Genetic uniqueness of the Waorani tribe from the Ecuadorian Amazon

Quantifying quality: The impact of measures of school quality on children's academic achievement across diverse societies

Recent decades have seen a rapid acceleration in global participation in formal education, due to worldwide initiatives aimed to provide school access to all children. Research in high income countries has shown that school quality indicators have a significant, positive impact on numeracy and literacy-skills required to participate in the increasingly globalized economy. Schools vary enormously in kind, resources, and teacher training around the world, however, and the validity of using diverse school quality measures in populations with diverse educational profiles remains unclear. First, we assessed whether children's numeracy and literacy performance across populations improves with age, as evidence of general school-related learning effects. Next, we examined whether several school quality measures related to classroom experience and composition, and to educational resources, were correlated with one another. Finally, we examined whether they were associated with children's (4-12-year-olds, N = 889) numeracy and literacy performance in 10 culturally and geographically diverse populations which vary in historical engagement with formal schooling. Across populations, age was a strong positive predictor of academic achievement. Measures related to classroom experience and composition were correlated with one another, as were measures of access to educational resources and classroom experience and composition. The number of teachers per class and access to writing materials were key predictors of numeracy and literacy, while the number of students per classroom, often linked to academic achievement, was not. We discuss these results in the context of maximising children's learning environments and highlight study limitations to motivate future research. RESEARCH HIGHLIGHTS: We examined the extent to which four measures of school quality were associated with one another, and whether they predicted children's academic achievement in 10 culturally and geographically diverse societies. Across populations, measures related to classroom experience and composition were correlated with one another as were measures of access to educational resources to classroom experience and composition. Age, the number of teachers per class, and access to writing materials were key predictors of academic achievement across populations. Our data have implications for designing efficacious educational initiatives to improve school quality globally.

HLA allelic diversity in the Waorani population of Ecuador: Its significance to their ancestry and migration

The Waorani, an isolated indigenous tribe in Ecuador, have long been characterized by limited genetic diversity, with few studies delving into their genetic background. Human Leukocyte Antigen (HLA) genes which are located in the human major histocompatibility complex (MHC) provides valuable insights into population evolution due to its highly polymorphic nature. However, little is known about the HLA diversity and ancestry of the Waorani population. In this study, we sequenced eight HLA genes using Next Generation Sequencing (NGS) from 134 Waorani individuals and obtained up to four-field HLA allele resolution. Cluster and phylogenetic analysis show that the Waorani are genetically distant from other Ecuador populations, but instead show genetic affinities with the Puyanawa and Terena tribes from Brazil, as well as the Mixe tribe from Mexico. The identification of alleles common within the Waorani population, previously linked to specific health conditions, notably paves the way for future association analyses. This extensive study, employing Next-Generation Sequencing (NGS) technology, significantly enriches the sparse and segmented understanding of HLA diversity in the South American region. Our findings enhance the global comprehension of human genetic diversity and underscore the value of studying indigenous populations. Such research is vital for deepening our insights into human migration patterns and evolutionary processes.

Clusters of rare disorders and congenital anomalies in South America

Objective

To map geographic clusters of rare disorders and congenital anomalies reported in South America.

Methods

Qualitative systematic review conducted in Medline/PubMed, Lilacs, and Scielo electronic databases to identify studies meeting eligibility criteria. The strategy resulted in 1 672 unique articles, from which 164 were selected for full reading by a pair of reviewers.

Results

Fifty-five articles reported at least one cluster of genetic disorders or congenital anomalies in South American territory. From these papers, 122 clusters were identified, of which half (61) were related to autosomal recessive disorders. Sixty-five (53.3%) of the clusters were located in Brazil.

Conclusions

The results of the review reinforce that rare diseases and congenital anomalies can occur in a non-random way in space, which is discussed in the perspective of the complex history of formation, social organization, and genetic structure of the South American population. Mapping clusters in population medical genetics can be an important public health tool, given that such places concentrate cases of rare diseases that frequently require multiprofessional, specialized care. Therefore, these results can support important agendas in public health related to rare diseases and congenital anomalies, such as health promotion and surveillance.

Hematological Parameters, Lipid Profile, and Cardiovascular Risk Analysis Among Genotype-Controlled Indigenous Kiwcha Men and Women Living at Low and High Altitudes

Introduction: Human adaptation to high altitude is due to characteristic adjustments at every physiological level. Differences in lipid profile and cardiovascular risk factors in altitude dwellers have been previously explored. Nevertheless, there are no reports available on genotype-controlled matches among different altitude-adapted indigenous populations.

Objective: To explore the possible differences in plasma lipid profile and cardiovascular risk among autochthonous Kiwcha people inhabitants of low and high-altitude locations.

Methodology: A cross-sectional analysis of plasmatic lipid profiles and cardiovascular risk factors in lowland Kiwchas from Limoncocha (230 m) and high-altitude Kiwchas from Oyacachi (3,800 m).

Results: In the low altitude group, 66% were women (n = 78) and 34% (n = 40) were men, whereas in the high altitude group, 59% (n = 56) were women and 41% (n = 41%) were men. We found the proportion of overweight and obese individuals to be higher among low altitude dwellers (p < 0.05). Red blood cells (RBCs), hemoglobin concentration, and SpO₂% were higher among high altitude dwellers and the erythrocyte size was found to be smaller at high altitude. The group located at low altitude also showed lower levels of plasma cholesterol, low-density lipoprotein (LDL), and high-density lipoprotein (HDL), but most of these differences are not influenced by gender or elevation.

Conclusions: Living at an altitude elicits well-known adaptive physiological changes such as erythrocyte count, hemoglobin concentration, hematocrit level, and serum glucose level. We also report clinical differences in the plasma lipid profile, with higher levels of cholesterol, HDL, and LDL in inhabitants of the Andes Mountain vs. their Amazonian basin peers. Despite this, we did not find significant differences in cardiovascular risk.

The Mitochondrial DNA Landscape of Modern Mexico

Mexico is a rich source for anthropological and population genetic studies with high diversity in ethnic and linguistic groups. The country witnessed the rise and fall of major civilizations, including the Maya and Aztec, but resulting from European colonization, the population landscape has dramatically changed. Today, the majority of Mexicans do not identify themselves as Indigenous but as admixed, and appear to have very little in common with their pre-Columbian predecessors. However, when the maternally inherited mitochondrial (mt)DNA is investigated in the modern Mexican population, this is not the case. Control region sequences of 2021 samples deriving from all over the country revealed an overwhelming Indigenous American legacy, with almost 90% of mtDNAs belonging to the four major pan-American haplogroups A2, B2, C1, and D1. This finding supports a very low European contribution to the Mexican gene pool by female colonizers and confirms the effectiveness of employing uniparental markers as a tool to reconstruct a country’s history. In addition, the distinct frequency and dispersal patterns of Indigenous American and West Eurasian clades highlight the benefit such large and country-wide databases provide for studying the impact of colonialism from a female perspective and population stratification. The importance of geographical database subsets not only for forensic application is clearly demonstrated.

Uniparental Lineages from the Oldest Indigenous Population of Ecuador: The Tsachilas

Together with Cayapas, the Tsachilas constitute the oldest population in the country of Ecuador and, according to some historians, they are the last descendants of the ancient Yumbos. Several anthropological issues underlie the interest towards this peculiar population: the uncertainty of their origin, their belonging to the Barbacoan linguistic family, which is still at the center of an intense linguistic debate, and the relations of their Yumbo ancestors with the Inca invaders who occupied their ancient territory. Our contribution to the knowledge of their complex past was the reconstruction of their genetic maternal and paternal inheritance through the sequencing of 70 entire mitochondrial genomes and the characterization of the non-recombinant region of the Y chromosome in 26 males. For both markers, we built comprehensive datasets of various populations from the surrounding geographical area, northwestern South America, NW, with a known linguistic affiliation, and we could then compare our sample against the overall variability to infer relationships with other Barbacoan people and with other NW natives. We found contrasting patterns of genetic diversity for the two markers, but generally, our results indicated a possible common origin between the Tsachilas, the Chachi, and other Ecuadorian and Colombian Barbacoans and are suggestive of an interesting ancient linkage to the Inca invaders in Yumbo country.

Current pool of ultimate collection of mitochondrial DNA from remnants of Kalash

The mitochondrial DNA (mtDNA) complete control region coverage of 111 individuals from Kalash population of Pakistan has been presented for forensic applications and to infer their genetic parameters. We detected in total 14 different haplotypes with only five unique and nine shared by more than one individual. This population has come up with quite lower haplotype diversity (0.8393) and very higher random match probability (0.1682), and ultimately lower power of discrimination (0.832). Additionally, haplogroup distribution reveals the genetic ancestry of Kalash, mainly from West Eurasia (98.8%) and very little from South Asia (0.9%). Neither African lineages nor East Asian genetic segments were detected among these Kalash. This study will contribute to the database development for forensic applications as well as to track the evolutionary highlights of this ethnic group.

Investigating genetic diversity in admixed populations from Ecuador

OBJECTIVES

According to demographic history, Ecuador has experienced shifts in its Native American populations caused by European colonization and the African slave trade. The continuous admixture events among Europeans, Native Americans, and Africans occurred differently in each region of the country, producing a stratified population. Thus, the aim of this study was to investigate the level of genetic substructure in the Ecuadorian Mestizo population.

MATERIALS AND METHODS

A total of 377 male and 209 female samples were genotyped for two sets of X-chromosomal markers (32 X-Indels and 12 X-STRs). Population analyses performed included Hardy-Weinberg equilibrium tests, LD analysis, PCA, pairwise F_ST s, and AMOVA.

RESULTS

Significant levels of LD were observed between markers separated by distances of less than 1 cM, as well as between markers separated by distances varying from 10.891 to 163.53 cM. Among Ecuadorian regions, Amazonia showed the highest average R² value.

DISCUSSION

When X-chromosomal and autosomal differentiation values were compared, a sex-biased admixture between European men and Native American and African women was revealed, as well as between African men and Native American women. Moreover, a distinct Native American ancestry was discernible in the Amazonian population, in addition to sex-biased gene flow between Amazonia and the Andes and Pacific coast regions. Overall, these results underline the importance of integrating X chromosome information to achieve a more comprehensive view of the genetic and demographic histories of South American admixed populations.

A Y-chromosomal survey of Ecuador's multi-ethnic population reveals new insights into the tri-partite population structure and supports an early Holocene age of the rare Native American founder lineage C3-MPB373

Ecuador is a multiethnic and pluricultural country with a complex history defined by migration and admixture processes. The present study aims to increase our knowledge on the Ecuadorian Native Amerindian groups and the unique South American Y-chromosome haplogroup C3-MPB373 through the analysis of up to 23 Y-chromosome STRs (Y-STRs) and several Y-SNPs in a sample of 527 Ecuadorians from 7 distinct populations and geographic areas, including Kichwa and non-Kichwa Native Amerindians, Mestizos and Afro-Ecuadorians. Our results reveal the presence of C3-MPB373 both in the Amazonian lowland Kichwa with frequencies up to 28 % and, for the first time, in notable proportions in Kichwa populations from the Ecuadorian highlands. The substantially higher frequencies of C3-MPB373 in the Amazonian lowlands found in Kichwa and Waorani individuals suggest a founder effect in that area. Notably, estimates for the time to the most recent common ancestor (TMRCA) in the range of 7.2-9.0 kya point to an ancient origin of the haplogroup and suggest an early Holocene expansion of C3-MPB373 into South America. Finally, the pairwise genetic distances (R_ST) separate the Kichwa Salasaka from all the other Native Amerindian and Ecuadorian groups, indicating a so far hidden diversity among the Kichwa-speaking populations and suggesting a more southern origin of this population. In sum, our study provides a more in-depth knowledge of the male genetic structure of the multiethnic Ecuadorian population, as well as a valuable reference dataset for forensic use.

Potential research ethics violations against an indigenous tribe in Ecuador: a mixed methods approach

Background

Biomedical and ethnographic studies among indigenous people are common practice in health and geographical research. Prior health research misconduct has been documented, particularly when obtaining genetic material. The objective of this study was to crossmatch previously published data with the perceptions of the Waorani peoples about the trading of their genetic material and other biological samples.

Methods

We conducted a mixed methods study design using a tailored 15-item questionnaire in 72 participants and in-depth interviews in 55 participants belonging to 20 Waorani communities about their experiences and perceptions of participating in biomedical research projects. Additionally, we conducted a systematic review of the literature in order to crossmatch the published results of studies stating the approval of an ethics committee and individual consent within their work.

Results

A total of 40 men (60%) and 32 women (40%), with a mean age of 57 ± 15 years agreed to be interviewed for inclusion. Five main categories around the violation of good clinical practices were identified, concerning the obtention of blood samples from a recently contacted Waorani native community within the Amazonian region of Ecuador. These themes are related to the lack of adequate communication between community members and researchers as well as the voluntariness to participate in health research. Additionally, over 40 years, a total of 38 manuscripts related to the use of biological samples in Waorani indigenous people were published. The majority of the studies (68%) did not state within their article obtaining research ethics board approval, and 71% did not report obtaining the informed consent of the participants prior to the execution of the project.

Conclusion

Clinical Research on the Waorani community in the Ecuadorian Amazon basin has been performed on several occasions. Unfortunately, the majority of these projects did not follow the appropriate ethical and professional standards in either reporting the results or fulfilling them. The results of our investigation suggest that biological material, including genetic material, has been used by researchers globally, with some omitting the minimum information required to guarantee transparency and good clinical practices. We highlight the importance of stating ethics within research to avoid breaches in research transparency.

The three-hybrid genetic composition of an Ecuadorian population using AIMs-InDels compared with autosomes, mitochondrial DNA and Y chromosome data

The history of Ecuador was marked by the arrival of Europeans with Africans, resulting in the mixture of Native Americans with Africans and Europeans. The present study contributes to the knowledge of the Ecuadorian mestizo population by offering information about ancestry and ethnic heterogeneity. Forty-six AIM-InDels (Ancestry Informative Insertion/Deletion Markers) were used to obtain information on 240 Ecuadorian individuals from three regions (Amazonia, the Highlands, and the Coast). As a result, the population involved a significant contribution from Native Americans (values up to 51%), followed by Europeans (values up to 33%) and Africans (values up to 13%). Furthermore, we compared the data obtained with nine previously reported scientific articles on autosomal, mitochondrial DNA and Y chromosomes. The admixture results correspond to Ecuador's historical background and vary slightly between regions.

Cultural Innovations Influence Patterns of Genetic Diversity in Northwestern Amazonia

Human populations often exhibit contrasting patterns of genetic diversity in the mtDNA and the nonrecombining portion of the Y-chromosome (NRY), which reflect sex-specific cultural behaviors and population histories. Here, we sequenced 2.3 Mb of the NRY from 284 individuals representing more than 30 Native American groups from Northwestern Amazonia (NWA) and compared these data to previously generated mtDNA genomes from the same groups, to investigate the impact of cultural practices on genetic diversity and gain new insights about NWA population history. Relevant cultural practices in NWA include postmarital residential rules and linguistic exogamy, a marital practice in which men are required to marry women speaking a different language. We identified 2,969 SNPs in the NRY sequences, only 925 of which were previously described. The NRY and mtDNA data showed different sex-specific demographic histories: female effective population size has been larger than that of males through time, which might reflect larger variance in male reproductive success. Both markers show an increase in lineage diversification beginning ∼5,000 years ago, which may reflect the intensification of agriculture, technological innovations, and the expansion of regional trade networks documented in the archaeological evidence. Furthermore, we find similar excesses of NRY versus mtDNA between-population divergence at both the local and continental scale, suggesting long-term stability of female versus male migration. We also find evidence of the impact of sociocultural practices on diversity patterns. Finally, our study highlights the importance of analyzing high-resolution mtDNA and NRY sequences to reconstruct demographic history, since this can differ considerably between sexes.

The Paleo-Indian Entry into South America According to Mitogenomes

Recent and compelling archaeological evidence attests to human presence ∼14.5 ka at multiple sites in South America and a very early exploitation of extreme high-altitude Andean environments. Considering that, according to genetic evidence, human entry into North America from Beringia most likely occurred ∼16 ka, these archeological findings would imply an extremely rapid spread along the double continent. To shed light on this issue from a genetic perspective, we first completely sequenced 217 novel modern mitogenomes of Native American ancestry from the northwestern area of South America (Ecuador and Peru); we then evaluated them phylogenetically together with other available mitogenomes (430 samples, both modern and ancient) from the same geographic area and, finally, with all closely related mitogenomes from the entire double continent. We detected a large number (N = 48) of novel subhaplogroups, often branching into further subclades, belonging to two classes: those that arose in South America early after its peopling and those that instead originated in North or Central America and reached South America with the first settlers. Coalescence age estimates for these subhaplogroups provide time boundaries indicating that early Paleo-Indians probably moved from North America to the area corresponding to modern Ecuador and Peru over the short time frame of ∼1.5 ka comprised between 16.0 and 14.6 ka.

Enclaves of genetic diversity resisted Inca impacts on population history

The Inca Empire is claimed to have driven massive population movements in western South America, and to have spread Quechua, the most widely-spoken language family of the indigenous Americas. A test-case is the Chachapoyas region of northern Peru, reported as a focal point of Inca population displacements. Chachapoyas also spans the environmental, cultural and demographic divides between Amazonia and the Andes, and stands along the lowest-altitude corridor from the rainforest to the Pacific coast. Following a sampling strategy informed by linguistic data, we collected 119 samples, analysed for full mtDNA genomes and Y-chromosome STRs. We report a high indigenous component, which stands apart from the network of intense genetic exchange in the core central zone of Andean civilization, and is also distinct from neighbouring populations. This unique genetic profile challenges the routine assumption of large-scale population relocations by the Incas. Furthermore, speakers of Chachapoyas Quechua are found to share no particular genetic similarity or gene-flow with Quechua speakers elsewhere, suggesting that here the language spread primarily by cultural diffusion, not migration. Our results demonstrate how population genetics, when fully guided by the archaeological, historical and linguistic records, can inform multiple disciplines within anthropology.

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.

The genetic evidence for human origin of Jivaroan shrunken heads in collections from the Polish museums

Advances in forensic identification using molecular genetics are helpful in resolving some historical mysteries. The aim of this study was to confirm the authenticity of shrunken-head artifacts exhibited by two Polish museums. Shrunken heads, known as tsantsas, were headhunting trophies of South American Indians (Jivaroan). A special preparation preserved their hair and facial appearance. However, it was quite common to offer counterfeit shrunken heads of sloths or monkeys to collectors of curiosities. We sampled small skin specimens of four shrunken-head skin from the museum collection from Warsaw and Krakow, Poland. Following genomic DNA isolation, highly polymorphic short tandem repeats were genotyped using a commercial chemistry and DNA sequencing analyzer. Haplogroups of human Y chromosome were identified. We obtained an informative genetic profile of genomic short tandem repeats from all the samples of shrunken heads. Moreover, amplification of amelogenin loci allowed for sex determination. All four studied shrunken heads were of human origin. In two ones, a shared Y-chromosome haplogroup Q characteristic for Indigenous Americans was detected. Another artifact was counterfeited because Y-chromosome haplogroup I2 was found, characteristic for the Southeastern European origin. Commercial genetic methods of identification can be applied successfully in studies on the origin and authenticity of some unusual collection items.

Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas

The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.

Helena, the hidden beauty: Resolving the most common West Eurasian mtDNA control region haplotype by massively parallel sequencing an Italian population sample

The analysis of mitochondrial (mt)DNA is a powerful tool in forensic genetics when nuclear markers fail to give results or maternal relatedness is investigated. The mtDNA control region (CR) contains highly condensed variation and is therefore routinely typed. Some samples exhibit an identical haplotype in this restricted range. Thus, they convey only weak evidence in forensic queries and limited phylogenetic information. However, a CR match does not imply that also the mtDNA coding regions are identical or samples belong to the same phylogenetic lineage. This is especially the case for the most frequent West Eurasian CR haplotype 263G 315.1C 16519C, which is observed in various clades within haplogroup H and occurs at a frequency of 3-4% in many European populations. In this study, we investigated the power of massively parallel complete mtGenome sequencing in 29 Italian samples displaying the most common West Eurasian CR haplotype - and found an unexpected high diversity. Twenty-eight different haplotypes falling into 19 described sub-clades of haplogroup H were revealed in the samples with identical CR sequences. This study demonstrates the benefit of complete mtGenome sequencing for forensic applications to enforce maximum discrimination, more comprehensive heteroplasmy detection, as well as highest phylogenetic resolution.

The expanded mtDNA phylogeny of the Franco-Cantabrian region upholds the pre-neolithic genetic substrate of Basques

The European genetic landscape has been shaped by several human migrations occurred since Paleolithic times. The accumulation of archaeological records and the concordance of different lines of genetic evidence during the last two decades have triggered an interesting debate concerning the role of ancient settlers from the Franco-Cantabrian region in the postglacial resettlement of Europe. Among the Franco-Cantabrian populations, Basques are regarded as one of the oldest and more intriguing human groups of Europe. Recent data on complete mitochondrial DNA genomes focused on macrohaplogroup R0 revealed that Basques harbor some autochthonous lineages, suggesting a genetic continuity since pre-Neolithic times. However, excluding haplogroup H, the most representative lineage of macrohaplogroup R0, the majority of maternal lineages of this area remains virtually unexplored, so that further refinement of the mtDNA phylogeny based on analyses at the highest level of resolution is crucial for a better understanding of the European prehistory. We thus explored the maternal ancestry of 548 autochthonous individuals from various Franco-Cantabrian populations and sequenced 76 mitogenomes of the most representative lineages. Interestingly, we identified three mtDNA haplogroups, U5b1f, J1c5c1 and V22, that proved to be representative of Franco-Cantabria, notably of the Basque population. The seclusion and diversity of these female genetic lineages support a local origin in the Franco-Cantabrian area during the Mesolithic of southwestern Europe, ∼10,000 years before present (YBP), with signals of expansions at ∼3,500 YBP. These findings provide robust evidence of a partial genetic continuity between contemporary autochthonous populations from the Franco-Cantabrian region, specifically the Basques, and Paleolithic/Mesolithic hunter-gatherer groups. Furthermore, our results raise the current proportion (≈15%) of the Franco-Cantabrian maternal gene pool with a putative pre-Neolithic origin to ≈35%, further supporting the notion of a predominant Paleolithic genetic substrate in extant European populations.

Young Alu insertions within the MHC class I region in native American populations: insights into the origin of the MHC-Alu repeats

OBJECTIVES

Genetic heterogeneity of two Amerindian populations (Jujuy province, Argentina, and Waorani tribe, Ecuador) was characterized by analyzing data on polymorphic Alu insertions within the human major histocompatibility complex (MHC) class I region (6p21.31), which are completely nonexistent in Native Americans. We further evaluated the haplotype distribution and genetic diversity among continental ancestry groups and their potential implications for the dating of the origin of MHC-Alus.

METHODS

Five MHC-Alu elements (AluMicB, AluTF, AluHJ, AluHG, and AluHF) were typed in samples from Jujuy (N = 108) and Waorani (N = 36). Allele and haplotype frequency data on worldwide populations were compiled to explore spatial structuring of the MHC-Alu diversity through AMOVA tests. We utilized the median-joining network approach to illustrate the continental distribution of the MHC-Alu haplotypes and their phylogenetic relationships.

RESULTS

Allele and haplotype distributions differed significantly between Jujuy and Waorani. The Waorani featured a low average heterozygosity attributable to strong population isolation. Overall, Alu markers showed great genetic heterogeneity both within and among populations. The haplotype distribution was distinctive of each continental ancestry group. Contrary to expectations, Africans showed the lowest MHC-Alu diversity.

CONCLUSIONS

Genetic drift mainly associated to population bottlenecks seems to be reflected in the low MHC-Alu diversity of the Amerindians, mainly in Waorani. Geographical structuring of the haplotype distribution supports the efficiency of the MHC-Alu loci as lineage (ancestry) markers. The markedly low Alu diversity of African populations relative to other continental clusters suggests that these MHC-Alus might have arisen after the anatomically modern humans expanded out of Africa.