The multiethnic ancestry of Bolivians as revealed by the analysis of Y-chromosome markers

Development and validation of YARN: A novel SE-400 MPS kit for East Asian paternal lineage analysis

Y-chromosomal short tandem repeat polymorphisms (Y-STRs) and Y-chromosomal single nucleotide polymorphisms (Y-SNPs) are valuable genetic markers used in paternal lineage identification and population genetics. Currently, there is a lack of an effective panel that integrates Y-STRs and Y-SNPs for studying paternal lineages, particularly in East Asian populations. Hence, we developed a novel Y-chromosomal targeted panel called YARN (Y-chromosome Ancestry and Region Network) based on multiplex PCR and a single-end 400 massive parallel sequencing (MPS) strategy, consisting of 44 patrilineage Y-STRs and 260 evolutionary Y-SNPs. A total of 386 reactions were validated for the effectiveness and applicability of YARN according to SWGDAM validation guidelines, including sensitivity (with a minimum input gDNA of 0.125 ng), mixture identification (ranging from 1:1-1:10), PCR inhibitor testing (using substances such as 50 μM hematin, 100 μM hemoglobin, 100 μM humic acid, and 2.5 mM indigo dye), species specificity (successfully distinguishing humans from other animals), repeatability study (achieved 100% accuracy), and concordance study (with 99.91% accuracy for 1121 Y-STR alleles). Furthermore, we conducted a pilot study using YARN in a cohort of 484 Han Chinese males from Huaiji County, Zhaoqing City, Guangdong, China (GDZQHJ cohort). In this cohort, we identified 52 different Y-haplogroups and 73 different surnames. We found weak to moderate correlations between the Y-haplogroups, Chinese surnames, and geographical locations of the GDZQHJ cohort (with λ values ranging from 0.050 to 0.340). However, when we combined two different categories into a new independent variable, we observed stronger correlations (with λ values ranging from 0.617 to 0.754). Overall, the YARN panel, which combines Y-STR and Y-SNP genetic markers, meets forensic DNA quality assurance guidelines and holds potential for East Asian geographical origin inference and paternal lineage analysis.

Insights into the Y chromosome human diversity in Uruguay

BACKGROUND

With regard to the origin of its population and microevolutionary processes, Uruguay exhibits distinctive features that distinguish it from other countries in Latin America, while at the same time sharing several similarities. In this article, we will focus on the variability of paternal genetic lineages in two geographical regions with different histories that can be considered as examples of distinct populations for the continent. In general terms, the genetic diversity is a result of different demographic processes related to the American conquest and colonisation. These resulted in distinct ancestral components which vary geographical and depend on the distribution by sex within these components. In Uruguay, native maternal haplogroups are significantly more frequent in the North. Although there are several studies about the geneticvariability of Uruguay, little is known about male genetic lineages.

AIMS

The aim of this work is to present an updated study of the male genetic variability of the Uruguayan population.

METHODS

We analyzed 13 biallelic markers and 27 STRs located in the male-specific region of the Y chromosome for 157 males: 98 from the capital, Montevideo, and 59 from Tacuarembó.

RESULTS

Almost all haplogroups found in both locations are European (99% and 93.2% respectively). One Sub-Saharan African haplogroup was found in Montevideo (1%) and 2 in Tacuarembó (3%), while Native haplogroups were found only in Tacuarembó, evidencing a strong sex-biased admixture. By crossing genetic and genealogical information we could relate European haplogroups with different waves and times of migrations.

DISCUSSION

Network analysis indicated a very diverse male population, suggesting that European migrants came from heterogeneous geographic locations and in different waves. Tacuarembó has closer population affinities with Iberian populations while Montevideo is more diverse. Male population expansion expansion, can be explained by the large number of migrants that arrived during the XIX century and the first half of the XX century.

CONCLUSIONS

The Uruguayan male gene pool is the result of several migration waves with diverse origins, with strong sex-biased admixture that can be explained by the European migration, the violence against the indigenous males, and the segregation of the Africansadmixture that can be explained due to European migration, violence against Natives, and segregation against African males.admixture that can be explained due to European migration, violence against Natives, and segregation against African males.admixture that can be explained due to European migration, violence against Natives, and segregation against African males.admixture that can be explained due to European migration, violence against Natives, and segregation of hte Africans.

An approach on the migratory processes in the north of Chile based on Y chromosome analysis

OBJECTIVES

Northern Chile is an area characterized by a complex cultural and demographic trajectory. During the last few centuries, this complex trajectory has become the destination of intra- and intercontinental migratory waves. In this study, we analyzed the Y chromosome to evaluate how migratory and admixture patterns have affected the genetic composition of the populations in northern Chile compared with other populations of the country.

METHODS

A total of 311 people from urban (Antofagasta and Calama), rural (Azapa and Camarones), and Native (Aymara and Atacameño) populations from northern Chile were characterized by 26 SNPs and the STR DYS393 of the Y chromosome, along with 69 individuals from Native populations (Mapuche, Pehuenche, and Huilliche) from southern Chile. In addition to characterizing the paternal lineages, multivariate analyses were performed to compare with published data from other Chilean populations.

RESULTS

Both the Antofagasta and Calama populations show differences compared with the rest of the Chilean population. On one side, Antofagasta shows a high diversity of non-Amerindian lineages, including the highest value for haplogroup I (12%) for all Chileans populations. Otherwise, Calama has the highest value of any Chilean urban population (31.9%) for Amerindian lineages, including the only Q-M3 sub-lineage detected in the entire sample. Regarding the Native population, Aymara presents the highest percentage of Q-M3 (94.4%).

CONCLUSIONS

The Y chromosome haplogroup distribution allowed us to identify recent migratory processes typical of the northern populations studied. These have shaped the demographic and cultural dynamics of local and migrant groups in the territory.

Demand for larger Y-STR reference databases in ethnic melting-pot countries: Argentina as a test case

The Y chromosome behaves as a single locus. Its genetic information is useful in forensic casework, deficiency kinship testing, and population genetics studies. Continuous increases of loci number within commercial kits forced modification of worldwide reference databases. In Pan American countries, like Argentina, diverse parental ethnic groups contributed to the extant admixed urban populations. We report 509 additional haplotypes of 23 Y-STRs from donors inhabiting urban areas of six Argentinean provinces: Buenos Aires, Santiago del Estero, Santa Cruz, Rio Negro, Santa Fe, and Formosa. To better understand the demographic landscape of the admixed urban paternal lineages, structural analysis was performed using published data from other Argentinean provinces. AMOVA by Rst distance and inferred haplogroups by two predictive online software methods based on haplotypes yielded complementary results with respect to detected population structure, probably due to the different proportions of the Native American Q3-M3 haplogroup in the studied samples. This situation, which is common to most North, Meso, and South American countries, underscores the need for the additional step of typing specific SNPs for haplogroup diagnosis. We propose organizing Y-STR haplotype reference databases according to the most frequent haplogroups detected in a given admixed population.

Native American gene continuity to the modern admixed population from the Colombian Andes: Implication for biomedical, population and forensic studies

Andean populations have variable degrees of Native American and European ancestry, representing an opportunity to study admixture dynamics in the populations from Latin America (also known as Hispanics). We characterized the genetic structure of two indigenous (Nasa and Pijao) and three admixed (Ibagué, Ortega and Planadas) groups from Tolima, in the Colombian Andes. DNA samples from 348 individuals were genotyped for six mitochondrial DNA (mtDNA), seven non-recombining Y-chromosome (NRY) region and 100 autosomal ancestry informative markers. Nasa and Pijao had a predominant Native American ancestry at the autosomal (92%), maternal (97%) and paternal (70%) level. The admixed groups had a predominant Native American mtDNA ancestry (90%), a substantial frequency of European NRY haplotypes (72%) and similar autosomal contributions from Europeans (51%) and Amerindians (45%). Pijao and nearby Ortega were indistinguishable at the mtDNA and autosomal level, suggesting a genetic continuity between them. Comparisons with multiple Native American populations throughout the Americas revealed that Pijao, had close similarities with Carib-speakers from distant parts of the continent, suggesting an ancient correlation between language and genes. In summary, our study aimed to understand Hispanic patterns of migration, settlement and admixture, supporting an extensive contribution of local Amerindian women to the gene pool of admixed groups and consistent with previous reports of European-male driven admixture in Colombia.

Historical records under the genetic evidence: "Chiriguano" tribe genesis as a test case

Historical records suggest that Chiriguano tribe is the result of a genetic admixture event. The process involved the arrival of Guaraní tribesmen descending from Amazonian region of Brazil along with groups of Arawak origin that inhabited the foothill plains of Bolivia. Later they arrived in Argentina at the beginning of the twentieth century. Aiming to test the historical records, we analysed a set of 46 samples collected at San Ramon de la Nueva Orán, Province of Salta, Argentina. A wide set of uni- and biparentally transmitted genetic markers were analysed, including 23 autosomal STRs; 46 AIM-DIPs and 24 AIM-SNPs all located at diverse autosomal chromosome locations; 23 Y-STRs and the entire mtDNA D-Loop sequence. Ancestry informative markers allowed for the detection of a strong Native American component in the genomes (> 94%), while all mtDNA haplotypes showed Native American characteristic motives, and 93% of Y-haplotypes belonged to the Q1a3a Y-haplogroup. The analysis of mitochondrial haplotypes and Y chromosome, although they did not match other populations, revealed a relationship between the Chiriguano and other groups of Guaraní and Arawak origin inhabiting Brazil and Bolivia, confirming, at least in part, the historical records describing the origins of Chiriguano tribal settlements in northwestern Argentina.

The geographic mosaic of Ecuadorian Y-chromosome ancestry

Ecuadorians originated from a complex mixture of Native American indigenous people with Europeans and Africans. We analyzed Y-chromosome STRs (Y-STRs) in a sample of 415 Ecuadorians (145 using the AmpFlSTR^® Yfiler™ system [Life Technologies, USA] and 270 using the PowerPlex^®Y23 system [Promega Corp., USA]; hereafter Yfiler and PPY23, respectively) representing three main ecological continental regions of the country, namely Amazon rainforest, Andes, and Pacific coast. Diversity values are high in the three regions, and the PPY23 exhibits higher discrimination power than the Yfiler set. While summary statistics, AMOVA, and R_ST distances show low to moderate levels of population stratification, inferred ancestry derived from Y-STRs reveal clear patterns of geographic variation. The major ancestry in Ecuadorian males is European (61%), followed by an important Native American component (34%); whereas the African ancestry (5%) is mainly concentrated in the Northwest corner of the country. We conclude that classical procedures for measuring population stratification do not have the desirable sensitivity. Statistical inference of ancestry from Y-STRS is a satisfactory alternative for revealing patterns of spatial variation that would pass unnoticed when using popular statistical summary indices.

Hepatitis C virus pharmacogenomics in Latin American populations: implications in the era of direct-acting antivirals

In recent years, great progress has been made in the field of new therapeutic options for hepatitis C virus (HCV) infection. The new direct-acting antiviral agents (DAAs) represent a great hope for millions of chronically infected individuals because their use may lead to excellent cure rates with fewer side effects. In Latin America, the high prevalence of HCV genotype 1 infection and the significant association of Native American ancestry with risk predictive single-nucleotide polymorphisms (SNPs) in IFNL4 and ITPA genes highlight the need to implement new treatment regimens in these populations. However, the universal accessibility to DAAs is still not a reality in the region as their high cost is one of the major, although not the only, limiting factors for their broad implementation. Therefore, under these circumstances, could the assessment of host genetic markers be a useful tool to prioritize DAA treatment until global access to these new drugs can be achieved? This review will summarize the scientific evidences and the potential implications of HCV pharmacogenomics in this rapidly evolving era of anti-HCV drug development.

Mapping the genomic mosaic of two 'Afro-Bolivians' from the isolated Yungas valleys

Background

Unraveling the ancestry of ‘Afro-American’ communities is hampered by the complex demographic processes that took place during the Transatlantic Slave Trade (TAST) and the (post-)colonization periods. ‘Afro-Bolivians’ from the subtropical Yungas valleys constitute small and isolated communities that live surrounded by the predominant Native American community of Bolivia. By genotyping >580,000 SNPs in two ‘Afro-Bolivians’, and comparing these genomic profiles with data compiled from more than 57 African groups and other reference ancestral populations (n = 1,161 in total), we aimed to disentangle the complex admixture processes undergone by ‘Afro-Bolivians’.

Results

The data indicate that these two genomes constitute a complex mosaic of ancestries that is approximately 80 % of recent African origin; the remaining ~20 % being European and Native American. West-Central Africa contributed most of the African ancestry to ‘Afro-Bolivians’, and this component is related to populations living along the Atlantic coast (i.e. Senegal, Ghana, Nigeria). Using tract length distribution of genomic segments attributable to distinct ancestries, we could date the time of admixture in about 400 years ago. This time coincides with the maximum importation of slaves to Bolivia to compensate the diminishing indigenous labor force needed for the development of the National Mint of Potosí.

Conclusions

Overall, the data indicate that the genome of ‘Afro-Bolivians’ was shaped by a complex process of admixture occurring in America among individuals originating in different West-Central African populations; their genomic mosaics received additional contributions of Europeans and local Native Americans (e.g. Aymaras).

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2520-x) contains supplementary material, which is available to authorized users.

Charting the Y-chromosome ancestry of present-day Argentinean Mennonites

Old Order Mennonite communities initially arose in Northern Europe (centered in the Netherlands) and derived from the Anabaptist movement of the 16th century. Mennonites migrated to the New World in the early 18th century, first to North America, and more recently to Mesoamerica and South America. We analyzed Y-chromosome short tandem repeats (STRs) and single nucleotide polymorphisms in males from a community of Mennonites, 'La Nueva Esperanza', which arrived to Argentina in 1985 from colonies in Bolivia and Mexico. Molecular diversity indices coupled with demographic simulations show that Mennonites have a reduced variability when compared with local Argentinean populations and 69 European population samples. Mennonite Y-STR haplotypes were mainly observed in Central Europe. In agreement, multidimensional scaling analyses based on RST genetic distances indicate that Mennonite Y-chromosomes are closely related to Central/Northern Europeans (the Netherlands, Switzerland and Denmark). In addition, statistical inferences made on the most likely geographic origin of Y-chromosome haplotypes point more specifically to the Netherlands as the populations that best represent the majority of the Mennonite Y-chromosomes. Overall, Y-chromosome variation of Mennonites shows the signatures of moderate reduction of variability when compared with source populations, which is in good agreement with their lifestyle in small endogamous demes. These genetic singularities could also help to understand disease conditions that are more prevalent among Mennonites.

Analysis of Y-chromosome STRs in Chile confirms an extensive introgression of European male lineages in urban populations

We analyzed the Y chromosome haplotypes (Yfiler) of 978 non-related Chilean males grouped in five sampling regions (Iquique, Santiago de Chile, Concepción, Temuco and Punta Arenas) covering main geo-political regions. Overall, 803 different haplotypes and 688 singletons were observed. Molecular diversity was moderately lower than in other neighboring countries (e.g. Argentina); and AMOVA analysis on Y-STR haplotypes showed that among variation within Chile accounted for only 0.25% of the total variation. Punta Arenas, in the southern cone, showed the lowest haplotype diversity, and discrimination capacity, and also the highest matching probability of the five Chilean samples, probably reflecting its more marked geographic isolation compared to the other regions. Multidimensional scaling (MDS) analysis based on RST genetic distances suggested a close proximity of Chilean Y-chromosome profiles to European ones. Consistently, haplogroups inferred from Y-STR profiles revealed that the Native American component constituted only 8% of all the haplotypes, and this component ranged from 5% in the Centre of the country to 9-10% in the South and 13% in the North, which is in good agreement with the distribution of Native American communities in these regions. AMOVA computed on inferred haplogroups confirmed the very low among variation observed in Chilean populations. The present project provides the first Chilean dataset to the international Y-chromosome STR Haplotype Reference Database (YHRD) and it is also the first reference database for Y-chromosome forensic casework of the country.

The Genomic Legacy of the Transatlantic Slave Trade in the Yungas Valley of Bolivia

During the period of the Transatlantic Slave Trade (TAST) some enslaved Africans were forced to move to Upper Peru (nowadays Bolivia). At first they were sent to Potosí, but later to the tropical Yungas valley where the Spanish colonizers established a so-called “hacienda system” that was based on slave labor, including African-descendants. Due to their isolation, very little attention has been paid so far to ‘Afro-Bolivian’ communities either within the research field of TAST or in genetic population studies. In this study, a total of 105 individuals from the Yungas were sequenced for their mitochondrial DNA (mtDNA) control region, and mitogenomes were obtained for a selected subset of these samples. We also genotyped 46 Ancestry Informative Markers (AIM) in order to investigate continental ancestry at the autosomal level. In addition, Y-chromosome STR and SNP data for a subset of the same individuals was also available from the literature. The data indicate that the partitioning of mtDNA ancestry in the Yungas differs significantly from that in the rest of the country: 81% Native American, 18% African, and 1% European. Interestingly, the great majority of ‘Afro-descendant’ mtDNA haplotypes in the Yungas (84%) concentrates in the locality of Tocaña. This high proportion of African ancestry in the Tocaña is also manifested in the Y-chromosome (44%) and in the autosomes (56%). In sharp contrast with previous studies on the TAST, the ancestry of about 1/3 of the ‘Afro-Bolivian’ mtDNA haplotypes can be traced back to East and South East Africa, which may be at least partially explained by the Arab slave trade connected to the TAST.

Genomic insights on the ethno-history of the Maya and the 'Ladinos' from Guatemala

Background

Guatemala is a multiethnic and multilingual country located in Central America. The main population groups separate ‘Ladinos’ (mixed Native American-African-Spanish), and Native indigenous people of Maya descent. Among the present-day Guatemalan Maya, there are more than 20 different ethnic groups separated by different languages and cultures. Genetic variation of these communities still remains largely unexplored. The principal aim of this study is to explore the genetic variability of the Maya and ‘Ladinos’ from Guatemala by means of uniparental and ancestry informative markers (AIMs).

Results

Analyses of uniparental genetic markers indicate that Maya have a dominant Native American ancestry (mitochondrial DNA [mtDNA]: 100%; Y-chromosome: 94%). ‘Ladino’, however, show a clear gender-bias as indicated by the large European ancestry observed in the Y-chromosome (75%) compared to the mtDNA (0%). Autosomal polymorphisms (AIMs) also mirror this marked gender-bias: (i) Native American ancestry: 92% for the Maya vs. 55% for the ‘Ladino’, and (ii) European ancestry: 8% for the Maya vs. 41% for the ‘Ladino’. In addition, the impact of the Trans-Atlantic slave trade on the present-day Guatemalan population is very low (and only occurs in the ‘Ladino’; mtDNA: 9%; AIMs: 4%), in part mirroring the fact that Guatemala has a predominant orientation to the Pacific Ocean instead of a Caribbean one. Sequencing of entire Guatemalan mitogenomes has led to improved Native American phylogeny via the addition of new haplogroups that are mainly observed in Mesoamerica and/or the North of South America.

Conclusions

The data reveal the existence of a fluid gene flow in the Mesoamerican area and a predominant unidirectional flow towards South America, most likely occurring during the Pre-Classic (1800 BC-200 AD) and the Classic (200–1000 AD) Eras of the Mesoamerican chronology, coinciding with development of the most distinctive and advanced Mesoamerican civilization, the Maya. Phylogenetic features of mtDNA data also suggest a demographic scenario that is compatible with moderate local endogamy and isolation in the Maya combined with episodes of gene exchange between ethnic groups, suggesting an ethno-genesis in the Guatemalan Maya that is recent and supported on a cultural rather than a biological basis.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1339-1) contains supplementary material, which is available to authorized users.