Human auditory ossicles as an alternative optimal source of ancient DNA.

DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provides optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluate the ossicles as an alternative source of ancient DNA. We show that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quantity and minimal differences in data quality across preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that they should be used when available to reduce damage to human remains. Our results identify another optimal skeletal element for ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that ancient DNA analysis will produce useable results.

Intra-tooth stable isotope analysis of dentine: a step toward addressing selective mortality in the reconstruction of life history in the archaeological record.

Intra-tooth stable isotope analysis of dentine provides a more sensitive means to examine infant and childhood life history in the past than conventional cross-sectional analyses that rely on age-at-death. In addition, reconstructions of early diet and life history using an intra-tooth approach circumvent potential problems associated with mortality bias, which may operate strongly during infancy and childhood. We present new intra-tooth stable carbon and nitrogen isotope profiles in dentine collagen of early forming permanent teeth in a sample of adults from the Medieval Nubian site of Kulubnarti. We interpret the profiles in terms of weaning behavior and dietary history, and we compare profiles generated from first molars and canines to explore the degree to which these tooth types correspond. We then compare the profiles to the occurrence of linear enamel hypoplasia to assess the relationship between the timing of the weaning process and stress events. Finally, we compare the longitudinal profiles to cross-sectional stable isotope data obtained from rib collagen to investigate how life histories might differ between those that survived into adulthood and those that did not. Results suggest that canine and first molar profiles are in broad agreement, that hypoplastic stress events occurred during rather than before or after the weaning process in our sample, and that survivors appear to have weaned earlier than the average non-survivor. We suggest that this approach may be useful for addressing the effects of selective mortality on reconstructions of early life history and the relationship between early life history and morbidity.

Irrigation and infection: the immunoepidemiology of schistosomiasis in ancient Nubia.

Schistosomiasis has been deemed "the most important water-based disease from a global public-health perspective" in modern populations. To better understand the burden of schistosomiasis in ancient populations, we conducted immunologic examinations of desiccated tissue samples from two ancient Nubian populations, Wadi Halfa (N = 46) and Kulubnarti (N = 191). Saqia irrigated agriculture increases the available habitat for the aquatic vector snails and the risk of exposure. On the basis of evidence regarding the impact of saqia irrigation on schistosomiasis prevalence and transmission in modern populations, we predicted that the prevalence of Schistosoma mansoni infection would be higher in Wadi Halfa (saqia irrigation) than Kulubnarti (annual flooding). We also predicted that peak infection prevalence would occur at an earlier age within the Wadi Halfa population than the Kulubnarti population and that in both populations the prevalence of schistosomiasis would be higher in males than females due to differential water contact. The prevalence of S. mansoni was greater in the Wadi Halfa population (26.1%) than at Kulubnarti (9.4%) (P = 0.002). However, peak prevalence of infection did not occur in a younger age category within the Wadi Halfa population; prevalence of infection peaked at 66.7% in the mature adult age group (46+ years) in the Wadi Halfa population and at 16% in the later child age group (6-10 years) in the Kulubnarti population. There were no statistically significant differences in prevalence between males and females of either population. The impact of human alteration of the environment on the transmission of schistosomiasis is clearly shown in these populations.

Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia.

Relatively little is known about Nubia's genetic landscape prior to the influence of the Islamic migrations that began in the late 1st millennium CE. Here, we increase the number of ancient individuals with genome-level data from the Nile Valley from three to 69, reporting data for 66 individuals from two cemeteries at the Christian Period (~650-1000 CE) site of Kulubnarti, where multiple lines of evidence suggest social stratification. The Kulubnarti Nubians had ~43% Nilotic-related ancestry (individual variation between ~36-54%) with the remaining ancestry consistent with being  introduced through Egypt and ultimately deriving from an ancestry pool like that found in the Bronze and Iron Age Levant. The Kulubnarti gene pool - shaped over a millennium - harbors disproportionately female-associated West Eurasian-related ancestry. Genetic similarity among individuals from the two cemeteries supports a hypothesis of social division without genetic distinction. Seven pairs of inter-cemetery relatives suggest fluidity between cemetery groups. Present-day Nubians are not directly descended from the Kulubnarti Nubians, attesting to additional genetic input since the Christian Period.