Meanwhile, the Chinese Ming dynasty fell to the rebellion of Li Zicheng (1606–1645) in 1644, yet his short-lived Shun dynasty was crushed by the Manchu invasion and the Han Chinese general Wu Sangui (1612–1678). China Daily states that when the following Qing dynasty replaced the Ming dynasty, it merely "strengthened administration of Tibet." However, Kolmaš states that the Dalai Lama was very observant of what was going on in China and accepted a Manchu invitation in 1640 to send envoys to their capital at Mukden in 1642, before the Ming collapsed. Dawa Norbu, William Rockhill, and George N. Patterson write that when the Shunzhi Emperor (r. 1644–1661) of the subsequent Qing dynasty invited the fifth Dalai Lama Lozang Gyatso to Beijing in 1652, Shunzhi treated the Dalai Lama as an independent sovereign of Tibet. Patterson writes that this was an effort of Shunzhi to secure an alliance with Tibet that would ultimately lead to the establishment of Manchu rule over Mongolia. In this meeting with the Qing emperor, Goldstein asserts that the Dalai Lama was not someone to be trifled with due to his alliance with Mongol tribes, some of which were declared enemies of the Qing. Van Praag states that Tibet and the Dalai Lama's power was recognized by the "Manchu Emperor, the Mongolian Khans and Princes, and the rulers of Ladakh, Nepal, India, Bhutan, and Sikkim."

Who did the the Chinese Ming dynasty fall to?