The population genomic legacy of the second plague pandemic

SummaryHuman 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 17th–19th 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 FST 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.Results and discussion STAR★Method

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 17th–19th 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 FST 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.publishedVersio

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 17th-19th 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 FST 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

Assessing human diet and movement in the Tongan maritime chiefdom using isotopic analyses.

The rise of stratified societies fundamentally influences the interactions between status, movement, and food. Using isotopic analyses, we assess differences in diet and mobility of individuals excavated from two burial mounds located at the `Atele burial site on Tongatapu, the main island of the Kingdom of Tonga (c. 500 - 150 BP). The first burial mound (To-At-1) was classified by some archaeologists as a commoner's mound while the second burial mound (To-At-2) was possibly used for interment of the chiefly class. In this study, stable isotope analyses of diet (δ13C, δ15N, and δ34S; n = 41) are used to asses paleodiet and 87Sr/86Sr ratios (n = 30) are analyzed to investigate individual mobility to test whether sex and social status affected these aspects of life. Our results show significant differences in diet between burial mounds and sexes. Those interred in To-At-2 displayed lower δ13C values, indicating they ate relatively more terrestrial plants (likely starchy vegetable staples) compared with To-At-1 individuals. Females displayed significantly lower δ15N values compared with males within the entire assemblage. No differences in δ34S values were observed between sexes or burial mound but it is possible that sea spray or volcanism may have affected these values. One individual displayed the strontium isotopic composition representative of a nonlocal immigrant (outside 2SD of the mean). This suggests the hegemonic control over interisland travel, may have prevented long-term access to the island by non-Tongans exemplifying the political and spiritual importance of the island of Tongatapu in the maritime chiefdom

The Life History of an Enslaved African:Multiple Isotope Evidence for Forced Childhood Migration from Africa to the Caribbean and Associated Dietary Change

Archaeological excavations of an enslaved African domestic area at the Spring Bay Flat plantation on the island of Saba, Dutch Caribbean, uncovered a small concentration of artefacts (shell, metal nails, animal bones and five human teeth) overlaid with a lock hinge, interpreted as a lockbox and its contents. Dental anthropological and multi-isotope (strontium, oxygen, carbon and nitrogen) analyses of the teeth revealed that they belonged to a single individual who originated from Africa and survived a period of pronounced nutritional stress as a juvenile. The results provide rare insights into the life history of an individual who probably experienced enslavement, (forced) migration from Africa and adaptation to plantation life in the colonial-era Caribbean

A Multi-Isotope Investigation of Human and Dog Mobility and Diet in the Pre-Colonial Antilles

The complex relationships between humans and dogs (Canis lupus familiaris) have a very deep and unique history. Dogs have accompanied humans as they colonised much of the world, and were introduced via human agency into the insular Caribbean where they became widespread throughout the Ceramic Age. It is likely that the dynamic interactions between humans, dogs, and their environments in the Caribbean were spatially, chronologically, and socially variable. However, almost no research has specifically addressed the nature, or potential variability, of human/dog interactions in this region. This study presents isotopic (strontium and carbon) evidence bearing on human and dog paleomobility and paleodietary patterns in the pre-colonial Caribbean. The isotope results illustrate a generally high degree of correspondence between human and dog dietary practices at all analysed sites but also slight differences in the relative importance of different dietary inputs. Striking parallels are also observed between the human and dog mobility patterns and shed light on broader networks of social interaction and exchange. Lastly, the paper addresses the possible utility and relevance of canine isotope data as proxies for inferring past human behaviours.Seventh Framework Programme (FP7)Archaeology of the America

87Sr/86Sr variability in Puerto Rico: geological complexity and the study of paleomobility

The temptation to use biogeochemical techniques to resolve issues of paleomigration is evident and well intentioned. Knowledge of radiogenic strontium isotope baselines in a region of interest is a sine qua non of such archaeological studies of paleomobility. Here, we present the first detailed study of baseline 87Sr/86Sr values for the island of Puerto Rico. The high degree of 87Sr/86Sr variability present in this corpus of modern Puerto Rican bedrock and terrestrial malacological samples (0.70406–0.70909) is a testament to the complex geology of that island. This diversity of 87Sr/86Sr values makes parsing issues of origin a difficult and highly contingent task. Given these complexities, regional studies seeking to assess paleomigration by such isotopic means should proceed with a great deal of caution.► 87Sr/86Sr signatures of Puerto Rican geological samples vary widely. ► Observed 87Sr/86Sr range subsumes variation reported for entire insular Caribbean. ► Complexity of Puerto Rican geology makes mapping of 87Sr/86Sr signatures difficult. ► Non-discrete geology of Puerto Rico makes tracking paleomobility highly problematic