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

Genetic history of Cambridgeshire before and after the Black Death

The extent of the devastation of the Black Death pandemic (1346-1353) on European populations is known from documentary sources and its bacterial source illuminated by studies of ancient pathogen DNA. What has remained less understood is the effect of the pandemic on human mobility and genetic diversity at the local scale. Here, we report 275 ancient genomes, including 109 with coverage >0.1×, from later medieval and postmedieval Cambridgeshire of individuals buried before and after the Black Death. Consistent with the function of the institutions, we found a lack of close relatives among the friars and the inmates of the hospital in contrast to their abundance in general urban and rural parish communities. While we detect long-term shifts in local genetic ancestry in Cambridgeshire, we find no evidence of major changes in genetic ancestry nor higher differentiation of immune loci between cohorts living before and after the Black Death.

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.

Phylogeographic history of mitochondrial haplogroup J in Scandinavia

BACKGROUND

Mitochondrial DNA haplogroup J is the third most frequent haplogroup in modern-day Scandinavia, although it did not originate there. To infer the genetic history of haplogroup J in Scandinavia, we examined worldwide mitogenome sequences using a maximum-likelihood phylogenetic approach.

METHODS

Haplogroup J mitogenome sequences were gathered from GenBank (n = 2245) and aligned against the ancestral Reconstructed Sapiens Reference Sequence. We also analyzed haplogroup J Viking Age sequences from the European Nucleotide Archive (n = 54). Genetic distances were estimated from these data and projected onto a maximum likelihood rooted phylogenetic tree to analyze clustering and branching dates.

RESULTS

Haplogroup J originated approximately 42.6 kya (95% CI: 30.0-64.7), with several of its earliest branches being found within the Arabian Peninsula and Northern Africa. J1b was found most frequently in the Near East and Arabian Peninsula, while J1c occurred most frequently in Europe. Based on phylogenetic dating, subhaplogroup J1c has its early roots in the Mediterranean and Western Balkans. Otherwise, the majority of the branches found in Scandinavia are younger than those seen elsewhere, indicating that haplogroup J dispersed relatively recently into Northern Europe, most plausibly with Neolithic farmers.

CONCLUSIONS

Haplogroup J appeared when Scandinavia was transitioning to agriculture over 6 kya, with J1c being the most common lineage there today. Changes in the distribution of haplogroup J mtDNAs were likely driven by the expansion of farming from West Asia into Southern Europe, followed by a later expansion into Scandinavia, with other J subhaplogroups appearing among Scandinavian groups as early as the Viking Age.

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.

Sexual stature difference fluctuations in pre- and post-Black Death London as an indicator of living standards

OBJECTIVES

The degree of sexual stature difference (SSD), the ratio of male to female height, is argued to be an indicator of living standards based on evidence that physical growth for males is more sensitive to environmental fluctuations. In a resource-poor environment, the degree of SSD is expected to be relatively low. The aim of this study is to comparatively assess SSD in medieval London in the context of repeated famine events and other environmental stressors before the Black Death (BD) and the improved living conditions that characterized the post-Black Death period.

METHODS

To test the hypothesis that a poor nutritional environment resulted in decreased SSD in medieval London, this study compares adult individuals from early pre-Black Death (c. 1000-1200), late pre-Black Death (c. 1200-1250) and post-Black Death (c. 1350-1540) cemetery contexts from London. Maximum tibial,femoral, and lower limb lengths were used as a proxy for stature, and SSD was calculated using the Chakraborty and Majumber index.

RESULTS

Compared to the late pre-BD period, we find a slighter higher degree of SSD in the post-BD period for all three stature proxies used. This increase is attributed to more exaggerated increases in stature for estimated males post-BD.

CONCLUSIONS

This study demonstrates the importance of examining variables that are considered indicators of living standards in light of factors like selective mortality, catch-up growth, and urban migration patterns. Future research needs to further investigate how cultural and biological processes influence the mechanisms that produce adult stature.

The population genomic legacy of the second plague pandemic

Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%-40%.¹ It is assumed that this high mortality affected the gene pools of these populations. First, local population crashes reduced genetic diversity. Second, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the etiologic agent (Yersinia pestis).² Third, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Norwegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods: (1) prior to the plague striking Trondheim in 1,349 CE, (2) the 17^th-19^th century, and (3) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large F_ST values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential reference bias on test statistics.

The plague’s impact paleodemographic and genetic measures in 15th to 16th century Gdańsk

Yersinia pestis caused plagues and haunted Gdańsk several times during the 15th and 16th centuries. This study focuses on the following demographic effects: 1/ distributions of deceased by age in a plagued city, 2/ parameters of the life tables, 3/ estimation of the natural increase. To assess genetic effects of the plague, measures of the opportunity for natural selection were considered. Skeletal remains of 283 people from the 15th – 16th century ossuary 3009 from the Dominican Monastery in Gdańsk provided research material. Yersinia pestis DNA in this skeletal material has already been found (Morozowa et al. 2017, 2020). Distributions of the deceased by age in the study sample were compared with those for Gdańsk before the plague and with those for the mass burial of plague victims in the 14th century Lübeck. Neither catastrophic mortality was found in the material studied, nor selective nature of the plague with regard to sex and age had been demonstrated. Using the Weiss method, the rate of natural increase r=–0.005 was reconstructed. With the wide dating range of the ossuary and the fact that it contains results of both the epidemic and “normal” mortality, the natural increase value at this level seems justified. There was a deterioration in the values of life tables parameters, especially life expectancy. Newborn life expectancy dropped to 19.5–22.6 years and for a 20-year-old to 17.7 years. The measures of opportunity for natural selection also deteriorated primarily due to child mortality: the biological state index Ibs values were low (within the 0.3–0.4 range) and values of the Im Crow’s index about 1.0. Natural selection also acted on adults as evidenced by values of the gross potential reproduction rate Rpot below 0.7. Demographically the study sample was at the level of the early Middle Ages rather than the Rennaisance.

Pleistocene mitogenomes reconstructed from the environmental DNA of permafrost sediments

Traditionally, paleontologists have relied on the morphological features of bones and teeth to reconstruct the evolutionary relationships of extinct animals.¹ In recent decades, the analysis of ancient DNA recovered from macrofossils has provided a powerful means to evaluate these hypotheses and develop novel phylogenetic models.² Although a great deal of life history data can be extracted from bones, their scarcity and associated biases limit their information potential. The paleontological record of Beringia³-the unglaciated areas and former land bridge between northeast Eurasia and northwest North America-is relatively robust thanks to its perennially frozen ground favoring fossil preservation.^4,5 However, even here, the macrofossil record is significantly lacking in small-bodied fauna (e.g., rodents and birds), whereas questions related to migration and extirpation, even among well-studied taxa, remain crudely resolved. The growing sophistication of ancient environmental DNA (eDNA) methods have allowed for the identification of species within terrestrial/aquatic ecosystems,^6-12 in paleodietary reconstructions,^13-19 and facilitated genomic reconstructions from cave contexts.^8,20-22 Murchie et al.^6,23 used a capture enrichment approach to sequence a diverse range of faunal and floral DNA from permafrost silts deposited during the Pleistocene-Holocene transition.²⁴ Here, we expand on their work with the mitogenomic assembly and phylogenetic placement of Equus caballus (caballine horse), Bison priscus (steppe bison), Mammuthus primigenius (woolly mammoth), and Lagopus lagopus (willow ptarmigan) eDNA from multiple permafrost cores spanning the last 30,000 years. We identify a diverse metagenomic spectra of Pleistocene fauna and identify the eDNA co-occurrence of distinct Eurasian and American mitogenomic lineages.

Collapse of the mammoth-steppe in central Yukon as revealed by ancient environmental DNA

The temporal and spatial coarseness of megafaunal fossil records complicates attempts to to disentangle the relative impacts of climate change, ecosystem restructuring, and human activities associated with the Late Quaternary extinctions. Advances in the extraction and identification of ancient DNA that was shed into the environment and preserved for millennia in sediment now provides a way to augment discontinuous palaeontological assemblages. Here, we present a 30,000-year sedimentary ancient DNA (sedaDNA) record derived from loessal permafrost silts in the Klondike region of Yukon, Canada. We observe a substantial turnover in ecosystem composition between 13,500 and 10,000 calendar years ago with the rise of woody shrubs and the disappearance of the mammoth-steppe (steppe-tundra) ecosystem. We also identify a lingering signal of Equus sp. (North American horse) and Mammuthus primigenius (woolly mammoth) at multiple sites persisting thousands of years after their supposed extinction from the fossil record.

Mitochondrial DNA Profiles of Individuals from a 12th Century Necropolis in Feldioara (Transylvania)

The genetic signature of modern Europeans is the cumulated result of millennia of discrete small-scale exchanges between multiple distinct population groups that performed a repeated cycle of movement, settlement, and interactions with each other. In this study we aimed to highlight one such minute genetic cycle in a sea of genetic interactions by reconstructing part of the genetic story of the migration, settlement, interaction, and legacy of what is today the Transylvanian Saxon. The analysis of the mitochondrial DNA control region of 13 medieval individuals from Feldioara necropolis (Transylvania region, Romania) reveals a genetically heterogeneous group where all identified haplotypes are different. Most of the perceived maternal lineages are of Western Eurasian origin, except for the Central Asiatic haplogroup C seen in only one sample. Comparisons with historical and modern populations describe the contribution of the investigated Saxon settlers to the genetic history of this part of Europe.

Toward a bioarchaeology of urbanization: Demography, health, and behavior in cities in the past

Urbanization is one of the most important settlement shifts in human history and has been the focus of research within bioarchaeology for decades. However, there have been limited attempts to synthesize the results of these studies in order to gain a broader perspective on whether or how urbanization affects the biology, demography, and behavior of humans, and how these potential effects are embodied in the human skeleton. This paper outlines how bioarchaeology is well-suited to examine urbanization in the past, and we provide an overview and examples of three main ways in which urbanization is studied in bioarchaeological research: comparison of (often contemporaneous) urban and rural sites, synchronic studies of the variation that exists within and between urban sites, and investigations of changes that occur within urban sites over time. Studies of urbanization, both within bioarchaeology and in other fields of study, face a number of limitations, including a lack of a consensus regarding what urban and urbanization mean, the assumed dichotomous nature of urban versus rural settlements, the supposition that urbanization is universally bad for people, and the assumption (at least in practice) of homogeneity within urban and rural populations. Bioarchaeologists can address these limitations by utilizing a wide array of data and methods, and the studies described here collectively demonstrate the complex, nuanced, and highly variable effects of urbanization.