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.

Tracking breastfeeding and weaning practices in ancient populations by combining carbon, nitrogen and oxygen stable isotopes from multiple non-adult tissues.

This paper explores the potential of combining different isotope systems from different tissues to improve resolution when reconstructing breastfeeding and weaning practices (BWP) in archaeology. Additionally, we tested whether changes in diet can be detected in deciduous teeth. Rib collagen samples from 22 infants/children from the archaeological site of Bacuranao I (Mayabeque, Cuba) were processed for nitrogen (δ15N) and carbon (δ13Cco) stable isotopes and assessed using a Bayesian model (WARN). In addition, enamel of 48 teeth from 30 infants/children were analyzed for oxygen (δ18Oen) and carbon (δ13Cen) stable isotopes. Data revealed that the timing of weaning cannot be characterized precisely by analyzing either δ18O or δ15N. While a depletion in both δ15N and δ13Cco is only evident after one year, the WARN model suggested that the weaning process started at around 3 months and ended around 1.7 years. Most teeth were enriched in δ18Oen compared to deciduous incisors, suggesting a breastfeeding signal. However, a high variability in δ18O was found between similar teeth from the same individuals. Higher enrichment in δ18Oen, and variability, was observed in tissues formed during the first six months of life. A δ13C enrichment of 1.0‰ was observed among deciduous teeth and ribs. While most individuals enriched in δ15N showed enrichment in δ13C, the δ18O values were more variable. Our data suggests that stable isotopes of deciduous teeth, especially δ13Cen, can be used to detect changes in diet during the weaning process. It is also possible that the δ18O enrichment observed in M1 is influenced by the effects of cooking techniques on weaning foods. The combination of multiple isotope systems and tissues overcome some of the limitations posed by single tissue approaches.

Assessing the preservation of biogenic strontium isotope ratios (87 Sr/86 Sr) 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 km2 ) 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.

Paleodietary reconstruction of endemic rodents from the precolumbian Dominican Republic: Discriminating wild feeding behavior from diets linked to human niche construction activities.

In the Greater Antilles, certain animal taxa that have long been theorized to have been managed by indigenous peoples prior to AD1492, the main candidates being a group of endemic caviomorph rodents known as hutias (Capromyinae). This isotopic study investigates the paleodiets of several species of endemic rodents from three late precolonial sites in the northern Dominican Republic: El Flaco (cal. ad 990-1452), El Carril (cal. ad 1030-1262), and La Entrada (cal. ad 840-900) to assess whether human influence over animal diets can be determined. We examined bone collagen carbon (δ13Cco) and nitrogen (δ15N) and tooth enamel carbon (δ13Cen) isotope values of three species of hutias, Isolobodon portoricensis, Isolobodon montanus, and Plagiodontia aedium, alongside edible rat (Brotomys sp.), and domestic guinea pig (Cavia porcellus). To estimate dietary source contributions, we employed a Bayesian dietary mixing model (FRUITS v.3.0) and ran three different permutations to assess the relative contributions of C3 or C4/CAM plants. The addition of an extra 79 wild C3 and 40 wild C4/CAM plant species' isotope values from published sources to an established isotopic foodweb for the Caribbean region enabled us to discriminate between wild and domestic C3 and C4/CAM plant food sources in two of these models. Our results provide evidence of the significant consumption of domestic C4/CAM plants by some animals. This likely represents maize (Zea mays) consumption, which is known to have been ubiquitously cultivated by indigenous peoples in the region. This is particularly the case for I. portoricensis, as FRUITS modeling suggests that a few individuals consumed C4/CAM plants well beyond their expected natural diets as determined from feeding studies of extant hutia species. This may indicate human influence over endemic rodent diets due to niche construction activities such as horticultural practices and may reflect either opportunistic feeding on human produce or the purposeful supplementation of hutia diets by humans.

Genomic insights into the early peopling of the Caribbean.

The Caribbean was one of the last regions of the Americas to be settled by humans, but where they came from and how and when they reached the islands remain unclear. We generated genome-wide data for 93 ancient Caribbean islanders dating between 3200 and 400 calibrated years before the present and found evidence of at least three separate dispersals into the region, including two early dispersals into the Western Caribbean, one of which seems connected to radiation events in North America. This was followed by a later expansion from South America. We also detected genetic differences between the early settlers and the newcomers from South America, with almost no evidence of admixture. Our results add to our understanding of the initial peopling of the Caribbean and the movements of Archaic Age peoples in the Americas.

Isotopic evidence for anthropogenic lead exposure on a 17th/18th century Barbadian plantation.

OBJECTIVES: To identify and characterize anthropogenic lead sources on a 17th/18th century Barbadian plantation and to test if lead isotope analyses can be used to identify the geographic origins of first-generation African captives. MATERIALS AND METHODS: We carried out lead (Pb) isotope analyses on dental enamel samples from 24 individuals from the Newton Plantation Cemetery in Barbados, which had previously been analyzed for strontium (Sr) and oxygen (O) isotope composition (Schroeder et al., American Journal of Physical Anthropology, 2009, 139:547-557) and Pb concentrations (Schroeder et al., American Journal of Physical Anthropology, 2013, 150:203-209. RESULTS: We are able to identify British Pb sources, and more specifically Bristol/Mendips Pb, as the most likely source of anthropogenic Pb on the plantation, highlighting the impact of the British Atlantic economy on the lives of enslaved peoples in Barbados during the period of plantation slavery. Furthermore, we find that there is only one clear outlier among seven individuals who had previously been identified as African-born based on their enamel Sr isotope composition (Schroeder et al., American Journal of Physical Anthropology, 2009, 139:547-557). All other individuals present a very homogenous Pb isotope composition, which overlaps with that of British Pb sources. CONCLUSION: Our results indicate that while Pb isotope analyses can help identify and further characterize the sources of anthropogenic Pb in plantation settings, they might not be suited for identifying the origins of African-born individuals in diasporic contexts.

A bioavailable strontium isoscape for Western Europe: A machine learning approach.

Strontium isotope ratios (87Sr/86Sr) are gaining considerable interest as a geolocation tool and are now widely applied in archaeology, ecology, and forensic research. However, their application for provenance requires the development of baseline models predicting surficial 87Sr/86Sr variations ("isoscapes"). A variety of empirically-based and process-based models have been proposed to build terrestrial 87Sr/86Sr isoscapes but, in their current forms, those models are not mature enough to be integrated with continuous-probability surface models used in geographic assignment. In this study, we aim to overcome those limitations and to predict 87Sr/86Sr variations across Western Europe by combining process-based models and a series of remote-sensing geospatial products into a regression framework. We find that random forest regression significantly outperforms other commonly used regression and interpolation methods, and efficiently predicts the multi-scale patterning of 87Sr/86Sr variations by accounting for geological, geomorphological and atmospheric controls. Random forest regression also provides an easily interpretable and flexible framework to integrate different types of environmental auxiliary variables required to model the multi-scale patterning of 87Sr/86Sr variability. The method is transferable to different scales and resolutions and can be applied to the large collection of geospatial data available at local and global levels. The isoscape generated in this study provides the most accurate 87Sr/86Sr predictions in bioavailable strontium for Western Europe (R2 = 0.58 and RMSE = 0.0023) to date, as well as a conservative estimate of spatial uncertainty by applying quantile regression forest. We anticipate that the method presented in this study combined with the growing numbers of bioavailable 87Sr/86Sr data and satellite geospatial products will extend the applicability of the 87Sr/86Sr geo-profiling tool in provenance applications.

Origins and genetic legacies of the Caribbean Taino.

The Caribbean was one of the last parts of the Americas to be settled by humans, but how and when the islands were first occupied remains a matter of debate. Ancient DNA can help answering these questions, but the work has been hampered by poor DNA preservation. We report the genome sequence of a 1,000-year-old Lucayan Taino individual recovered from the site of Preacher's Cave in the Bahamas. We sequenced her genome to 12.4-fold coverage and show that she is genetically most closely related to present-day Arawakan speakers from northern South America, suggesting that the ancestors of the Lucayans originated there. Further, we find no evidence for recent inbreeding or isolation in the ancient genome, suggesting that the Lucayans had a relatively large effective population size. Finally, we show that the native American components in some present-day Caribbean genomes are closely related to the ancient Taino, demonstrating an element of continuity between precontact populations and present-day Latino populations in the Caribbean.

Investigating human geographic origins using dual-isotope (87Sr/86Sr, δ18O) assignment approaches.

Substantial progress in the application of multiple isotope analyses has greatly improved the ability to identify nonlocal individuals amongst archaeological populations over the past decades. More recently the development of large scale models of spatial isotopic variation (isoscapes) has contributed to improved geographic assignments of human and animal origins. Persistent challenges remain, however, in the accurate identification of individual geographic origins from skeletal isotope data in studies of human (and animal) migration and provenance. In an attempt to develop and test more standardized and quantitative approaches to geographic assignment of individual origins using isotopic data two methods, combining 87Sr/86Sr and δ18O isoscapes, are examined for the Circum-Caribbean region: 1) an Interval approach using a defined range of fixed isotopic variation per location; and 2) a Likelihood assignment approach using univariate and bivariate probability density functions. These two methods are tested with enamel isotope data from a modern sample of known origin from Caracas, Venezuela and further explored with two archaeological samples of unknown origin recovered from Cuba and Trinidad. The results emphasize both the potential and limitation of the different approaches. Validation tests on the known origin sample exclude most areas of the Circum-Caribbean region and correctly highlight Caracas as a possible place of origin with both approaches. The positive validation results clearly demonstrate the overall efficacy of a dual-isotope approach to geoprovenance. The accuracy and precision of geographic assignments may be further improved by better understanding of the relationships between environmental and biological isotope variation; continued development and refinement of relevant isoscapes; and the eventual incorporation of a broader array of isotope proxy data.