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Analysis of admixture in Native American populations from Colombia
Abstract
The current Colombian population is the result of genetic admixture between Native Americans, Europeans and Africans. Around 82% of the population is considered admixed, 15% are Afro-Colombians and just 3% are Native Americans. There are about 81 native groups in Colombia. In this work, a sample of 121 non-related individuals from three Native American groups were analysed for 46 ancestry informative InDel markers. One of these groups was the Pijaos that, because of their combative nature, was almost exterminated during European conquest and colonial times. The other two studied groups belong to communities that have been less subjected to admixture with non-Natives. The Barí, known as "Motilones" or "Dobukubi", is a Native group that inhabits the Serranía del Perija, Norte de Santander, since pre-Colombian times. They still keep their original language, the Barí-ara, which belongs to the Chibcha family. We have also studied a sample of Natives from Guainía, formed by different groups that migrated from the Amazonia and Orinoquian regions, including the Desana, Curripaco, Puinave, Cubeo, Guaunano and Tucano, all belonging to Tucano and Arawak linguistic groups. This study allow determining genotypic and allelic frequencies for 46 ancestry informative InDels and to estimate Native American, European and African admixture proportions in three Colombian native communities. The results showed a very low European and African admixture in the Barí and Guainia native groups in contrast to the high levels of admixture presented by the Pijao.
... Dye-labeled amplified fragments were separated and detected using an ABI3130 Genetic Analyzer (Life Technologies), and automated allele calls were obtained with GeneMapper v.3.2 (Life Technologies). This panel showed to be highly informative to analyze genetic admixture in different Latin-American populations, including Argentina [16], Brazil [25], Bolivia [26] and Colombia [27,28]. ...
... Allele frequency estimations, Hardy-Weinberg exact tests, and population differentiation tests were performed using the Arlequin software v.3.5.2 [29]. Population genetic analyses were carried out comparing our five populations with an additional six Argentinian populations [16] and six South American populations from Brazil [25], Bolivia [26] and Colombia [27,28]. Genetic distances (F ST ) between populations across 46 AIM-Indel markers were visualized in a multi-dimensional scaling (MDS) plot performed with the R v3.1.1 ...
... Using data from the 46 AIM-Indels, pairwise F ST genetic distances were calculated between the five Patagonian populations from this study, and samples from six Argentinian provinces [16], six South American populations from Brazil [25], Bolivia [26] and Colombia [27,28], as well as the European, African and Native American HGDP-CEPH reference populations [23] (S5 Table). ...
Objectives
We aimed to contribute to the understanding of the ancient geographic origins of the uniparentally inherited markers in modern admixed Argentinian populations from central Patagonia with new information provided for the city of Trelew. We attempted to highlight the importance of combining different genetic markers when studying population history.
Methods
The mtDNA control region sequence was typified in 89 individuals and 12 Y-STR and 15 Y-SNP loci were analyzed in 66 males. With these data, analysis of molecular variance and Network analyses were carried out. We exhaustively compared the modern data with ancient mtDNA information. Finally, we tested the differences in continental origins estimated by uniparental and previously published biparental markers.
Results
Native American mtDNAs (53.9%) increased when maternal ancestors were born in the northern (81.8%) and southern (58.5%) regions of Argentina or in Chile (77.8%). Population substructure was only observed for Y-chromosome haplotypes. Some mtDNA haplogroups have been present in the area for at least ca. 2762–2430 and ca. 500 (D1g and D1g4 haplogroups) and ca. 6736 and ca. 6620 (C1b and C1c haplogroups) years, respectively. In contrast, haplogroups B2i2 and C1b13, frequent in modern Patagonia populations, had not been found in previous ancient DNA studies of the region.
Conclusions
The results suggest that Native American ancestry is well preserved in the region. Trelew samples had characteristic native mtDNA haplogroups previously described in Chilean and Argentine Patagonian populations, but not observed in ancient samples until now. These findings support the idea that these lineages have a recent regional origin. Finally, the estimated proportions of continental ancestry depend on the genetic marker analyzed.
... Dye-labeled amplified fragments were separated and detected using an ABI3130 Genetic Analyzer (Life Technologies), and automated allele calls were obtained with GeneMapper v.3.2 (Life Technologies). This panel showed to be highly informative to analyze genetic admixture in different Latin-American populations, including Argentina [16], Brazil [25], Bolivia [26] and Colombia [27,28]. ...
... Allele frequency estimations, Hardy-Weinberg exact tests, and population differentiation tests were performed using the Arlequin software v.3.5.2 [29]. Population genetic analyses were carried out comparing our five populations with an additional six Argentinian populations [16] and six South American populations from Brazil [25], Bolivia [26] and Colombia [27,28]. Genetic distances (F ST ) between populations across 46 AIM-Indel markers were visualized in a multi-dimensional scaling (MDS) plot performed with the R v3.1.1 ...
... Using data from the 46 AIM-Indels, pairwise F ST genetic distances were calculated between the five Patagonian populations from this study, and samples from six Argentinian provinces [16], six South American populations from Brazil [25], Bolivia [26] and Colombia [27,28], as well as the European, African and Native American HGDP-CEPH reference populations [23] (S5 Table). ...
... Dye-labeled amplified fragments were separated and detected using an ABI3130 Genetic Analyzer (Life Technologies), and automated allele calls were obtained with GeneMapper v.3.2 (Life Technologies). This panel showed to be highly informative to analyze genetic admixture in different Latin-American populations, including Argentina [16], Brazil [25], Bolivia [26] and Colombia [27,28]. ...
... Allele frequency estimations, Hardy-Weinberg exact tests, and population differentiation tests were performed using the Arlequin software v.3.5.2 [29]. Population genetic analyses were carried out comparing our five populations with an additional six Argentinian populations [16] and six South American populations from Brazil [25], Bolivia [26] and Colombia [27,28]. Genetic distances (F ST ) between populations across 46 AIM-Indel markers were visualized in a multi-dimensional scaling (MDS) plot performed with the R v3.1.1 ...
... Using data from the 46 AIM-Indels, pairwise F ST genetic distances were calculated between the five Patagonian populations from this study, and samples from six Argentinian provinces [16], six South American populations from Brazil [25], Bolivia [26] and Colombia [27,28], as well as the European, African and Native American HGDP-CEPH reference populations [23] (S5 Table). ...
As in other Latin American populations, Argentinians are the result of the admixture amongst different continental groups, mainly from America and Europe, and to a lesser extent from Sub-Saharan Africa. However, it is known that the admixture processes did not occur homogeneously throughout the country. Therefore, considering the importance for anthropological, medical and forensic researches, this study aimed to investigate the population genetic structure of the Argentinian Patagonia, through the analysis of 46 ancestry informative markers, in 433 individuals from five different localities. Overall, in the Patagonian sample, the average individual ancestry was estimated as 35.8% Native American (95% CI: 32.2–39.4%), 62.1% European (58.5–65.7%) and 2.1% African (1.7–2.4%). Comparing the five localities studied, statistically significant differences were observed for the Native American and European contributions, but not for the African ancestry. The admixture results combined with the genealogical information revealed intra-regional variations that are consistent with the different geographic origin of the participants and their ancestors. As expected, a high European ancestry was observed for donors with four grandparents born in Europe (96.8%) or in the Central region of Argentina (85%). In contrast, the Native American ancestry increased when the four grandparents were born in the North (71%) or in the South (61.9%) regions of the country, or even in Chile (60.5%). In summary, our results showed that differences on continental ancestry contribution have different origins in each region in Patagonia, and even in each locality, highlighting the importance of knowing the origin of the participants and their ancestors for the correct interpretation and contextualization of the genetic information.
... For analysis, we included data from Native Colombian populations that were previously studied for the same AIM-Indel markers. These included (i) Natives living in the Cauca region; (ii) Emberá-Chami living in the Antioquia Department; (iii) Natives living in Guainía; (iv) Motilón-Barí living in Norte de Santander; (v) and Pijao from the Tolima Department [16,29]. These Native groups are from different departments (see Fig 1 in Ossa et al. [29]) and belong to diverse linguistic/ethnic groups: Barbacoan (Guambiano and Coconuco from Cauca), Chibchan (Motilón-Barí; Nasa from Cauca), Chocoan (Emberá-Chamí), Tucanoan (Tucano, Cubeo, Guanano and Desana from Guanía) and Arawakan (Curripaco from Guainía). ...
... These included (i) Natives living in the Cauca region; (ii) Emberá-Chami living in the Antioquia Department; (iii) Natives living in Guainía; (iv) Motilón-Barí living in Norte de Santander; (v) and Pijao from the Tolima Department [16,29]. These Native groups are from different departments (see Fig 1 in Ossa et al. [29]) and belong to diverse linguistic/ethnic groups: Barbacoan (Guambiano and Coconuco from Cauca), Chibchan (Motilón-Barí; Nasa from Cauca), Chocoan (Emberá-Chamí), Tucanoan (Tucano, Cubeo, Guanano and Desana from Guanía) and Arawakan (Curripaco from Guainía). Additionally, to perform ancestry analysis, we used reference data available for HGDP-CEPH samples from African, European and Native American populations [25]. ...
... The genotyping results obtained for the 761 Colombian samples from the present work and the 121 samples from the Native groups examined in Ossa et al. [29] are listed in S1 Table. The genotypes from the remaining 93 samples are available in Xavier et al. [16]. ...
The ancestry of the Colombian population comprises a large number of well differentiated Native communities belonging to diverse linguistic groups. In the late fifteenth century, a process of admixture was initiated with the arrival of the Europeans, and several years later, Africans also became part of the Colombian population. Therefore, the genepool of the current Colombian population results from the admixture of Native Americans, Europeans and Africans. This admixture occurred differently in each region of the country, producing a clearly stratified population. Considering the importance of population substructure in both clinical and forensic genetics, we sought to investigate and compare patterns of genetic ancestry in Colombia by studying samples from Native and non-Native populations living in its 5 continental regions: the Andes, Caribe, Amazonia, Orinoquía, and Pacific regions. For this purpose, 46 AIM-Indels were genotyped in 761 non-related individuals from current populations. Previously published genotype data from 214 Colombian Natives from five communities were used for population comparisons. Significant differences were observed between Native and non-Native populations, among non-Native populations from different regions and among Native populations from different ethnic groups. The Pacific was the region with the highest African ancestry, Amazonia harboured the highest Native ancestry and the Andean and Orinoquían regions showed the highest proportion of European ancestry. The Andean region was further sub-divided into 6 sub-regions: North East, Central West, Central East, West, South West and South East. Among these regions, the South West region showed a significantly lower European admixture than the other regions. Hardy-Weinberg equilibrium and variance values of ancestry among individuals within populations showed a potential stratification of the Pacific population.
... Usaquén, 2012;Ansari-Pour et al., 2016;Bedoya et al., 2006;Bortolini, Salzano, & Thomas, 2003;Carvajal-Carmona et al., 2000;Garavito et al., 2015;Ibarra et al., 2014;Martínez et al., 2017;Mesa et al., 2000;Noguera et al., 2014;Ossa et al., 2015Ossa et al., , 2016Rodas, Gelvez, & Keyeux, 2013;Rojas et al., 2010;Rojas, Roa, Briceño, Guaneme, & Gómez, 2011;Urbano, Portilla, Builes, Gusmão, & Sierra-Torres, 2016;Xavier et al., 2015;Yunis, Acevedo, Campo, & Yunis, 2013). These studies showed that urban populations have high levels of non-native admixture, and Native American, African, and European ancestries vary across the country. ...
Colombia, located in the north of the South American subcontinent is a country of great interest for population genetic studies given its high ethnic and cultural diversity represented by the admixed population, 102 indigenous peoples and African descent populations. In this study, an analysis of the genetic structure and ancestry was performed based on 46 ancestry informative INDEL markers (AIM‐INDELs) and considering the genealogical and demographic variables of 451 unrelated individuals belonging to nine Native American, two African American, and four multiple ancestry populations. Measures of genetic diversity, ancestry components, and genetic substructure were analyzed to build a population model typical of the northernmost part of the South American continent. The model suggests three types of populations: Native American, African American, and multiple ancestry. The results support hypotheses posed by other authors about issues like the peopling of South America and the existence of two types of Native American ancestry. This last finding could be crucial for future research on the peopling of Colombia and South America in that a single origin of all indigenous communities should not be assumed. It then would be necessary to consider other events that could explain their genetic variability and complexity throughout the continent.
... En una familia con cinco hijos, al menos dos de los niños serán idénticos a hla. 12,15,16 Respecto al síndrome de Usher afecta genes que participan en la formación de los haces del pelo auditivo y el anclaje a filamentos de actina, en otras palabras, los genes ush codifican proteínas motoras, de andamiaje, moléculas de adhesión y receptores transmembrana. 17 conclusIones La aparición de enfermedades autosómicas recesivas se ve influenciada por limitaciones geográficas y socioeconómicas debido al aumento de uniones matrimoniales endogámicas, Colombia no está exenta, siendo el tercer país en Suramérica después de bra-sil y Venezuela en presentar consanguinidad, lo que favorece la expresión de alelos deletéreos recesivos. ...
El síndrome de Usher es una enfermedad autosómica recesiva que se caracteriza por presentar retinitis pigmentosa, hipoacusia neurosensorial congénita y disfunción vestibular. El propósito de este trabajo es realizar la caracterización de hla en una familia colombiana
endogámica que presenta síndrome de Usher. La metodología consiste en que con un previo consentimiento informado se realizó una genealogía de la familia y a cuatro pacientes confirmados clínicamente con síndrome de Usher y a cuatro fenotípicamente sanos se les tomó 5 ml de sangre periférica en tubos de venopunción con edta para luego realizar el aislamiento del dna por la técnica de salting out, conservados en buffer te a -8 °C y ajustada la muestra a una concentración de 8 μg/ml. Posteriormente a través de la técnica de pcr-ssp de mediana resolución se caracterizaron los antígenos de hla *a, *b, *drb1 y *dqb1. Los resultados obtenidos indican que la familia oriunda del Departamento del Huila presenta una marcada endogamia detectándose que todos los hermanos afectados, sus padres son hermanos también y una de las parejas a su vez tuvo una niña afectada, por lo que sus abuelos y padres son hermanos. En lo referente al hla, los alelos más frecuentemente encontrados fueron a30 b42 dr1 dq5 y a3 b45 dr12 y dq7, que no están asociados a la enfermedad. Estos resultados sugieren que dada la endogamia que muestra esta familia se presenta una gran acumulación de polimorfismos y mutaciones, por lo que es necesario realizar un proceso de asesoría genética para disminuir el riesgo de recurrencia.
... In most comparisons, significant differences (p < 0.0002) were obtained between São Paulo and other populations [20]. Additionally, São Paulo showed lower genetic distances with European populations (0.0120 ≤ F ST ≤ 0.0169) than with Native Americans or Sub-Saharan African populations. ...
X-chromosomal markers can be useful in some forensic cases, where the analysis of the autosomal markers is not conclusive. In this study, a population sample of 500 unrelated individuals born in São Paulo State was characterized for 32 X-InDel markers. No deviations from the Hardy–Weinberg equilibrium were detected, except for MID1361. The 32 X-InDels showed an accumulated power of discrimination of 0.9999999999993 in females and 0.99999993 in males and an exclusion chance of 0.999996 in trios and 0.99995 in duos. São Paulo showed lower genetic distances to the Colombian admixed and European populations than to Native American, Asian, or African populations. Ancestry analysis revealed 41.8% European, 31.6% African, and 26.6% Native American contributions. Segregation analysis was performed in 101 trios, and the mutation rate was estimated to be low.
Genetic diversity of present American populations results from very complex demographic events involving different types and degrees of admixture. Through the analysis of lineage markers such as mtDNA and Y chromosome it is possible to recover the original Native American haplotypes, which remained identical since the admixture events due to the absence of recombination. However, the decrease in the effective population sizes and the consequent genetic drift effects suffered by these populations during the European colonization resulted in the loss or under-representation of a substantial fraction of the Native American lineages. In this study, we aim to clarify how the diversity and distribution of uniparental lineages vary with the different demographic characteristics (size, degree of isolation) and the different levels of admixture of extant Native groups in Colombia. We present new data resulting from the analyses of mtDNA whole control region, Y chromosome SNP haplogroups and STR haplotypes, and autosomal ancestry informative insertion-deletion polymorphisms in Colombian individuals from different ethnic and linguistic groups. The results demonstrate that populations presenting a high proportion of non-Native American ancestry have preserved nevertheless a substantial diversity of Native American lineages, for both mtDNA and Y chromosome. We suggest that, by maintaining the effective population sizes high, admixture allowed for a decrease in the effects of genetic drift due to Native population size reduction and thus resulting in an effective preservation of the Native American non-recombining lineages.
Ancestry-informative markers (AIMs) show high allele frequency divergence between different ancestral or geographically distant populations. These genetic markers are especially useful in inferring the likely ancestral origin of an individual or estimating the apportionment of ancestry components in admixed individuals or populations. The study of AIMs is of great interest in clinical genetics research, particularly to detect and correct for population substructure effects in case-control association studies, but also in population and forensic genetics studies.
This work presents a set of 46 ancestry-informative insertion deletion polymorphisms selected to efficiently measure population admixture proportions of four different origins (African, European, East Asian and Native American). All markers are analyzed in short fragments (under 230 basepairs) through a single PCR followed by capillary electrophoresis (CE) allowing a very simple one tube PCR-to-CE approach.
HGDP-CEPH diversity panel samples from the four groups, together with Oceanians, were genotyped to evaluate the efficiency of the assay in clustering populations from different continental origins and to establish reference databases. In addition, other populations from diverse geographic origins were tested using the HGDP-CEPH samples as reference data. The results revealed that the AIM-INDEL set developed is highly efficient at inferring the ancestry of individuals and provides good estimates of ancestry proportions at the population level.
In conclusion, we have optimized the multiplexed genotyping of 46 AIM-INDELs in a simple and informative assay, enabling a more straightforward alternative to the commonly available AIM-SNP typing methods dependent on complex, multi-step protocols or implementation of large-scale genotyping technologies.
We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci. The new model accounts for the correlations between linked loci that arise in admixed populations (“admixture linkage disequilibium”). This modification has several advantages, allowing (1) detection of admixture events farther back into the past, (2) inference of the population of origin of chromosomal regions, and (3) more accurate estimates of statistical uncertainty when linked loci are used. It is also of potential use for admixture mapping. In addition, we describe a new prior model for the allele frequencies within each population, which allows identification of subtle population subdivisions that were not detectable using the existing method. We present results applying the new methods to study admixture in African-Americans, recombination in Helicobacter pylori, and drift in populations of Drosophila melanogaster. The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu.
We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.
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We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci-e.g. , seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/ approximately pritch/home. html.
We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci. The new model accounts for the correlations between linked loci that arise in admixed populations ("admixture linkage disequilibium"). This modification has several advantages, allowing (1) detection of admixture events farther back into the past, (2) inference of the population of origin of chromosomal regions, and (3) more accurate estimates of statistical uncertainty when linked loci are used. It is also of potential use for admixture mapping. In addition, we describe a new prior model for the allele frequencies within each population, which allows identification of subtle population subdivisions that were not detectable using the existing method. We present results applying the new methods to study admixture in African-Americans, recombination in Helicobacter pylori, and drift in populations of Drosophila melanogaster. The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu.
Lenguas indígenas de Colombia
- Instituto Caro Y Cuervo