Population trends and the transition to agriculture: Global processes as seen from North America.

Agriculture-specifically an intensification of the production of readily stored food and its distribution-has supported an increase in the global human population throughout the Holocene. Today, with greatly accelerated of growth during recent centuries, we have reached about 8 billion people. Human skeletal and archaeobotanical remains clarify what occurred over several millennia of profound societal and population change in small-scale societies once distributed across the North American midcontinent. Stepwise, not gradual, changes in the move toward an agriculturally based life, as indicated by plant remains, left a demographic signal reflecting age-independent ([Formula: see text]) mortality as estimated from skeletons. Designated the age-independent component of the Siler model, it is tracked through the juvenility index (JI), which is increasingly being used in studies of archaeological skeletons. Usually interpreted as a fertility indicator, the JI is more responsive to age-independent mortality in societies that dominated most of human existence. In the midcontinent, the JI increased as people transitioned to a more intensive form of food production that prominently featured maize. Several centuries later, the JI declined, along with a reversion to a somewhat more diverse diet and a reduction in overall population size. Changes in age-independent mortality coincided with previously recognized increases in intergroup conflict, group movement, and pathogen exposure. Similar rises and falls in JI values have been reported for other parts of the world during the emergence of agricultural systems.

The efficacy of whole human genome capture on ancient dental calculus and dentin.

OBJECTIVES: Dental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques. MATERIALS AND METHODS: Total DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in-solution hybridization capture and high-throughput sequencing. RESULTS: Total DNA from calculus exceeded that of dentin in all cases, and although the proportion of human DNA was generally lower in calculus, the absolute human DNA content of calculus and dentin was not significantly different. Whole genome enrichment resulted in up to four-fold enrichment of the human endogenous DNA content for both dentin and dental calculus libraries, albeit with some loss in complexity. Recovering more on-target reads for the same sequencing effort generally improved the quality of downstream analyses, such as sex and ancestry estimation. For nonhuman DNA, comparison of phylum-level microbial community structure revealed few differences between precapture and postcapture libraries, indicating that off-target sequences in human genome-enriched calculus libraries may still be useful for oral microbiome reconstruction. DISCUSSION: While ancient human dental calculus does contain endogenous human DNA sequences, their relative proportion is low when compared with other skeletal tissues. Whole genome enrichment can help increase the proportion of recovered human reads, but in this instance enrichment efficiency was relatively low when compared with other forms of capture. We conclude that further optimization is necessary before the method can be routinely applied to archaeological samples.

Cranial vault trauma and selective mortality in medieval to early modern Denmark.

To date, no estimates of the long-term effect of cranial vault fractures on the risk of dying have been generated from historical or prehistoric skeletons. Excess mortality provides a perspective on the efficacy of modern treatment, as well as the human cost of cranial injuries largely related to interpersonal violence in past populations. Three medieval to early modern Danish skeletal samples are used to estimate the effect of selective mortality on males with cranial vault injuries who survived long enough for bones to heal. The risk of dying for these men was 6.2 times higher than it was for their uninjured counterparts, estimated through a simulation study based on skeletal observations. That is about twice the increased risk of dying experienced by modern people with traumatic brain injuries. The mortality data indicate the initial trauma was probably often accompanied by brain injury. Although the latter cannot be directly observed in skeletal remains, it can be inferred through the relative risks of dying. The ability to identify the effects of selective mortality in this skeletal sample indicates it must be taken into account in paleopathological research. The problem is analogous to extrapolating from death register data to modern communities, so epidemiological studies based on mortality data have the same inherent possibility of biases as analyses of ancient skeletons.

Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus.

OBJECTIVES: Archaeological dental calculus is a rich source of host-associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis. MATERIALS AND METHODS: Extracted DNA from six individuals at the 700-year-old Norris Farms #36 cemetery in Illinois was enriched for mtDNA using in-solution capture techniques, followed by Illumina high-throughput sequencing. RESULTS: Full mitogenomes (7-34×) were successfully reconstructed from dental calculus for all six individuals, including three individuals who had previously tested negative for DNA preservation in bone using conventional PCR techniques. Mitochondrial haplogroup assignments were consistent with previously published findings, and additional comparative analysis of paired dental calculus and dentine from two individuals yielded equivalent haplotype results. All dental calculus samples exhibited damage patterns consistent with ancient DNA, and mitochondrial sequences were estimated to be 92-100% endogenous. DNA polymerase choice was found to impact error rates in downstream sequence analysis, but these effects can be mitigated by greater sequencing depth. DISCUSSION: Dental calculus is a viable alternative source of human DNA that can be used to reconstruct full mitogenomes from archaeological remains. Am J Phys Anthropol 160:220-228, 2016. © 2016 The Authors American Journal of Physical Anthropology Published by Wiley Periodicals, Inc.

Sex estimation from modern American humeri and femora, accounting for sample variance structure.

OBJECTIVES: A new procedure for skeletal sex estimation based on humeral and femoral dimensions is presented, based on skeletons from the United States. The approach specifically addresses the problem that arises from a lack of variance homogeneity between the sexes, taking into account prior information about the sample's sex ratio, if known. MATERIAL AND METHODS: Three measurements useful for estimating the sex of adult skeletons, the humeral and femoral head diameters and the humeral epicondylar breadth, were collected from 258 Americans born between 1893 and 1980 who died within the past several decades. RESULTS: For measurements individually and collectively, the probabilities of being one sex or the other were generated for samples with an equal distribution of males and females, taking into account the variance structure of the original measurements. The combination providing the best estimates correctly classifies 88.3% of the skeletons, with 10.8% considered unknown and 0.9% assigned to the wrong sex. DISCUSSION: Probabilities of correct assignments are a better means of categorizing individuals as male or female than the sectioning points commonly used in skeletal studies. That is because it is possible to estimate the observer's certainty that the individual represented by measured bones was one sex or the other. A computer program is available that simultaneously considers samples of unequal sex composition. It is useful when there is contextual information available about the nature of skeletal samples (e.g., a mass burial from a battle or genocide).

Conflict and societal change in late prehistoric eastern North America.

As recently as the 1980s, archeologists focusing on prehistoric eastern North America paid little attention to intergroup conflict. Today the situation is quite different, as indicated by this Special Issue. Archeologists now face three principal challenges: to document the temporal and spatial distribution of evidence of conflict; to identify the cultural and environmental conditions associated with variation in the nature and frequency of warfare over long periods of time and large geographical areas; and to determine the extent to which intergroup tensions contributed to or resulted from changes in sociopolitical complexity, economic systems, and population size and distribution. We present data from habitation and mortuary sites in the Eastern Woodlands, notably the midcontinent, that touch on all three issues. Palisaded sites and victims of attacks indicate the intensity of conflicts varied over time and space. Centuries-long intervals of either high or low intergroup tensions can be attributed to an intensification or relaxation of pressure on resources that arose in several ways, such as changes in local population density; technological innovations, including subsistence practices; and the natural environment.

Mapping bone microstructure trace element composition: Sr, Ba, Cu, and Pb in an early modern Danish skeleton.

OBJECTIVES: A Geographical Information System (GIS) approach enhances the acquisition, management, and analysis of trace element data from cortical bone. A high-resolution spatial dimension expands the research potential of Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) data from cortical bone cross-sections. The chemical characterization of hundreds of osteons, notably sequences of superimposed osteons, permits more exacting studies of individual life histories than is possible with analyses of bulk bone samples. METHODS: A GIS procedure was used to estimate Sr, Ba, Pb, and Cu concentrations, originally generated through LA-ICP-MS, for bone microstructural features, notably fragmentary and intact osteons, in a human femoral cross-section. The skeleton is from Ribe, Denmark, and dates to the early modern period. RESULTS: Postmortem chemical alteration was limited to the bone's outer and inner margins. Two dietary indicators, Sr and Ba, and two socioeconomic indicators, Pb and Cu, measured for individual osteons were correlated with one another. Osteon sequences indicate concentrations of all four elements increased late in life for this individual. CONCLUSIONS: The application of GIS procedures expedites fine-grained analyses of variation in the distribution of trace elements in bone microstructure identifiable in cortical bone cross-sections. It provides an efficient means of extracting the most information possible from LA-ICP-MS data about the lives of people in the past. Combining the two procedures makes it easier to track exposure to elements such as Pb across the part of an individual's life represented by osteon sequences.

Transition analysis: a validation study with known-age modern American skeletons.

Transition Analysis-a recent skeletal age-estimation procedure (Boldsen et al.: Paleodemography: age distributions from skeletal samples (2002) 73-106)-is evaluated using 252 known-age modern American males and females from the Bass Donated Collection and Mercyhurst forensic cases. The pubic symphysis worked best for estimating age, followed by the sacroiliac joint and cranial sutures. Estimates based on all skeletal characteristics are influenced by the choice of prior distribution, although its effect is dwarfed by both the inaccuracy and imprecision of age estimates. Age intervals are narrowest for young adults, but are surprisingly short in old age as well. When using an informative prior distribution, the greatest uncertainty occurs from the late 40s into the 70s. Transition Analysis estimates do not perform as well as experience-based assessments, indicating the existing procedure is too narrowly focused on commonly used pelvic and cranial structures.

Paleodemography: From archaeology and skeletal age estimation to life in the past.

Much of paleodemography, an interdisciplinary field with strong ties to archaeology, among other disciplines, is oriented toward clarifying the life experiences of past people and why they changed over time. We focus on how human skeletons contribute to our understanding of preindustrial demographic regimes, including when changes took place that led to the world as we know it today. Problems with existing paleodemographic practices are highlighted, as are promising directions for future work. The latter requires both better age estimates and innovative methods to handle data appropriately. Age-at-death estimates for adult skeletons are a particular problem, especially for adults over 50 years that undoubtedly are mistakenly underrepresented in published studies of archaeological skeletons. Better age estimates for the entirety of the lifespan are essential to generate realistic distributions of age at death. There are currently encouraging signs that after about a half-century of intensive, and sometimes contentious, research, paleodemography is poised to contribute much to understandings of evolutionary processes, the structure of past populations, and human-disease interaction, among other topics.

Twenty-first century bioarchaeology: Taking stock and moving forward.

This article presents outcomes from a Workshop entitled "Bioarchaeology: Taking Stock and Moving Forward," which was held at Arizona State University (ASU) on March 6-8, 2020. Funded by the National Science Foundation (NSF), the School of Human Evolution and Social Change (ASU), and the Center for Bioarchaeological Research (CBR, ASU), the Workshop's overall goal was to explore reasons why research proposals submitted by bioarchaeologists, both graduate students and established scholars, fared disproportionately poorly within recent NSF Anthropology Program competitions and to offer advice for increasing success. Therefore, this Workshop comprised 43 international scholars and four advanced graduate students with a history of successful grant acquisition, primarily from the United States. Ultimately, we focused on two related aims: (1) best practices for improving research designs and training and (2) evaluating topics of contemporary significance that reverberate through history and beyond as promising trajectories for bioarchaeological research. Among the former were contextual grounding, research question/hypothesis generation, statistical procedures appropriate for small samples and mixed qualitative/quantitative data, the salience of Bayesian methods, and training program content. Topical foci included ethics, social inequality, identity (including intersectionality), climate change, migration, violence, epidemic disease, adaptability/plasticity, the osteological paradox, and the developmental origins of health and disease. Given the profound changes required globally to address decolonization in the 21st century, this concern also entered many formal and informal discussions.

Tuberculosis in medieval and early modern Denmark: A paleoepidemiological perspective.

Millions of people worldwide have sickened and died from tuberculosis in recent centuries. Yet for most of human existence, the impact of tuberculosis on society is largely unknown. It is, indeed, unknowable without methods suitable for estimating disease prevalence in skeletal samples. Here such a procedure is applied to medieval and early modern Danish skeletons, and it shows how disease prevalence varied with differences in socioeconomic conditions. The approach is based on sensitivity and specificity estimates from modern skeletons. To augment our understanding of tuberculosis in Danish history, 713 adult skeletons were examined, all from Ribe. Tuberculosis increased from 17% to 40% in the medieval to early modern periods in Ribe. Low status (29%) people were more likely to contract the disease than those of high status (10%). The general model, derived from the modern expression of tuberculosis, fits the early modern sample better than it does the medieval skeletons. Differences in the model's fit indicate the skeletal expression changed over time. Notably, rib lesions increased in frequency from the medieval to early modern periods. The approach developed here can provide insights into host-pathogen relationships and disease expression in future work with tuberculosis and other diseases that affect the skeleton.

The association between skeletal lesions and tuberculosis diagnosis using a probabilistic approach.

Sensitivity and specificity estimates for 18 skeletal lesions were generated from modern skeletons for future paleoepidemiological analyses of tuberculosis prevalence in archaeological samples. A case-control study was conducted using 480 skeletons from 20th century American skeletal collections. One-half of the skeletons were documented tuberculosis cases (Terry Collection). The remaining age and sex-matched skeletons were controls (Bass Collection). The association between 18 candidate skeletal lesions and tuberculosis was established by comparing lesion distributions in case and control groups. Lesion indicators at six locations - visceral surface of ribs, ventral vertebral bodies, lateral part of ilium, acetabular fossa, iliac auricular surface, and ulna olecranon process - occurred significantly more often among cases than in controls, and were associated with one another. The most useful indicator proved to be a bony reaction on ventral thoracic and lumbar vertebral bodies. Its presence means a 53.3% probability of a true tuberculosis diagnosis. Because of the nature of the reference sample - 20th century American cases - sensitivity and specificity estimates will better estimate disease prevalence in archaeological samples from cultural settings where pulmonary tuberculosis predominated. The general approach of this proof-of-concept study is applicable to other diseases that occur commonly and affect bone.

Selective mortality in middle-aged American women with Diffuse Idiopathic Skeletal Hyperostosis (DISH).

OBJECTIVE: A mortality sample of white American male and female skeletons was examined to illustrate a simple means of identifying skeletal conditions associated with an increased risk of dying relatively early in adulthood and to determine if males and females with Diffuse Idiopathic Skeletal Hyperostosis (DISH) displayed the same general age-specific pattern of mortality. METHODS: Age-specific probability distributions for DISH were generated from 416 white Americans who died from the 1980s to the present, and whose remains were donated to the University of Tennessee Forensic Anthropology Center. The age-specific frequency of DISH is analyzed using an empirical smoothing algorithm. Doing so allows for the identification of deviations (i.e., local maxima) from monotonically increasing age-specific probabilities. RESULTS: In females (N = 199), there is a peak in the frequency of individuals with DISH around 60 years of age where 37.0% of the individuals have DISH. It is matched only by the frequency (38.7%) in the oldest females, those over 85 years old. In contrast, DISH frequencies for males (N = 217) increase monotonically with advancing age, reaching 62.5% in the ≥86 years age group. There was an association between DISH and high body weight in women, particularly those who died before they reached the age of 75. CONCLUSIONS: Early-onset DISH in white American women is associated with an increased risk of dying indicated by a local maximum in the probability curve. Should this finding be replicated in additional mortality samples and the reason DISH is associated with early death is established, beyond being heavy, this radiologically visible ossification of the spine could be a potential component of health-monitoring programs for middle-aged women.

Differential preservation of endogenous human and microbial DNA in dental calculus and dentin.

Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach. Overall, we find DNA from dental calculus is consistently more abundant and less contaminated than DNA from dentin. The majority of DNA in dental calculus is microbial and originates from the oral microbiome; however, a small but consistent proportion of DNA (mean 0.08 ± 0.08%, range 0.007-0.47%) derives from the host genome. Host DNA content within dentin is variable (mean 13.70 ± 18.62%, range 0.003-70.14%), and for a subset of dentin samples (15.21%), oral bacteria contribute > 20% of total DNA. Human DNA in dental calculus is highly fragmented, and is consistently shorter than both microbial DNA in dental calculus and human DNA in paired dentin samples. Finally, we find that microbial DNA fragmentation patterns are associated with guanine-cytosine (GC) content, but not aspects of cellular structure.

Life not death: Epidemiology from skeletons.

Analytically sophisticated paleoepidemiology is a relatively new development in the characterization of past life experiences. It is based on sound paleopathological observations, accurate age-at-death estimates, an explicit engagement with the nature of mortality samples, and analytical procedures that owe much to epidemiology. Of foremost importance is an emphasis on people, not skeletons. Transforming information gleaned from the dead, a biased sample of individuals who were once alive at each age, into a form that is informative about past life experiences has been a major challenge for bioarchaeologists, but recent work shows it can be done. The further development of paleoepidemiology includes essential contributions from paleopathology, archaeology or history (as appropriate), and epidemiology.

Humeral and femoral head diameters in recent white American skeletons.

Osteologists often rely on single measurements, such as humeral and femoral head diameters, to estimate sex, especially when skeletons are incomplete. Measurements of 237 Bass Donated Collection skeletons provide a means of distinguishing white American females from males based on a modern sample: humeral head, female mean 42.1 mm, male mean 49.0 mm; and femoral head, female mean 42.2 mm, male mean 48.4 mm. Probabilities that bones at 1-mm increments came from females (p(f)) are estimated (p(m) = 1 - p(f)). An overrepresentation of one sex in the skeletons that are examined influences the probability that a bone of a certain size is from a female or male. So, probabilities are also estimated for samples consisting of an unequal number of males and females. Sample composition has its greatest effect when one sex dominates the remains that are the subject of investigation.

Conflict and death in a late prehistoric community in the American Midwest.

Over the past two decades, it has been recognized that the effects of intergroup conflict in prehistoric small-scale societies were greater than previously thought. Osteological evidence provides otherwise unobtainable information on the number of people who were killed, and who was most likely to become a casualty. One such site is Norris Farms #36 in the American Midwest, dating to ca. AD 1300. Skeletal evidence of injuries (blunt force trauma and arrow wounds), body mutilation (scalping, decapitation, and dismemberment), and scavenger damage indicate that one-third of the adults died in a series of ambushes, although children were mostly spared. Both young and old adults were killed, and the age distributions of the male and female victims were similar. Individuals with disabilities that interfered with mobility were more likely to be killed than their healthier counterparts. This level of conflict-related mortality almost certainly had an effect on the community's ability to conduct its affairs and, indeed, to survive as a viable economic and social group.