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.

Emergence, continuity, and evolution of Yersinia pestis throughout medieval and early modern Denmark.

The historical epidemiology of plague is controversial due to the scarcity and ambiguity of available data.1,2 A common source of debate is the extent and pattern of plague re-emergence and local continuity in Europe during the 14th-18th century CE.3 Despite having a uniquely long history of plague (∼5,000 years), Scandinavia is relatively underrepresented in the historical archives.4,5 To better understand the historical epidemiology and evolutionary history of plague in this region, we performed in-depth (n = 298) longitudinal screening (800 years) for the plague bacterium Yersinia pestis (Y. pestis) across 13 archaeological sites in Denmark from 1000 to 1800 CE. Our genomic and phylogenetic data captured the emergence, continuity, and evolution of Y. pestis in this region over a period of 300 years (14th-17th century CE), for which the plague-positivity rate was 8.3% (3.3%-14.3% by site). Our phylogenetic analysis revealed that the Danish Y. pestis sequences were interspersed with those from other European countries, rather than forming a single cluster, indicative of the generation, spread, and replacement of bacterial variants through communities rather than their long-term local persistence. These results provide an epidemiological link between Y. pestis and the unknown pestilence that afflicted medieval and early modern Europe. They also demonstrate how population-scale genomic evidence can be used to test hypotheses on disease mortality and epidemiology and help pave the way for the next generation of historical disease research.

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.

A life history approach to stature and body proportions in medieval Danes.

Developmental plasticity, or the ability of physiological development to change in response to environmental pressures (external and internal), results in permanent physiological changes that can shape the later life health experiences of an individual. The timing of non-specific stress in relation to growth and development is critical to this interaction. Dental enamel provides detailed information on the timing of non-specific stress experiences, which may be considered in relation to growth in other physiological systems developing at the same time to elucidate the impact of one on the other. Examples of parallel developing systems include the immune, nervous, cardiovascular, respiratory, renal, and digestive systems (Chamley et al. 2005; MacGregor 2008; Bee & Boyd 2010). This research investigates these patterns through the consideration markers of enamel growth disruption known as accentuated striae of Retzius (AS) in relation to stature and body proportions in human skeletal remains. Anthropometrics and dental samples were collected from two medieval Danish cemetery samples. Residuals were calculated using linear regression from stature in the grave and all metrics were considered in relation to a total number of AS for each individual. A life course approach was also taken by considering AS at different stages of crown development in relation to each metric. Results indicate potential associations between AS and skeletal metrics (particularly tibial length and stature). These are most apparent in relation to AS rates in enamel developing from approximately 2 to 4.8 years of age. These results point to the utility of taking a life course approach in which enamel development is considered in relation to patterns of skeletal growth. Certain limitations and the need for further developments are highlighted by the nature of the results.

Stressing out in medieval Denmark: An investigation of dental enamel defects and age at death in two medieval Danish cemeteries.

The influence of early life stress on later life experiences has become a major focus of research in medicine and more recently in bioarchaeology. Dental enamel, which preserves a record of childhood stress events, represents an important resource for this investigation when paired with the information from adult skeletal remains, such as age at death. The purpose of this research was to use a life history approach to the exploration of sex differences in the relationship between childhood stress and adult longevity by examining accentuated striae of Retzius (AS). A medieval Danish sample (n=70) drawn from the rural cemetery of Sejet and the urban cemetery of Ole Wormsgade was considered for AS and age at death. The results suggest sex differences in survivorship, with more stress being associated with reduced survivorship in males and increased survivorship in females. A consideration of AS formation time also suggests a difference in the impact of developmental timing between males and females. These results are interpreted in terms of differential frailty and selective mortality, drawing in both biomedical and cultural perspectives.