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Genetic diversity of HLA system in two populations from San Luis Potosí, Mexico: San Luis Potosí City and rural San Luis Potosí
Human Immunology xxx (xxxx) xxx–xxx
Contents lists available at ScienceDirect
Human Immunology journal homepage: www.elsevier.com/locate/humimm
Genetic diversity of HLA system in two populations from San Luis Potosí, Mexico: San Luis Potosí City and rural San Luis Potosí Diana Iraíz Hernández-Zaragozaa,b,1, Tirzo Jesús Rodríguez-Munguíac,1, Rodrigo Barqueraa,d, ,1, Carmen Adalid-Sáinze,1, Esteban Arrieta-Bolañosf,1, Stephen Claytond,1, Hanna Pacheco-Ubaldoa, Liliana González-Medinaa, Abraham Lona-Sáncheza, Alicia Bravo-Acevedog, Guadalupe Aquino-Rubioc, Marisela del Rocío González-Martínezh, Héctor Delgado-Aguirree, Néstor Escareño-Montieli, Yolanda Jaramillo-Rodríguezj, Antonio Salgado-Adamej, ⁎ Federico Juárez-de la Cruzi, Joaquín Zúñigak,l, , Edmond J. Yunism, Carolina Bekker-Méndezn, Julio Granadoso ⁎
a
Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico Immunogenetics Unit, Técnicas Genéticas Aplicadas a la Clínica (TGAC), Mexico City, Mexico c Molecular Biology Laboratory, Hospital General “Norberto Treviño Zapata”, Dirección de Servicios de Salud de Tamaulipas, Ciudad Victoria, Tamaulipas, Mexico d Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Germany e Laboratory of Histocompatibility, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico f Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany g Blood Bank, UMAE Hospital de Gineco Obstetricia No. 4 “Luis Castelazo Ayala”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico h Microbiology Department, Faculty of Medicine, Universidad Autónoma de Coahuila, Torreón, Coahuila, Mexico i Department of Transplantation, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico j Direction of Health Education and Research, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico k Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico l Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico m Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA n Immunology and Infectology Research Unit, Infectology Hospital, Centro Médico Nacional “La Raza”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico o Department of Transplantation, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán” (INCMNSZ), Mexico City, Mexico b
ARTICLE INFO
ABSTRACT
Keywords: HLA Immunogenetics Population genetics San Luis Potosí Admixture
We studied HLA class I (HLA-A, -B) and class II (HLA-DRB1, -DQB1) alleles by PCR-SSP based typing in 117 Mexicans from the state of San Luis Potosí living in the city of San Luis Potosí (N = 30) and rural communities (N = 87), to obtain information regarding allelic and haplotypic frequencies. We find that the most frequent haplotypes in the state include 13 Native American, six European, two African and two Asian haplotypes. Admixture estimates revealed that the main genetic components are Native American (52.72 ± 0.66% by ML; 48.29% of Native American haplotypes) and European (34.62 ± 4.28% by ML; 32.48% of European haplotypes), and a relatively high African genetic component (12.66 ± 4.61% by ML; 10.26% of African haplotypes).
The state of San Luis Potosí is located in the northern part of the central region of Mexico (Fig. 1). The state of San Luis Potosí borders seven entities: the North with Zacatecas, Nuevo León and Tamaulipas; to the East with Tamaulipas and Veracruz; to the South with Hidalgo,
Querétaro and Guanajuato; and to the West with Zacatecas. It has 58 municipalities, organized into four geographical regions with their own physical, cultural and economic characteristics: a) Huasteca region, b) Middle region, c) Central region, d) San Luis Potosí highlands.
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). Laboratory of Immunobiology and Genetics, Research Division, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calz. De Tlalpan 4502, Bellisario Domínguez Sección XVI, 14080 Tlalpan, Mexico City, Mexico (J. Zúñiga). E-mail addresses: [email protected] (R. Barquera), [email protected] (J. Zúñiga). URLs: http://www.shh.mpg.de/en (R. Barquera), http://www.iner.salud.gob.mx (J. Zúñiga). 1 These authors contributed equally to the present work. https://doi.org/10.1016/j.humimm.2019.07.291 Received 8 July 2019; Accepted 14 July 2019 0198-8859/ © 2019 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.
Please cite this article as: Diana Iraíz Hernández-Zaragoza, et al., Human Immunology, https://doi.org/10.1016/j.humimm.2019.07.291
Human Immunology xxx (xxxx) xxx–xxx
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Fig. 1. Location of San Luis Potosí and admixture proportions for the state of San Luis Potosí [composed by the following populations: Mexico San Luis Potosí, San Luis Potosí city, N = 30, Allele Frequencies Net Database Identifier (AFND-ID): 3487; Mexico San Luis Potosí Rural, N = 87, AFND-ID: 3586]. 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].
However, only six municipalities exceed 90,000 inhabitants: San Luis Potosi, Matehuala, Rioverde, Tamazunchale, Soledad de Graciano Sánchez and Ciudad Valles. About 58.73% of the total population live in urban centers; 30% of which live in the capital city of San Luis Potosí. In San Luis Potosí state more than 630,000 people are considered indigenous (23.2% of the total population), being the Huasteca region the place where the three municipalities with the largest indigenous population are located (San Antonio 97.2%, Tanlajas 94.4%, and Coxcatlán 94.4%). Of the speakers of indigenous languages, 54.7% speak Nahuatl and 39.1% Huasteco. Only 0.04% of the population consider themselves as Afro-descendant [1]. According to paleoecology studies, during the Late Pleistocene San Luis Potosí presented favorable characteristics for human settlement, such as Rancho de la Amapola in the town of Cedral, which, being a marshy area, trapped animals in search of water. Animal and human remains were found during the first excavations of the site [2] suggesting that the hunter-gatherer groups could take advantage of this trap to hunt. During the Pre Hispanic period the state is divided between the two main cultural zones (Aridoamérica and Mesoamérica), the northern part was inhabited by Otomíes and Chichimecas, while eastern and southeastern San Luis Potosí were inhabited by Huastecos, Pames and Nahuas. The European conquerors discovered large gold and silver deposits and began the colonization of the territory that was inhabited by Huachichil groups, more closely related to Chichimecas [3]. In 1592 the city of San Luis Potosí was founded, “San Luis” in honor of King Louis IX of France and “Potosí” because it was expected that the riches of its mines would be similar to those found in the homonymous city in Bolivia. In addition to the mining activity, the growth of livestock areas prompted two situations: first, the pacification of the north of the country by transplanting pacifying indigenous communities (mainly Tlaxcaltecan and Purépecha) to northern areas where the Chichimec groups continued to maintain wars; and second, a semi-desertification for the creation of pastures for livestock grazing, which peaked in the San Luis Potosí area around 1630 [3]. During the Colonial period, the hacienda systems were the main form of settlement. The hacienda towns were communities settled around the haciendas or
within their territorial limits, and formed population centers with a very varied social composition, composed of tenants, day laborers, shepherds, artisans, muleteers and weavers, that often exceeded a thousand inhabitants. However, these did not have recognition nor the rights that the indigenous communities had; on the contrary, they were only seen as the workforce for the haciendas and the interest in the growth of their population was to preserve this labor force. However by the mid-nineteenth century the situation changed, the population was more than could be kept under control and this led to a series of uprisings against landowners. In addition, the Reform war and the French Intervention created favorable political conditions in the region to install legislation by local governments instead of communal lands [4]. Due to its geographical location, San Luis Potosí has always been an intermediate point in the communication networks between the three main cities of the country: Guadalajara, Monterrey and Mexico City; it is also the intersection in the routes between four maritime ports: Manzanillo, Mazatlán, Altamira and Tampico; and has a large network of roads and highways that allow a large flow of people throughout the length and breadth of its territory. The city of San Luis Potosí has become a cluster of metalworking industry, which has driven social and economic growth; however, in general terms, the state is in third place as a center for the exodus (expulsion makes it sound as if they are forced to leave, or is that the case?) of the population, a situation that has been maintained since 1940, with the state of Nuevo León being its main migratory destination [5]. For the present work, we analyzed HLA class I (HLA-A, -B) and class II (HLA-DRB1, -DQB1) PCR-SSP based typings in 117 Mexicans from the state of San Luis Potosí [composed by the following populations: Mexico San Luis Potosí, San Luis Potosí city, N = 30, Allele Frequencies Net Database Identifier (AFND-ID): 3487; Mexico San Luis Potosí Rural, N = 87, AFND-ID: 3586]. In addition to the individual populations we also show data for these combined populations. The latter are not held on AFND to prevent duplication 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, 2
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be used as workforce for mining, agriculture and husbandry activities in the state [11]. The proportions of Asian MPA haplotypes remain relatively constant in the three datasets analyzed: 6.84% for the state of San Luis Potosí, 3.33% for San Luis Potosí City and 8.05% for the rural areas. Although not documented in large numbers in San Luis Potosí, there were some Asian immigrants reaching the central part of Mexico throughout the colonial period but also a ten-fold increase in Asian population from 1895 to 1910 [12,13]. This Asian presence can explain the proportion of Asian haplotypes found in the datasets analyzed. All data from our sample sets, both frequencies and individual genotypes, can be found at The Allele Frequency Net Database website (www.allelefrequencies. net) [14].
please refer to [6] 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 San Luis Potosí 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 [6] 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 13 Native American (HLA ~ A*02 ~ B*35 ~ DRB1*08 ~ DQB1*04, A*68 ~ B*40:02 ~ DRB1*08 ~ DQB1*04, A*02 ~ B*15:01 ~ DRB1*04 ~ DQB1*03:02, A*24 ~ B*35 ~ DRB1*16 ~ DQB1*03:01, A*31 ~ B*35 ~ DRB1*04 ~ DQB1*03:02, A*02 ~ B*35 ~ DRB1*04 ~ DQB1 *03:02, A*02 ~ B*40:02 ~ DRB1*08 ~ DQB1*04, A*02 ~ B*48 ~ DRB1*04 ~ DQB1*03:02, A*02 ~ B*51 ~ DRB1*08 ~ DQB1*04, A*24 ~ B*35 ~ DRB1*08 ~ DQB1*04, A*24 ~ B*39 ~ DRB1*16 ~ DQB1*03:01, A*68 ~ B*35 ~ DRB1*08 ~ DQB1*04 and A*68 ~ B*40:02 ~ DRB1*04 ~ DQB1*03:02), six European (HLA ~ A*33 ~ B*14:02 ~ DRB1*01 ~ DQB1*05, A*01 ~ B*08 ~ DRB1*03:01 ~ DQB1*02, A*24 ~ B*35 ~ DRB1*11 ~ DQB1*03:01, A*26 ~ B*14:01 ~ DRB1*13 ~ DQB1*06, A*29 ~ B*44 ~ DRB1*07 ~ DQB1*02 and A*68 ~ B*14:02 ~ DRB1*01 ~ DQB1*05), two African (HLA ~ A*66 ~ B*41 ~ DRB1*11 ~ DQB1*03:01 and A*23 ~ B*45 ~ DRB1*15 ~ DQB1*06) and two Asian (HLA ~ A*23 ~ B*49 ~ DRB1*11 ~ DQB1*03:01 and A*02 ~ B*50 ~ DRB1*07 ~ DQB1*02; the latter probably Eurasian) haplotypes. Admixture estimates revealed that the main genetic components are Native American (52.72 ± 0.66% by ML; 48.29% of Native American haplotypes) and European (34.62 ± 4.28% by ML; 32.48% of European haplotypes), and a relatively high African genetic component (12.66 ± 4.61% by ML; 10.26% of African haplotypes). A study using blood groups as genetic estimators in mixed ancestry population from San Luis Potosí [7] found 75.64 ± 5.42% of European ancestry and 24.60 ± 5.42% of Native American ancestry in their sample. Another study using 13 short tandem repeats (STRs) as a genetic estimator for admixture analysis in a closely related population [8] showed somewhat different results: 54.99 ± 3.44% of European, 39.99 ± 2.57% of Native American and 5.02 ± 2.82% of African contributions. These two studies resemble more the results for San Luis Potosí City than the ones here reported for the whole state (see below). A different study using ancestry informative markers (AIMs) in a similar population [9] found 56% of Native American, 38% of European and 6% of African contribution, results that resemble more closely the estimations obtained with HLA. The admixture estimates for both San Luis Potosí city and the rural areas show very dissimilar African (San Luis Potosí city 0.00 ± 9.87% by the ML method and 11.67% by estimating the proportion of African haplotypes vs. rural areas 16.79 ± 6.50% by the ML method and 9.77% by estimating the proportion of African haplotypes; Fig. 1) and European (San Luis Potosí city: 51.23 ± 9.58% by the ML method and 38.33% by estimating the proportion of European haplotypes vs. Rural areas: 29.58 ± 5.67% by the ML method and 30.46% by estimating the proportion of European haplotypes) ancestries, but similar Native American (San Luis Potosí city: 48.77 ± 1.58% by the ML method and 45.00% by estimating the proportion of Native American haplotypes vs. Rural areas: 53.63 ± 1.11% by the ML method and 49.43% by estimating the proportion of Native American haplotypes) proportions. These results are in line with previous evidence stating Native American and African ancestries are more represented in rural areas than in urban settings [10]. The important presence of African haplotypes in San Luis Potosí can be explained by the massive involuntary migration of African enslaved human workforce that happened during the Colonial period to
Appendix A. Supplementary data Supplementary data to this article can be found online at https:// doi.org/10.1016/j.humimm.2019.07.291. References [1] Instituto Nacional de Estadística y Geografía (INEGI), Conociendo San Luis Potosí, sixth ed., Instituto Nacional de Estadística y Geografía, Mexico, 2016. [2] J.L. Lorenzo, L. Mirambell, Preliminary report on archaeological and paleoenvironmental studies in the area of El Cedral, San Luis Potosi, Mexico, 1977-1980, New Evidence for the Pleistocene Paleo-Indian Archaeology in Mexico Peopling of the Americas, 1985, pp. 107–114. [3] D. Frye, The native peoples of northeastern Mexico, in: R.E.W. Adams, M.J. MacLeod (Eds.), The Cambridge History of the Native Peoples of the Americas Mesoamerica, Cambridge University Press, Cambridge, 2008, pp. 89–135. [4] J.C.S. Montiel, De poblados de hacienda a municipios en el altiplano de San Luis Potosí, Estudios de Historia Moderna y Contemporánea de México, Enero-Juni (2006). [5] J. Sobrino, Migración interna en México durante el siglo XX, first ed., Consejo Nacional de Población, Mexico City, 2010 http://www.conapo.gob.mx. [6] R. Barquera, D.I. Hernández Zaragoza, A. Bravo Acevedo, E. Arrieta Bolaños, S. Clayton, V. Acuña Alonzo, et al., The immunogenetic diversity of the HLA system in Mexico correlates with underlying population genetic structure, Human Immunol. (2019). [7] R.M. Cerda-Flores, G.K. Kshatriya, S.A. Barton, C.H. Leal-Garza, R. Garza-Chapa, W.J. Schull, et al., Genetic structure of the populations migrating from San Luis Potosi and Zacatecas to Nuevo León in Mexico, Human Biol. 63 (1991) 309–327. [8] R.M. Cerda-Flores, B. Budowle, L. Jin, S.A. Barton, R. Deka, R. Chakraborty, Maximum likelihood estimates of admixture in Northeastern Mexico using 13 short tandem repeat loci, Am. J. Human Biol. 14 (2002) 429–439, https://doi.org/10. 1002/ajhb.10058. [9] M.L. Martinez-Fierro, J. Beuten, R.J. Leach, E.J. Parra, M. Cruz-Lopez, H. RangelVillalobos, et al., Ancestry informative markers and admixture proportions in northeastern Mexico, J. Human Genet. 54 (2009) 504–509, https://doi.org/10. 1038/jhg.2009.65. [10] B.Z. González-Sobrino, A.P. Pintado-Cortina, L. Sebastián-Medina, F. MoralesMandujano, A.V. Contreras, Y.E. Aguilar, et al., Genetic diversity and differentiation in urban and indigenous populations of Mexico: patterns of mitochondrial DNA and Y-chromosome lineages, Biodemogr. Soc. Biol. 62 (2016) 53–72, https://doi.org/ 10.1080/19485565.2015.1117938. [11] Ú. Camba Ludlow, Imaginarios ambiguos, realidades contradictorias: conductas y representaciones de los negros y mulatos novohispanos, Siglos XVI y XVII, COLMEX, Mexico City, 2008. [12] D. Oropeza, La migración asiática libre al centro del virreinato novohispano, 1565–1700, Relaciones Estudios de Historia y Sociedad 37 (2017) 347, https://doi. org/10.24901/rehs.v37i147.181. [13] J.J. Gómez Izquierdo, El movimiento antichino en México (1871-1934) : problemas del racismo y del nacionalismo durante la Revolución Mexicana, Instituto Nacional de Antropología e Historia, Mexico City, 1992. [14] E.J.M. dos Santos, A. McCabe, F.F. Gonzalez-Galarza, A.R. Jones, D. Middleton, Allele frequencies net database: improvements for storage of individual genotypes and analysis of existing data, Human Immunol. 77 (2016) 238–248, https://doi. org/10.1016/j.humimm.2015.11.013. [15] Google, Google Earth Pro ©, 2019. earth.google.com.
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Contents lists available at ScienceDirect
Human Immunology journal homepage: www.elsevier.com/locate/humimm
Genetic diversity of HLA system in two populations from San Luis Potosí, Mexico: San Luis Potosí City and rural San Luis Potosí Diana Iraíz Hernández-Zaragozaa,b,1, Tirzo Jesús Rodríguez-Munguíac,1, Rodrigo Barqueraa,d, ,1, Carmen Adalid-Sáinze,1, Esteban Arrieta-Bolañosf,1, Stephen Claytond,1, Hanna Pacheco-Ubaldoa, Liliana González-Medinaa, Abraham Lona-Sáncheza, Alicia Bravo-Acevedog, Guadalupe Aquino-Rubioc, Marisela del Rocío González-Martínezh, Héctor Delgado-Aguirree, Néstor Escareño-Montieli, Yolanda Jaramillo-Rodríguezj, Antonio Salgado-Adamej, ⁎ Federico Juárez-de la Cruzi, Joaquín Zúñigak,l, , Edmond J. Yunism, Carolina Bekker-Méndezn, Julio Granadoso ⁎
a
Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico Immunogenetics Unit, Técnicas Genéticas Aplicadas a la Clínica (TGAC), Mexico City, Mexico c Molecular Biology Laboratory, Hospital General “Norberto Treviño Zapata”, Dirección de Servicios de Salud de Tamaulipas, Ciudad Victoria, Tamaulipas, Mexico d Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Germany e Laboratory of Histocompatibility, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico f Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany g Blood Bank, UMAE Hospital de Gineco Obstetricia No. 4 “Luis Castelazo Ayala”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico h Microbiology Department, Faculty of Medicine, Universidad Autónoma de Coahuila, Torreón, Coahuila, Mexico i Department of Transplantation, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico j Direction of Health Education and Research, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico k Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico l Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico m Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA n Immunology and Infectology Research Unit, Infectology Hospital, Centro Médico Nacional “La Raza”, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico o Department of Transplantation, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán” (INCMNSZ), Mexico City, Mexico b
ARTICLE INFO
ABSTRACT
Keywords: HLA Immunogenetics Population genetics San Luis Potosí Admixture
We studied HLA class I (HLA-A, -B) and class II (HLA-DRB1, -DQB1) alleles by PCR-SSP based typing in 117 Mexicans from the state of San Luis Potosí living in the city of San Luis Potosí (N = 30) and rural communities (N = 87), to obtain information regarding allelic and haplotypic frequencies. We find that the most frequent haplotypes in the state include 13 Native American, six European, two African and two Asian haplotypes. Admixture estimates revealed that the main genetic components are Native American (52.72 ± 0.66% by ML; 48.29% of Native American haplotypes) and European (34.62 ± 4.28% by ML; 32.48% of European haplotypes), and a relatively high African genetic component (12.66 ± 4.61% by ML; 10.26% of African haplotypes).
The state of San Luis Potosí is located in the northern part of the central region of Mexico (Fig. 1). The state of San Luis Potosí borders seven entities: the North with Zacatecas, Nuevo León and Tamaulipas; to the East with Tamaulipas and Veracruz; to the South with Hidalgo,
Querétaro and Guanajuato; and to the West with Zacatecas. It has 58 municipalities, organized into four geographical regions with their own physical, cultural and economic characteristics: a) Huasteca region, b) Middle region, c) Central region, d) San Luis Potosí highlands.
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). Laboratory of Immunobiology and Genetics, Research Division, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calz. De Tlalpan 4502, Bellisario Domínguez Sección XVI, 14080 Tlalpan, Mexico City, Mexico (J. Zúñiga). E-mail addresses: [email protected] (R. Barquera), [email protected] (J. Zúñiga). URLs: http://www.shh.mpg.de/en (R. Barquera), http://www.iner.salud.gob.mx (J. Zúñiga). 1 These authors contributed equally to the present work. https://doi.org/10.1016/j.humimm.2019.07.291 Received 8 July 2019; Accepted 14 July 2019 0198-8859/ © 2019 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.
Please cite this article as: Diana Iraíz Hernández-Zaragoza, et al., Human Immunology, https://doi.org/10.1016/j.humimm.2019.07.291
Human Immunology xxx (xxxx) xxx–xxx
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Fig. 1. Location of San Luis Potosí and admixture proportions for the state of San Luis Potosí [composed by the following populations: Mexico San Luis Potosí, San Luis Potosí city, N = 30, Allele Frequencies Net Database Identifier (AFND-ID): 3487; Mexico San Luis Potosí Rural, N = 87, AFND-ID: 3586]. 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].
However, only six municipalities exceed 90,000 inhabitants: San Luis Potosi, Matehuala, Rioverde, Tamazunchale, Soledad de Graciano Sánchez and Ciudad Valles. About 58.73% of the total population live in urban centers; 30% of which live in the capital city of San Luis Potosí. In San Luis Potosí state more than 630,000 people are considered indigenous (23.2% of the total population), being the Huasteca region the place where the three municipalities with the largest indigenous population are located (San Antonio 97.2%, Tanlajas 94.4%, and Coxcatlán 94.4%). Of the speakers of indigenous languages, 54.7% speak Nahuatl and 39.1% Huasteco. Only 0.04% of the population consider themselves as Afro-descendant [1]. According to paleoecology studies, during the Late Pleistocene San Luis Potosí presented favorable characteristics for human settlement, such as Rancho de la Amapola in the town of Cedral, which, being a marshy area, trapped animals in search of water. Animal and human remains were found during the first excavations of the site [2] suggesting that the hunter-gatherer groups could take advantage of this trap to hunt. During the Pre Hispanic period the state is divided between the two main cultural zones (Aridoamérica and Mesoamérica), the northern part was inhabited by Otomíes and Chichimecas, while eastern and southeastern San Luis Potosí were inhabited by Huastecos, Pames and Nahuas. The European conquerors discovered large gold and silver deposits and began the colonization of the territory that was inhabited by Huachichil groups, more closely related to Chichimecas [3]. In 1592 the city of San Luis Potosí was founded, “San Luis” in honor of King Louis IX of France and “Potosí” because it was expected that the riches of its mines would be similar to those found in the homonymous city in Bolivia. In addition to the mining activity, the growth of livestock areas prompted two situations: first, the pacification of the north of the country by transplanting pacifying indigenous communities (mainly Tlaxcaltecan and Purépecha) to northern areas where the Chichimec groups continued to maintain wars; and second, a semi-desertification for the creation of pastures for livestock grazing, which peaked in the San Luis Potosí area around 1630 [3]. During the Colonial period, the hacienda systems were the main form of settlement. The hacienda towns were communities settled around the haciendas or
within their territorial limits, and formed population centers with a very varied social composition, composed of tenants, day laborers, shepherds, artisans, muleteers and weavers, that often exceeded a thousand inhabitants. However, these did not have recognition nor the rights that the indigenous communities had; on the contrary, they were only seen as the workforce for the haciendas and the interest in the growth of their population was to preserve this labor force. However by the mid-nineteenth century the situation changed, the population was more than could be kept under control and this led to a series of uprisings against landowners. In addition, the Reform war and the French Intervention created favorable political conditions in the region to install legislation by local governments instead of communal lands [4]. Due to its geographical location, San Luis Potosí has always been an intermediate point in the communication networks between the three main cities of the country: Guadalajara, Monterrey and Mexico City; it is also the intersection in the routes between four maritime ports: Manzanillo, Mazatlán, Altamira and Tampico; and has a large network of roads and highways that allow a large flow of people throughout the length and breadth of its territory. The city of San Luis Potosí has become a cluster of metalworking industry, which has driven social and economic growth; however, in general terms, the state is in third place as a center for the exodus (expulsion makes it sound as if they are forced to leave, or is that the case?) of the population, a situation that has been maintained since 1940, with the state of Nuevo León being its main migratory destination [5]. For the present work, we analyzed HLA class I (HLA-A, -B) and class II (HLA-DRB1, -DQB1) PCR-SSP based typings in 117 Mexicans from the state of San Luis Potosí [composed by the following populations: Mexico San Luis Potosí, San Luis Potosí city, N = 30, Allele Frequencies Net Database Identifier (AFND-ID): 3487; Mexico San Luis Potosí Rural, N = 87, AFND-ID: 3586]. In addition to the individual populations we also show data for these combined populations. The latter are not held on AFND to prevent duplication 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, 2
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be used as workforce for mining, agriculture and husbandry activities in the state [11]. The proportions of Asian MPA haplotypes remain relatively constant in the three datasets analyzed: 6.84% for the state of San Luis Potosí, 3.33% for San Luis Potosí City and 8.05% for the rural areas. Although not documented in large numbers in San Luis Potosí, there were some Asian immigrants reaching the central part of Mexico throughout the colonial period but also a ten-fold increase in Asian population from 1895 to 1910 [12,13]. This Asian presence can explain the proportion of Asian haplotypes found in the datasets analyzed. All data from our sample sets, both frequencies and individual genotypes, can be found at The Allele Frequency Net Database website (www.allelefrequencies. net) [14].
please refer to [6] 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 San Luis Potosí 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 [6] 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 13 Native American (HLA ~ A*02 ~ B*35 ~ DRB1*08 ~ DQB1*04, A*68 ~ B*40:02 ~ DRB1*08 ~ DQB1*04, A*02 ~ B*15:01 ~ DRB1*04 ~ DQB1*03:02, A*24 ~ B*35 ~ DRB1*16 ~ DQB1*03:01, A*31 ~ B*35 ~ DRB1*04 ~ DQB1*03:02, A*02 ~ B*35 ~ DRB1*04 ~ DQB1 *03:02, A*02 ~ B*40:02 ~ DRB1*08 ~ DQB1*04, A*02 ~ B*48 ~ DRB1*04 ~ DQB1*03:02, A*02 ~ B*51 ~ DRB1*08 ~ DQB1*04, A*24 ~ B*35 ~ DRB1*08 ~ DQB1*04, A*24 ~ B*39 ~ DRB1*16 ~ DQB1*03:01, A*68 ~ B*35 ~ DRB1*08 ~ DQB1*04 and A*68 ~ B*40:02 ~ DRB1*04 ~ DQB1*03:02), six European (HLA ~ A*33 ~ B*14:02 ~ DRB1*01 ~ DQB1*05, A*01 ~ B*08 ~ DRB1*03:01 ~ DQB1*02, A*24 ~ B*35 ~ DRB1*11 ~ DQB1*03:01, A*26 ~ B*14:01 ~ DRB1*13 ~ DQB1*06, A*29 ~ B*44 ~ DRB1*07 ~ DQB1*02 and A*68 ~ B*14:02 ~ DRB1*01 ~ DQB1*05), two African (HLA ~ A*66 ~ B*41 ~ DRB1*11 ~ DQB1*03:01 and A*23 ~ B*45 ~ DRB1*15 ~ DQB1*06) and two Asian (HLA ~ A*23 ~ B*49 ~ DRB1*11 ~ DQB1*03:01 and A*02 ~ B*50 ~ DRB1*07 ~ DQB1*02; the latter probably Eurasian) haplotypes. Admixture estimates revealed that the main genetic components are Native American (52.72 ± 0.66% by ML; 48.29% of Native American haplotypes) and European (34.62 ± 4.28% by ML; 32.48% of European haplotypes), and a relatively high African genetic component (12.66 ± 4.61% by ML; 10.26% of African haplotypes). A study using blood groups as genetic estimators in mixed ancestry population from San Luis Potosí [7] found 75.64 ± 5.42% of European ancestry and 24.60 ± 5.42% of Native American ancestry in their sample. Another study using 13 short tandem repeats (STRs) as a genetic estimator for admixture analysis in a closely related population [8] showed somewhat different results: 54.99 ± 3.44% of European, 39.99 ± 2.57% of Native American and 5.02 ± 2.82% of African contributions. These two studies resemble more the results for San Luis Potosí City than the ones here reported for the whole state (see below). A different study using ancestry informative markers (AIMs) in a similar population [9] found 56% of Native American, 38% of European and 6% of African contribution, results that resemble more closely the estimations obtained with HLA. The admixture estimates for both San Luis Potosí city and the rural areas show very dissimilar African (San Luis Potosí city 0.00 ± 9.87% by the ML method and 11.67% by estimating the proportion of African haplotypes vs. rural areas 16.79 ± 6.50% by the ML method and 9.77% by estimating the proportion of African haplotypes; Fig. 1) and European (San Luis Potosí city: 51.23 ± 9.58% by the ML method and 38.33% by estimating the proportion of European haplotypes vs. Rural areas: 29.58 ± 5.67% by the ML method and 30.46% by estimating the proportion of European haplotypes) ancestries, but similar Native American (San Luis Potosí city: 48.77 ± 1.58% by the ML method and 45.00% by estimating the proportion of Native American haplotypes vs. Rural areas: 53.63 ± 1.11% by the ML method and 49.43% by estimating the proportion of Native American haplotypes) proportions. These results are in line with previous evidence stating Native American and African ancestries are more represented in rural areas than in urban settings [10]. The important presence of African haplotypes in San Luis Potosí can be explained by the massive involuntary migration of African enslaved human workforce that happened during the Colonial period to
Appendix A. Supplementary data Supplementary data to this article can be found online at https:// doi.org/10.1016/j.humimm.2019.07.291. References [1] Instituto Nacional de Estadística y Geografía (INEGI), Conociendo San Luis Potosí, sixth ed., Instituto Nacional de Estadística y Geografía, Mexico, 2016. [2] J.L. Lorenzo, L. Mirambell, Preliminary report on archaeological and paleoenvironmental studies in the area of El Cedral, San Luis Potosi, Mexico, 1977-1980, New Evidence for the Pleistocene Paleo-Indian Archaeology in Mexico Peopling of the Americas, 1985, pp. 107–114. [3] D. Frye, The native peoples of northeastern Mexico, in: R.E.W. Adams, M.J. MacLeod (Eds.), The Cambridge History of the Native Peoples of the Americas Mesoamerica, Cambridge University Press, Cambridge, 2008, pp. 89–135. [4] J.C.S. Montiel, De poblados de hacienda a municipios en el altiplano de San Luis Potosí, Estudios de Historia Moderna y Contemporánea de México, Enero-Juni (2006). [5] J. Sobrino, Migración interna en México durante el siglo XX, first ed., Consejo Nacional de Población, Mexico City, 2010 http://www.conapo.gob.mx. [6] R. Barquera, D.I. Hernández Zaragoza, A. Bravo Acevedo, E. Arrieta Bolaños, S. Clayton, V. Acuña Alonzo, et al., The immunogenetic diversity of the HLA system in Mexico correlates with underlying population genetic structure, Human Immunol. (2019). [7] R.M. Cerda-Flores, G.K. Kshatriya, S.A. Barton, C.H. Leal-Garza, R. Garza-Chapa, W.J. Schull, et al., Genetic structure of the populations migrating from San Luis Potosi and Zacatecas to Nuevo León in Mexico, Human Biol. 63 (1991) 309–327. [8] R.M. Cerda-Flores, B. Budowle, L. Jin, S.A. Barton, R. Deka, R. Chakraborty, Maximum likelihood estimates of admixture in Northeastern Mexico using 13 short tandem repeat loci, Am. J. Human Biol. 14 (2002) 429–439, https://doi.org/10. 1002/ajhb.10058. [9] M.L. Martinez-Fierro, J. Beuten, R.J. Leach, E.J. Parra, M. Cruz-Lopez, H. RangelVillalobos, et al., Ancestry informative markers and admixture proportions in northeastern Mexico, J. Human Genet. 54 (2009) 504–509, https://doi.org/10. 1038/jhg.2009.65. [10] B.Z. González-Sobrino, A.P. Pintado-Cortina, L. Sebastián-Medina, F. MoralesMandujano, A.V. Contreras, Y.E. Aguilar, et al., Genetic diversity and differentiation in urban and indigenous populations of Mexico: patterns of mitochondrial DNA and Y-chromosome lineages, Biodemogr. Soc. Biol. 62 (2016) 53–72, https://doi.org/ 10.1080/19485565.2015.1117938. [11] Ú. Camba Ludlow, Imaginarios ambiguos, realidades contradictorias: conductas y representaciones de los negros y mulatos novohispanos, Siglos XVI y XVII, COLMEX, Mexico City, 2008. [12] D. Oropeza, La migración asiática libre al centro del virreinato novohispano, 1565–1700, Relaciones Estudios de Historia y Sociedad 37 (2017) 347, https://doi. org/10.24901/rehs.v37i147.181. [13] J.J. Gómez Izquierdo, El movimiento antichino en México (1871-1934) : problemas del racismo y del nacionalismo durante la Revolución Mexicana, Instituto Nacional de Antropología e Historia, Mexico City, 1992. [14] E.J.M. dos Santos, A. McCabe, F.F. Gonzalez-Galarza, A.R. Jones, D. Middleton, Allele frequencies net database: improvements for storage of individual genotypes and analysis of existing data, Human Immunol. 77 (2016) 238–248, https://doi. org/10.1016/j.humimm.2015.11.013. [15] Google, Google Earth Pro ©, 2019. earth.google.com.
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