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Concept: Indigenous peoples of the Americas

741

The explosive pandemic of Zika virus infection occurring throughout South America, Central America, and the Caribbean (see map) and potentially threatening the United States is the most recent of four unexpected arrivals of important arthropod-borne viral diseases in the Western Hemisphere over the past 20 years. It follows dengue, which entered this hemisphere stealthily over decades and then more aggressively in the 1990s; West Nile virus, which emerged in 1999; and chikungunya, which emerged in 2013. Are the successive migrations of these viruses unrelated, or do they reflect important new patterns of disease emergence? Furthermore, are there secondary health consequences . . .

Concepts: United States, North America, South America, Americas, Latin America, Caribbean, Central America, Indigenous peoples of the Americas

314

 To estimate differences in annual income of physicians in the United States by race and sex adjusted for characteristics of physicians and practices.

Concepts: United States, Poverty in the United States, U.S. state, Race, White American, Household income in the United States, European American, Indigenous peoples of the Americas

299

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.

Concepts: DNA, Regression analysis, United States, Brazil, South America, Americas, Latin America, Indigenous peoples of the Americas

213

The genus Capsicum is New World in origin and represents a complex of a wide variety of both wild and domesticated taxa. Peppers or fruits of Capsicum species rarely have been identified in the paleoethnobotanical record in either Meso- or South America. We report here confirmation of Capsicum sp. residues from pottery samples excavated at Chiapa de Corzo in southern Mexico dated from Middle to Late Preclassic periods (400 BCE to 300 CE). Residues from 13 different pottery types were collected and extracted using standard techniques. Presence of Capsicum was confirmed by ultra-performance liquid chromatography (UPLC)/MS-MS Analysis. Five pottery types exhibited chemical peaks for Capsicum when compared to the standard (dihydrocapsaicin). No peaks were observed in the remaining eight samples. Results of the chemical extractions provide conclusive evidence for Capsicum use at Chiapas de Corzo during a 700 year period (400 BCE-300 CE). Presence of Capsicum in different types of culinary-associated pottery raises questions how chili pepper could have been used during this early time period. As Pre-Columbian cacao products sometimes were flavored using Capsicum, the same pottery sample set was tested for evidence of cacao using a theobromine marker: these results were negative. As each vessel that tested positive for Capsicum had a culinary use we suggest here the possibility that chili residues from the Chiapas de Corzo pottery samples reflect either paste or beverage preparations for religious, festival, or every day culinary use. Alternatively, some vessels that tested positive merely could have been used to store peppers. Most interesting from an archaeological context was the presence of Capsicum residue obtained from a spouted jar, a pottery type previously thought only to be used for pouring liquids.

Concepts: Mexico, Capsicum, Capsaicin, Chili pepper, Black pepper, Indigenous peoples of the Americas, Mexican cuisine, Jalapeño

194

The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, we investigate the population genetic history of this region by characterizing patterns of genome-wide variation among 330 individuals from three of the Greater Antilles (Cuba, Puerto Rico, Hispaniola), two mainland (Honduras, Colombia), and three Native South American (Yukpa, Bari, and Warao) populations. We combine these data with a unique database of genomic variation in over 3,000 individuals from diverse European, African, and Native American populations. We use local ancestry inference and tract length distributions to test different demographic scenarios for the pre- and post-colonial history of the region. We develop a novel ancestry-specific PCA (ASPCA) method to reconstruct the sub-continental origin of Native American, European, and African haplotypes from admixed genomes. We find that the most likely source of the indigenous ancestry in Caribbean islanders is a Native South American component shared among inland Amazonian tribes, Central America, and the Yucatan peninsula, suggesting extensive gene flow across the Caribbean in pre-Columbian times. We find evidence of two pulses of African migration. The first pulse-which today is reflected by shorter, older ancestry tracts-consists of a genetic component more similar to coastal West African regions involved in early stages of the trans-Atlantic slave trade. The second pulse-reflected by longer, younger tracts-is more similar to present-day West-Central African populations, supporting historical records of later transatlantic deportation. Surprisingly, we also identify a Latino-specific European component that has significantly diverged from its parental Iberian source populations, presumably as a result of small European founder population size. We demonstrate that the ancestral components in admixed genomes can be traced back to distinct sub-continental source populations with far greater resolution than previously thought, even when limited pre-Columbian Caribbean haplotypes have survived.

Concepts: Africa, United States, North America, Caribbean, Puerto Rico, Slavery, Indigenous peoples of the Americas, Atlantic slave trade

188

For the last 500 years, the Americas have been a melting pot both for genetically diverse humans and for the pathogenic and commensal organisms associated with them. One such organism is the stomach-dwelling bacterium Helicobacter pylori, which is highly prevalent in Latin America where it is a major current public health challenge because of its strong association with gastric cancer. By analyzing the genome sequence of H. pylori isolated in North, Central and South America, we found evidence for admixture between H. pylori of European and African origin throughout the Americas, without substantial input from pre-Columbian (hspAmerind) bacteria. In the US, strains of African and European origin have remained genetically distinct, while in Colombia and Nicaragua, bottlenecks and rampant genetic exchange amongst isolates have led to the formation of national gene pools. We found three outer membrane proteins with atypical levels of Asian ancestry in American strains, as well as alleles that were nearly fixed specifically in South American isolates, suggesting a role for the ethnic makeup of hosts in the colonization of incoming strains. Our results show that new H. pylori subpopulations can rapidly arise, spread and adapt during times of demographic flux, and suggest that differences in transmission ecology between high and low prevalence areas may substantially affect the composition of bacterial populations.

Concepts: Gene, Bacteria, United States, Helicobacter pylori, North America, South America, Americas, Indigenous peoples of the Americas

177

Most individuals throughout the Americas are admixed descendants of Native American, European, and African ancestors. Complex historical factors have resulted in varying proportions of ancestral contributions between individuals within and among ethnic groups. We developed a panel of 446 ancestry informative markers (AIMs) optimized to estimate ancestral proportions in individuals and populations throughout Latin America. We used genome-wide data from 953 individuals from diverse African, European, and Native American populations to select AIMs optimized for each of the three main continental populations that form the basis of modern Latin American populations. We selected markers on the basis of locus-specific branch length to be informative, well distributed throughout the genome, capable of being genotyped on widely available commercial platforms, and applicable throughout the Americas by minimizing within-continent heterogeneity. We then validated the panel in samples from four admixed populations by comparing ancestry estimates based on the AIMs panel to estimates based on genome-wide association study (GWAS) data. The panel provided balanced discriminatory power among the three ancestral populations and accurate estimates of individual ancestry proportions (R² > 0.9 for ancestral components with significant between-subject variance). Finally, we genotyped samples from 18 populations from Latin America using the AIMs panel and estimated variability in ancestry within and between these populations. This panel and its reference genotype information will be useful resources to explore population history of admixture in Latin America and to correct for the potential effects of population stratification in admixed samples in the region.

Concepts: United States, Spanish language, North America, South America, Americas, Latin America, Nicaragua, Indigenous peoples of the Americas

168

WITH ANALYSES OF ENTIRE MITOGENOMES, STUDIES OF NATIVE AMERICAN MITOCHONDRIAL DNA (MTDNA) VARIATION HAVE ENTERED THE FINAL PHASE OF PHYLOGENETIC REFINEMENT: the dissection of the founding haplogroups into clades that arose in America during and after human arrival and spread. Ages and geographic distributions of these clades could provide novel clues on the colonization processes of the different regions of the double continent. As for the Southern Cone of South America, this approach has recently allowed the identification of two local clades (D1g and D1j) whose age estimates agree with the dating of the earliest archaeological sites in South America, indicating that Paleo-Indians might have reached that region from Beringia in less than 2000 years. In this study, we sequenced 46 mitogenomes belonging to two additional clades, termed B2i2 (former B2l) and C1b13, which were recently identified on the basis of mtDNA control-region data and whose geographical distributions appear to be restricted to Chile and Argentina. We confirm that their mutational motifs most likely arose in the Southern Cone region. However, the age estimate for B2i2 and C1b13 (11-13,000 years) appears to be younger than those of other local clades. The difference could reflect the different evolutionary origins of the distinct South American-specific sub-haplogroups, with some being already present, at different times and locations, at the very front of the expansion wave in South America, and others originating later in situ, when the tribalization process had already begun. A delayed origin of a few thousand years in one of the locally derived populations, possibly in the central part of Chile, would have limited the geographical and ethnic diffusion of B2i2 and explain the present-day occurrence that appears to be mainly confined to the Tehuelche and Araucanian-speaking groups.

Concepts: South America, Americas, Latin America, Chile, Patagonia, Indigenous peoples of the Americas, Southern Cone, Operation Condor

140

The impact of changing climate on terrestrial and underwater archaeological sites, historic buildings, and cultural landscapes can be examined through quantitatively-based analyses encompassing large data samples and broad geographic and temporal scales. The Digital Index of North American Archaeology (DINAA) is a multi-institutional collaboration that allows researchers online access to linked heritage data from multiple sources and data sets. The effects of sea-level rise and concomitant human population relocation is examined using a sample from nine states encompassing much of the Gulf and Atlantic coasts of the southeastern United States. A 1 m rise in sea-level will result in the loss of over >13,000 recorded historic and prehistoric archaeological sites, as well as over 1000 locations currently eligible for inclusion on the National Register of Historic Places (NRHP), encompassing archaeological sites, standing structures, and other cultural properties. These numbers increase substantially with each additional 1 m rise in sea level, with >32,000 archaeological sites and >2400 NRHP properties lost should a 5 m rise occur. Many more unrecorded archaeological and historic sites will also be lost as large areas of the landscape are flooded. The displacement of millions of people due to rising seas will cause additional impacts where these populations resettle. Sea level rise will thus result in the loss of much of the record of human habitation of the coastal margin in the Southeast within the next one to two centuries, and the numbers indicate the magnitude of the impact on the archaeological record globally. Construction of large linked data sets is essential to developing procedures for sampling, triage, and mitigation of these impacts.

Concepts: Oceanography, Anthropology, Archaeology, Indigenous peoples of the Americas, Prehistory, National Register of Historic Places, Archaeological record, Archaeological site

140

Archaeological and palaeoecological studies throughout the Americas have documented widespread landscape and environmental transformation during the pre-Columbian era. The highly dynamic Formative (or Neolithic) period in northern Chile (ca. 3700-1550 yr BP) brought about the local establishment of agriculture, introduction of new crops (maize, quinoa, manioc, beans, etc.) along with a major population increase, new emergent villages and technological innovations. Even trees such as the Algarrobos (Prosopis section Algarobia) may have been part of this transformation. Here, we provide evidence that these species were not native to the Atacama Desert of Chile (18-27°S), appearing only in the late Holocene and most likely due to human actions. We assembled a database composed of 41 taxon specific AMS radiocarbon dates from archaeobotanical and palaeoecological records (rodent middens, leaf litter deposits), as well an extensive bibliographical review comprising archaeobotanical, paleoecological, phylogenetic and taxonomic data to evaluate the chronology of introduction and dispersal of these trees. Although Algarrobos could have appeared as early as 4200 yr BP in northernmost Chile, they only became common throughout the Atacama over a thousand years later, during and after the Formative period. Cultural and natural factors likely contributed to its spread and consolidation as a major silvicultural resource.

Concepts: South America, Americas, Chile, Indigenous peoples of the Americas, Mexico City, Atacama Desert, Desert, Pre-Columbian era