A Reassessment of the Impact of European Contact on the Structure of Native American Genetic Diversity

Cardiovascular physiology and pathophysiology at high altitude

Oxygen is vital for cellular metabolism; therefore, the hypoxic conditions encountered at high altitude affect all physiological functions. Acute hypoxia activates the adrenergic system and induces tachycardia, whereas hypoxic pulmonary vasoconstriction increases pulmonary artery pressure. After a few days of exposure to low oxygen concentrations, the autonomic nervous system adapts and tachycardia decreases, thereby protecting the myocardium against high energy consumption. Permanent exposure to high altitude induces erythropoiesis, which if excessive can be deleterious and lead to chronic mountain sickness, often associated with pulmonary hypertension and heart failure. Genetic factors might account for the variable prevalence of chronic mountain sickness, depending on the population and geographical region. Cardiovascular adaptations to hypoxia provide a remarkable model of the regulation of oxygen availability at the cellular and systemic levels. Rapid exposure to high altitude can have adverse effects in patients with cardiovascular diseases. However, intermittent, moderate hypoxia might be useful in the management of some cardiovascular disorders, such as coronary heart disease and heart failure. The aim of this Review is to help physicians to understand the cardiovascular responses to hypoxia and to outline some recommendations that they can give to patients with cardiovascular disease who wish to travel to high-altitude destinations.

Genetic characterization of a collection of Tsantsas from Ecuadorian museums

Tsantsas are shrunken human heads originally made for ceremonial purposes by Amazonian indigenous groups of the Shuar and Achuar family, previously called Jivaroan tribes. A significant demand of these objects during the first half of the 20th century led to the manufacture of counterfeit shrunken heads for commercial purposes. For museums where these collections are held, as well as for the indigenous groups who claim their ownership, it is important to identify the origin and authenticity of these tsantsas. We hypothesized that a collection of 14 tsantsas from 3 different museum collections in Ecuador are human and aimed to characterize their sex and potential origin. We amplified the amelogenin gene and performed a high resolution melting analysis to determine their human origin and characterize their sex. We also analyzed a fragment (16209-16402) from the HVR-1 region to identify the mtDNA haplogroups present in the tsantsa collection. Our exploratory results show that all the tsantsas are human and that the collection is comprised of 13 males and 1 female. A total of seven mtDNA haplogroups were found among the tsantsa collection using the mtDNA EMPOP database. These results show a predominance of the Amerindian mtDNA haplogroups B, C and D. Additional principal component analysis, genetic distance tree and haplotype network analyses suggest a relationship between the tsantsa specimens and Native American groups.

Genetic assessment reveals no population substructure and divergent regional and sex-specific histories in the Chachapoyas from northeast Peru

Many native populations in South America have been severely impacted by two relatively recent historical events, the Inca and the Spanish conquest. However decisive these disruptive events may have been, the populations and their gene pools have been shaped markedly also by the history prior to the conquests. This study focuses mainly on the Chachapoya peoples that inhabit the montane forests on the eastern slopes of the northern Peruvian Andes, but also includes three distinct neighboring populations (the Jívaro, the Huancas and the Cajamarca). By assessing mitochondrial, Y-chromosomal and autosomal diversity in the region, we explore questions that have emerged from archaeological and historical studies of the regional culture (s). These studies have shown, among others, that Chachapoyas was a crossroads for Coast-Andes-Amazon interactions since very early times. In this study, we examine the following questions: 1) was there pre-Hispanic genetic population substructure in the Chachapoyas sample? 2) did the Spanish conquest cause a more severe population decline on Chachapoyan males than on females? 3) can we detect different patterns of European gene flow in the Chachapoyas region? and, 4) did the demographic history in the Chachapoyas resemble the one from the Andean area? Despite cultural differences within the Chachapoyas region as shown by archaeological and ethnohistorical research, genetic markers show no significant evidence for past or current population substructure, although an Amazonian gene flow dynamic in the northern part of this territory is suggested. The data also indicates a bottleneck c. 25 generations ago that was more severe among males than females, as well as divergent population histories for populations in the Andean and Amazonian regions. In line with previous studies, we observe high genetic diversity in the Chachapoyas, despite the documented dramatic population declines. The diverse topography and great biodiversity of the northeastern Peruvian montane forests are potential contributing agents in shaping and maintaining the high genetic diversity in the Chachapoyas region.

Ancient DNA Reconstructs the Genetic Legacies of Precontact Puerto Rico Communities

Indigenous peoples have occupied the island of Puerto Rico since at least 3000 BC. Due to the demographic shifts that occurred after European contact, the origin(s) of these ancient populations, and their genetic relationship to present-day islanders, are unclear. We use ancient DNA to characterize the population history and genetic legacies of precontact Indigenous communities from Puerto Rico. Bone, tooth, and dental calculus samples were collected from 124 individuals from three precontact archaeological sites: Tibes, Punta Candelero, and Paso del Indio. Despite poor DNA preservation, we used target enrichment and high-throughput sequencing to obtain complete mitochondrial genomes (mtDNA) from 45 individuals and autosomal genotypes from two individuals. We found a high proportion of Native American mtDNA haplogroups A2 and C1 in the precontact Puerto Rico sample (40% and 44%, respectively). This distribution, as well as the haplotypes represented, supports a primarily Amazonian South American origin for these populations and mirrors the Native American mtDNA diversity patterns found in present-day islanders. Three mtDNA haplotypes from precontact Puerto Rico persist among Puerto Ricans and other Caribbean islanders, indicating that present-day populations are reservoirs of precontact mtDNA diversity. Lastly, we find similarity in autosomal ancestry patterns between precontact individuals from Puerto Rico and the Bahamas, suggesting a shared component of Indigenous Caribbean ancestry with close affinity to South American populations. Our findings contribute to a more complete reconstruction of precontact Caribbean population history and explore the role of Indigenous peoples in shaping the biocultural diversity of present-day Puerto Ricans and other Caribbean islanders.

Colonialism and the co-evolution of ethnic and genetic structure in New Mexico

OBJECTIVE

Socially constructed ethnic identities are frequently rooted in beliefs about common descent that form when people with disparate cultures, languages, and biology come into contact. This study explores connections between beliefs about common descent, as represented by ethnic nomenclatures, and histories of migration and isolation ascertained from genomic data in New Mexicans of Spanish-speaking descent (NMS).

MATERIALS AND METHODS

We interviewed 507 NMS who further identified using one of seven ethnic terms that they associated with beliefs about connections to past ancestors. For groups of individuals who identified using each term, we estimated biogeographic ancestry, fit admixture models to ancestry distributions, and partitioned genetic distance into admixture and drift components.

RESULTS

Regardless of which ethnic term they used, all NMS had appreciable Native American (avg. 27%) and European ancestry (avg.71%). However, individuals who identified using terms associated with beliefs connecting them to colonial-period Spanish ancestors had significantly higher European ancestry than individuals who identified using terms associated with ancestral connections to post-colonial-period migrants from Mexico. Model-fitting analyses show that this ancestry difference reflects post-colonial gene flow with non-NMS European Americans, not colonial-period gene flow with Spaniards. Drift, not admixture, accounted for most of the genetic distance between NMS who expressed connections to Mexican versus Spanish ancestors, reflecting relative isolation of New Mexico and Mexico through the 19th century.

DISCUSSION

Patterns of genomic diversity in NMS are consistent with beliefs about common descent in showing that New Mexico was isolated for generations following initial colonization. They are inconsistent with these beliefs in showing that all NMS have substantial European and Native American ancestry, and in showing that a proportion of European ancestry derives from post-colonial-period admixture with non-NMS European Americans. Our findings provide insights into the construction of ethnic identity in contexts of migration and isolation in New Mexico and, potentially, throughout human prehistory.

Associations between ethnic identity, regional history, and genomic ancestry in New Mexicans of Spanish-speaking descent

This study examines associations between ethnic identity, regional history, and genomic ancestry in New Mexicans of Spanish-speaking descent (NMS). In structured interviews, we asked 507 NMS to select from a list of eight ethnic identity terms identified in previous research. We estimated genomic ancestry for each individual from 291,917 single nucleotide polymorphisms (SNPs) and compared genomic ancestry, age, and birthplace between groups of individuals who identified using each ethnic identity term. Eighty-eight per cent of NMS who identified as "Hispanic," "Nuevomexicano/a," and "Spanish," on average, were born in New Mexico, as were the vast majority of their parents and grandparents. Thirty-three per cent of NMS who identified as "Mexican" and "Mexican American" were born in Mexico, as were 59 per cent of their parents and 67 per cent of their grandparents. Average Native American and African ancestry proportions in "Hispanic" (0.26, 0.02, respectively), "Spanish" (0.25, 0.01), and "Nuevomexicano/a" (0.24, 0.01) NMS were significantly lower than in "Mexican American" (0.37, 0.04) NMS. Significant age differences between older "Spanish" and younger "Nuevomexicano/a" individuals, combined with widespread use of the term "Hispanic," may reflect ongoing nomenclature changes. Patterns of correspondence between ethnic identity, ethnic nomenclatures, and genomic ancestry reflect historical patterns of migration, colonization, and cultural change.

Social-group identity and population substructure in admixed populations in New Mexico and Latin America

We examined the relationship between continental-level genetic ancestry and racial and ethnic identity in an admixed population in New Mexico with the goal of increasing our understanding of how racial and ethnic identity influence genetic substructure in admixed populations. Our sample consists of 98 New Mexicans who self-identified as Hispanic or Latino (NM-HL) and who further categorized themselves by race and ethnic subgroup membership. The genetic data consist of 270 newly-published autosomal microsatellites from the NM-HL sample and previously published data from 57 globally distributed populations, including 13 admixed samples from Central and South America. For these data, we 1) summarized the major axes of genetic variation using principal component analyses, 2) performed tests of Hardy Weinberg equilibrium, 3) compared empirical genetic ancestry distributions to those predicted under a model of admixture that lacked substructure, 4) tested the hypotheses that individuals in each sample had 100%, 0%, and the sample-mean percentage of African, European, and Native American ancestry. We found that most NM-HL identify themselves and their parents as belonging to one of two groups, conforming to a region-specific narrative that distinguishes recent immigrants from Mexico from individuals whose families have resided in New Mexico for generations and who emphasize their Spanish heritage. The “Spanish” group had significantly lower Native American ancestry and higher European ancestry than the “Mexican” group. Positive F_IS values, PCA plots, and heterogeneous ancestry distributions suggest that most Central and South America admixed samples also contain substructure, and that this substructure may be related to variation in social identity. Genetic substructure appears to be common in admixed populations in the Americas and may confound attempts to identify disease-causing genes and to understand the social causes of variation in health outcomes and social inequality.