Bernardo Arriaza

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.

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.

The Frequency and Antiquity of Prehistoric Coca-Leaf-Chewing Practices in Northern Chile: Radioimmunoassay of a Cocaine Metabolite in Human-Mummy Hair

Coca-leaf chewing results in absorption of part of its cocaine content. Following absorption, cocaine and/or its stable metabolic product benzoylecgonine (BZE) may enter the chewers hair follicles and subsequently be incorporated into the hair shafts. This article reports that a recently developed radioimmunoassay is capable of detecting BZE in hair samples from ancient, spontaneously mummified human remains. Results are provided from tests on hair samples of 163 individuals, representatives of populations from seven different cultures living at coastal and low valley sites in northern Chile during the past 4,000 years. These indicate that coca-leaf-chewing practices began in this area about 2,000 years ago. The practice seems to have been common in several subsequent cultural groups. In one of these—Maitas Chiribaya—the majority of both adult men and women indulged in this practice. Coca-leaf-chewing women probably transferred BZE to their fetuses and nursing infants.

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.

The origin and evolution of maize in the Southwestern United States

The origin of maize (Zea mays mays) in the US Southwest remains contentious, with conflicting archaeological data supporting either coastal(1-4) or highland(5,6) routes of diffusion of maize into the United States. Furthermore, the genetics of adaptation to the new environmental and cultural context of the Southwest is largely uncharacterized(7). To address these issues, we compared nuclear DNA from 32 archaeological maize samples spanning 6,000 years of evolution to modern landraces. We found that the initial diffusion of maize into the Southwest about 4,000 years ago is likely to have occurred along a highland route, followed by gene flow from a lowland coastal maize beginning at least 2,000 years ago. Our population genetic analysis also enabled us to differentiate selection during domestication for adaptation to the climatic and cultural environment of the Southwest, identifying adaptation loci relevant to drought tolerance and sugar content.

Spondylolysis in prehistoric human remains from Guam and its possible etiology.

This study reports the findings of complete bilateral separation of the neural arch (spondylolysis) in 176 inhumations from the Hyatt Site, Tumon Bay, which is located on the west side of the island of Guam. Skeletons were excavated and analyzed by the Paul H. Rosendahl Inc. (PHRI) team in 1989-1990. The inhumations were associated with the pre-European Latte Period (circa 1,200-1,521 A.D.). This period was characterized by the use of large stone pillars, called latte sets, for the construction of houses. Of the 176 individuals, only 38 adult skeletons had complete spines, and 21% (8/38) of these had evidence of spondylolysis in their lumbar vertebrae, particularly in L-5. The age of the eight individuals range from 30 to 50 years. No children were found with spondylolysis. Of the males 29.4% (5/17) had spondylolysis, as did 14.3% (3/21) of the females. However, the difference between the sexes was not statistically significant. Though the sample is small, it is suggested that the high incidence of lumbar spondylolysis found in these ancient Chamorros was related to lower back traumatic events. The transport of latte stones, involving hyperextension and torque of the lower back, while dragging the stones, probably contributed to the development of microfractures in the spine and subsequent spondylolysis. If this hypothesis is correct, then both males and females appear to have been participants in an organized community labor force. It is predicted that similar frequencies of spondylolysis will be found at other Latte sites.

PALEOEPIDEMIOLOGY OF INTESTINAL PARASITES AND LICE IN PRE-COLUMBIAN SOUTH AMERICA

Some human parasites originated in prehominid ancestors in Africa. Nematode species, such as Enterobius vermicularis (pinworm), hookworms and Trichuris trichiura are shared by humans and other close phylogenetic primates (Pan and Gorilla), showing that they infected a common ancestor to this group. When humans migrated from Africa to other continents they carried these parasites wherever climate conditions allowed parasite transmission from host to host. Other parasites, however, were acquired throughout human biological and social evolutive history when new territories were occupied. Paleoparasitology data is a valuable source to recover emergence and disappearance of parasite infections through analysis of archaeological remains. Parasites can be used as biological markers of prehistoric human migrations. They are also indicators of diet, as parasite life cycles are related to specific kinds of food consumed by human groups in the different habitats they occupied. We review paleoparasitological findings in South America, comparing human-host and intestinal parasites with life conditions and environmental relationships through time.

ARSENIASIS AS AN ENVIRONMENTAL HYPOTHETICAL EXPLANATION FOR THE ORIGIN OF THE OLDEST ARTIFICIAL MUMMIFICATION PRACTICE IN THE WORLD

En este ensayo se postula que el origen de la momificacion de los Chinchorro, la mas antigua del mundo, fue provocado por un envenenamiento cronico con arsenico. Hace 7.000 anos la gente Chinchorro comenzo a momificar intencionalmente a fetos e infantes y no sabemos por que. Los Chinchorro vivian en un medio ambiente extremadamente toxico con aguas de rio que contienen niveles de arsenico de 1.000 µg/L, es decir, 100 veces mas de los niveles recomendados para la salud. El arsenicismo produce abortos espontaneos y el nacimiento de ninos prematuros y resulta interesante que las primeras momias Chinchorro son todos infantes. Entonces el arsenicismo trajo como consecuencia que las mujeres Chinchorro tuvieran tasas de abortos probablemente 30 veces mas altas que cualquier poblacion. Se postula entonces que arsenicismo es una posible hipotesis medioambiental que explicaria el origen de esta singular practica de momificar a los muertos y porque comienzan a momificar a los infantes. Es decir, esta practica de momificar a los muertos surgio como una respuesta cultural frente a un fenomeno medioambiental que diezmaba a la poblacion

Deep sequencing of RNA from ancient maize kernels.

The characterization of biomolecules from ancient samples can shed otherwise unobtainable insights into the past. Despite the fundamental role of transcriptomal change in evolution, the potential of ancient RNA remains unexploited – perhaps due to dogma associated with the fragility of RNA. We hypothesize that seeds offer a plausible refuge for long-term RNA survival, due to the fundamental role of RNA during seed germination. Using RNA-Seq on cDNA synthesized from nucleic acid extracts, we validate this hypothesis through demonstration of partial transcriptomal recovery from two sources of ancient maize kernels. The results suggest that ancient seed transcriptomics may offer a powerful new tool with which to study plant domestication.