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Tschinkel K, Verano J, Prieto G. Two cases of smallpox from 1540 CE circum-contact (early colonial) Northern Coastal Peru. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2024; 45:35-45. [PMID: 38653101 DOI: 10.1016/j.ijpp.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 03/30/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
OBJECTIVE This project seeks to create a differential diagnosis for lesions found on the skeletal remains of two children as a means to explore the presence of viral disease in 16th- century Peru. MATERIALS Extremely well-preserved human remains of two children who died between the ages of 1-2 years old, recovered from the circum-contact (∼1540 CE) cemetery in Huanchaco, Peru. METHODS Macroscopic and radiographic analysis. RESULTS Both individuals present with cortical thickening, symmetrical destructive lesions, metaphyseal expansion, perforations, exposure of the medullary cavity, resorption of metaphyseal ends and necrosis of the long bones, and deposited reactive new bone. These features are consistent with osteomyelitis variolosa and bacterial osteomyelitis. CONCLUSIONS Three features of Individuals IG-124 and IG-493 suggest a highly consistent diagnosis of osteomyelitis variolosa: multiple skeletal lesions, the historical context of the area, and the high mortality rate of non-adults in the circum-contact cemetery. SIGNIFICANCE Although viral infections are ubiquitous and well documented historically, their etiologies are often difficult to determine in archaeological populations. Orthopoxvirus variola (smallpox) is one of the many viruses whose archaeological impact is still under explored in skeletal remains. LIMITATIONS The absence of smallpox in other children from the Huanchaco cemetery creates difficulty in ascertaining true prevalence rates or information on potential outbreaks. SUGGESTIONS FOR FURTHER RESEARCH Further research analyzing aDNA from calculus and/or residues using a DIP-GC-MS method might create a better understanding of how smallpox spread through the region.
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Affiliation(s)
- Khrystyne Tschinkel
- Anthropology Department, Tulane University, Dinwiddie Hall 101 6823 St. Charles Ave, New Orleans, LA 70118, USA.
| | - John Verano
- Anthropology Department, Tulane University, Dinwiddie Hall 101 6823 St. Charles Ave, New Orleans, LA 70118, USA
| | - Gabriel Prieto
- Anthropology Department, University of Florida, P.O. Box 117305, Gainesville, LA 32611-7305, USA
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2
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Medina-Muñoz SG, Ortega-Del Vecchyo D, Cruz-Hervert LP, Ferreyra-Reyes L, García-García L, Moreno-Estrada A, Ragsdale AP. Demographic modeling of admixed Latin American populations from whole genomes. Am J Hum Genet 2023; 110:1804-1816. [PMID: 37725976 PMCID: PMC10577084 DOI: 10.1016/j.ajhg.2023.08.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 08/17/2023] [Accepted: 08/23/2023] [Indexed: 09/21/2023] Open
Abstract
Demographic models of Latin American populations often fail to fully capture their complex evolutionary history, which has been shaped by both recent admixture and deeper-in-time demographic events. To address this gap, we used high-coverage whole-genome data from Indigenous American ancestries in present-day Mexico and existing genomes from across Latin America to infer multiple demographic models that capture the impact of different timescales on genetic diversity. Our approach, which combines analyses of allele frequencies and ancestry tract length distributions, represents a significant improvement over current models in predicting patterns of genetic variation in admixed Latin American populations. We jointly modeled the contribution of European, African, East Asian, and Indigenous American ancestries into present-day Latin American populations. We infer that the ancestors of Indigenous Americans and East Asians diverged ∼30 thousand years ago, and we characterize genetic contributions of recent migrations from East and Southeast Asia to Peru and Mexico. Our inferred demographic histories are consistent across different genomic regions and annotations, suggesting that our inferences are robust to the potential effects of linked selection. In conjunction with published distributions of fitness effects for new nonsynonymous mutations in humans, we show in large-scale simulations that our models recover important features of both neutral and deleterious variation. By providing a more realistic framework for understanding the evolutionary history of Latin American populations, our models can help address the historical under-representation of admixed groups in genomics research and can be a valuable resource for future studies of populations with complex admixture and demographic histories.
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Affiliation(s)
- Santiago G Medina-Muñoz
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | - Diego Ortega-Del Vecchyo
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de Mexico, Juriquilla, Querétaro 76230, Mexico
| | | | | | | | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico.
| | - Aaron P Ragsdale
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico; Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA.
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3
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De Oliveira TC, Secolin R, Lopes-Cendes I. A review of ancestrality and admixture in Latin America and the caribbean focusing on native American and African descendant populations. Front Genet 2023; 14:1091269. [PMID: 36741309 PMCID: PMC9893294 DOI: 10.3389/fgene.2023.1091269] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/09/2023] [Indexed: 01/21/2023] Open
Abstract
Genomics can reveal essential features about the demographic evolution of a population that may not be apparent from historical elements. In recent years, there has been a significant increase in the number of studies applying genomic epidemiological approaches to understand the genetic structure and diversity of human populations in the context of demographic history and for implementing precision medicine. These efforts have traditionally been applied predominantly to populations of European origin. More recently, initiatives in the United States and Africa are including more diverse populations, establishing new horizons for research in human populations with African and/or Native ancestries. Still, even in the most recent projects, the under-representation of genomic data from Latin America and the Caribbean (LAC) is remarkable. In addition, because the region presents the most recent global miscegenation, genomics data from LAC may add relevant information to understand population admixture better. Admixture in LAC started during the colonial period, in the 15th century, with intense miscegenation between European settlers, mainly from Portugal and Spain, with local indigenous and sub-Saharan Africans brought through the slave trade. Since, there are descendants of formerly enslaved and Native American populations in the LAC territory; they are considered vulnerable populations because of their history and current living conditions. In this context, studying LAC Native American and African descendant populations is important for several reasons. First, studying human populations from different origins makes it possible to understand the diversity of the human genome better. Second, it also has an immediate application to these populations, such as empowering communities with the knowledge of their ancestral origins. Furthermore, because knowledge of the population genomic structure is an essential requirement for implementing genomic medicine and precision health practices, population genomics studies may ensure that these communities have access to genomic information for risk assessment, prevention, and the delivery of optimized treatment; thus, helping to reduce inequalities in the Western Hemisphere. Hoping to set the stage for future studies, we review different aspects related to genetic and genomic research in vulnerable populations from LAC countries.
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Affiliation(s)
- Thais C. De Oliveira
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
- The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Rodrigo Secolin
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
- The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Iscia Lopes-Cendes
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
- The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
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4
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Collen EJ, Johar AS, Teixeira JC, Llamas B. The immunogenetic impact of European colonization in the Americas. Front Genet 2022; 13:918227. [PMID: 35991555 PMCID: PMC9388791 DOI: 10.3389/fgene.2022.918227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
The introduction of pathogens originating from Eurasia into the Americas during early European contact has been associated with high mortality rates among Indigenous peoples, likely contributing to their historical and precipitous population decline. However, the biological impacts of imported infectious diseases and resulting epidemics, especially in terms of pathogenic effects on the Indigenous immunity, remain poorly understood and highly contentious to this day. Here, we examine multidisciplinary evidence underpinning colonization-related immune genetic change, providing contextualization from anthropological studies, paleomicrobiological evidence of contrasting host-pathogen coevolutionary histories, and the timings of disease emergence. We further summarize current studies examining genetic signals reflecting post-contact Indigenous population bottlenecks, admixture with European and other populations, and the putative effects of natural selection, with a focus on ancient DNA studies and immunity-related findings. Considering current genetic evidence, together with a population genetics theoretical approach, we show that post-contact Indigenous immune adaptation, possibly influenced by selection exerted by introduced pathogens, is highly complex and likely to be affected by multifactorial causes. Disentangling putative adaptive signals from those of genetic drift thus remains a significant challenge, highlighting the need for the implementation of population genetic approaches that model the short time spans and complex demographic histories under consideration. This review adds to current understandings of post-contact immunity evolution in Indigenous peoples of America, with important implications for bettering our understanding of human adaptation in the face of emerging infectious diseases.
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Affiliation(s)
- Evelyn Jane Collen
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Angad Singh Johar
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
| | - João C. Teixeira
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- School of Culture History and Language, The Australian National University, Canberra, ACT, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT, Australia
- Telethon Kids Institute, Indigenous Genomics Research Group, Adelaide, SA, Australia
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The genomic landscape of Mexican Indigenous populations brings insights into the peopling of the Americas. Nat Commun 2021; 12:5942. [PMID: 34642312 PMCID: PMC8511047 DOI: 10.1038/s41467-021-26188-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/22/2021] [Indexed: 12/30/2022] Open
Abstract
The genetic makeup of Indigenous populations inhabiting Mexico has been strongly influenced by geography and demographic history. Here, we perform a genome-wide analysis of 716 newly genotyped individuals from 60 of the 68 recognized ethnic groups in Mexico. We show that the genetic structure of these populations is strongly influenced by geography, and our demographic reconstructions suggest a decline in the population size of all tested populations in the last 15-30 generations. We find evidence that Aridoamerican and Mesoamerican populations diverged roughly 4-9.9 ka, around the time when sedentary farming started in Mesoamerica. Comparisons with ancient genomes indicate that the Upward Sun River 1 (USR1) individual is an outgroup to Mexican/South American Indigenous populations, whereas Anzick-1 was more closely related to Mesoamerican/South American populations than to those from Aridoamerica, showing an even more complex history of divergence than recognized so far.
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Historic and bioarchaeological evidence supports late onset of post-Columbian epidemics in Native California. Proc Natl Acad Sci U S A 2021; 118:2024802118. [PMID: 34260380 DOI: 10.1073/pnas.2024802118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Catastrophic decline of Indigenous populations in the Americas following European contact is one of the most severe demographic events in the history of humanity, but uncertainty persists about the timing and scale of the collapse, which has implications for not only Indigenous history but also the understanding of historical ecology. A long-standing hypothesis that a continent-wide pandemic broke out immediately upon the arrival of Spanish seafarers has been challenged in recent years by a model of regional epidemics erupting asynchronously, causing different rates of population decline in different areas. Some researchers have suggested that, in California, significant depopulation occurred during the first two centuries of the post-Columbus era, which led to a "rebound" in native flora and fauna by the time of sustained European contact after 1769. Here, we combine a comprehensive prehistoric osteological dataset (n = 10,256 individuals) with historic mission mortuary records (n = 23,459 individuals) that together span from 3050 cal BC to AD 1870 to systematically evaluate changes in mortality over time by constructing life tables and conducting survival analysis of age-at-death records. Results show that a dramatic shift in the shape of mortality risk consistent with a plague-like population structure began only after sustained contact with European invaders, when permanent Spanish settlements and missions were established ca. AD 1770. These declines reflect the syndemic effects of newly introduced diseases and the severe cultural disruption of Indigenous lifeways by the Spanish colonial system.
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Ham AC, Temple DH, Klaus HD, Hunt DR. Evaluating life history trade-offs through the presence of linear enamel hypoplasia at Pueblo Bonito and Hawikku: A biocultural study of early life stress and survival in the Ancestral Pueblo Southwest. Am J Hum Biol 2020; 33:e23506. [PMID: 32924230 DOI: 10.1002/ajhb.23506] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVES Due to the indelible nature of enamel, bioarchaeologists use linear enamel hypoplasia (LEH) to detect early investments in surviving stress and have identified an association between LEH presence and constraints in growth and maintenance as well as an increased susceptibility to future stress events. This study evaluates heterogenous frailty and susceptibility to death in relation to episodes of early life stress, as reflected by LEH presence, in the Ancestral Pueblo Southwest. This study hypothesizes that LEH presence will be associated with decreased survivorship and an increased likelihood of mortality in both samples. MATERIALS AND METHODS This study uses two samples, one from Pueblo Bonito (A.D. 800-1200; n = 28) and the second from Hawikku (A.D. 1300-1680; n = 103). Kaplan-Meier survival analysis with a log-rank test was used to evaluate the effect of LEH presence on survivorship for the two samples. RESULTS Survival analysis reveals statistically significant differences in mortality risk between individuals with and without LEH for the Hawikku sample, but no significant differences for the Pueblo Bonito sample. CONCLUSION The results demonstrate differences in the response to early life stress at the Hawikku and Pueblo Bonito sites, likely reflecting context. The Pueblo Bonito sample represents a high-status group, and survival following LEH may be the result of cultural buffering. Hawikku dates to a period associated with increased levels of disease and malnutrition as well as Spanish colonization. This environment may have exacerbated mortality risk for individuals in the region who survived early life stress and signifies the consequences of European colonialism in the New World.
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Affiliation(s)
- Allison C Ham
- Department of Anthropology, University of South Carolina, Columbia, South Carolina, USA
| | - Daniel H Temple
- Department of Sociology and Anthropology, George Mason University, Fairfax, Virginia, USA
| | - Haagen D Klaus
- Department of Sociology and Anthropology, George Mason University, Fairfax, Virginia, USA
| | - David R Hunt
- Physical Anthropology Division, Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
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Kyle B, Shehi E, Koçi M, Reitsema LJ. Bioarchaeological reconstruction of physiological stress during social transition in Albania. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2020; 30:118-129. [PMID: 32653862 DOI: 10.1016/j.ijpp.2020.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/17/2020] [Accepted: 06/20/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVE We test the hypothesis that physiological stress increased in response to increasing social turmoil following waves of colonization and social transition. The ways local conditions, including variation in geography, environment, and levels of urbanization impact physiological stress are also explored. MATERIALS In Albania, the historic period is a sequence of different waves of colonization. Skeletal data come from three Albanian archaeological sites: Apollonia (n = 231), Durrës (n = 246), and Lofkënd (n = 129). METHODS Prevalence of cribra orbitalia, porotic hyperostosis, linear enamel hypoplasia, and periosteal new bone formation are analyzed using chi-square and logistic regression tests. RESULTS We observe increased skeletal manifestations of physiological stress between prehistoric and historic groups, but physiological stress is generally consistent through time. CONCLUSIONS General increase in skeletal pathology between prehistoric and historic periods corresponds to broad increases in political unrest associated with colonization spanning the entire historic period. However, little difference in physiological stress across colonization episodes (Greek, Roman, Byzantine, Bulgarian, Ottoman) suggests skeletal health is affected similarly by colonization, regardless of particularities in method and type of colonial control. SIGNIFICANCE Examining human response to social change across broad time scales is useful in identifying broad patterns in the human experience. LIMITATIONS Exploring variation across broad time scales and multiple sites is potentially problematic because confounding factors could impact results and interpretations. SUGGESTIONS FOR FURTHER RESEARCH Environmental, social, and geographic differences, likely impacted the lives and lifestyles of individuals living in the past and should be explored further to understand the nuances in local response to colonization.
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Affiliation(s)
- Britney Kyle
- University of Northern Colorado, Department of Anthropology, Campus Box 90, Greeley, CO, 80639, USA.
| | - Eduard Shehi
- Instituti Arkeologjik Tirane (Albanian Institute of Archaeology, Tirana), Sheshi Nene Tereza, 1001, Tirane, Albania.
| | - Marlon Koçi
- University of Central Florida, Department of Anthropology, 4000 Central Florida Blvd., Howard Phillips Hall Room 309, Orlando, FL, 32816, USA.
| | - Laurie J Reitsema
- University of Georgia, Department of Anthropology, 250 Baldwin Hall, Athens, GA, 30602, USA.
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Garland CJ. Implications of accumulative stress burdens during critical periods of early postnatal life for mortality risk among Guale interred in a colonial era cemetery in Spanish Florida (ca. AD 1605-1680). AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 172:621-637. [PMID: 32064605 DOI: 10.1002/ajpa.24020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 01/24/2020] [Accepted: 01/29/2020] [Indexed: 11/12/2022]
Abstract
OBJECTIVE Research situated within the Developmental Origins of Health and Disease demonstrates that stressors are correlated with future mortality risk, especially if experienced frequently and during early periods of postnatal life. This study examines if the developmental timing and frequency of early life stressors influenced mortality risk for Indigenous Guale in Spanish Florida during the 17th century. MATERIALS AND METHODS The present study examines internal enamel microgrowth disruptions (accentuated lines-AL) from Guale individuals (n = 52) interred at Mission Santa Catalina de Guale on St. Catherines Island, Georgia (AD 1605-1680). Teeth were thin-sectioned and microscopically analyzed to document AL variables as predictors of age-at-death. RESULTS Individuals with AL died earlier than those without AL. This difference, however, was not significant. Individuals who exhibit AL formed during their first year of life died on average three times earlier than those who did not. The frequency of AL and age-at-first-AL are significantly correlated with age-at-death, and Cox hazard analyses indicates that individuals with early forming and frequent AL had increased risks of early death. DISCUSSION This study emphasizes how the lived experiences of Guale children shaped demographic patterns during the 17th century. The survival of early life stressors resulted in life history trade-offs and increased risks for early death. Mortality risks were exacerbated for individuals who experienced frequent stressors during the earliest periods of life. This underscores a role for bioarchaeology in understanding of how accumulative stress burdens during the earliest years of postnatal life may influence mortality risk.
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Affiliation(s)
- Carey J Garland
- Department of Anthropology, University of Georgia, Athens, Georgia, USA
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Wilson WM, Bulkan J, Piperata BA, Hicks K. Secular trends in adult stature among the Makushi of Guyana in the 20th Century. Am J Hum Biol 2019; 31:e23285. [DOI: 10.1002/ajhb.23285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 05/02/2019] [Accepted: 06/07/2019] [Indexed: 11/06/2022] Open
Affiliation(s)
- Warren M. Wilson
- Department of Anthropology and ArchaeologyUniversity of Calgary Calgary Alberta Canada
| | - Janette Bulkan
- Department of Forest Resources ManagementUniversity of British Columbia Vancouver British Columbia Canada
| | | | - Kathryn Hicks
- Department of AnthropologyThe University of Memphis Memphis Tennessee
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Abstract
Beginning some 10,000 years ago, humans began a dramatic alteration in living conditions relating especially to the shift in lifeway from foraging to farming. In addition to the initiation of and increasing focus on the production and consumption of domesticated plant carbohydrates, this revolutionary transformation in diet occasioned a decline in mobility and an increased size and agglomeration of populations in semipermanent or permanent settlements. These changes in life conditions presented an opportunity for increased transmission of pathogenic microbes from host to host, such as those that cause major health threats affecting most of the 7.5 billion members of our species today. This article discusses the bioarchaeology of infectious disease, focusing on tuberculosis, treponematosis, dental caries, and periodontitis, all of which continue to contribute to high levels of morbidity and mortality among the world's populations today.
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Affiliation(s)
- Clark Spencer Larsen
- Department of Anthropology, Ohio State University, Columbus, Ohio 43210-1106, USA
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Skelly E, Kapellas K, Cooper A, Weyrich LS. Consequences of colonialism: A microbial perspective to contemporary Indigenous health. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 167:423-437. [DOI: 10.1002/ajpa.23637] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Emily Skelly
- Australian Centre for Ancient DNA, School of Biological Sciences University of Adelaide Adelaide South Australia Australia
| | - Kostas Kapellas
- Australian Research Centre for Population Oral Health, Adelaide Dental School University of Adelaide Adelaide South Australia Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences University of Adelaide Adelaide South Australia Australia
| | - Laura S. Weyrich
- Australian Centre for Ancient DNA, School of Biological Sciences University of Adelaide Adelaide South Australia Australia
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Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico. Nat Ecol Evol 2018; 2:520-528. [PMID: 29335577 DOI: 10.1038/s41559-017-0446-6] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 12/07/2017] [Indexed: 11/08/2022]
Abstract
Indigenous populations of the Americas experienced high mortality rates during the early contact period as a result of infectious diseases, many of which were introduced by Europeans. Most of the pathogenic agents that caused these outbreaks remain unknown. Through the introduction of a new metagenomic analysis tool called MALT, applied here to search for traces of ancient pathogen DNA, we were able to identify Salmonella enterica in individuals buried in an early contact era epidemic cemetery at Teposcolula-Yucundaa, Oaxaca in southern Mexico. This cemetery is linked, based on historical and archaeological evidence, to the 1545-1550 CE epidemic that affected large parts of Mexico. Locally, this epidemic was known as 'cocoliztli', the pathogenic cause of which has been debated for more than a century. Here, we present genome-wide data from ten individuals for Salmonella enterica subsp. enterica serovar Paratyphi C, a bacterial cause of enteric fever. We propose that S. Paratyphi C be considered a strong candidate for the epidemic population decline during the 1545 cocoliztli outbreak at Teposcolula-Yucundaa.
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A time transect of exomes from a Native American population before and after European contact. Nat Commun 2016; 7:13175. [PMID: 27845766 PMCID: PMC5116069 DOI: 10.1038/ncomms13175] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 09/07/2016] [Indexed: 12/20/2022] Open
Abstract
A major factor for the population decline of Native Americans after European contact has been attributed to infectious disease susceptibility. To investigate whether a pre-existing genetic component contributed to this phenomenon, here we analyse 50 exomes of a continuous population from the Northwest Coast of North America, dating from before and after European contact. We model the population collapse after European contact, inferring a 57% reduction in effective population size. We also identify signatures of positive selection on immune-related genes in the ancient but not the modern group, with the strongest signal deriving from the human leucocyte antigen (HLA) gene HLA-DQA1. The modern individuals show a marked frequency decrease in the same alleles, likely due to the environmental change associated with European colonization, whereby negative selection may have acted on the same gene after contact. The evident shift in selection pressures correlates to the regional European-borne epidemics of the 1800s. A First Nation population declined after European contact, likely as a result of infectious disease. Here, researchers partner with indigenous communities to analyse ancient and modern Native American exomes, and find a shift in selection pressure on immune genes, correlated to European-borne epidemics.
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Temple DH, Goodman AH. Bioarcheology has a “health” problem: Conceptualizing “stress” and “health” in bioarcheological research. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2014; 155:186-91. [DOI: 10.1002/ajpa.22602] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 08/10/2014] [Accepted: 08/10/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Daniel H. Temple
- Department of Sociology and Anthropology; George Mason University; Fairfax VA 22030-4444
| | - Alan H. Goodman
- School of Natural Science, Hampshire College; Amherst MA 01002-3372
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Subsistence strategy changes: the evidence of entheseal changes. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2013; 64:491-508. [PMID: 24028816 DOI: 10.1016/j.jchb.2013.08.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 07/18/2013] [Indexed: 11/22/2022]
Abstract
Changes in subsistence strategy have caused some of the profoundest changes to the structure and health of humans. This study aims to test whether these changes have reduced work-load as assessed by entheseal changes. Entheseal changes, formerly called musculoskeletal stress markers, are thought to reflect muscle usage throughout life, although it is widely agreed that they have a multifactorial origin. This paper uses a meta-analysis of comparable published data to plot trends in time by muscle, enthesis type and sex. The results show that agriculturalists have the lowest scores for entheseal changes, with hunte-gatherers next highest and those working in industry the highest. These findings are the same for males and females, for most muscles and muscle groups. However, entheseal changes are highly correlated with increased age and the age distributions of the samples analysed could not be compared. It is, therefore, possible that differences in age distribution of the samples are one of the reasons for this finding. Recommendations are provided to reduce this and other limitations for future meta-analyses.
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Georges L, Seidenberg V, Hummel S, Fehren-Schmitz L. Molecular characterization of ABO blood group frequencies in pre-Columbian Peruvian highlanders. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012; 149:242-9. [DOI: 10.1002/ajpa.22115] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 06/15/2012] [Indexed: 12/28/2022]
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Vercellotti G, Piperata BA. The use of biocultural data in interpreting sex differences in body proportions among rural Amazonians. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012; 147:113-27. [PMID: 22120650 PMCID: PMC3357059 DOI: 10.1002/ajpa.21636] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 10/10/2011] [Indexed: 11/07/2022]
Abstract
Variation in height and body proportions is relatively well-understood at the inter-population level, but less is known about intra-population variation. This study explores intra-population variation in body proportions among 172 (88 female; 84 male) adult rural Amazonians. We test the hypotheses that: (1) stunting is associated with changes in proportions and fatness; (2) the sexes express different proportions in response to similar environmental stress; and (3) female growth is negatively affected by the costs of reproduction. We examined height, sitting height, and total leg length in subsamples based on sex and nutritional status (stunted/nonstunted) in relation to biocultural factors including access to food and healthcare and female reproductive history parameters. Differences in proportions were examined using the Quick-Test (Tsutakawa and Hewett: Biometrics 33 (1977) 215-219); correlation analyses were used to detect associations between anthropometric data and body fatness, and female reproductive history parameters. We found significantly higher rates of stunting among females (X(2) = 5.31; P = 0.02; RR = 1.4). Stunted individuals exhibited relatively shorter legs than nonstunted individuals (P = 0.02), although this was not found in within-sex analyses. A significant negative correlation was found between leg length index and fatness (P < 0.01). Lastly, females exhibited relatively shorter legs than males (P = 0.0003) and, among females, height and leg length were significantly positively correlated with age-at-first-birth (P < 0.02) suggesting that adolescent pregnancy may negatively affect growth in this population. Our findings provide insights for the study of intra-population variation in body proportions and highlight the importance of biocultural data in interpreting the pattern of variation observed in living and past populations.
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Native Americans experienced a strong population bottleneck coincident with European contact. Proc Natl Acad Sci U S A 2011; 108:20444-8. [PMID: 22143784 DOI: 10.1073/pnas.1112563108] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genetic and demographic impact of European contact with Native Americans has remained unclear despite recent interest. Whereas archeological and historical records indicate that European contact resulted in widespread mortality from various sources, genetic studies have found little evidence of a recent contraction in Native American population size. In this study we use a large dataset including both ancient and contemporary mitochondrial DNA to construct a high-resolution portrait of the Holocene and late Pleistocene population size of indigenous Americans. Our reconstruction suggests that Native Americans suffered a significant, although transient, contraction in population size some 500 y before the present, during which female effective size was reduced by ∼50%. These results support analyses of historical records indicating that European colonization induced widespread mortality among indigenous Americans.
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Covey RA, Childs G, Kippen R. Dynamics of Indigenous Demographic Fluctuations. CURRENT ANTHROPOLOGY 2011. [DOI: 10.1086/660010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Murphy MS, Gaither C, Goycochea E, Verano JW, Cock G. Violence and weapon-related trauma at Puruchuco-Huaquerones, Peru. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2010; 142:636-49. [DOI: 10.1002/ajpa.21291] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Klaus HD, Spencer Larsen C, Tam ME. Economic intensification and degenerative joint disease: life and labor on the postcontact north coast of Peru. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2009; 139:204-21. [PMID: 19140181 DOI: 10.1002/ajpa.20973] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This study tests the hypothesis that the colonial economy of the Lambayeque region of northern coastal Peru was associated with a mechanically strenuous lifestyle among the indigenous Mochica population. To test the hypothesis, we documented the changes in the prevalence of degenerative joint disease (or DJD) in human remains from the late pre-Hispanic and colonial Lambayeque Valley Complex. Comparisons were made using multivariate odds ratios calculated across four age classes and 11 principle joint systems corresponding to 113 late pre-Hispanic and 139 postcontact adult Mochica individuals. Statistically significant patterns of elevated postcontact DJD prevalence are observed in the joint systems of the shoulder, elbow, wrist, and knee. More finely grained comparison between temporal phases indicates that increases in prevalence were focused immediately following contact in the Early/Middle Colonial period. Analysis of DJD by sex indicates postcontact males experienced greater DJD prevalence than females. Also, trends between pre- and postcontact females indicate nearly universally elevated DJD prevalence among native colonial women. Inferred altered behavioral uses of the upper body and knee are contextualized within ecological, ethnohistoric, and ethnoarchaeological frameworks and appear highly consistent with descriptions of the local postcontact economy. These patterns of DJD appear to stem from a synergism of broad, hemispheric level sociopolitical alterations, specific changes to Mochica activity and behavior, regional economic intensification, and local microenvironmental characteristics, which were all focused into these biological outcomes by the operation of a colonial Spanish political economy on the north coast of Peru from A.D. 1536 to 1751.
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Affiliation(s)
- Haagen D Klaus
- Behavioral Science Department, Utah Valley University, Orem, Utah 84058, USA.
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Klaus HD, Tam ME. Contact in the Andes: bioarchaeology of systemic stress in colonial Mórrope, Peru. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2009; 138:356-68. [PMID: 18951404 DOI: 10.1002/ajpa.20944] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The biocultural interchange between the Eastern and Western Hemispheres beginning in the late fifteenth century initiated an unprecedented adaptive transition for Native Americans. This article presents findings from the initial population biological study of contact in the Central Andes of Peru using human skeletal remains. We test the hypothesis that as a consequence of Spanish colonization, the indigenous Mochica population of Mórrope on the north coast of Peru experienced elevated systemic biological stress. Using multivariate statistical methods, we examine childhood stress reflected in the prevalence of linear enamel hypoplasias and porotic hyperostosis, femoral growth velocity, and terminal adult stature. Nonspecific periosteal infection prevalence and D(30+)/D(5+) ratio estimations of female fertility characterized adult systemic stress. Compared to the late pre-Hispanic population, statistically significant patterns of increased porotic hyperostosis and periosteal inflammation, subadult growth faltering, and depressed female fertility indicate elevated postcontact stress among both children and adults in Mórrope. Terminal adult stature was unchanged. A significant decrease in linear enamel hypoplasia prevalence may not indicate improved health, but reflect effects of high-mortality epidemic disease. Various lines of physiological, archaeological, and ethnohistoric evidence point to specific socioeconomic and microenvironmental factors that shaped these outcomes, but the effects of postcontact population aggregation in this colonial town likely played a fundamental role in increased morbidity. These results inform a model of postcontact coastal Andean health outcomes on local and regional scales and contribute to expanding understandings of the diversity of indigenous biological variation in the postcontact Western Hemisphere.
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Affiliation(s)
- Haagen D Klaus
- Behavioral Science Department, Utah Valley University, 800 West University Parkway, Orem, UT 84058, USA.
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Eggers S, Petronilho CC, Brandt K, Jericó-Daminello C, Filippini J, Reinhard KJ. How does a riverine setting affect the lifestyle of shellmound builders in Brazil? HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2008; 59:405-27. [PMID: 19027113 DOI: 10.1016/j.jchb.2008.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Accepted: 04/27/2008] [Indexed: 10/21/2022]
Abstract
The contact of inland and coastal prehistoric groups in Brazil is believed to have been restricted to regions with no geographical barrier, as is the case in the Ribeira de Iguape valley. The inland osteological collection from the riverine shellmound Moraes (5800-4500 BP) represents a unique opportunity to test this assumption for this region. Despite cultural similarities between riverine and coastal shellmounds, important ecological and site distribution differences are expected to impact on lifestyle. The purpose of this study is thus to document and interpret health and lifestyle indicators in Moraes in comparison to coastal shellmound groups. Specifically we test if the rare evidence of fish and mollusc remains in the riverine shellmound led to (a) higher caries rates and (b) lower auditory exostosis frequency and (c) if the small size of the riverine shellmound translates into reduced demographic density and thus rarity of communicable infectious diseases. Of the three hypotheses, (a) was confirmed, (b) was rejected and (c) was partly rejected. Bioanthropological similarities between Moraes and coastal shellmounds include auditory exostoses with equally high frequencies; significantly more frequent osteoarthritis in upper than in lower limbs; cranial and dental morphological affinities and low frequencies of violent trauma. However, there are also important differences: Moraes subsisted on a much broader protein diet and consumed more cariogenic food, but showed a stature even shorter than coastal groups. Thus, despite the contact also suggested by treponematoses in both site types, there was enough time for the people at the riverine site to adapt to local conditions.
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Affiliation(s)
- S Eggers
- Laboratório de Antropologia Biológica, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-900 São Paulo, Brazil.
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Abstract
Disparities in health status between American Indians and other groups in the United States have persisted throughout the 500 years since Europeans arrived in the Americas. Colonists, traders, missionaries, soldiers, physicians, and government officials have struggled to explain these disparities, invoking a wide range of possible causes. American Indians joined these debates, often suggesting different explanations. Europeans and Americans also struggled to respond to the disparities, sometimes working to relieve them, sometimes taking advantage of the ill health of American Indians. Economic and political interests have always affected both explanations of health disparities and responses to them, influencing which explanations were emphasized and which interventions were pursued. Tensions also appear in ongoing debates about the contributions of genetic and socioeconomic forces to the pervasive health disparities. Understanding how these economic and political forces have operated historically can explain both the persistence of the health disparities and the controversies that surround them.
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Affiliation(s)
- David S Jones
- Center for the Study of Diversity in Science, Technology, and Medicine, Massachusetts Institute of Technology 02139, USA.
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Hutchinson DL, Norr L. Nutrition and health at contact in late prehistoric central Gulf Coast Florida. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2006; 129:375-86. [PMID: 16323191 DOI: 10.1002/ajpa.20300] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This paper presents an analysis of human remains from Tatham Mound, a dual-component mortuary site from central Gulf Coast Florida. The human remains from Tatham are significant because they come from a limited time period during the initial contact with Europeans at AD 1525-1550. Dietary reconstruction demonstrates that at the time of European contact, maize was not a predominant dietary item. Low frequencies for several dental and skeletal pathological indicators are consistent with relatively good health as compared to other Southeastern late prehistoric and protohistoric populations. Despite the limited time period represented by the mound population, critical interactions occurred between Native Americans and Spaniards, as indicated by skeletal elements severed by metal weapons. The Tatham population is significant because it is one of the earliest studied populations contacted by Europeans in North America, and the only one with well-documented sharp-force trauma that represents intergroup hostility.
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Affiliation(s)
- Dale L Hutchinson
- Department of Anthropology and Research Laboratories of Archaeology, University of North Carolina,Chapel Hill, North Carolina 27599-3115, USA.
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Keenleyside A. Skeletal evidence of health and disease in pre-contact Alaskan Eskimos and Aleuts. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 1998; 107:51-70. [PMID: 9740301 DOI: 10.1002/(sici)1096-8644(199809)107:1<51::aid-ajpa5>3.0.co;2-g] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
There have been relatively few paleopathological studies of arctic populations to date, compared to other regions of North America. Studies aimed at elucidating patterns of health and disease in arctic peoples prior to contact and assessing inter- and intraregional differences in disease patterns have been particularly few. In the present study, five pre-contact skeletal samples (N = 193), representing 4 Eskimo populations from northern coastal Alaska and 1 Aleut population from the eastern Aleutian Islands, were examined macroscopically for the following indicators of health status: cribra orbitalia, porotic hyperostosis, trauma, infection, dental caries, abscesses, antemortem tooth loss, periodontal disease, and dental attrition. In addition, archeological and epidemiological data were used to help reconstruct the health of these populations. The goals of the analysis were 2-fold: 1) to assess the pre-contact health of North Alaskan Eskimos and Aleuts in order to provide a baseline comparison for the post-contact health of these groups, and 2) to determine if any differences in disease patterns exist between the Eskimos and Aleuts that might be related to differences in their physical environment, subsistence patterns, and cultural practices. The analysis revealed that both groups suffered from a variety of health problems prior to contact, including iron deficiency anemia, trauma, infection, and various forms of dental pathology. Statistical comparisons of the 2 groups revealed that Eskimos and Aleuts had different patterns of health and disease prior to contact. Most notably, the Aleuts had a significantly higher frequency of cranial trauma and infracranial infection than the Eskimos, while the latter had a significantly higher frequency of enamel hypoplasia. An examination of the physical and cultural environment of the 2 groups reveals several possible explanations for these differences, including warfare, subsistence pursuits, and housing practices. The documentation of these differences indicates that variability in pre-contact disease patterns can be identified between hunter-gatherer populations living in similar environments and exhibiting similar general lifestyles.
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Affiliation(s)
- A Keenleyside
- Department of Classics, Royal Holloway College, University of London, Egham, Surrey, United Kingdom.
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Hanson DB, Butler BM. A biocultural perspective on Marianas prehistory: recent trends in bioarchaeological research. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 1997; 104:271-90. [PMID: 9408537 DOI: 10.1002/(sici)1096-8644(199711)104:3<271::aid-ajpa2>3.0.co;2-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Fifteen years ago, the biohistory of Micronesia was still a blank slate relative to other regions of the Pacific. Since 1980, however, the Mariana Islands, one of the largest island chains in Micronesia, have been the focus of intensive archaeological investigation and human remains have been ubiquitous components of the archaeological assemblages recovered from the islands of Guam, Rota, Tinian, and Saipan. These investigations have provided us with a wealth of new data that will contribute substantially to our understanding of population adaptation to island ecosystems in this part of the Pacific. Much of the recent bioarchaeological research in the Marianas is the product of archaeological mitigation rather than directed research. Consequently, many of our research efforts have been articulated with the needs of cultural resource management (CRM) where research designs focus on several general problem areas: 1) subsistence adaptation with emphasis on the contribution of marine vs. terrestrial resources and the role of pelagic, or deep-ocean resources in the marine component of the diet; 2) regional (upland vs. coastal; interisland) and temporal variation in subsistence/settlement; and 3) geomorphologic variation in coastal sediments, particularly as influenced by storm events.
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Affiliation(s)
- D B Hanson
- Bioengineering Department, Forsyth Dental Center, Boston, Massachusetts 02115, USA.
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