Modern strains of Mycobacterium tuberculosis from the Americas are closely related to those from Europe, supporting the assumption that human tuberculosis was introduced post-contact1. This notion, however, is incompatible with archaeological evidence of pre-contact tuberculosis in the New World2. Comparative genomics of modern isolates suggests that M. tuberculosis attained its worldwide distribution following human dispersals out of Africa during the Pleistocene epoch3, although this has yet to be confirmed with ancient calibration points. Here we present three 1,000-year-old mycobacterial genomes from Peruvian human skeletons, revealing that a member of the M. tuberculosis complex caused human disease before contact. The ancient strains are distinct from known human-adapted forms and are most closely related to those adapted to seals and sea lions. Two independent dating approaches suggest a most recent common ancestor for the M. tuberculosis complex less than 6,000 years ago, which supports a Holocene dispersal of the disease. Our results implicate sea mammals as having played a role in transmitting the disease to humans across the ocean.

Linear hypoplasia of the deciduous teeth is rare in most human populations, but common where nutritional status is poor. Deciduous enamel hypoplasia, hypocalcification, and hypoplasia-related caries are described in Middle and Late Woodland skeletal series from the Lower Illinois Valley. Gross enamel defects that can be referred to pre-natal development are found in 83 of 170 children under six years of age at death. Circular caries secondary to hypoplasia is significantly more common in the Late Woodland series, reflecting the apparent higher cariogenicity of Late Woodland diets. There is a significant association between prenatal dental defects and bony evidence for anemia and infectious disease. Children with enamel defects show relatively higher weaning age mortality than those without. These relationships suggest that at least moderate levels of malnutrition existed in Illinois Woodland populations.

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Fossorialism is a beneficial adaptation for brooding, predator avoidance and protection from extreme climate. The abundance of fossilised burrow casts from the Early Triassic of southern Africa is viewed as a behavioural response by many tetrapods to the harsh conditions following the Permo-Triassic mass-extinction event. However, scarcity of vertebrate remains associated with these burrows leaves many ecological questions unanswered. Synchrotron scanning of a lithified burrow cast from the Early Triassic of the Karoo unveiled a unique mixed-species association: an injured temnospondyl amphibian (Broomistega) that sheltered in a burrow occupied by an aestivating therapsid (Thrinaxodon). The discovery of this rare rhinesuchid represents the first occurrence in the fossil record of a temnospondyl in a burrow. The amphibian skeleton shows signs of a crushing trauma with partially healed fractures on several consecutive ribs. The presence of a relatively large intruder in what is interpreted to be a Thrinaxodon burrow implies that the therapsid tolerated the amphibian’s presence. Among possible explanations for such unlikely cohabitation, Thrinaxodon aestivation is most plausible, an interpretation supported by the numerous Thrinaxodon specimens fossilised in curled-up postures. Recent advances in synchrotron imaging have enabled visualization of the contents of burrow casts, thus providing a novel tool to elucidate not only anatomy but also ecology and biology of ancient tetrapods.

Hutchinson's incisors and Moon's molars are specific lesions of congenital syphilis. The extensive but fragmentary clinical literature on these conditions describes reduced dimensions and thin enamel in the permanent incisors and first molars, crowding and infolding of the first molar cusps, notching of the upper incisors, and apical hypoplasias of the permanent canines. A Barbados slave cemetery (ca. 1660-1820 AD) includes three individuals with these features, suggesting a frequency at birth of congenital syphilis in the population approaching 10%. These three cases show triple the frequency of all hypoplasias and more than seven times the frequency of pitting hypoplasia present in the remainder of the series. The recognizable congenital syphilis cases account for much of the remarkably high frequency of hypoplasias in the series as a whole. We infer that syphilis contributed substantially to morbidity, infant mortality, and infertility in this population. Presence or absence of congenital syphilis may account for much of the variability in health and mortality seen among nineteenth century African-American populations.