By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilization’s decline, its people mixed with individuals in the southeast to form one of the two main ancestral populations of South Asia, whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around 4000 years ago, spread via Central Asia to form the other main ancestral population. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the distinctive features shared between Indo-Iranian and Balto-Slavic languages.

The deep population history of East Asia remains poorly understood due to a lack of ancient DNA data and sparse sampling of present-day people 1 , 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.

Based on the crop trial data during 1981-2009 at 57 agricultural experimental stations across the North Eastern China Plain (NECP) and the middle and lower reaches of Yangtze River (MLRYR), we investigated how major climate variables had changed and how the climate change had affected crop growth and yield in a setting in which agronomic management practices were taken based on actual weather. We found a significant warming trend during rice growing season, and a general decreasing trend in solar radiation (SRD) in the MLRYR during 1981-2009. Rice transplanting, heading, and maturity dates were generally advanced, but the heading and maturity dates of single rice in the MLRYR (YZ_SR) and NECP (NE_SR) were delayed. Climate warming had a negative impact on growth period lengths at about 80% of the investigated stations. Nevertheless, the actual growth period lengths of YZ_SR and NE_SR, as well as the actual length of reproductive growth period (RGP) of early rice in the MLRYR (YZ_ER), were generally prolonged due to adoption of cultivars with longer growth period to obtain higher yield. In contrast, the actual growth period length of late rice in the MLRYR (YZ_LR) was shortened by both climate warming and adoption of early mature cultivars to prevent cold damage and obtain higher yield. During 1981-2009, climate warming and decrease in SRD changed the yield of YZ_ER by -0.59 to 2.4%; climate warming during RGP increased the yield of YZ_LR by 8.38-9.56%; climate warming and decrease in SRD jointly reduced yield of YZ_SR by 7.14-9.68%; climate warming and increase in SRD jointly increased the yield of NE_SR by 1.01-3.29%. Our study suggests that rice production in China has been affected by climate change, yet at the same time changes in varieties continue to be the major factor driving yield and growing period trends.

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