Vivien G. Standen

Genomic evidence for the Pleistocene and recent population history of Native Americans

Genetic history of Native Americans Several theories have been put forth as to the origin and timing of when Native American ancestors entered the Americas. To clarify this controversy, Raghavan et al. examined the genomic variation among ancient and modern individuals from Asia and the Americas. There is no evidence for multiple waves of entry or recurrent gene flow with Asians in northern populations. The earliest migrations occurred no earlier than 23,000 years ago from Siberian ancestors. Amerindians and Athabascans originated from a single population, splitting approximately 13,000 years ago. Science, this issue 10.1126/science.aab3884 Genetic variation within ancient and extant Native American populations informs on their migration into the Americas. INTRODUCTION The consensus view on the peopling of the Americas is that ancestors of modern Native Americans entered the Americas from Siberia via the Bering Land Bridge and that this occurred at least ~14.6 thousand years ago (ka). However, the number and timing of migrations into the Americas remain controversial, with conflicting interpretations based on anatomical and genetic evidence. RATIONALE In this study, we address four major unresolved issues regarding the Pleistocene and recent population history of Native Americans: (i) the timing of their divergence from their ancestral group, (ii) the number of migrations into the Americas, (iii) whether there was ~15,000 years of isolation of ancestral Native Americans in Beringia (Beringian Incubation Model), and (iv) whether there was post-Pleistocene survival of relict populations in the Americas related to Australo-Melanesians, as suggested by apparent differences in cranial morphologies between some early (“Paleoamerican”) remains and those of more recent Native Americans. We generated 31 high-coverage modern genomes from the Americas, Siberia, and Oceania; 23 ancient genomic sequences from the Americas dating between ~0.2 and 6 ka; and SNP chip genotype data from 79 present-day individuals belonging to 28 populations from the Americas and Siberia. The above data sets were analyzed together with published modern and ancient genomic data from worldwide populations, after masking some present-day Native Americans for recent European admixture. RESULTS Using three different methods, we determined the divergence time for all Native Americans (Athabascans and Amerindians) from their Siberian ancestors to be ~20 ka, and no earlier than ~23 ka. Furthermore, we dated the divergence between Athabascans (northern Native American branch, together with northern North American Amerindians) and southern North Americans and South and Central Americans (southern Native American branch) to be ~13 ka. Similar divergence times from East Asian populations and a divergence time between the two branches that is close in age to the earliest well-established archaeological sites in the Americas suggest that the split between the branches occurred within the Americas. We additionally found that several sequenced Holocene individuals from the Americas are related to present-day populations from the same geographical regions, implying genetic continuity of ancient and modern populations in some parts of the Americas over at least the past 8500 years. Moreover, our results suggest that there has been gene flow between some Native Americans from both North and South America and groups related to East Asians and Australo-Melanesians, the latter possibly through an East Asian route that might have included ancestors of modern Aleutian Islanders. Last, using both genomic and morphometric analyses, we found that historical Native American groups such as the Pericúes and Fuego-Patagonians were not “relicts” of Paleoamericans, and hence, our results do not support an early migration of populations directly related to Australo-Melanesians into the Americas. CONCLUSION Our results provide an upper bound of ~23 ka on the initial divergence of ancestral Native Americans from their East Asian ancestors, followed by a short isolation period of no more than ~8000 years, and subsequent entrance and spread across the Americas. The data presented are consistent with a single-migration model for all Native Americans, with later gene flow from sources related to East Asians and, indirectly, Australo-Melanesians. The single wave diversified ~13 ka, likely within the Americas, giving rise to the northern and southern branches of present-day Native Americans. Population history of present-day Native Americans. The ancestors of all Native Americans entered the Americas as a single migration wave from Siberia (purple) no earlier than ~23 ka, separate from the Inuit (green), and diversified into “northern” and “southern” Native American branches ~13 ka. There is evidence of post-divergence gene flow between some Native Americans and groups related to East Asians/Inuit and Australo-Melanesians (yellow). How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative “Paleoamerican” relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

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

Native American population history is reexamined using a large data set of pre-Columbian mitochondrial genomes. 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.

Trauma in the preceramic coastal populations of northern Chile: violence or occupational hazards?

One hundred and forty-four Chinchorro skeletons, stored at the Museo Arqueol¿ogico San Miguel de Azapa in Arica, Chile, were examined to test the following alternative hypotheses concerning skeletal trauma: either observed trauma was a consequence of interpersonal violence, or was the result of work-related accidents. Trauma found in subadults was rare, with 1.8% (1/55) contrasted with 30% (27/89) in the adult population. The location of most adult trauma was the skull with 24.6% (17/69), followed by the upper extremities with 8. 7% (7/80), the trunk with 2.9% (2/68), and the lower extremities with the least trauma at 1.1% (1/89). Skull trauma corresponded to well-healed, semicircular fractures, with males being three times more affected than females at 34.2% (13/38) and 12.9% (4/31), respectively. Most fractures were nonlethal, appearing to have been caused by impacts from stones, suggesting interpersonal violence rather than accidents. This study indicates that the egalitarian, maritime, hunter-gatherer Chinchorro culture (circa 4000 years B.P.) may not have lived as peacefully as once thought.

Emergence of social complexity among coastal hunter-gatherers in the Atacama Desert of northern Chile

The emergence of complex cultural practices in simple hunter-gatherer groups poses interesting questions on what drives social complexity and what causes the emergence and disappearance of cultural innovations. Here we analyze the conditions that underlie the emergence of artificial mummification in the Chinchorro culture in the coastal Atacama Desert in northern Chile and southern Peru. We provide empirical and theoretical evidence that artificial mummification appeared during a period of increased coastal freshwater availability and marine productivity, which caused an increase in human population size and accelerated the emergence of cultural innovations, as predicted by recent models of cultural and technological evolution. Under a scenario of increasing population size and extreme aridity (with little or no decomposition of corpses) a simple demographic model shows that dead individuals may have become a significant part of the landscape, creating the conditions for the manipulation of the dead that led to the emergence of complex mortuary practices.

External auditory exostosis in prehistoric Chilean populations: a test of the cold water hypothesis.

Over one thousand prehistoric crania (n = 1,149) from northern Chile were analyzed to determine if the presence of external auditory exostosis (EAE) was a type of subsistence-induced pathology, a consequence of habitual fishing in the cold water of the Pacific Ocean, rather than genetically determined. To test this occupational hypothesis, the sample was divided according to chronology, type of economy, site elevation, and sex. The crania came from 43 sites, including the coast, lowland valleys (100-2,000 m), and highlands (2,000 to 4,000 m) with a time frame of 7,000 B.C. to the Inca era (1500 A.D.). There was a significant association between EAE, environment, and sex. The coastal inhabitants had the highest prevalence of EAE with 30.7% (103/336), followed by 2.3% (6/24) for the valley people and 0% (0/549) for highlanders. Coastal and valley men were significantly more affected than their female counterparts. Contrary to expectations, there was no significant association between EAE and economy and/or chronology. In the Arica area, the early Chinchorro fishers, without agriculture, had 27.7% (26/94) EAE, the subsequent agro-pastoralists, 42.7% (32/75), and the late Arican agro-pastoral fishers had 35.6% (36/101) EAE. Apparently, with the advent of agriculture, the coastal Arican populations increased their ocean harvests, rather than decreased them, to gain a surplus in order to trade with nonmaritime groups.

Mid-Holocene climate and culture change in the South Central Andes

This chapter reviews the history of study and the current status of Mid-Holocene climatic and cultural change in the South Central Andes, which host a wide range of different habitats from Pacific coastal areas up to extremely harsh cold and dry environments of the high mountain plateau, the altiplano or the puna. Paleoenvironmental information reveals high amplitude and rapid changes in effective moisture during the Holocene period and, consequently, dramatically changing environmental conditions. Therefore, this area is suitable to study the response of hunting and gathering societies to environmental changes, because the smallest variations in the climatic conditions have large impacts on resources and the living space of humans. This chapter analyzes environmental and paleoclimatic information from lake sediments, ice cores, pollen profiles, and geomorphic processes and relates these with the cultural and geographic settlement patterns of human occupation in the different habitats in the area of southern Peru, southwest Bolivia, northwest Argentina, and north Chile and puts in perspective of the early and late Holocene to present a representative range of environmental and cultural changes. It has been found that the largest changes took place around 9000 cal yr BP when the humid early Holocene conditions were replaced by extremely arid but highly variable climatic conditions. These resulted in a marked decrease of human occupation, “ecological refuges,” increased mobility, and an orientation toward habitats with relatively stable resources (such as the coast, the puna seca, and “ecological refuges”).

GEOGLIFOS Y TRÁFICO PREHISPÁNICO DE CARAVANAS DE LLAMAS EN EL DESIERTO DE ATACAMA (NORTE DE CHILE)

Este estudio aporta nuevos antecedentes empiricos, resultado de las excavaciones de cuatro campamentos de uso transitorio y dos entierros humanos, asociados a sitios con geoglifos, ubicados a lo largo de una ruta caravanera prehispanica de 150 km, que conecto a los oasis de Pica con la costa del oceano Pacifico. Puesto que la mayoria de estos sitios se encuentra en territorios deserticos sin recursos, asociados a contextos tales como coprolitos de llamas y hojas de maices, argumentamos que fueron componentes directos del trafico caravanero. Esta ruta estuvo vinculada al intenso trafico macrorregional de larga distancia po r donde circulaban bienes economicos y suntuarios procedentes de los mas diversos ambientes (selva-altiplano-oasis-pampacosta). Las seis dataciones de radiocarbono, obtenidas de los contextos excavados, indicarian que, si bien la mayoria de los geoglifos de la transecta de estudio fueron elaborados durante el periodo del Desarrollo Regional (900-1.450 anos d.C.), cierta s rutas transdeserticas ya estaban en uso, al menos desde el Arcaico Tardio (1.300 anos a.C.), por parte de cazadores, pescadores y recolectores. Palabras claves: geoglifos, caravanas de llamas, rutas de trafico prehistorico, campamentos transitorios, dataciones absolutas. This study brings new empirical evidence, resulting from the excavation of four transitory camp sites and two human burials associated with geoglyphs, and found along a prehispanic caravan path of 150 km long, connecting the Pica oasis with the Pacific coastal ocean in the Atacama desert in northern Chile. Since the majority of these sites are found in resourceless desertic areas and are associated to contexts such as llama coprolites and corn leaves, we argue that these sites were direct components of caravan trafficking. This route was linked to an intensive long distance macro-regional traffic associated with the circulations of economic and sumptuary goods from diverse origins, including the selva, altiplano, oasis, pampa and coast. Radiocarbon dates obtained at the excavations indicate that even though most of the geoglyphs were created during the Desarrollo Regional period (900-1,450 yrs. A.D.) some transdesertic routes were already used, from at least the Late Archaic Period (1,300 B.C.) by hunters, fishers and gatherers.

Análisis de Adn Mitocondrial en Momias del Norte de Chile avala Hipótesis de Orígen Amazónico de Poblaciones Andinas

La hipotesis del origen amazonico de las poblaciones andinas basada en el analisis de marcadores geneticos nucleares es contrastada haciendo uso de ADN mitocondrial antiguo aislado de restos esqueletales de poblaciones prehistoricas del Valle de Azapa, Arica, Chile. Se analizaron 42 muestras de las cuales 32 rindieron amplificados para los cuatro marcadores amerindios permitiendo su tipificacion. La distribucion de haplogrupos (A: 31,2 %, B: 21,9 %, C: 31,2 %, D: 3,1 % y otros 12,5 %) relaciona geneticamente a las poblaciones estudiadas con grupos amazonicos y andinos actuales. El numero de muestras analizadas no permite aun una subdivision por fases cronologicas con el objeto de poner a prueba las hipotesis planteadas por arqueologos y bioantropologos para explicar la microevolucion biocultural de las poblaciones estudiadas

EL PROCESO MICROEVOLUTIVO DE LA POBLACIÓN NATIVA ANTIGUA DE ARICA

Se estudia la afinidad biologica entre grupos prehistoricos de la costa y del valle de Azapa (Norte de Chile). La muestra esta constituida por 245 craneos pertenecientes a diferentes periodos (Arcaico Tardio, Intermedio Temprano, Medio, Intermedio Tardio y Tardio) del desarrollo de la poblacion. Empleando caracteres continuos y aplicando diferentes tecnicas de analisis multivariado (distancias biologicas, analisis discriminante canonico y tecnicas de agrupamientos) se evaluaron las relaciones biologicas entre muestras de las fases Chinchorro, Alto Ramirez, El Laucho, Tiwanaku, Maytas, Cabuza, Gentilar, San Miguel e Inca. Los resultados muestran una evidente diferenciacion entre los grupos que vivian en la costa y en el valle. En las fases finales se observa una mayor integracion entre ambas areas, aunque la diferencia entre ellas permanece. Se interpreta la historia del poblamiento nativo de Arica como el resultado de por lo menos dos eventos colonizadores principales: uno vinculado con el establecimiento de grupos pescadores costeros y otro con el afincamiento y desarrollo de grupos pastores y agricultores que alcanzan un indudable predominio hasta epocas tardias. Ambos grupos tienen un origen genetico comun en una poblacion arcaica ancestral y se diferenciaron gradualmente en ambientes diferentes por la accion de factores evolutivos (sistematicos y aleatorios) y culturales, los cuales continuaron operando en el nuevo escenario

Possible influence of the ENSO phenomenon on the pathoecology of diphyllobothriasis and anisakiasis in ancient Chinchorro populations

Current clinical data show a clear relationship between the zoonosis rates of Diphyllobothrium pacificum and Anisakis caused by the El Niño Southern Oscillations (ENSO) phenomenon along the Chilean coast. These parasites are endemic to the region and have a specific habitat distribution. D. pacificum prefers the warmer waters in the northern coast, while Anisakis prefers the colder waters of Southern Chile. The ENSO phenomenon causes a drastic inversion in the seawater temperatures in this region, modifying both the cool nutrient-rich seawater and the local ecology. This causes a latitudinal shift in marine parasite distribution and prevalence, as well as drastic environmental changes. The abundance of human mummies and archaeological coastal sites in the Atacama Desert provides an excellent model to test the ENSO impact on antiquity. We review the clinical and archaeological literature debating to what extent these parasites affected the health of the Chinchorros, the earliest settlers of this region. We hypothesise the Chinchorro and their descendants were affected by this natural and cyclical ENSO phenomenon and should therefore present fluctuating rates of D. pacificum and Anisakis infestations.