A Paleogenomic Reconstruction of the Deep Population History of the Andes.

There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today's genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000-500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin. VIDEO ABSTRACT.

The role of dietary calcium in the etiology of childhood rickets in the past and the present.

For more than two centuries, lack of sunlight has been understood to cause vitamin D deficiency and documented as a primary cause of rickets. As such, evidence of rickets in the archeological record has been used as a proxy for vitamin D status in past individuals and populations. In the last decade, a clinical global consensus has emerged wherein it is recognized that dietary calcium deficiency also plays a role in the manifestation of rickets and classic skeletal deformities may not form if dietary calcium is normal even if vitamin D is deficient. This disease is now clinically called "nutritional rickets" to reflect the fact that rickets can take calcium deficiency-predominant or vitamin D deficiency-predominant forms. However, there are currently no paleopathological studies wherein dietary calcium deficiency is critically considered a primary etiology of the disease. We review here the interplay of calcium, vitamin D, and phosphorous in bone homeostasis, examine the role of dietary calcium in human health, and critically explore the clinical literature on calcium deficiency-predominant rickets. Finally, we report a case of rickets from the late Formative Period (~2500-1500 years ago) of the Atacama Desert and argue the disease in this infant is likely an example of calcium deficiency-predominant rickets. We conclude that most archeological cases of rickets are the result of multiple micronutrient deficiencies that compound to manifest in macroscopic skeletal lesions. For clinicians, these factors are important for implementing best treatment practice, and for paleopathologists they are necessary for appropriate interpretation of health in past communities.

Five thousand years of bellyaches: Exploring boron concentration in ancient populations of the Atacama Desert.

OBJECTIVES: This study explores whether ancient Atacama Desert populations in northern Chile were exposed to endemic boron contamination. MATERIALS AND METHODS: Using Laser Ablation-Inductively Coupled Plasma-Mass Spectrometry (LA-ICP-MS), we studied 144 strands of ancient mummy hair, ranging from 3000 B.C. to 1500 A.D., excavated from the Lluta, Azapa, and Camarones valleys in northern Chile. We tested whether these ancient populations showed signs of significant boron concentration in hair tissue. RESULTS: On average, all individuals from these valleys showed high boron concentrations, ranging from 1.5 to 4 times above the average boron concentration in contemporary hair (baseline <0.85 µg/g). The boron concentration in mummy hair varied according to the main geographic areas mentioned above. CONCLUSIONS: The rivers of northern Chile have high geogenic boron concentrations. They contain 38 times above the recommended limit for human consumption. Geogenic boron contamination likely played a role in population morbidity and the types of crops that were cultivated in antiquity. The ancient populations were chronically affected by boron overexposure, suggesting that ancient geogenic water contamination should be considered when discussing the biocultural trajectories of ancient populations.

Violence in hunters, fishermen, and gatherers of the Chinchorro culture: Archaic societies of the Atacama Desert (10,000-4,000 cal yr BP).

OBJECTIVES: This article addresses evidence of violence imbedded in both soft and hard tissues from early populations of hunters, fishermen, and gatherers, known as the Chinchorro culture, who lived between 10,000 and 4,000 cal yr BP, along the coast of the Atacama Desert, one of the driest environments on Earth. Our study is aimed to test two hypotheses (a) that interactions and violent behaviors increased through time as population density and social complexity augmented; and (b) that violence was more prevalent between local Chinchorro groups and groups from other inland locations. MATERIAL AND METHODS: Two lines of data were analyzed: (1) bioarchaeology, through the quantification of physical traces of interpersonal violence in skeletons and mummies from a sample of 136 adult individuals and, (2) isotopic chemical analysis (strontium) of individuals with traces of trauma in order to determine their local or foreign origin. RESULTS: Violence among Chinchorro populations was ubiquitous and remained invariant over time, with a remarkable skew to male (about 25% above female across the complete sample). Moreover, the chemical signature of individuals with traces of violence was not of foreign origin. DISCUSSION: The violence exerted by the Chinchorro groups was not related to increased population size, nor social complexity and was mostly restricted to individuals coming from the same coastal habitat. That is, our data suggest that violence was constant across the Archaic period among the Chinchorro, implying that violent behavior was part of the sociocultural repertory of these populations, likely associated to mechanisms to resolve conflicts and social tensions.

Living in poisoning environments: Invisible risks and human adaptation.

This article describes the hidden natural chemical contaminants present in a unique desert environment and their health consequences on ancient populations. Currently, millions of people are affected worldwide by toxic elements such as arsenic. Using data gathered from Atacama Desert mummies, we discuss long-term exposure and biocultural adaptation to toxic elements. The rivers that bring life to the Atacama Desert are paradoxically laden with arsenic and other minerals that are invisible and tasteless. High intake of these toxic elements results in severe health and behavioral problems, and even death. We demonstrate that Inca colonies, from Camarones 9 site, were significantly affected by chemical contaminants in their food and water. It appears however, some modern-day Andean populations resist the elevated levels of arsenic exposure as a result of positive selection mediated via the arsenic methyltransferase enzyme and display more tolerance to high chemical doses. This article further debate the effects of natural pollution and biocultural adaptation of past populations.

Macroscopic features of scurvy in human skeletal remains: A literature synthesis and diagnostic guide.

The past two decades have seen a proliferation in bioarchaeological literature on the identification of scurvy, a disease caused by chronic vitamin C deficiency, in ancient human remains. This condition is one of the few nutritional deficiencies that can result in diagnostic osseous lesions. Scurvy is associated with low dietary diversity and its identification in human skeletal remains can provide important contextual information on subsistence strategy, resource allocation, and human-environmental interactions in past populations. A large and robust methodological body of work on the paleopathology of scurvy exists. However, the diagnostic criteria for this disease employed by bioarchaeologists have not always been uniform. Here we draw from previous research on the skeletal manifestations of scurvy in adult and juvenile human skeletal remains and propose a weighted diagnostic system for its identification that takes into account the pathophysiology of the disease, soft tissue anatomy, and clinical research. Using a sample of individuals from the prehistoric Atacama Desert in Northern Chile, we also provide a practical example of how diagnostic value might be assigned to skeletal lesions of the disease that have not been previously described in the literature.

Let's talk about stress, baby! Infant-feeding practices and stress in the ancient Atacama desert, Northern Chile.

AIMS AND OBJECTIVES: The transition to an agricultural economy is often presumed to involve an increase in female fertility related to changes in weaning practice. In particular, the availability of staple crops as complementary foods is hypothesized to allow earlier weaning in agricultural populations. In this study, our primary aim is to explore whether this model fits the agricultural transition in the Atacama Desert using incremental isotopic analysis. A secondary aim of this study is to identify isotopic patterns relating to weaning, and assess how these may be differentiated from those relating to early life stress. MATERIALS AND METHODS: We use incremental isotopic analysis of dentine to examine changes in δ15 N and δ13 C values from infancy and childhood in sites of the Arica region (n = 30). We compare individuals from pre-agricultural and agricultural phases to establish isotopic patterns and relate these patterns to maternal diet, weaning trajectory and physiological stress. RESULTS: We find that there is no evidence for systematic temporal or geographic variation in incremental isotopic results. Instead, results from all time periods are highly variable, with weaning completed between 1.5 and 3.5 years. Characteristics of the incremental profiles indicate that both in utero and postnatal stress were a common part of the infant experience in the Atacama. DISCUSSION: In the Atacama Desert it appears that the arrival of agricultural crops did not result in uniform shifts in weaning behavior. Instead, infant and child diet seems to have been dictated by the broad-spectrum diets of the mothers, perhaps as a way of mitigating the stresses of the harsh desert environment.

Investigating cranial morphological variation of early human skeletal remains from Chile: A 3D geometric morphometric approach.

OBJECTIVES: Archaeological and genetic research has demonstrated that the Pacific Coast was a key route in the early colonization of South America. Research examining South American skeletons >8000 cal BP has revealed differences in cranial morphology between early and late Holocene populations, which may reflect distinct migration events and/or populations. However, genetic, cultural, and some skeletal data contradict this model. Given these discrepancies, this study examines ∼9000 years of prehistory to test the hypothesis that Early skeletons have a distinct cranial morphology from later skeletons. MATERIALS AND METHODS: Using 3D digital models, craniofacial landmarks, and geometric morphometric analyses, we compared Early Holocene crania (n = 4) to later Chilean samples (n = 90) frequently absent in continental assessments of craniofacial variation. PCA, Mahalanobis distances, posterior and typicality probabilities were used to examine variation. RESULTS: Two of the earliest skeletons from northern Chile show clear affinities to individuals from later sites in the same region. However, the hypothesis cannot be rejected as one Early individual from northern Chile and one individual from inland Patagonia did not always show clear affinities to coastal populations. DISCUSSION: Biological affinities among northern populations and other regions of Chile align with genetic and archaeological data, supporting cultural and biological continuity along the Pacific Coast. In Patagonia, archaeological data are in accordance with skeletal differences between the Early inland steppe individual and coastal populations. This study incorporates 3D methods and skeletal datasets not widely used in assessments of biological affinity, thus contributing to a critical body of research examining the ancient population history of western South America.

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.

Violence in fishing, hunting, and gathering societies of the Atacama Desert coast: A long-term perspective (10,000 BP-AD 1450).

In this study, we examine the long-term trajectory of violence in societies that inhabited the coast of the Atacama Desert in northern Chile using three lines of evidence: bioarchaeology, geoarchaeology and socio-cultural contexts (rock art, weapons, and settlement patterns). These millennia-old populations adopted a way of life, which they maintained for 10,000 years, based on fishing, hunting, and maritime gathering, complementing this with terrestrial resources. We analyzed 288 adult individuals to search for traumas resulting from interpersonal violence and used strontium isotopes 87Sr/86Sr as a proxy to evaluate whether individuals that showed traces of violence were members of local or non-local groups. Moreover, we evaluated settlement patterns, rock art, and weapons. The results show that the violence was invariant during the 10,000 years in which these groups lived without contact with the western world. During the Formative Period (1000 BC-AD 500), however, the type of violence changed, with a substantial increase in lethality. Finally, during the Late Intermediate Period (AD 1000-1450), violence and lethality remained similar to that of the Formative Period. The chemical signal of Sr shows a low frequency of individuals who were coastal outsiders, suggesting that violence occurred between local groups. Moreover, the presence of weapons and rock art depicting scenes of combat supports the notion that these groups engaged in violence. By contrast, the settlement pattern shows no defensive features. We consider that the absence of centralized political systems could have been a causal factor in explaining violence, together with the fact that these populations were organized in small-scale grouping. Another factor may have been competition for the same resources in the extreme environments of the Atacama Desert. Finally, from the Formative Period onward, we cannot rule out a certain level of conflict between fishers and their close neighbors, the horticulturalists.

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.

Prehistoric polydactylism: Biological evidence and rock art representation from the Atacama Desert in northern Chile.

A review of the bioarchaeological collections from the site Morro de Arica in northern Chile allowed the identification of two cases of human polydactyly. Both cases are from the Chinchorro culture, hunters, fishers, and gatherers with a maritime orientation who inhabited the coast of the Atacama Desert (9000-3400 BP). Additionally, the analyses of 75 rock art sites in the area, from the Formative to Late Intermediate Periods (3000-550 BP), allowed the identification of hands and feet with six digits. Given the bioarchaeological record of polydactyly, it is highly probable that the rock art images were based on real individuals with polydactyly. However, the Sr chemical signal in a juvenile with polydactyly is the same as the Sr chemical signal in the rest of the individuals buried in the same site, proving that all the individuals were born and lived on the coast. We discuss the idea that, although these anomalies could have been the result of genetic mutations, endogamy and exposition to ecotoxic environments could also be at play within the Chinchorro groups.

Comparative study of the claws of Pediculus humanus capitis between archaeological and modern specimens.

Metric data of the claws of archaeological specimens of Pediculus humanus capitis (dating between 1500 B.C. and A.D. 1500) and modern lice specimens coming from school children were analyzed and compared. Both sets of samples come from Arica in northern Chile. The overall sample is comprised of 14 archaeological specimens (6 females and 8 males) of Pediculus humanus capitis and 22 modern specimens (13 females and 9 males). All specimens were studied with scanning electron microscopy (SEM), uncoated, using variable pressure mode. The objective of this study was to metrically analyze the first couple of clutches of ancient and modern adult lice specimens (width and length of the tibio-tarsal claw and tarsus length) to test if morphological changes have taken place throughout time in these anatomical elements. We found that archaeological male and female specimens presented significant differences in the tibio-tarsal width (right and left). When comparing data between archaeological and modern male specimens, statistically significant differences were found in almost all the parameters studied, except for the right tarsal length. On the other hand, archaeological and modern female specimens showed no statistically significant change in the variables studied. In brief, our data suggest that modern male specimens have undergone a process of claw reduction, but females have maintained the same dimensions.

Scurvy at the agricultural transition in the Atacama desert (ca 3600-3200 BP): nutritional stress at the maternal-foetal interface?

Studies of contemporary populations have demonstrated an association between decreased dietary diversity due to resource scarcity or underutilization and an increase in diseases related to poor micronutrient intake. With a reduction of dietary diversity, it is often the women and children in a population who are the first to suffer the effects of poor micronutrient status. Scurvy, a disease of prolonged vitamin C deficiency, is a micronutrient malnutrition disorder associated with resource scarcity, low dietary diversity, and/or dependence on high carbohydrate staple-foods. The aim of this paper is to assess the potential impact of nutritional transition on the prevalence of diseases of nutritional insufficiency in an archaeological sample. Here, we report palaeopathological findings from an Early Formative Period transitional site located in coastal Northern Chile (Quiani-7). The subadult cohort from this site is composed of four perinates who exhibit a number of non-specific skeletal changes suggestive of a systemic pathological condition. One of these is associated with an adult female exhibiting diagnostic skeletal lesions of scurvy. We argue that the lesions exhibited by these perinates may represent maternal transmission of vitamin C deficiency but acknowledge that there are difficulties in applying current diagnostic criteria for scurvy to individuals this young.

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.

Reevaluating Harris lines--a comparison between Harris lines and enamel hypoplasia.

This study examines the association between Harris lines and enamel hypoplasia. This association is analyzed in terms of: 1) presence/absence of these markers in each individual, and 2) age of the individuals at the time of Harris lines and enamel hypoplasias formation. Data from two archaeological groups (Azapa-71 and Azapa-140) from northern Chile were analyzed. The results indicate Harris lines and enamel hypoplasias are not associated in terms of presence/absence. Moreover, the estimated age of the individuals at the time of Harris lines and enamel hypoplasia formation shows that these two markers have a very different distribution. While enamel hypoplasias clustered between ages 3 and 5, Harris lines were more commonly formed during the first year of life, as well as during adolescence, which are the periods of most accelerated growth. We propose that Harris lines are a result of a normal, rather than abnormal, saltatory growth process.

Study of archaeological nits/eggs of Pediculus humanus capitis by scanning electron microscopy.

This paper presents and discusses archaeological samples of Pediculus humanus capitis nits/eggs in Arica, northern Chile, dating between 2000 B.C. and A.D. 500. Eight samples of nits/eggs taken directly from seven mummified bodies of both the valley and the coast of Arica, were collected and studied. Samples were analysed with scanning electron microscopy (SEM), uncoated, using low and variable pressure modes. The aim was to study the morphology of the nits/eggs, the different degrees of preservation and their research potential. All samples were in good external condition and due to manipulation before SEM analysis, the oldest ones were fractured allowing the observation in situ of the hatching ad portas of an embryo. This inside view of the egg allowed observation and identification of microstructures of the embryo such as abdominal and thoracic spiracles and claws. In the most recent and best preserved samples, external structures characteristic of the egg such as aeropyles and operculum were observed. SEM can contribute significantly to the study of ectoparasites that affected ancient American populations and in this particular case to illustrate the stages and morphology of Andean archaeological specimens of P. humanus capitis.

On head lice and social interaction in archaic Andean coastal populations.

Archaic mummies from northern Chile were examined for the presence of Pediculus humanus capitis. The excellent preservation of mummies and louse nits/eggs permitted a study of the degree of head lice infestation. We studied 63 Chinchorro mummies (ca. 5000-3000 years B.P.) from the Arica-Camarones coast. An area of 2cm×2cm on each mummy's head was systematically inspected for louse nits/eggs. Hairs with nits/eggs and lice were collected and analyzed using optic and scanning electronic microscopy. About 79% (50/63) of the mummies resulted positive for pediculosis, with an average of 2.1nits/eggs/cm2 per positive individual. Microscopic analyses revealed the micromorphology of all developmental stages, including eggs/nits, nymphal instars and adults. Chinchorro people lived in small huts increasing the transmission of ectoparasites. Considering that head lice thrive in crowded conditions, their prevalence could be used as an bioindicator to assess and debate cultural behavior (e.g., degree of crowdedness and sedentism) and to study paleoepidemiology in prehistoric populations.

Severe head lice infestation in an Andean mummy of Arica, Chile.

Pediculus humanus capitis is an ancient human parasite, probably inherited from pre-hominid times. Infestation appears as a recurrent health problem throughout history, including in pre-Columbian populations. Here, we describe and discuss the occurrence of pre-Columbian pediculosis in the Andean region of the Atacama Desert. Using a light microscope and scanning electron microscopy, we studied a highly infested Maitas Chiribaya mummy from Arica in northern Chile dating to 670-990 calibrated years A.D. The scalp and hair of the mummy were almost completely covered by nits and adult head lice. Low- and high-vacuum scanning electron microscopy revealed a well-preserved morphology of the eggs. In addition, the excellent preservation of the nearly 1,000-yr-old adult head lice allowed us to observe and characterize the head, antennae, thorax, abdomen, and legs. Leg segmentation, abdominal spiracles, and sexual dimorphism also were clearly observed. The preservation of the ectoparasites allowed us to examine the micromorphology using scanning electron microscopy; the opercula, aeropyles, and spiracles were clearly visible. This case study provides strong evidence that head lice were a common nuisance for Andean farmers and herders. Head lice are transmitted by direct head-to-head contact; thus, this ancient farmer and herder was potentially infesting other people. The present study contributes to the body of research focusing on lice in ancient populations.