Reply to Barton et al: signatures of natural selection during the Black Death.

Barton et al.1 raise several statistical concerns regarding our original analyses2 that highlight the challenge of inferring natural selection using ancient genomic data. We show here that these concerns have limited impact on our original conclusions. Specifically, we recover the same signature of enrichment for high FST values at the immune loci relative to putatively neutral sites after switching the allele frequency estimation method to a maximum likelihood approach, filtering to only consider known human variants, and down-sampling our data to the same mean coverage across sites. Furthermore, using permutations, we show that the rs2549794 variant near ERAP2 continues to emerge as the strongest candidate for selection (p = 1.2×10-5), falling below the Bonferroni-corrected significance threshold recommended by Barton et al. Importantly, the evidence for selection on ERAP2 is further supported by functional data demonstrating the impact of the ERAP2 genotype on the immune response to Y. pestis and by epidemiological data from an independent group showing that the putatively selected allele during the Black Death protects against severe respiratory infection in contemporary populations.

Evolution of immune genes is associated with the Black Death.

Infectious diseases are among the strongest selective pressures driving human evolution1,2. This includes the single greatest mortality event in recorded history, the first outbreak of the second pandemic of plague, commonly called the Black Death, which was caused by the bacterium Yersinia pestis3. This pandemic devastated Afro-Eurasia, killing up to 30-50% of the population4. To identify loci that may have been under selection during the Black Death, we characterized genetic variation around immune-related genes from 206 ancient DNA extracts, stemming from two different European populations before, during and after the Black Death. Immune loci are strongly enriched for highly differentiated sites relative to a set of non-immune loci, suggesting positive selection. We identify 245 variants that are highly differentiated within the London dataset, four of which were replicated in an independent cohort from Denmark, and represent the strongest candidates for positive selection. The selected allele for one of these variants, rs2549794, is associated with the production of a full-length (versus truncated) ERAP2 transcript, variation in cytokine response to Y. pestis and increased ability to control intracellular Y. pestis in macrophages. Finally, we show that protective variants overlap with alleles that are today associated with increased susceptibility to autoimmune diseases, providing empirical evidence for the role played by past pandemics in shaping present-day susceptibility to disease.

Genetic resiliency and the Black Death: No apparent loss of mitogenomic diversity due to the Black Death in medieval London and Denmark.

OBJECTIVES: In the 14th century AD, medieval Europe was severely affected by the Great European Famine as well as repeated bouts of disease, including the Black Death, causing major demographic shifts. This high volatility led to increased mobility and migration due to new labor and economic opportunities, as evidenced by documentary and stable isotope data. This study uses ancient DNA (aDNA) isolated from skeletal remains to examine whether evidence for large-scale population movement can be gleaned from the complete mitochondrial genomes of 264 medieval individuals from England (London) and Denmark. MATERIALS AND METHODS: Using a novel library-conserving approach to targeted capture, we recovered 264 full mitochondrial genomes from the petrous portion of the temporal bones and teeth and compared genetic diversity across the medieval period within and between English (London) and Danish populations and with contemporary populations through population pairwise ΦST analysis. RESULTS: We find no evidence of significant differences in genetic diversity spatially or temporally in our dataset, yet there is a high degree of haplotype diversity in our medieval samples with little exact sequence sharing. DISCUSSION: The mitochondrial genomes of both medieval Londoners and medieval Danes suggest high mitochondrial diversity before, during and after the Black Death. While our mitochondrial genomic data lack geographically correlated signals, these data could be the result of high, continual female migration before and after the Black Death or may simply indicate a large female effective population size unaffected by the upheaval of the medieval period. Either scenario suggests a genetic resiliency in areas of northwestern medieval Europe.

Frailty and famine: Patterns of mortality and physiological stress among victims of famine in medieval London.

OBJECTIVES: Famine can be defined as a shortage of foodstuffs that instigates widespread excess mortality due to starvation, infectious disease, and social disruption. Like other causes of catastrophic mortality, famine has the potential to be selective. This study examines how famines in medieval London were selective with respect to previous stress, age, and sex. METHODS: This study compares famine burials to nonfamine (attritional) burials from the St Mary Spital cemetery, London (c. 1120-1540 AD). We evaluate the associations between age, sex, and skeletal stress indicators [cribra orbitalia, linear enamel hypoplasia (LEH), and periosteal lesions] using hierarchical log-linear analysis. Additionally, sex is modeled as a covariate affecting the Gompertz hazard of mortality. RESULTS: Significant associations exist between famine burials and LEH and between attritional burials and periosteal lesions, independent of age or sex. Sex did not significantly affect risk of mortality in the 12th-13th centuries. However, males interred in attritional burials c. 1400-1539 AD faced a lower risk of mortality compared to females. DISCUSSION: The LEH results suggest that early exposure to stressors increased frailty in the context of famine. The periosteal lesion results suggest that individuals were more likely to survive stressors and thus form these lesions under nonfamine conditions. Hazard analysis suggests that a cultural or biological transformation during this period affected sex differences in mortality. Possible causes include the selective mortality during the Black Death, which might have influenced risks of mortality among survivors, or unequal distribution of improvements in standards of living after the epidemic. Am J Phys Anthropol 160:272-283, 2016. © 2016 Wiley Periodicals, Inc.

Coming of age in Roman Britain: Osteological evidence for pubertal timing.

OBJECTIVES: Puberty is a key transitional phase of the human life course, with important biological and social connotations. Novel methods for the identification of the pubertal growth spurt and menarche in skeletal remains have recently been proposed (Shapland and Lewis, 2013, 2014). In this study we applied the methods to two Romano-British cemetery samples (1st-early 5th centuries AD) in order to investigate the timing of puberty during this period and further assess the veracity of the methods. MATERIALS AND METHODS: Shapland and Lewis' methods (2013, 2014) were applied to 38 adolescents (aged 8-20 years) from the British cemetery sites of Roman London (1st-early 5th centuries AD) and Queenford Farm, Oxfordshire (4th-early 5th centuries AD). RESULTS: Overall, the Romano-British males and females experienced the onset of puberty at similar ages to modern European adolescents, but subsequently experienced a longer period of pubertal development. Menarche occurred between the ages of 15 and 17 years for these Romano-British females, around 2 to 4 years later than for present-day European females. DISCUSSION: The observed Romano-British pattern of pubertal timing has various possible explanations, including exposure to environmental stressors in early urban environments. The pattern of pubertal timing is largely congruent with social age transitions alluded to in ancient texts and funerary evidence for this period. While there are limitations to the application of these techniques to archaeological samples, they were successfully applied in this study, and may have important implications for understandings of past life courses, as well as providing a long-term perspective on pubertal timing and biocultural interactions.

Sex differentials in caries frequencies in Medieval London.

OBJECTIVE: Tooth decay is one of the most common oral infections observed in skeletal assemblages. Sex differentials in caries frequency are commonly examined, with most studies finding that females tend to have a higher frequency of carious lesions (caries) compared to males. Less research has examined differences in caries between males and females with respect to age in past populations. Findings from living populations indicate that caries frequencies are higher in females, at least in part, because of the effects of estrogen and pregnancy. We are interested in the interaction of age, sex, and caries in medieval London, during a period of repeated famines, which might have exacerbated underlying biological causes of caries sex differentials. DESIGN: We examined caries in adults from two medieval London cemeteries dating to c. 1120-1539 AD: St. Mary Spital (n=291) and St. Mary Graces (n=80) to test the hypothesis that males and females have different caries frequencies irrespective of age. The association between maxillary molar caries and sex was tested using hierarchical log-linear analysis to control for the effects of age on caries frequencies. RESULTS: The results indicate a higher frequency of maxillary molar caries in females (P<0.00), and that the age distribution of caries differs between the sexes (P=0.01), with a consistent increase in frequency with age for females until late adulthood, but not males. CONCLUSIONS: The difference in caries frequencies is not explained by differences in the age distributions of the sexes. Differences in the age patterns of caries for males and females could be the result of biological factors that present during reproductive age, differences in diet, or differential access to resources during famine.

Urban-rural differences in Roman Dorset, England: A bioarchaeological perspective on Roman settlements.

In the Roman period, urban and rural ways of living were differentiated philosophically and legally, and this is the first regional study of these contrasting life-ways. Focusing on frailty and mortality risk, we investigated how these differed by age, sex, and status, using coffin type as a proxy for social status. We employed skeletal data from 344 individuals: 150 rural and 194 urban (1st-5th centuries A.D.) from Dorset, England. Frailty and mortality risk were examined using indicators of stress (cribra orbitalia, porotic hyperostosis, nonspecific periostitis, and enamel hypoplastic defects), specific metabolic and infectious diseases (rickets, scurvy, and tuberculosis), and dental health (carious lesions and calculus). These variables were studied using Chi-square, Siler model of mortality, Kaplan-Meier analysis, and the Gompertz model of adult mortality. Our study found that overall, mortality risk and survivorship did not differ between cemetery types but when the data were examined by age, mortality risk was only significantly higher for urban subadults. Demographic differences were found, with urban cemeteries having more 0-10 and >35 year olds, and for health, urban cemeteries had significantly higher frequencies of enamel hypoplastic defects, carious lesions, and rickets. Interestingly, no significant difference in status was observed between rural and urban cemeteries. The most significant finding was the influence of the skeletal and funerary data from the Poundbury sites, which had different demographic profiles, significantly higher frequencies of the indicators of stress and dental health variables. In conclusion, there are significant health, demographic, and mortality differences between rural and urban populations in Roman Britain.

Evidence of skeletal treponematosis from the medieval burial ground of St. Mary Spital, London, and implications for the origins of the disease in Europe.

Treponematosis is a syndrome of chronic infectious diseases. There has been much debate on its origins and spread, particularly with regard to venereal syphilis, an unsightly and debilitating disease in preantibiotic populations. The osteological analysis of 5,387 individuals excavated by Museum of London Archaeology from the medieval burial ground of St. Mary Spital in London (dated c 1120-1539) provided an unprecedented opportunity to investigate the nature and prevalence of disease over a period of time. Twenty-five individuals were found with suspected treponematosis, originating from all but the earliest period of the burial ground. Descriptions of affected individuals from each period, together with supporting images, are provided. In this work, particular emphasis was given to the distribution of lesions on the skeleton and the variation in patterns by sex and over time. Little change was observed in the distribution of bony change between individuals dated to pre- and post-Columbian periods. However, a dramatic rise in the prevalence of the disease in the final period (c 1400-1539) may reflect documentary reports of a European epidemic from the late 15th century.

Medieval monastic mortality: hazard analysis of mortality differences between monastic and nonmonastic cemeteries in England.

Scholarship on life in medieval European monasteries has revealed a variety of factors that potentially affected mortality in these communities. Though there is some evidence based on age-at-death distributions from England that monastic males lived longer than members of the general public, what is missing from the literature is an explicit examination of how the risks of mortality within medieval monastic settings differed from those within contemporaneous lay populations. This study examines differences in the hazard of mortality for adult males between monastic cemeteries (n = 528) and non-monastic cemeteries (n = 368) from London, all of which date to between AD 1050 and 1540. Age-at-death data from all cemeteries are pooled to estimate the Gompertz hazard of mortality, and "monastic" (i.e., buried in a monastic cemetery) is modeled as a covariate affecting this baseline hazard. The estimated effect of the monastic covariate is negative, suggesting that individuals in the monastic communities faced reduced risks of dying compared to their peers in the lay communities. These results suggest better diets, the positive health benefits of religious behavior, better living conditions in general in monasteries, or selective recruitment of healthy or higher socioeconomic status individuals.

Status and health in Roman Dorset: the effect of status on risk of mortality in post-conquest populations.

The Roman conquest of Britain was previously shown to have negatively impacted health, particularly for children, older adults, and men. We build upon this previous research by investigating the effect that status had on risks of mortality within the Roman Britain populations of Dorset. This study incorporates a sample of 291 individuals excavated from several cemeteries in the county of Dorset dating between the first to early fifth centuries AD. To assess the effect of status on risks of mortality, burial type was used as a proxy for status and modeled as a covariate affecting the Siler and Gompertz-Makeham models of mortality. The results of these analyses indicate that high-status individuals, particularly children, had a lower mortality risk compared to lower-status groups; and for those buried in urban cemeteries, higher-status individuals of all age-groups had a lower mortality risk. As with our previous study (Redfern and DeWitte: Am J Phys Anthropol 144 (2011) 269-285), we found that male mortality risk was higher than females, which we consider to reflect underlying sex-differences in immunity and disease response.

Brief communication: developmental dysplasia of the hip in medieval London.

Developmental dysplasia of the hip (DDH) is a spectrum of disease starting in childhood and in many cases persisting into adulthood. The spectrum ranges from acetabular dysplasia, through hip subluxation to dislocation. The aim of this research was to determine the prevalence and pathoanatomy of acetabular dysplasia and subluxation in excavated human skeletal remains, to complement past research on dislocation in DDH. The material under study was the medieval cemetery of St. Mary Spital in London, in use from c.1100 to 1539 AD. A series of 572 adults with both hips preserved were analyzed. Acetabular dysplasia was indicated by a shallow acetabulum with upward sloping roof. Subluxation was suggested by degenerative change along the margin of the acetabulum suggestive of labral tears, and degenerative change in the outer part of the acetabular roof suggestive of osteoarthritis. The prevalence of DDH (acetabular dysplasia, subluxation, or dislocation) was 1.7%. Because this a congenital musculoskeletal disorder of relatively high frequency, with significant variation in prevalence between populations around the world, it is a topic that warrants targeted research from physical anthropologists studying past populations.

A new approach to the study of Romanization in Britain: a regional perspective of cultural change in late iron age and roman dorset using the siler and gompertz-makeham models of mortality.

This is the first study of health in the Roman Empire to use the Siler and Gompertz-Makeham models of mortality to investigate the health consequences of the 43 AD conquest of Britain. The study examined late Iron Age and Romano-British populations (N = 518) from Dorset, England, which is the only region of Britain to display continuity in inhumation burial practice and cemetery use throughout the two periods. Skeletal evidence for frailty was assessed using cribra orbitalia, porotic hyperostosis, periosteal lesions, enamel hypoplasia, dental caries, tuberculosis, and rickets. These health variables were chosen for analysis because they are reliable indicators of general health for diachronic comparison (Steckel and Rose: The backbone of history: health and nutrition in the western hemisphere (2002)) and are associated with the introduction of urbanism in Britain during the Roman period (Redfern: J Rom Archaeol Supp Series 64 (2007) 171-194; Redfern: Britannia 39 (2008a) 161-191; Roberts and Cox: Health and disease in Britain: from prehistory to the present day (2003)). The results show that levels of frailty and mortality were lower in the late Iron Age period, and no sex differences in mortality was present. However, post-conquest, mortality risk increased for children and the elderly, and particularly for men. The latter finding challenges received wisdom concerning the benefits of incorporation into the Empire and the higher status of the male body in the Roman world. Therefore, we conclude that the consequences of urbanism, changes in diet, and increased population heterogeneity negatively impacted health, to the extent that the enhanced cultural buffering of men did not outweigh underlying sex differences in biology that advantage women.

A demographic analysis of Maiden Castle hillfort: Evidence for conflict in the late Iron Age and early Roman period.

The late Iron Age human remains from the British hillfort of Maiden Castle are frequently cited within the archaeological and bioarchaeological literature as providing evidence for conflict. This interpretation is based on osteological work undertaken in the late 1930s. In order to test the validity of using this sample in conflict research, the authors undertook a detailed analysis of the site's demography in comparison with contemporary late Iron Age attritional cemeteries from Dorset (England) and additional conflict mortality data. These results showed that the 1st century BC to 1st century AD samples conformed to a catastrophic profile, as greater numbers of young adult males had been buried during this phase of occupation. In combination with new bioarchaeological findings and the identification of an embedded Roman projectile weapon, we conclude that individuals had died during an episode of warfare, one of which probably included the Roman conquest of 43AD.

The prevalence of dislocation in developmental dysplasia of the hip in Britain over the past thousand years.

BACKGROUND: The aim of this study is to determine whether dislocation in developmental dysplasia of the hip (DDH) is changing in prevalence over time. This would allow us to see if modern improvements in diet, health, and obstetric care had any effect upon the likelihood of developing DDH. METHODS: The material used was a large medieval skeletal collection excavated from Britain (6580 hips). The cemetery was in use from approximately AD 1100 to 1530. RESULTS: The prevalence in the medieval series was found to be 2.7 per 1000. DISCUSSION: This prevalence was comparable with published clinical series from 20th century Britain, with no statistical difference found on chi2 test. CONCLUSIONS: It is concluded that hip dislocation secondary to DDH does not seem to be changing significantly in prevalence over the centuries, despite improvements in many other aspects of health over this time.