Genomic Insights into the Formation of Human Populations in East Asia

厦门大学人类学研究所、厦门大学生命科学学院细胞应激生物学国家重点实验室王传超教授课题组与哈佛医学院David Reich教授团队合作，联合全球43个单位的85位共同作者组成的国际合作团队通过古DNA精细解析东亚人群形成历史。研究人员利用古DNA数据检验了东亚地区农业和语言共扩散理论，综合考古学、语言学等证据，该研究系统性地重构了东亚人群的形成、迁徙和混合历史。这是目前国内开展的东亚地区最大规模的考古基因组学研究，此次所报道的东亚地区古人基因组样本量是以往国内研究机构所发表的样本量总和的两倍，改变了东亚地区尤其是中国境内考古基因组学研究长期滞后的局面。 该研究是由王传超教授团队与哈佛医学院（David Reich教授）、德国马普人类历史科学研究所（Johannes Krause教授）、复旦大学现代人类学教育部重点实验室（李辉教授和金力院士）、维也纳大学进化人类学系（Ron Pinhasi副教授）、南洋理工大学人文学院（Hui-Yuan Yeh助理教授）、俄罗斯远东联邦大学科学博物馆（Alexander N Popov研究员）、西安交通大学（张虎勤教授）、蒙古国国家博物馆研究中心、乌兰巴托国立大学考古系、华盛顿大学人类学系、台湾成功大学考古所、加州大学人类学系等全球43个单位的85位共同作者组成的国际合作团队联合完成的。厦门大学人类学研究所、厦门大学生命科学学院细胞应激生物学国家重点实验室为论文第一完成单位。厦门大学人类学研究所韦兰海副教授、胡荣助理教授、郭健新博士后、何光林博士后和杨晓敏硕士参与了研究工作。The deep population history of East Asia remains poorly understood due to a lack of ancient DNA data and sparse sampling of present-day people1,2. We report genome-wide data from 166 East Asians dating to 6000 BCE-1000 CE and 46 present-day groups. Hunter-gatherers from Japan, the Amur River Basin, and people of Neolithic and Iron Age Taiwan and the Tibetan plateau are linked by a deeply-splitting lineage likely reflecting a Late Pleistocene coastal migration. We follow Holocene expansions from four regions. First, hunter-gatherers of Mongolia and the Amur River Basin have ancestry shared by Mongolic and Tungusic language speakers but do not carry West Liao River farmer ancestry contradicting theories that their expansion spread these proto-languages. Second, Yellow River Basin farmers at ～3000 BCE likely spread Sino-Tibetan languages as their ancestry dispersed both to Tibet where it forms up ～84% to some groups and to the Central Plain where it contributed ～59-84% to Han Chinese. Third, people from Taiwan ～1300 BCE to 800 CE derived ～75% ancestry from a lineage also common in modern Austronesian, Tai-Kadai and Austroasiatic speakers likely deriving from Yangtze River Valley farmers; ancient Taiwan people also derived ～25% ancestry from a northern lineage related to but different from Yellow River farmers implying an additional north-to-south expansion. Fourth, Yamnaya Steppe pastoralist ancestry arrived in western Mongolia after ～3000 BCE but was displaced by previously established lineages even while it persisted in western China as expected if it spread the ancestor of Tocharian Indo-European languages. Two later gene flows affected western Mongolia: after ～2000 BCE migrants with Yamnaya and European farmer ancestry, and episodic impacts of later groups with ancestry from Turan.We thank David Anthony, Ofer Bar-Yosef, Katherine Brunson, Rowan Flad, Pavel Flegontov,Qiaomei Fu, Wolfgang Haak, Iosif Lazaridis, Mark Lipson, Iain Mathieson, Richard Meadow,Inigo Olalde, Nick Patterson, Pontus Skoglund, Dan Xu, and the four reviewers for valuable comments. We thank Naruya Saitou and the Asian DNA Repository Consortium for sharing genotype data from present-day Japanese groups. We thank Toyohiro Nishimoto and Takashi Fujisawa from the Rebun Town Board of Education for sharing the Funadomari Jomon samples, and Hideyo Tanaka and Watru Nagahara from the Archeological Center of Chiba City who are excavators of the Rokutsu Jomon site. The excavations at Boisman-2 site (Boisman culture), the Pospelovo-1 site (Yankovsky culture), and the Roshino-4 site (Heishui Mohe culture) were funded by the Far Eastern Federal University and the Institute of History,Archaeology and Ethnology Far Eastern Branch of the Russian Academy of Sciences; research on Pospelovo-1 is funded by RFBR project number 18-09-40101. C.C.W was funded by the Max Planck Society, the National Natural Science Foundation of China (NSFC 31801040), the Nanqiang Outstanding Young Talents Program of Xiamen University (X2123302), the Major project of National Social Science Foundation of China (20&ZD248), a European Research Council (ERC) grant to Dan Xu (ERC-2019-ADG-883700-TRAM) and Fundamental Research Funds for the Central Universities (ZK1144). O.B. and Y.B. were funded by Russian Scientific Foundation grant 17-14-01345. H.M. was supported by the grant JSPS 16H02527. M.R. and C.C.W received funding from the ERC under the European Union’s Horizon 2020 research and innovation program (grant No 646612) to M.R. The research of C.S. is supported 30 by the Calleva Foundation and the Human Origins Research Fund. H.L was funded NSFC (91731303, 31671297), B&R International Joint Laboratory of Eurasian Anthropology (18490750300). J.K. was funded by DFG grant KR 4015/1-1, the Baden Württemberg Foundation, and the Max Planck Institute. Accelerator Mass Spectrometry radiocarbon dating work was supported by the National Science Foundation (NSF) (BCS-1460369) to D.J.K. and B.J.C. D.R. was funded by NSF grant BCS-1032255, NIH (NIGMS) grant GM100233, the Paul M. Allen Frontiers Group, John Templeton Foundation grant 61220, a gift from Jean-Francois Clin, and the Howard Hughes Medical Institute. 该研究得到了国家自然科学基金“中国东南各族群的遗传混合”、国家社科基金重大项目“多学科视角下的南岛语族的起源和形成研究”、厦门大学南强青年拔尖人才支持计划A类、中央高校基本科研业务费等资助

Three-Phase-Based Approach to Develop a River Health Prediction and Early Warning System to Guide River Management

To effectively manage a river system, systematic tracking and diagnosing the change and risks of a river system are essentially required to efficiently conserve or restore its conditions. Hence, this study focuses on how to integrate current status assessment, trend prediction, and cause diagnosis in river health to guide early warning decision-making in river protection and management. This study has presented a three-phase approach by coupling spatial with nonspatial information in a highly systematic and reliable way, and an early warning system has been designed. In phase I, the current health status is assessed and nowcasted by using the order degree of each indicator. In phase II, health predictors, including the single perspective-based health index (HI) (e.g., water quality index (WQI) and index of biotic integrity (IBI)) and multi-perspective-based health index, have been forecasted under normal conditions or emerging conditions using predictive models. In phase III, key causal factors threatening the river health have been identified to enable early notification and to address unexpected events before occurrence. Although different modeling methods can be used in each phase to demonstrate this concept, we tested the model of partial least square regression (PLSR) associated with time series. Additionally, the three-phase approach has been integrated with geographic information system (GIS) and a decision support system (DSS) to develop a river health prediction and early warning system (RHP-EWS), an automatic prediction and decision-making tool. This tool was implemented to deal with the landing of typhoon “Maria” in 2018 into the Shanxi River watershed in China. Because of the timely responses and decisions, the drinking water supply was not influenced. However, the models should be extended to other river systems for testing and improvement at different temporal or spatial scales

Yields, Quality and Metal Accumulation of Chinese Cabbage Irrigated with Diary Effluent

Abstract: In order to investigate the short-term effects of wastewater (dairy effluent) and EM treated wastewater on cabbage quality (vitamin C, nitrate), yield, Nitrogen (N) and Phosphorous (P) uptakes and heavy metals (i.e., Hg, Pb and Cd) accumulation in Cabbage, field experiments were conducted with the following irrigation treatments: Clean Water (CW), Waste Water (WW), Reclaimed Water-EM treated wastewater (RW), Clear Water-wastewater rotation (C/W) and clear water-treated wastewater rotation (C/R). The results showed that: yield of cabbages, concentration of total N and P in cabbages could be improved in treatment irrigated with both untreated and EM treated dairy effluent, especially in treatments RW and C/R. Heavy metals in cabbages irrigated with/without dairy effluent showed non-significant difference. The highest nitrate was obtained with C/W treatment and the lowest was obtained with the RW treatment. With integrate comparative study of nutrition, nitrate and heavy metal, EM treated dairy effluent is more suitable to irrigate cabbage than raw dairy effluent. And the cabbages under RW and C/W treatment grew better than other treatments. It is suggested that the EM treated wastewater can be used as a safe alternative for irrigation of cabbages edible

Gas Chromatography/Mass Spectrometry-Based Metabolomic Profiling Reveals Alterations in Mouse Plasma and Liver in Response to Fava Beans.

Favism is a life-threatening hemolytic anemia resulting from the intake of fava beans by susceptible individuals with low erythrocytic glucose 6-phosphate dehydrogenase (G6PD) activity. However, little is known about the metabolomic changes in plasma and liver after the intake of fava beans in G6PD normal and deficient states. In this study, gas chromatography/mass spectrometry was used to analyze the plasma and liver metabolic alterations underlying the effects of fava beans in C3H- and G6PD-deficient (G6PDx) mice, and to find potential biomarkers and metabolic changes associated with favism. Our results showed that fava beans induced oxidative stress in both C3H and G6PDx mice. Significantly, metabolomic differences were observed in plasma and liver between the control and fava bean treated groups of both C3H and G6PDx mice. The levels of 7 and 21 metabolites in plasma showed significant differences between C3H-control (C3H-C)- and C3H fava beans-treated (C3H-FB) mice, and G6PDx-control (G6PDx-C)- and G6PDx fava beans-treated (G6PDx-FB) mice, respectively. Similarly, the levels of 7 and 25 metabolites in the liver showed significant differences between C3H and C3H-FB, and G6PDx and G6PDx-FB, respectively. The levels of oleic acid, linoleic acid, and creatinine were significantly increased in the plasma of both C3H-FB and G6PDx-FB mice. In the liver, more metabolic alterations were observed in G6PDx-FB mice than in C3H-FB mice, and were involved in a sugar, fatty acids, amino acids, cholesterol biosynthesis, the urea cycle, and the nucleotide metabolic pathway. These findings suggest that oleic acid, linoleic acid, and creatinine may be potential biomarkers of the response to fava beans in C3H and G6PDx mice and therefore that oleic acid and linoleic acid may be involved in oxidative stress induced by fava beans. This study demonstrates that G6PD activity in mice can affect their metabolic pathways in response to fava beans

Distribution Pattern and Structure of Vascular Plant Communities in Riparian Areas and Their Response to Soil Factors: A Case Study of Baoan Lake, Hubei Province, China

The vascular plant community in a riparian area is the main substrate and vehicle of many ecological functions for the lakeshores of grass-type shallow lakes. However, there is still a lack of knowledge regarding the responses of vascular plants to soil factors of the habitat in riparian areas, which restricts the ecological adaptation management for riparian vegetation. In this work, a typical grass-type shallow lake (Baoan Lake) in the Yangtze Basin in Central China was taken as the study area. We describe the plant species distribution and community structure in riparian areas under two habitat types (lake and tributary) and their responses to soil factors. The results showed that (1) the soil chemical factors have a significant effect on the distribution and community structure of vascular plants, even though there was a significant interaction among three group factors of soil habitats; (2) compared with other factors, the total nitrogen (TN) and available phosphorus (AP) have the most significant correlations with the distribution of vascular plants; (3) the rate of soil nutrient sorption determines the distribution of vascular species, closely related to the biological characteristics of plants and the microbial enzymatic activity in soil; and (4) vascular plant diversity and the proportion of perennial plants were generally higher in the lakeshore areas than in the tributaries and showed a low-high-low “hump-shaped” species richness and diversity distribution. The Shannon-Wiener index value increased with the increasing soil-available phosphorus in the surface soil layer. Therefore, this study advanced our knowledge of the species distribution and diversity patterns of lakeshores and tributaries, providing scientific and theoretical guidance for the biodiversity conservation and sustainable ecosystem management of grass-type shallow lakes

Distribution Pattern and Structure of Vascular Plant Communities in Riparian Areas and Their Response to Soil Factors: A Case Study of Baoan Lake, Hubei Province, China

The vascular plant community in a riparian area is the main substrate and vehicle of many ecological functions for the lakeshores of grass-type shallow lakes. However, there is still a lack of knowledge regarding the responses of vascular plants to soil factors of the habitat in riparian areas, which restricts the ecological adaptation management for riparian vegetation. In this work, a typical grass-type shallow lake (Baoan Lake) in the Yangtze Basin in Central China was taken as the study area. We describe the plant species distribution and community structure in riparian areas under two habitat types (lake and tributary) and their responses to soil factors. The results showed that (1) the soil chemical factors have a significant effect on the distribution and community structure of vascular plants, even though there was a significant interaction among three group factors of soil habitats; (2) compared with other factors, the total nitrogen (TN) and available phosphorus (AP) have the most significant correlations with the distribution of vascular plants; (3) the rate of soil nutrient sorption determines the distribution of vascular species, closely related to the biological characteristics of plants and the microbial enzymatic activity in soil; and (4) vascular plant diversity and the proportion of perennial plants were generally higher in the lakeshore areas than in the tributaries and showed a low-high-low “hump-shaped” species richness and diversity distribution. The Shannon-Wiener index value increased with the increasing soil-available phosphorus in the surface soil layer. Therefore, this study advanced our knowledge of the species distribution and diversity patterns of lakeshores and tributaries, providing scientific and theoretical guidance for the biodiversity conservation and sustainable ecosystem management of grass-type shallow lakes

Spatiotemporal variations and gradient functions of water turbidity in shallow lakes

Shallow lakes are prone to water quality deterioration and are difficult to manage. Turbidity is a physical parameter commonly used to estimate water quality. Revealing the spatiotemporal variations in turbidity can help determine the risk areas of water turbidity to achieve efficient protection and management of water resources. Here, we conducted continuous field observations and monitoring of turbidity in Baoan Lake (114°39′–114°46′E, 30°12′–30°18′N), a shallow lake (average depth: 2.27 m) in southeastern Hubei Province, China, from July 2019 to May 2022, to perform gradient analysis and determine risk levels of water turbidity. Results showed that the average turbidity of the Baoan Lake varied within the range of 9.0–48.8 NTU. Water turbidity fluctuated, reaching peaks in summer or autumn, and troughs in winter. The overall variation of water turbidity in spring and summer ranged within 15 NTU, while in autumn and winter it was over 29 NTU. The turbidity of Zhuti and Qiaodun Lakes (ZL and QL, respectively) was often higher than that of Xiaosihai and Biandantang Lakes (XL and BL, respectively), showing a turbidity decrease from southeast to northwest, especially in winter. A gradient function describing the spatial variation in turbidity was summarized. The parameters of the function had implicit meanings for spatial variations in turbidity. Parameter a influenced the form of the fitting curve. Parameters b and c reflected the range of turbidity values. The two points of the second derivative of the function were considered to indicate the radius of the risk area in a concentric manner. The methodology proposed to identify the risk levels of water turbidity entails the calculation of the risk values for different seasons. Thus, this study provides a new tool for quantifying spatial gradient variation of water turbidity and a new method for determining high-risk areas and risk levels of water turbidity

Temporal Variation and Spatial Distribution in the Water Environment Helps Explain Seasonal Dynamics of Zooplankton in River-Type Reservoir

Integrated assessment of the water environment has become widespread in many rivers, lakes, and reservoirs; however, aquatic organisms in freshwater are often overlooked in this process. Zooplankton, as primary consumers, are sensitive and responsive to changes in the water environment. Water and zooplankton samples were collected on-site at Shanxi Reservoir quarterly to determine 12 water environmental indicators and to quantify the abundance of zooplankton of Cladocera, Copepoda and Rotifera by using the ZooScan zooplankton image-scanning analysis system, combined with OLYMPUS BX51 using machine learning recognition classification. The aim was to explore the relationship between water environmental factors and zooplankton through their spatial and temporal heterogeneity. Through principal component analysis, redundancy analysis and cluster analysis, variations in the factors driving zooplankton population growth in different seasons could be identified. At the same time, different taxa of zooplankton can form clusters with related water environmental factors during the abundant water period in summer and the dry water period in winter. Based on long-term monitoring, zooplankton can be used as a comprehensive indicator for water environment and water ecological health evaluation, as well as providing scientific support for regional water resources deployment and management

Temporal Variation and Spatial Distribution in the Water Environment Helps Explain Seasonal Dynamics of Zooplankton in River-Type Reservoir

Integrated assessment of the water environment has become widespread in many rivers, lakes, and reservoirs; however, aquatic organisms in freshwater are often overlooked in this process. Zooplankton, as primary consumers, are sensitive and responsive to changes in the water environment. Water and zooplankton samples were collected on-site at Shanxi Reservoir quarterly to determine 12 water environmental indicators and to quantify the abundance of zooplankton of Cladocera, Copepoda and Rotifera by using the ZooScan zooplankton image-scanning analysis system, combined with OLYMPUS BX51 using machine learning recognition classification. The aim was to explore the relationship between water environmental factors and zooplankton through their spatial and temporal heterogeneity. Through principal component analysis, redundancy analysis and cluster analysis, variations in the factors driving zooplankton population growth in different seasons could be identified. At the same time, different taxa of zooplankton can form clusters with related water environmental factors during the abundant water period in summer and the dry water period in winter. Based on long-term monitoring, zooplankton can be used as a comprehensive indicator for water environment and water ecological health evaluation, as well as providing scientific support for regional water resources deployment and management