Human Immunology xxx (xxxx) xxx–xxx

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Human Immunology
journal homepage: www.elsevier.com/locate/humimm

Genetic diversity of HLA system in two populations from Morelos, Mexico:

Cuernavaca and rural Morelos
Andrea Ortega-Yáñeza,1, Rodrigo Barquerab,c, ,1, Laura Curiel-Gilesd,1,
⁎

Julio César Martínez-Álvareze,1, Rosa María Macías-Medranof,1, Esteban Arrieta-Bolañosg,1,

Stephen Claytonb,1, Alicia Bravo-Acevedoh,1, Diana Iraíz Hernández-Zaragozac,i,
Alexander Immelb,j, María del Rosario Vega-Martínezk, Gamaliel Benítez-Arvizul,
María Araceli Arrazola-Garcíae, Agustín Jericó Arriaga-Pereaf, Eva Dolores Juárez-Cortésf,
Vicencio Juárez-Barretom, Norma Salgado-Galiciak, Bárbara Novelo-Garzan, Joaquín Zúñigao,p,
Edmond J. Yunisq, Carolina Bekker-Méndezr, Julio Granadoss, ,1
⁎

a
Department of Developmental Genetics and Molecular Physiology, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Cuernavaca,
Morelos, Mexico
b
Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
c
Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
d
Forensic Anthropology Area, Fiscalía General del Estado de Morelos, Cuenavaca, Morelos, Mexico
e
HLA Laboratory, Central Blood Bank, Hospital de Especialidades, Unidad Médica de Alta Especialidad (UMAE) Centro Médico Nacional “Siglo XXI”, Instituto Mexicano
del Seguro Social (IMSS), Mexico City, Mexico
f
Histocompatibility Laboratory, Central Blood Bank, Centro Médico Nacional “La Raza”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
g
Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
h
Blood Bank, UMAE Hospital de Gineco Obstetricia No. 4 “Luis Castelazo Ayala”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
i
Immunogenetics Unit, Técnicas Genéticas Aplicadas a la Clínica (TGAC), Mexico City, Mexico
j
Institute of Clinical Molecular Biology (IKMB), Kiel University, University Hospital, Schleswig-Holstein, Germany
k
Molecular Biology and Histocompatibility Laboratory, Hospital Central Sur de Alta Especialidad, Petróleos Mexicanos (PEMEX), Mexico City, Mexico
l
Central Blood Bank, Hospital de Especialidades, Unidad Médica de Alta Especialidad (UMAE) Centro Médico Nacional “Siglo XXI”, Instituto Mexicano del Seguro Social
(IMSS), Mexico City, Mexico
m
Blood Bank, Hospital Infantil de México “Federico Gómez”, Mexico City, Mexico
n
Medical Infrastructure Planning Committee, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
o
Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
p
Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
q
Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
r
Immunology and Infectology Research Unit, Infectology Hospital, Centro Médico Nacional “La Raza”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
s
Department of Transplantation, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán” (INCMNSZ), Mexico City, Mexico

ARTICLE INFO ABSTRACT

Keywords: We studied HLA class I (HLA-A, -B) and class II (HLA-DRB1, -DQB1) alleles by PCR-SSP based typing in 112
HLA Mexicans from the state of Morelos living in the city of Cuernavaca (N = 82) and rural communities (N = 30), to
Immunogenetics obtain information regarding allelic and haplotypic frequencies. The most frequent haplotypes in Morelos in-
Population genetics clude seven Native American, one European, one African and one Asian haplotype. Admixture estimates revealed
Morelos
that the main genetic components in Morelos are Native American (60.43 ± 2.22% by ML; 53.57% of Native
Admixture

Abbreviations: HLA, Human Leukocyte Antigen; MPA, Most-Probable Ancestry; LD, Linkage Disequilibrium
⁎
Corresponding authors at: Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
(R. Barquera). Department of Transplantation, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán” (INCMNSZ), Vasco de Quiroga 15, Belisario
Domínguez Sección XVI, 14080 Tlalpan, CDMX, Mexico (J. Granados).
E-mail addresses: barquera@shh.mpg.de (R. Barquera), julgrate@yahoo.com (J. Granados).
URLs: http://www.shh.mpg.de/en (R. Barquera), http://www.innsz.mx (J. Granados).
1
These authors contributed equally to the present work.

https://doi.org/10.1016/j.humimm.2019.07.289
Received 8 July 2019; Accepted 13 July 2019
0198-8859/ © 2019 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

Please cite this article as: Andrea Ortega-Yáñez, et al., Human Immunology, https://doi.org/10.1016/j.humimm.2019.07.289
A. Ortega-Yáñez, et al.
American haplotypes) and European (39.58 ± 3.70% by ML; 27.68% of European haplotypes), and a virtually
absent African genetic component (0.00 ± 4.93% by ML; but 11.16% of African haplotypes).
The State of Morelos is divided into 33 municipalities, has an area of
4961 Km2, which represents 0.25% of the total Mexican national ter-
ritory. Located in the south-central part of the country, Morelos is
bordered to the north by Mexico City and the State of Mexico, to the
east and southeast by Puebla, and to the south and southwest by
Guerrero. In 2015, the state of Morelos had 1,903,811 inhabitants. The
population of the state represents 1.6% of the population of Mexico.
Two out of every 100 inhabitants aged 3 years and over in Morelos are
speakers of an indigenous language. The most common indigenous
languages in the state are: Nahuatl (63.5%) and Mixtec (18.6%). About
28.1% of the population of the state is considered indigenous and 0.4%
is considered Afro-descendant [1,2].
Records of the first permanent human settlements in the Morelos
Valley date from around 1500 BCE [3]. Some authors point out that it
was in Morelos where Tamoanchan was located, a mythical place from
where it is believed that the human groups that populated the central
area of the country, mainly Teotihuacán, originated [4]. In places like
Chalcatzingo, there is evidence of a strong Olmec influence (900 and
800 BCE), this given that the monumental stones carved and the
sculpture of Chalcatzingo have a style similar to the bas-reliefs of the
Venta in Tabasco. The first settlements in Xochicalco are dated to 1300
BCE, thriving between 650 CE and 900 CE. The social organization of
the site, characterized by the settlement of neighborhoods according to
the social level and ethnic origin, as well as a similarity between state
institutions, is known to have had a great influence from Teotihuacán.
Likewise, due to its geographical position, Xochicalco regulated the
agricultural commercial exchange coming from Oaxaca, the south of
Guerrero and the Morelos Valley. Around 700 CE, and thanks to its
agricultural self-sufficiency, the site was able to increase its power by
building urban works, such as streets, walls and bastions. The fall of
Xochicalco coincided with the migration of Nahuatlacan tribes from the
north of the country in search of better environmental conditions. From
seven Nahuatlacan tribes (i.e. Xochimilcas, Chalcas, Tepanecas, Col-
huas, Tlaxcaltecas, Tlahuicas, and Mexicas), the Tlahuicas and Xochi-
milcas were the ones who settled in Morelos, founding Cuauhnáhuac
(the state’s capital city of Cuernavaca), and forming the base of the
indigenous population in the region at the time of the arrival of the
conquerors [3,5]. By the middle of the 15th century, Cuauhnáhuac, as
well as other settlements in the Morelos valley, became tributary tribes
of the Triple Alliance, with cotton weaving being the most important
product to be taxed [3,5].
Upon the arrival of the Europeans in 1519, and the subsequent years
of struggle for conquest, the most important prehispanic Morelos peo-
ples (Huaxtepec, Yecapixtla, Yautepec and Cuauhnáuhac) fell under the
jurisdiction of Hernán Cortés. By 1523 he founded the first state sugar
mill in Tlaltenango, laying the foundations of an industry that prevails
until today as a characteristic economic activity in the state. After the
death of Cortés in 1547, his son Martín Cortés inherited his father's
business, thus boosting the sugar estates in an ambitious manner, to the
extent that it was necessary to bring slave labor from Africa and Cuba.
Around the year 1600, there was also the development of mining ac-
tivity, extracting silver from Huautla and Miacatlán [5]. In 1646 when
the audience of Mexico was created, the current territory of the State
was divided between that audience and the intendancy of Puebla. By
1786, the organization of New Spain was again changed, creating 12
provinces and separating the current territory of Morelos as an in-
dependent entity between the provinces of Mexico and Puebla [5].
By 1980, Morelos became an important migrant population at-
tractor from other states of the country (mainly Guerrero), as was the
case for other states in the central region of Mexico. By the year 2000,
2
Human Immunology xxx (xxxx) xxx–xxx
over 25% of the people living in Morelos were born in a different state
of the country, especially inhabitants coming from Mexico City [6].
For the present work, we analyzed HLA class I (HLA-A, -B) and class II
(HLA-DRB1, -DQB1) PCR-SSP based typings in 112 Mexicans from the
state of Morelos [composed by the following populations: Mexico
Morelos, Cuernavaca, N = 82, Allele Frequencies Net Database Identifier
(AFND-ID): 3464; Mexico Morelos Rural, N = 30, AFND-ID: 3593]. In
addition to the individual populations we also show data for these
combined populations. The latter are not held on AFND to prevent du-
plication of data. Maximum-likelihood (ML) frequencies for alleles and
four-locus haplotypes were estimated using an Expectation-Maximization
algorithm. For a comprehensive review on the methods, such as sample
collection, HLA typing and statistical analyses, please refer to [7] in this
same issue. For the frequencies of HLA-A, -B, -DRB1 and -DQB1 and
haplotypic data for the sample sets of the state of Morelos please refer to
the Supplementary Information: Supplementary Tables 1–7. For data on
Hardy-Weinberg equilibrium (HWE) please see Supplementary
Information: Supplementary Table 8 of this work and Supplementary
Information: Supplementary Table 9 in [7] in this same issue. We find
that the most frequent haplotypes for the state (haplotypic frequency,
H.F. > 1.0%, arbitrarily; Supplementary Table 5) include seven Native
American (HLA ~ A*02 ~ B*35 ~ DRB1*08 ~ DQB1*04, A*02 ~ B*39 ~
DRB1*04 ~ DQB1*03:02, A*02 ~ B*40:02 ~ DRB1*04 ~ DQB1*03:02,
A*24 ~ B*40:02 ~ DRB1*04 ~ DQB1*03:02, A*31 ~ B*39 ~ DRB1*
04 ~ DQB1*03:02, A*68 ~ B*39 ~ DRB1*04 ~ DQB1*03:02 and A*02 ~
B*15:01 ~ DRB1*04 ~ DQB1*03:02), one European (HLA ~ A*01 ~
B*08 ~ DRB1*03:01 ~ DQB1*02), one Eurasian (HLA ~ A*30 ~ B*13 ~
DRB1*07 ~ DQB1*02) and one African (HLA ~ A*02 ~ B*41 ~
DRB1*13 ~ DQB1*03:01) haplotypes. Admixture estimates revealed that
the main genetic components in Morelos are Native American
(60.43 ± 2.22% by the ML method and 53.57% of Native American
haplotypes) and European (39.58 ± 3.70% by the ML method and
27.68% of European haplotypes), and a virtually absent African genetic
component (0.00 ± 4.93% by the ML method but 11.16% of African
haplotypes). Previous reports on the central area of Mexico with short
tandem repeats (STRs) as genetic estimators [8] show different estima-
tions for the first two components: 52% of European ancestry, 39% of
Native American ancestry and 9% of African ancestry. Paternal lineage
data obtained by analyzing Y chromosome haplogroups in a similar
sample [9] show a 41% of European and 21% of Native American hap-
lotypes, while African contribution was estimated at 7%.
The admixture for both Cuernavaca and the rural areas follow
comparable patterns: although they both have evidence of very low
African contribution as determined by the ML method (Cuernavaca
1.22 ± 1.72% vs. rural areas 0.00 ± 15.60%; Fig. 1), both Native
American (Cuernavaca: 59.77 ± 2.11% by the ML method and 54.88%
by estimating the proportion of Native American haplotypes vs. Rural
areas: 60.49 ± 6.77% by the ML method and 50.00% by estimating the
proportion of Native American haplotypes) and European (Cuernavaca:
39.01 ± 0.88% by the ML method and 25.61% by estimating the
proportion of European haplotypes vs. Rural areas: 39.51 ± 16.33% by
the ML method and 33.33% by estimating the proportion of European
haplotypes) ancestries follow very similar distributions and contradict
previous evidence stating Native American ancestry is more re-
presented in rural areas than in urban settings [10].
The proportions of African and Asian MPA haplotypes remain re-
latively constant in the three datasets analyzed: while at the level of the
state a proportion of 11.16% of African haplotypes can be observed, in
Cuernavaca this proportion was estimated to be 9.76% and is even
higher in the rural areas (15.00%). Asian haplotypes show a low
A. Ortega-Yáñez, et al.
Fig. 1. Location of Morelos and admixture proportions for the state of Morelos [composed by the following populations: Mexico Morelos, Cuernavaca, N = 82, Allele
Frequencies Net Database Identifier (AFND-ID): 3464; Mexico Morelos Rural, N = 30, AFND-ID: 3593]. Admixture proportions were estimated by ML using HLA-A,
-B and -DRB1 frequencies as genetic estimators. Green refers to the proportion of European contribution, purple to Native American contribution and yellow depicts
African contribution. Map modified from Google Maps Pro [15].
proportion in the three datasets (6.25% for the state of Morelos, 7.93%
for Cuernavaca and 1.67% for the rural areas). The important presence
of African haplotypes in Morelos can be explained by the massive in-
voluntary migration of African enslaved human workforce that hap-
pened during the Colonial period to work in the sugar mills of the state
[5,11]. Although not documented in large numbers in Morelos, there
were some Asian immigrants reaching the central part of Mexico
throughout the colonial period but also during the first hundred years
after independence in 1821 [12,13]. This Asian presence can explain
the proportion of Asian haplotypes found in the datasets analyzed.
One of the important contributions of this work is to provide data of
the genetic variation of the population that inhabits the state of Morelos
which are scarce when compared to other states of the country. All data
from our sample sets, both frequencies and individual genotypes, can be
found at The Allele Frequency Net Database website (www.allele-
frequencies.netwww.allelefrequencies.net) [14].
Appendix A. Supplementary data
Supplementary data to this article can be found online at https://
doi.org/10.1016/j.humimm.2019.07.289.
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