'TB or not TB': the conundrum of pre-European contact tuberculosis in the Pacific.

Tuberculosis (TB) is a major global health threat, infecting one-third of the world's population. Despite this prominence, the age, origin and spread of the disease have been topics of contentious debate. Molecular studies suggest that Mycobacterium tuberculosis 'sensu stricto', the most common strain of TB infecting humans today, originated in Africa and from there spread into Europe and Asia. The M. tuberculosis strains most commonly found across the Pacific and the Americas today are most closely related to European strains, supporting a hypothesis that the disease only reached these regions relatively recently via European sailors or settlers. However, this hypothesis is inconsistent with palaeopathological evidence of TB-like lesions in human remains from across the Pacific that predate European contact. Similarly, genetic evidence from pre-European South American mummies challenges the notion of a European introduction of the disease into the Pacific. Here, we review the complex evidence for the age and origin of TB in the Pacific, and discuss key gaps in our knowledge and how these may be addressed. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.

Author Correction: Ancient DNA of Guinea Pigs (Cavia spp.) Indicates a Probable New Center of Domestication and Pathways of Global Distribution.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Ancient DNA of Guinea Pigs (Cavia spp.) Indicates a Probable New Center of Domestication and Pathways of Global Distribution.

Guinea pigs (Cavia spp.) have a long association with humans. From as early as 10,000 years ago they were a wild food source. Later, domesticated Cavia porcellus were dispersed well beyond their native range through pre-Columbian exchange networks and, more recently, widely across the globe. Here we present 46 complete mitogenomes of archaeological guinea pigs from sites in Peru, Bolivia, Colombia, the Caribbean, Belgium and the United States to elucidate their evolutionary history, origins and paths of dispersal. Our results indicate an independent centre of domestication of Cavia in the eastern Colombian Highlands. We identify a Peruvian origin for the initial introduction of domesticated guinea pigs (Cavia porcellus) beyond South America into the Caribbean. We also demonstrate that Peru was the probable source of the earliest known guinea pigs transported, as part of the exotic pet trade, to both Europe and the southeastern United States. Finally, we identify a modern reintroduction of guinea pigs to Puerto Rico, where local inhabitants use them for food. This research demonstrates that the natural and cultural history of guinea pigs is more complex than previously known and has implications for other studies regarding regional to global-scale studies of mammal domestication, translocation, and distribution.

Complex history of dog (Canis familiaris) origins and translocations in the Pacific revealed by ancient mitogenomes.

Archaeological evidence suggests that dogs were introduced to the islands of Oceania via Island Southeast Asia around 3,300 years ago, and reached the eastern islands of Polynesia by the fourteenth century AD. This dispersal is intimately tied to human expansion, but the involvement of dogs in Pacific migrations is not well understood. Our analyses of seven new complete ancient mitogenomes and five partial mtDNA sequences from archaeological dog specimens from Mainland and Island Southeast Asia and the Pacific suggests at least three dog dispersal events into the region, in addition to the introduction of dingoes to Australia. We see an early introduction of dogs to Island Southeast Asia, which does not appear to extend into the islands of Oceania. A shared haplogroup identified between Iron Age Taiwanese dogs, terminal-Lapita and post-Lapita dogs suggests that at least one dog lineage was introduced to Near Oceania by or as the result of interactions with Austronesian language speakers associated with the Lapita Cultural Complex. We did not find any evidence that these dogs were successfully transported beyond New Guinea. Finally, we identify a widespread dog clade found across the Pacific, including the islands of Polynesia, which likely suggests a post-Lapita dog introduction from southern Island Southeast Asia.

Ancient mitogenomes of Phoenicians from Sardinia and Lebanon: A story of settlement, integration, and female mobility.

The Phoenicians emerged in the Northern Levant around 1800 BCE and by the 9th century BCE had spread their culture across the Mediterranean Basin, establishing trading posts, and settlements in various European Mediterranean and North African locations. Despite their widespread influence, what is known of the Phoenicians comes from what was written about them by the Greeks and Egyptians. In this study, we investigate the extent of Phoenician integration with the Sardinian communities they settled. We present 14 new ancient mitogenome sequences from pre-Phoenician (~1800 BCE) and Phoenician (~700-400 BCE) samples from Lebanon (n = 4) and Sardinia (n = 10) and compare these with 87 new complete mitogenomes from modern Lebanese and 21 recently published pre-Phoenician ancient mitogenomes from Sardinia to investigate the population dynamics of the Phoenician (Punic) site of Monte Sirai, in southern Sardinia. Our results indicate evidence of continuity of some lineages from pre-Phoenician populations suggesting integration of indigenous Sardinians in the Monte Sirai Phoenician community. We also find evidence of the arrival of new, unique mitochondrial lineages, indicating the movement of women from sites in the Near East or North Africa to Sardinia, but also possibly from non-Mediterranean populations and the likely movement of women from Europe to Phoenician sites in Lebanon. Combined, this evidence suggests female mobility and genetic diversity in Phoenician communities, reflecting the inclusive and multicultural nature of Phoenician society.

Origins and dispersals of Pacific peoples: evidence from mtDNA phylogenies of the Pacific rat.

The human settlement of the Pacific in general, and the origin of the Polynesians in particular, have been topics of debate for over two centuries. Polynesian origins are most immediately traced to people who arrived in the Fiji, Tonga, and Samoa region approximately 3,000 B.P. and are clearly associated with the Lapita Cultural Complex. Although this scenario of the immediate origins of the Polynesians is generally accepted, the debate on the ultimate origin of the Polynesians and the Lapita cultural complex continues. Our previous research has shown that analyses of mtDNA variation in the Pacific rat (Rattus exulans), often transported as a food item in the colonizing canoes, are valuable for tracing prehistoric human migration within Polynesia. Here we present mtDNA phylogenies based on approximately 240 base pairs of the d-loop from both archaeological and modern samples collected from Island Southeast Asia and the Pacific. We identify three major haplogroups, two of which occur in the Pacific. Comparing our results with Lapita models of Oceanic settlement, we are able to reject two often cited but simplistic models, finding support instead for multifaceted models incorporating a more complex view of the Lapita intrusion. This study is unique and valuable in that R. exulans is the only organism associated with the Lapita dispersal for which there are sufficient ancient and extant populations available for genetic analysis. By tracking population changes through time, we can understand more fully the settlement process and population interactions in both Near and Remote Oceania.

Patterns of prehistoric human mobility in polynesia indicated by mtDNA from the Pacific rat.

Human settlement of Polynesia was a major event in world prehistory. Despite the vastness of the distances covered, research suggests that prehistoric Polynesian populations maintained spheres of continuing interaction for at least some period of time in some regions. A low level of genetic variation in ancestral Polynesian populations, genetic admixture (both prehistoric and post-European contact), and severe population crashes resulting from introduction of European diseases make it difficult to trace prehistoric human mobility in the region by using only human genetic and morphological markers. We focus instead on an animal that accompanied the ancestral Polynesians on their voyages. DNA phylogenies derived from mitochondrial control-region sequences of Pacific rats (Rattus exulans) from east Polynesia are presented. A range of specific hypotheses regarding the degree of interaction within Polynesia are tested. These include the issues of multiple contacts between central east Polynesia and the geographically distinct archipelagos of New Zealand and Hawaii. Results are inconsistent with models of Pacific settlement involving substantial isolation after colonization and confirm the value of genetic studies on commensal species for elucidating the history of human settlement.

Ancient DNA from Polynesian rats: extraction, amplification and sequence from single small bones.

The human colonisation of Polynesia was a major event in world prehistory. It represents one of the last human population migrations, and one which required crossing major water barriers. Though the subject of Pacific population origins has been approached by scholars from numerous fields for nearly a century, recent years have seen the problem addressed by human geneticists. Since the initial report describing the recovery of DNA from skeletal remains, ancient DNA studies have also focused on the Pacific region. In this paper we present the results of ancient DNA analyses of Rattus exulans, an animal that was transported by ancestral Polynesians through the Pacific to the far reaches of the Polynesian triangle. Analysis of DNA of R. exulans skeletal remains has many advantages over studies of ancient human remains, yet the one drawback has been the recovery of ancient DNA from single bones of these very small rodents. We have successfully modified standard extraction protocols for ancient DNA and have consistently extracted, amplified and sequenced mitochondrial DNA (mtDNA) from less than 0.1 g of R. exulans bone and tooth samples recovered from archaeological sites throughout the Pacific, ranging from 400 to 2000 years old.