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

87Sr/86Sr data indicate human post-juvenile residence mobility decreases over time-elapsed since initial Holocene island colonization in the Pacific and Caribbean

During the Holocene colonization of islands in the Pacific and Caribbean by agropastoral and horticulturalist communities, a variety of proxies (material, genetic, zoogeographic etc.) indicate substantial inter-island and inter-community contact. It has been suggested that this contact represents an adaptive response to mitigate intrinsic demographic fragility during the initial phases of island colonization, and that this exogamous imperative faded in the aftermath of initial dispersal as overall population density increased. Here, we evaluate this model by synthesizing and comparing increasingly available 87Sr/86Sr data from funerary populations in the Pacific and Caribbean. After performing basic hygienic discrimination, we conclude that the Caribbean data—both from across the region, and on an intra-site/island basis—lend support to this model, with high early in-migration succeeded by comparatively low in-migration in a relationship which, based on chi-square tests, is statistically significant (1, N = 290) = 4.046, p = 0.044). The Pacific situation is more complex, with data from the Bismarck Archipelago and northern Solomon Islands skewing the analysis. However, in considering these data in detail, we demonstrate that there are reasons to suppose that the Pacific data may also tentatively support a model of high rates of in-migration being replaced later in settlement histories by comparatively low rates. We conclude by highlighting future directions for this incipient research program

Assessing the preservation of biogenic strontium isotope ratios (⁸⁷Sr/⁸⁶Sr) in the pars petrosa ossis temporalis of unburnt human skeletal remains: A case study from Saba

RATIONALE: Strontium isotope ((87)Sr/(86)Sr) analysis of skeletal remains has become a powerful tool in archaeological studies of human migration and mobility. Owing to its resistance to post‐mortem alteration, dental enamel is the preferred sampling material used for (87)Sr/(86)Sr analysis in bioarchaeological provenance research, although recent studies have demonstrated that cremated bone is also generally resistant to diagenesis. This paper presents the results of a pilot study exploring the potential of unburnt petrous bone (pars petrosa) as a reservoir of biogenic (diagenetically unaltered) strontium, as the otic capsule or bony labyrinth within the petrous bone is extremely dense and is thought to be unable to remodel after early childhood, potentially providing an alternative for dental enamel. METHODS: From an individual from a colonial‐era (18th century) site on the island of Saba in the Caribbean for whom previous enamel (87)Sr/(86)Sr results had indicated non‐local origins, multiple locations (n = 4) on the petrous were sampled and measured for strontium isotope composition. Saba (13 km(2)) has been extensively mapped for baseline strontium isotopes (n = 50) with (87)Sr/(86)Sr varying from ca 0.7065 to 0.7090, whereas enamel (87)Sr/(86)Sr (n = 3) ranged from 0.7104 to 0.7112. RESULTS: All four petrous (87)Sr/(86)Sr ratios (0.7111–0.7122) are consistently and considerably higher than the local bioavailable range, and very similar to the enamel (87)Sr/(86)Sr. These results provide initial evidence that unburnt petrous bones may preserve biogenic strontium, at least in this specific burial context. CONCLUSIONS: While more research in diverse burial conditions is needed to validate this observation, if confirmed, it would have broader implications for sample selection strategies in bioarchaeological studies using the strontium isotope method

Assessing the preservation of biogenic strontium isotope ratios (87Sr/86Sr) in the pars petrosa ossis temporalis of unburnt human skeletal remains: A case study from Saba

Rationale: Strontium isotope (87Sr/86Sr) analysis of skeletal remains has become a powerful tool in archaeological studies of human migration and mobility. Owing to its resistance to post-mortem alteration, dental enamel is the preferred sampling material used for 87Sr/86Sr analysis in bioarchaeological provenance research, although recent studies have demonstrated that cremated bone is also generally resistant to diagenesis. This paper presents the results of a pilot study exploring the potential of unburnt petrous bone (pars petrosa) as a reservoir of biogenic (diagenetically unaltered) strontium, as the otic capsule or bony labyrinth within the petrous bone is extremely dense and is thought to be unable to remodel after early childhood, potentially providing an alternative for dental enamel. Methods: From an individual from a colonial-era (18th century) site on the island of Saba in the Caribbean for whom previous enamel 87Sr/86Sr results had indicated non-local origins, multiple locations (n = 4) on the petrous were sampled and measured for strontium isotope composition. Saba (13 km2) has been extensively mapped for baseline strontium isotopes (n = 50) with 87Sr/86Sr varying from ca 0.7065 to 0.7090, whereas enamel 87Sr/86Sr (n = 3) ranged from 0.7104 to 0.7112. Results: All four petrous 87Sr/86Sr ratios (0.7111–0.7122) are consistently and considerably higher than the local bioavailable range, and very similar to the enamel 87Sr/86Sr. These results provide initial evidence that unburnt petrous bones may preserve biogenic strontium, at least in this specific burial context. Conclusions: While more research in diverse burial conditions is needed to validate this observation, if confirmed, it would have broader implications for sample selection strategies in bioarchaeological studies using the strontium isotope method

Human and hutia (Isolobodon portoricensis) interactions in pre-Columbian Hispaniola:The isotopic and morphological evidence

There are certain animal candidates for which researchers have long speculated as having been managed, or possibly domesticated, by indigenous peoples in the pre-Columbian Caribbean, the primary candidate being some members of a group of caviomorph rodents known as hutia (Capromyinae). This study comprises an isotopic and morphological investigation of the potential management of an extinct species endemic to Hispaniola, the Puerto Rican hutia (Isolobodon portoricensis). For comparisons, isotopic analysis was conducted of bone collagen samples examining carbon (∂13Cco) and nitrogen (∂15N) values of I. portoricensis with two other species of endemic hutia, guinea pig (Cavia porcellus), Antillean slider (Trachemys stejnegeri), rhinoceros iguana (Cyclura cornuta) and edible rat (Brotomys sp.) from four sites in the Dominican Republic: El Flaco, El Carril, El Cabo and La Entrada. This data was compared to human and dog collagen values available from El Flaco to assess similarities between these groups. Osteometric data was recorded for hutia mandibles, allowing for body mass estimations (n = 230). The findings suggest that some Isolobodon portoricensis specimens possessed carbon (δ13Cco) values similar to humans and dogs at El Flaco, possibly associated with the consumption of agriculturally produced maize. This research does not indicate whether domestication or management of this species was occurring, at least not in a systematic way. Concurrence with palaeoenvironmental and zooarchaeological data from the region in which El Flaco and El Carril are located indicate that indigenous agricultural practices may have affected populations of hutia, perhaps by attracting them and supporting them within anthropogenic mosaic landscapes. The data also suggests that some degree of either purposeful feeding or scavenging from human agricultural plots was occurring and supports some degree of commensalism between humans and Puerto Rican hutia at these sites

Advancing the Study of Amerindian Ecodynamics in the Caribbean: Current Perspectives

Archaeology of the America

An Isotopic and Morphometric Examination of Island Dogs (Canis familiaris):Comparing Dietary and Mobility Patterns in the Precolumbian Caribbean

In precolumbian insular Caribbean archaeological sites, domestic dog (Canis familiaris) remains have been recovered from varied contexts, such as formal burials, in refuse deposits, and as modified artifacts, indicating their complex and multifaceted role within indigenous societies. In this study, isotopic and morphometric analyses provide biochemical and morphological correlations to assess this differential treatment. We examined collagen values (n = 21) of carbon (δ13Cco) and nitrogen (δ15N), and enamel values (n = 81) of carbon (δ13Cen), oxygen (δ18Oen), and strontium (87Sr/86Sr) of dog remains from 16 precolumbian sites. Five comparative parameters were used to assess dietary variations between different groups: buried versus nonburied, local versus nonlocal, Greater versus Lesser Antilles, chronology, and modified versus unmodified remains. The only statistically significant difference in diets was between local and nonlocal dogs. Sufficient data were available to conduct isotopic mixing models using the FRUITS statistical program on four individuals for which depositional and morphological data were available. Results of dietary modeling indicate an unexpectedly heavy reliance on plant foods consistent with intentional feeding. This approach highlights the utility of combining isotope analysis, dietary models, morphometrics, and depositional context to provide comprehensive biographic overviews of individual animals