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Chapter 1 Population Historyof the Giant Panda The giant panda (Ailuropoda melanoleuca) has an evolutionary history of approximately 8 million years£¬ and its direct ancestors can be traced back to the primal panda (Ailurarctos lufengensis and Ailurarctos yuanmouensis) in the late Miocene (Qiu and Qi£¬ 1989). In the late Pliocene to early Pleistocene£¬ the pygmy panda (Ailuropoda microta) appeared and then evolved into the baconi panda (Ailuropoda melanoleuca baconi) during the middle-late Pleistocene (Wang£¬ 1974). The extant species (or subspecies) of the giant panda (A. melanoleuca) is believed to have arisen in the Holocene. From pygmy panda to baconi panda and finally to extant panda£¬ their body sizes have undergone changes from small to large and then to small again. A traditional view based on these changes holds that the giant panda is on the way to an ¡°evolutionary dead end¡± (Pei£¬ 1965£¬ 1974). However£¬ the evolutionary history of giant pandas£¬ especially their population fluctuations and divergences and the underlying mechanisms have long remained mysterious. Scientists try to infer their population fluctuations using the number and distribution of fossils excavated; however£¬ it is difficult to reveal the true popu lation dynamics due to the limited fossil numbers discovered. With the development of genomics£¬ scientists now have the opportunity to accurately uncover patterns of population fluctuations and divergences with extensive genomic information passed down from their ancestors. Based upon the giant panda whole genome sequencing project in which we were involved (Li et al.£¬ 2010)£¬ we conducted the population genomics study of giant pandas for the first time. In this study£¬ we unveiled their effective population size (Ne) changes and population divergence events from the primal£¬ pygmy£¬ baconi pandas to the extant panda. Furthermore£¬ we clarified that the Quaternary climate fluctuations were primary drivers of their population fluctuations and divergences£¬ while human activities since the Last Glacial Maximum and Holocene were responsible for severe population collapses and endangerment of the species. These results indicated that the current endangered status of giant pandas was mainly caused by the paleoclimatic changes and recent anthropogenic activities (Zhao et al.£¬ 2013; Wu et al.£¬ 2014).