
and Amerindian). Am J Phys Anthropol 125:85– 89, 2004.
©
2004 Wiley-Liss, Inc.
southernmost part of Chile in the beginning of the
twentieth century, and Germans arrived around the
middle of the nineteenth century in another region
of the South. Although these groups were more balanced in terms of male-female ratio, their genetic
contribution was not great enough to alter the asymmetry that characterized the original admixture
pattern. Thus it follows that the Y chromosomes of
the Chilean population must be mainly of Spanish
origin, while autosomal chromosomes must be of
Grant sposnor: D.I.D., Universidad de Chile; Grant number: ENL2000/03.
*Correspondence to: L. Cifuentes, Programa de Genética Humana,
ICBM, Facultad de Medicina, Universidad de Chile, P.O. Box 70061,
Santiago 7, Chile. E-mail: lcifuent@machi.med.uchile.cl
Received 29 August 2001; accepted 21 July 2003.
DOI 10.1002/ajpa.10380
Published online 12 January 2004 in Wiley InterScience (www.
interscience.wiley.com).
86
L. CIFUENTES ET AL.
mixed (European and aboriginal) origin (Cifuentes
et al., 1999).
Many population studies have been conducted on
the Chilean population of mixed origin; all were
based on genetic markers located on autosomal chromosomes (Cifuentes et al., 1988). They showed that
the present Chilean population has an aboriginal
(Amerindian) admixture of around 40% (Valenzuela
et al., 1987). This percentage depends on the socioeconomic stratum: it is fairly small (typically less
than 10%) in the upper strata, and greater in lower
strata (Valenzuela, 1988).
Genetic markers located in nonautosomal regions
of the genome have not been studied in the Chilean
mixed population. The DYS19 locus is a microsatellite located in the short arm of the Y chromosome.
Its population diversity is due to a variable number
of GATA tandem repeats (Santos et al., 1993), from
186 bp (13 or A allele) to 202 bp (17 or E allele)
(Roewer et al., 1992); there are also other minor
alleles (Z). The 13 or A allele from this locus is the
most common allele in Amerindian populations,
while the 14 or B allele is the most common in
European populations. The DYS199 locus is a single-base change (C 3 T). The T allele has been found
only in Native American populations, where it is
predominant and is in linkage disequilibrium with
the 186-bp allele of the DYS19 locus (Underhill et
al., 1996).
The goal of this paper is to study the DYS19 and
DYS199 loci in two Chilean population samples of
mixed ancestry, and compare the magnitude of the
aboriginal admixture based on these two genetic
markers, which are located in the nonrecombinant
region of the Y chromosome, with estimates based
on autosomal genetic markers. We chose these genetic markers because their allele frequencies are
quite different in the Spanish (González-Neira et al.,
2000) and South American aboriginal populations
(Santos et al., 1996; Bianchi et al., 1997; Underhill
et al., 1996), which make them a reliable tool to
estimate the ethnic admixture in the Chilean population.
SUBJECTS AND METHODS
Two samples of male blood donors from Santiago,
the capital of Chile, were studied. One sample consisted of male blood donors from a low socioeconomic
stratum (according to a standard questionnaire;
Sepúlveda, 1960) who visited the San José Hospital
in the northern area of Santiago (N ⫽ 99) (Acuña et
al., 2000). The second sample consisted of male blood
donors from a high socioeconomic stratum who visited the Las Condes Clinic (N ⫽ 88). An appropriate
informed consent was obtained from each donor,
following the guidelines of the University of Chile
School of Medicine Ethics Board. They were typed
for the ABO and Rh (locus D) blood groups according
to standard procedures.
DNA was extracted from blood samples using the
organic method described by Comey et al. (1994).
The DNA was quantified by means of electrophoresis, employing 1% agarose gels, ethidium bromide
staining, and comparison with known standards of
molecular weight. To genotype the DYS19 locus,
amplification was made from a 50-ng DNA template,
using the primers described by Roewer and Epplen
(1992). As a negative control, we simultaneously
amplified a DNA sample of a female. The polymerase chain reaction (PCR) was carried out in a Perkin-Elmer thermal cycler for 25 cycles. Each cycle
consisted of 30 sec at 94°C for denaturation, 30 sec
at 65°C for primer annealing, and 90 sec at 72°C for
primer extension. After amplification, the samples
were stored at 4°C. Samples were resolved in 6%
native polyacrylamide gels. Following electrophoresis, fragments were visualized using highly sensitive
silver staining, according to the method of Budowle
et al. (1995). Allele identification was carried out by
comparing each fragment against an allelic ladder
constructed from a mixture of the different alleles
detected in several individuals. The DYS199 locus
was typed by means of two amplification reactions
for each sample, using between 15–25 ng of DNA
with the specific primers described by Underhill et
al. (1996). Thirty-five cycles using the following twostep PCR regime were performed: 94°C for 30 sec,
and 61°C for 20 sec. Ten microliters of the specific
201-bp product were run in an 1% agarose gel, and
UV-visualized by ethidium bromide-staining.
Gene frequencies for the ABO and Rh system were
estimated according to the Bernstein method, assuming Hardy-Weinberg equilibrium (CavalliSforza and Bodmer, 1971). The frequencies for Ychromosome haplotypes constructed from the
DYS19 and DYS199 loci were estimated by direct
count (Nei, 1987), and the standard errors were
calculated assuming a binomial distribution (Steel
and Torrie, 1980). The percentage of aboriginal (Amerindian) admixture in each genetic marker was
estimated using Bernstein’s method (Cavalli-Sforza
and Bodmer, 1971), based on gene frequency data
from ancestral populations already published. These
estimates were made based on the assumption that
allele frequencies from current Spanish and Amerindian populations are similar to those of the Spanish conquerors and Amerindians who met in the
Chilean territory five centuries ago.
RESULTS
Table 1 shows the frequencies for the Y-chromosome haplotypes constructed from the DYS19 and
DYS199 loci in the Chilean samples (San José Hospital, HSJ; Las Condes Clinic, CLC). Table 1 demonstrates that the main haplotype was DYS19*14/
DYS199 C (as is often the case with European
populations). Nevertheless, the presence of the
DYS19*13/DYS199 T haplotype in these two Chilean mixed samples is an evidence of an Amerindian
ethnic component, mainly in the HSJ sample. The T
allele from the DYS199 locus (which has been reported only in Amerindians populations) had a very
87
DYS19 AND DYS199 LOCI IN CHILEAN POPULATION
TABLE 1. Y-chromosome haplotype frequencies constructed from DYS19 and DYS199 loci
in two Chilean samples of mixed ancestry
San José Hospital (N ⫽ 99)
Haplotype
DYS19*12/DYS199
DYS19*13/DYS199
DYS19*14/DYS199
DYS19*15/DYS199
DYS19*16/DYS199
DYS19*17/DYS199
DYS19*13/DYS199
DYS19*14/DYS199
DYS19*15/DYS199
DYS19*16/DYS199
DYS19*17/DYS199
C
C
C
C
C
C
T
T
T
T
T
Las Condes Clinic (N ⫽ 88)
Frequency
Standard error
Frequency
Standard error
0.0110
0.2198
0.5275
0.1429
0.0550
0.0000
0.0219
0.0000
0.0219
0.0000
0.0000
0.01093
0.04341
0.05234
0.03668
0.02389
0.00000
0.01537
0.00000
0.01537
0.00000
0.00000
0.0000
0.0455
0.6705
0.1363
0.1023
0.0000
0.0227
0.0227
0.0000
0.0000
0.0000
0.00000
0.02220
0.05011
0.03658
0.03230
0.00000
0.01589
0.01589
0.00000
0.00000
0.00000
TABLE 2. Gene frequencies of ABO and Rh system and percentage of aboriginal admixture
in two Chilean samples of mixed ancestry1
Gene frequencies in
San José Hospital
Allele
Spanish2
Aboriginal3
Gene
frequency
A
B
O
Rh D
Rh d
0.2864
0.0670
0.6465
0.5937
0.4063
0.0678
0.0000
0.9322
1.0000
0.0000
0.2143
0.0354
0.7575
0.7202
0.2798
Las Condes Clinic
Aboriginal
admixture (%)
Gene
frequency
Aboriginal
admixture (%)
32.98
47.16
38.85
31.13
31.13
0.2395
0.0455
0.7149
0.6855
0.3145
21.45
32.09
23.94
22.59
22.59
1
San José Hospital, low socioeconomic stratum; Las Condes Clinic, high socioeconomic stratum.
Campillo (1976).
3
Llop and Rothhammer (1988).
2
low frequency in both Chilean samples. The high
frequency of the DYS19*13/DYS199 C haplotype observed in HSJ is surprising: it is considerably
greater than that of either of the supposedly ancestral populations.
Table 2 shows the gene frequencies of the Rh and
ABO blood groups for the two samples studied and
the estimates of aboriginal admixture in the samples studied, based on these two genetic systems.
These autosomal genetic markers are useful tools to
estimate the genetic admixture between European
and Amerindian populations because of the large
differences in allele frequencies between these two
ethnic groups. The gene frequencies from the Spanish and Amerindian populations used to estimate
the aboriginal admixture are those published by
Campillo (1976) and Llop and Rothhammer (1988).
The percentage of aboriginal admixture was 38.17%
for the ABO system (doing a weighted average using
the admixture estimate of each allele) and 31.13%
for the Rh system in HSJ (low socioeconomic stratum), and 23.71% and 22.59% in the CLC sample,
respectively. These values are consistent with the
admixture estimates published for different socioeconomic strata in the Chilean population (Valenzuela, 1988).
Table 3 shows the percentage of aboriginal admixture in the samples based on haplotype frequencies
from the DYS19 and DYS199 loci. To estimate the
aboriginal admixture, we collected data from the
literature for each ancestral population: the South
American aborigines (Underhill et al., 1996; Bianchi
et al., 1997, 1998; Di Pierri et al., 1998) and the
Spanish population (Gonzalez-Neira et al., 2000;
Kayser et al., 1997). The weighted average percentages of aboriginal admixture in the HSJ sample
were 15.83%, and 6.91% in the CLC sample. It can
be seen that the aboriginal admixture is lower in the
high socioeconomic stratum sample (CLC), in accordance with data already published for autosomal
loci (Valenzuela, 1988). The percentage of aboriginal
admixture is lower in the Y-chromosome loci than
the percentages found in the autosomal loci for both
samples studied.
DISCUSSION
The Y-chromosome haplotype frequencies based on
the DYS19 and DYS199 loci in the Chilean samples
are consistent with the historical background of the
population under consideration. The high frequency of
the DYS19*14/DYS199 C haplotype is evidence of a
preponderant European (Spanish) component. However, the DYS19*13/DYS199T haplotype reflects the
aboriginal (Amerindian) components.
We cannot explain the high frequency of the
DYS19 *13/DYS199 C haplotype observed in HSJ;
this frequency is greater than those reported for
European populations. This result cannot be explained by technical errors, for if that were the case
we should also have observed the same result in the
sample from Clı́nica Las Condes. While it is possible
that the original inhabitants of this region of Chile
had allele frequencies different from those of the
South American Indians used as the reference pop-
88
L. CIFUENTES ET AL.
TABLE 3. Percentage of aboriginal admixture in Y-chromosome haplotypes constructed from DYS199 and DYS19 loci of a Chilean
mixed population, based on comparison with allele frequencies in Spanish and Amerindian populations1
Frequencies in populations
Chilean mixed samples
Haplotype
DYS19*12/DYS199
DYS19*13/DYS199
DYS19*14/DYS199
DYS19*15/DYS199
DYS19*16/DYS199
DYS19*17/DYS199
DYS19*12/DYS199
DYS19*13/DYS199
DYS19*14/DYS199
DYS19*15/DYS199
Total2
C
C
C
C
C
C
T
T
T
T
Aboriginal admixture(%)
Spanish
Amerindian
HSJ
CLC
HSJ
CLC
0.0000
0.0942
0.6993
0.1449
0.0435
0.0181
0.0000
0.0000
0.0000
0.0000
276.0
0.0000
0.0101
0.0202
0.0202
0.0000
0.0000
0.0101
0.7980
0.1212
0.0202
99.0
0.0110
0.2198
0.5275
0.1429
0.0550
0.0000
0.0000
0.0219
0.0000
0.0219
99.0
0.0000
0.0455
0.6705
0.1363
0.1023
0.0000
0.0000
0.0227
0.0227
0.0000
88.0
0.00
⬍0.00
25.30
1.60
⬍0.00
100.00
0.00
2.70
0.00
⬎100.00
99.0
0.00
57.91
4.24
6.90
⬍0.00
100.00
0.00
2.85
18.73
0.00
88.0
1
HSJ, San José Hospital; CLC, Las Condes Clinic.
Number of Y chromosomes from each population. Frequencies for Spanish and Amerindian populations correspond to pooled data
already published (see text).
2
ulation, or that there has been some selective force
operating to favor this haplotype, there is currently
no available evidence to support either of these hypotheses. Another possibility is the postcolonial incorporation of an atypical European-descent population to the northern area of Santiago. However,
there is no historical information to support this
idea.
The percentage of aboriginal admixture found in
the Chilean samples for Y-chromosome haplotypes
based on the DYS19 and DYS199 loci is much lower
than the percentage of Amerindian ethnic component described for autosomal regions of the genome
in the Chilean population. Again, this result agrees
with the historical background of the population
studied, which indicates an asymmetrical system of
mating between ancestral populations. This asymmetry also predicts that the proportion of the indigenous component in the mixed Chilean population
should be greater for genes located in the X chromosome, and greater still for mitochondrial genes. This
hypothesis is supported by a recent study of polymorphisms in mitochondrial DNA (Rocco et al.,
2002), which reported that 84% of the haplogroups
in a similar mixed Chilean population were of Amerindian origin. This situation may also be found in
other populations of mixed origin. Previous studies
in other South American populations with an aboriginal component greater than that found in the
Chilean population also demonstrated directionality
of marriages. For example, the genetic admixture
with Amerindians is much lower for the Y chromosome than for other regions of the genome in the
Peruvian Quechuas (Rodrı́guez-Delfin et al., 2001).
A similar situation was reported in terms of the
contribution of indigenous females to the formation
of the Belém population (Brazilian Amazon region).
Here, it was found that the contribution of females is
10 times higher than that of indigenous men (Dos
Santos et al., 1999).
This study demonstrated one of the consequences,
in terms of population genetics, of an asymmetric
pattern of genome admixture between the ancestral
European and Amerindian source populations. The
autosomal Amerindian component of the Chilean
population is around 40%, while the Amerindian Y
component appears to be less than 20%. In the case
of the Chilean population, we suggest that it is important to consider the different patterns of ancestry
of the different regions of the genome when making
risk assessment of Y chromosome-based genetic diseases that depend on ethnic origin (Osterlund et al.,
2000).
ACKNOWLEDGMENTS
We are indebted to Prof. Lafayette Eaton for correcting our English usage and making helpful comments.
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