Project description:The shift from a hunter-gatherer (HG) to an agricultural (AG) mode of subsistence is believed to have been associated with profound changes in the burden and diversity of pathogens across human populations. Yet, the extent to which the advent of agriculture impacted the evolution of the human immune system remains unknown. Here we present a comparative study of variation in the transcriptional responses of peripheral blood mononuclear cells (PBMCs) to bacterial and viral stimuli between the Batwa, a rainforest hunter-gatherer, and the Bakiga, an agriculturalist population from Central Africa. We observed increased divergence between hunter-gatherers and farmers in the transcriptional response to viruses compared to that for bacterial stimuli. We demonstrate that a significant fraction of these transcriptional differences are under genetic control, and we show that positive natural selection has helped to shape population differences in immune regulation. Unexpectedly, we found stronger signatures of recent natural selection in the rainforest hunter-gatherers, which argues against the popularized notion that shifts in pathogen exposure due to the advent of agriculture imposed radically heightened selective pressures in agriculturalist populations.
Project description:Ancient genome-wide DNA from France highlights the complexity of interactions between Mesolithic hunter-gatherers and Neolithic farmers
Project description:The deadly maltreated body of Vittrup Man was deposited in a Danish bog, probably as part of a ritualised sacrifice. It happened between c. 3300 and 3100 cal years BC, i.e., during the period of the local farming-based Funnel Beaker Culture. In terms of skull morphological features he differs from the majority of the contemporaneous farmers found in Denmark, and associates with hunter-gatherers, who inhabited Scandinavia during the previous millennia. His skeletal remains were selected for transdisciplinary analysis to reveal his life-history in terms of a population historical perspective. We report the combined results of an integrated set of genetic, isotopic, physical anthropological and archaeological analytical approaches. Strontium signature suggests a foreign birthplace that could be in Norway or Sweden. In addition, enamel oxygen isotope values indicate that as a child he lived in a colder climate, i.e., to the north of the regions inhabited by farmers. Genomic data in fact demonstrates that he is closely related to Mesolithic humans known from Norway and Sweden. Moreover, dietary stable isotope analyses on enamel and bone collagen demonstrate a fisher-hunter way of life in his childhood and a diet typical of farmers later on. Such a volatile life-history is also reflected by proteomic analysis of hardened organic deposits on his teeth, indicating the consumption of forager food (seal, whale and marine fish) as well as farmer food (sheep/goat). From a dietary isotopic transect of one of his teeth it is shown that his transfer between societies of foragers and farmers took place near to the end of his late teenage years.
Project description:The extensive peat bogs of Southern Scandinavia have yielded rich Mesolithic archaeological assemblages, which has informed prehistoric studies for more than a century. Central to this has been the first recognizably Mesolithic culture, the Maglemose (c. 11,000 - 8,000 BP), first described in 1903 which has become a yardstick against which all other Early Mesolithic cultures have been compared. Despite the excellent preservation of organic material, we have for the first time conducted a combined investigation of the typology, species composition and absolute chronology of Maglemose bone points. A demonstrable and significant change in barb morphology can be directly linked to a significant paucity of finds in Southern Scandinavia around 10,300 cal BP, potentially linked to climate change. Peptide mass fingerprinting (ZooMS) reveals that the majority of bone points are made from cervids and bovines. The ribs of bovines; for instance, are more frequently utilized following the hiatus. Furthermore, the marked change in barbed bone point morphology coincides with a change in lithic technology. This change in material culture has been shown to arrive archaeologically with eastern pioneers and colonisations through Fennoscandinavia. We, therefore, propose that the Maglemose culture in Southern Scandinavia is fundamentally divided into an Early Complex (c. 11,600 - 10,300 cal BP) and a Late Complex (c. 10,300 - 8,600 cal BP): the former characterized by percussion blade production and “fine-barbed bone points” and the latter characterized by the innovations of pressure-blade production and “larger barbed bone points”. Finally, through these integrated analyses we are able to show that a single artifact type can be used as a proxy for human populations as well as inferences on potential climate changes.
Project description:Chewing betel nut is an important risk factor for the carcinogenesis of tongue squamous cell carcinoma (TSCC), but the mechanism is still unknown.To screen the lncRNAs associated with betel nut chewing-induced TSCC and identify potential biomarkers for the TSCC, we collected 5 pairs of TSCC and paracancerous tissues and monitored the resultant lncRNA and mRNA expression profiles using an lncRNA microarray. All 5 patients have a history of areca nut chewing.
Project description:The genetic structure of the indigenous hunter-gatherer peoples of Southern Africa, the oldest known lineage of modern man, holds an important key to understanding humanity's early history. Previously sequenced human genomes have been limited to recently diverged populations. Here we present the first complete genome sequences of an indigenous hunter-gatherer from the Kalahari Desert and of a Bantu from Southern Africa, as well as protein-coding regions from an additional three hunter-gatherers from disparate regions of the Kalahari. We characterize the extent of whole-genome and exome diversity among the five men, reporting 1.3 million novel DNA differences genome-wide, and 13,146 novel amino-acid variants. These data allow genetic relationships among Southern African foragers and neighboring agriculturalists to be traced more accurately than was previously possible. Adding the described variants to current databases will facilitate inclusion of Southern Africans in medical research efforts.
Project description:The genetic structure of the indigenous hunter-gatherer peoples of Southern Africa, the oldest known lineage of modern man, holds an important key to understanding humanity's early history. Previously sequenced human genomes have been limited to recently diverged populations. Here we present the first complete genome sequences of an indigenous hunter-gatherer from the Kalahari Desert and of a Bantu from Southern Africa, as well as protein-coding regions from an additional three hunter-gatherers from disparate regions of the Kalahari. We characterize the extent of whole-genome and exome diversity among the five men, reporting 1.3 million novel DNA differences genome-wide, and 13,146 novel amino-acid variants. These data allow genetic relationships among Southern African foragers and neighboring agriculturalists to be traced more accurately than was previously possible. Adding the described variants to current databases will facilitate inclusion of Southern Africans in medical research efforts. Copy number differences between NA18507 and KB1 were predicted from the depth of whole-genome shotgun sequence reads. These predictions were then validated using array-CGH using a a genome-wide design as well as a custom design targeted at specific regions of copy number difference