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MHC Class II Haplotypes of Colombian Amerindian Tribes

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MHC Class II Haplotypes of Colombian Amerindian Tribes Genetics and Molecular Biology, 36, 2, 158-166 (2013) Copyright © 2013, Sociedade Brasileira de Genética. Printed in Brazil www.sbg.org.br Research Article MHC Class II haplotypes of Colombian Amerindian tribes Juan J. Yunis1,2,3, Edmond J. Yunis4 and Emilio Yunis3 1Departamento de Patología, Facultad de Medicina e Instituto de Genética, Universidad Nacional de Colombia, Ciudad Universitaria, Bogotá, Colombia. 2Grupo de Identificación Humana e Inmunogenética, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia. 3Instituto de Genética, Servicios Médicos Yunis Turbay y Cia, Bogotá, Colombia. 4Brigham and Womens Hospital, Department of Pathology, Harvard Medical School, Boston, USA. Abstract We analyzed 1041 individuals belonging to 17 Amerindian tribes of Colombia, Chimila, Bari and Tunebo (Chibcha linguistic family), Embera, Waunana (Choco linguistic family), Puinave and Nukak (Maku-Puinave linguistic fami- lies), Cubeo, Guanano, Tucano, Desano and Piratapuyo (Tukano linguistic family), Guahibo and Guayabero (Guayabero Linguistic Family), Curripaco and Piapoco (Arawak linguistic family) and Yucpa (Karib linguistic family). for MHC class II haplotypes (HLA-DRB1, DQA1, DQB1). Approximately 90% of the MHC class II haplotypes found among these tribes are haplotypes frequently encountered in other Amerindian tribes. Nonetheless, striking differ- ences were observed among Chibcha and non-Chibcha speaking tribes. The DRB1*04:04, DRB1*04:11, DRB1*09:01 carrying haplotypes were frequently found among non-Chibcha speaking tribes, while the DRB1*04:07 haplotype showed significant frequencies among Chibcha speaking tribes, and only marginal frequencies among non-Chibcha speaking tribes. Our results suggest that the differences in MHC class II haplotype frequency found among Chibcha and non-Chibcha speaking tribes could be due to genetic differentiation in Mesoamerica of the an- cestral Amerindian population into Chibcha and non-Chibcha speaking populations before they entered into South America. Keywords: MHC, Class II, Amerindians, Colombia, linguistic. Received: August 28, 2012; Accepted: January 29, 2013. Introduction and Jews. These Mestizo populations are located in the An- The arrival of Native American through Beringia oc- dean, Pacific, Atlantic regions and, in a minor degree, in the curred around 12,000-15,000 years before present based on Orinoquian and Amazonian regions. On the other hand, archeological, mtDNA, and Y-chromosome microsatellites populations with a higher proportion of African ancestry, haplotypes/SNP studies (Crawford 1988; Salzano and Cal- derived from slave trading during the 17th and 18th centu- legari-Jaques 1988; Santos et al., 1996; Bonatto and Sal- ries, are located in the Pacific coast, Caribbean coast and is- zano 1997a; 1997b; Santos et al., 1999; Dillehay 2009; lands. The Amerindian populations, with 81 tribes are O’Rourke and Raff 2010). Recent studies using high reso- located in the plains (Orinoquian region), Amazonian jun- lution SNP genotyping analysis indicate that Native Ameri- gle and in some regions of the Colombian Andes. In Amer- can populations, including all Amerindian populations ica, Brazil has the highest number of Amerindian tribes derived from an Asian ancestral populations with at least followed by Colombia (81 Tribes), Mexico (68 tribes) and two additional streams of gene flow from Asia (Reich et al., Venezuela (20 tribes) (Salzano and Callegari-Jaques 1988; 2012). Yunis et al., 1994, 2001). The population of Colombia is highly diverse (Yunis Different studies of MHC class-I and class-II alleles et al., 2000). The majority of the Colombian contemporary in Amerindian populations have been carried out for an- population derived from Spaniards and Amerindians ad- thropological as well as evolutionary studies (Layrisse et mixture, with a lower contribution of other European al., 1973; Kostyu and Amos 1981; Williams et al., 1981; (French, Italian, German, and Portuguese) as well as Arabs, Vullo et al., 1984; Gorodezky et al., 1985; Long et al., 1991; Petzl-Erler et al., 1993; Tsuneto et al., 2003; Parolin and Carnese 2009; Arnaiz-Villena et al., 2010, 2011; Var- Send correspondence to Juan J. Yunis. Departamento de Pato- logía, Facultad de Medicina, Universidad Nacional de Colombia, gas-Alarcon et al., 2011). New MHC class I and class II al- Bogotá, Colombia. E-mail: [email protected]. leles have been identified in North and South Amerindian Yunis et al. 159 communities (Belich et al., 1992; Watkins et al., 1992; Zhang et al., 1993; Layrisse et al., 1997; Mack and Erlich 1998). The analysis of MHC along with other genetic mark- ers such as mtDNA, Y-chromosome haplotypes and SNP might provide important information regarding the peo- pling of the continent. Due to its geographical location, Co- lombia was a necessary stepping-stone for entrance of Amerindian populations into South America. Thus, the study of the actual living Amerindian populations in Co- lombia should shed some light regarding migrations, ad- mixture, and linguistic relationship. We have previously reported the MHC class II data obtained from four Amerindian tribes located in the north- ern section of Colombia (Arhuaco, Arsario, Kogui and Wayuu) (Yunis et al., 1994), as well as the MHC class II re- sults obtained from three Amerindian tribes located in the southwest section of Colombia (Guambiano, Paez and Ingano) (Yunis et al., 2001). In these reports we found a correlation between genetics and linguistic affiliation for the Chibcha speaking tribes, demonstrating that the Guam- biano and Paez Amerindian tribes (formerly classified as Chibcha speaking populations) are not genetically related to the Chibcha speaking tribes of northern Colombia (Yunis et al., 1994, 2001). Figure 1 - Geographical location of Amerindian tribes of Colombia (see Table 1). Lines within the country identify the natural regions of Colom- Here, we report the MHC class II haplotype data bia. Different shapes were used to identify the linguistic affiliation of each (DRB1, DQA1 and DQB1) from 17 additional Amerindian tribe. Numbers identify each population. Chibcha speaking populations: tribes located in the Amazonian, Orinoquian, Pacific and Chimila (1), Barí (2), Tunebo (3); Choco speaking populations: Wau- nana/Noanama (4) and Embera/Katio (5); Karib speaking population: Perija mountain range regions of Colombia, plus an analy- Yucpa/Yuko (6); Arawak speaking populations: Curripaco (7) and Pia- sis with the data from those seven Amerindian tribes previ- poco (8); Guahibo speaking populations: Guahibos/Sikuane (9) and Gua- ously reported. Significant differences between Chibcha yabero (10); Maku speaking populations: Nukak (11) and Puinave (12); speaking tribes and non-Chibcha speaking tribes were Tukano speaking populations: Cubeo (13), Guanano/Wanano (14), Tu- cano (15), Desano (16), Piratapuyo (17). found. These results suggest that the genetic differentiation between Chibcha and non-Chibcha Amerindian groups oc- curred in Mesoamerica before they entered and spread habitants of the Orinoquian flats, the Amazonian, the pa- throughout South America. cific region and the Perija Mountain range. DNA isolation Material and Methods DNA was isolated from ACD (anticoagulant citrate Populations studied dextrose) preserved blood by a quick lysis method (Ka- wasaki 1990), or by a salting-out method with minor modi- We have analyzed 1041 individuals from 17 different fications (Miller et al., 1988). Amerindian tribes of Colombia that belong to 7 different linguistic families (Arawak, Chibcha, Choco, Guahibo, Ka- PCR Amplifications rib, Maku and Tukano) (Figure 1, Table 1). Blood samples MHC class II typing was carried as described before. were collected between 1989-1992 after proper informed The second exon of the DRB1 generic locus, and the DQA1 consent was obtained, including the approval of each Chief and DQB1 loci were amplified by PCR from genomic or Governors of each Tribe. The analysis included the data DNA. The primers and conditions used in this study have obtained from the Arhuaco, Koguí, Arsario (Chibcha), been published elsewhere (Salazar et al., 1992; Yunis et al., Wayuu (Arawak), Ingano (Quechua), Paez and Guambiano 1992, 1994, 2001). In addition, allele specific amplifica- (no linguistic classification at present) tribes had been re- tions for DRB1*15/16 and DRB1*04 were performed as ported previously (Yunis et al., 1994, 2001). Among each described before (Yunis et al., 1994). tribe there were unrelated individuals and family groups The DRB generic and high resolution (except for based on the information derived when the samples were DRB1*04 alleles), DQA1 and DQB1 alleles were deter- obtained. The geographical location and their linguistic af- mined in the locus-specific PCR amplified products by filiation are shown in Table 1. Most of these tribes are in- sequence-specific oligonucleotide probe hybridization 160 MHC Class II in Amerindians Table 1 - Number of individuals (N), linguistic family affiliation (based on Ruhlen, 1991) and geographical location of Amerindian Colombian Tribes an- alyzed. Tribe N Linguistic family Geographical location Number in Figure 1 CHIMILA 88 CHIBCHA Sierra Nevada Santa Marta 1 BARI 90 CHIBCHA Perija Mountain Range 2 TUNEBO/ U’WA 29 CHIBCHA Orinoquian region 3 EMBERA/CATIO 73 CHOCO Pacific region 4 WAUNANA/NOANAMA 60 CHOCO Pacific region 5 YUCPA 47 KARIB Perija Mountain Range 6 CURRIPACO 49 ARAWAK Orinoquian region 7 PIAPOCO 25 ARAWAK Orinoquian region 8 GUAHIBOS/SIKUANE 34 GUAHIBO
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