Food resources of the Khog Gzung site on the Tibetan Plateau revealed by sedimentary ancient DNA

Traditional zooarchaeological and archaeobotanical methods based on morphological identification of the excavated faunal and floral remains have been broadly used in reconstructing ancient subsistence economies. However, the accuracy and reliability of these methods rely heavily on the preservation state of the remains. By sequencing the ancient DNA of plants,animals, and microorganisms preserved in sediment, sedimentary ancient DNA(sedaDNA) now offers a novel approach for reconstructing the taxa composition dated back to hundreds of thousands of years. Yet, its application in open-air archaeological sites is rarely reported. In this study, we attempted to apply sedaDNA shotgun metagenomics on the archaeological deposits of the Khog Gzung site(an open-air site dated to 3160–2954 cal yr BP) on the Tibetan Plateau, and then compared the reconstructed taxonomic composition to the unearthed remains. Results showed that most of the crops and domestic animals identified by the two approaches, such as barley(Hordeum vulgare) and sheep(Ovis aries), are in general consistent. Some species, such as foxtail millet(Setaria italica), however, were only detected by sedaDNA. In addition, a variety of microorganisms were also detected by the sedaDNA. The two approaches combined revealed diversified food resources at the Khog Gzung site, which included crops such as millet, barley and wheat, domestic animals such as sheep and cattle, and likely also wild animals from fishing and hunting. Our data proves that sedaDNA has a great potential in reconstructing the faunal and floral compositions from archaeological deposits, therefore laying the foundation for its border applications.

Bacterial Diversity in Alpine Lakes: A Review from the Third Pole Region

Microorganisms are unique among all of the living organisms because of their high population size, advanced genetic diversity, short generation time, and quick response to the small change in environmental conditions. Remote alpine lakes of the Third Pole region provide the unique habitat for microorganisms acting as a natural laboratory and offering the information about the ecological roles of microorganisms. Many researchers focused on microbial communities as well as the impact of physicochemical, biological and hydrological parameters in lakes of this region since decades but the comprehensive review focusing on bacterial diversity and the role of environmental parameters still lacks. Here we reviewed bacterial diversity in lakes of the Third Pole region by analyzing 16 S rRNA clone libraries accessed from previous research findings. A total of 5 388 bacterial 16 S rRNA gene sequences were analyzed and classified into different phylogenetic groups. The average relative abundance of dominant taxa includes Betaproteobacteria(19%), Bacteroidetes(18%), Gammaproteobacteria(16%), Actinobacteria(15%), Alphaproteobacteria(14%), Cyanobacteria(7%), and Firmicutes(5%). Several adaptational strategies were adopted by these dominant bacterial groups in order to accommodate in the respective habitat. Nevertheless, lake water properties like temperature, pH, salinity, incident UV radiation, turbidity, and nutrients also played role in bacterial diversity.

Indica rice spread to the Tibetan Plateau in the 700s CE

Asian cultivated rice(Oryza sativa)has two main subspecies,indica(O.sativa sub.indica)and japonica(O.sativa sub.japonica).Japonica rice was domesticated in the middle and lower reaches of the Yangtze River in China,while indica appeared around 4000 a BP in northern south Asia after hybridization between introduced japonica and indigenous proto-indica.When and how indica rice spread into China is still barely understood,although it is cultivated widely in southern China today.Here we report on the earliest,definite indica rice remains in China,including charred seeds,phytoliths,and ancient DNA,from the newly investigated Kongsangqiao site at an elevation of 2676 m above sea level in Tibet,along with a charcoal study that reveals the vegetation and climate during of human occupation.AMS radiocarbon dating of charred indica rice grains suggests the remains are from the 8th century(700s CE).The dominant identified charcoal fragments are Himalayan pine(Pinus wallichiana),from which a rather cold climate is inferred where indica rice could not be grown in situ,suggesting it was likely brought to the site.Both archaeological and literature records thus support that indica rice,fully domesticated in northern south Asia,had spread to the southern margin of the Tibetan Plateau via parts of the ancient Tang-Tubo Road,Tubo-Nepal Road,by at least the 8th century CE.