J Syst Evol

• Research Articles •    

Phylogeography and introgression between Pinus kesiya and Pinus yunnanensis in Southeast Asia

Jie Gao1,2*, Kyle W. Tomlinson2,3, Wei Zhao4, Baosheng Wang2,5, Ralph Sedricke Lapuz2,3, Jing‐Xin Liu1, Bonifacio O. Pasion2,3, Bach T. Hai6, Souvick Chanthayod7, Jin Chen1, and Xiao‐Ru Wang4   

  1. 1 CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, Yunnan, China
    2 Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun 666303, Yunnan, China
    3 Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, Yunnan, China
    4 Department of Ecology and Environmental Science, UPSC, Umeå University, Umeå 90187, Sweden
    5 Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
    6 Cat Tien National Park, Vietnam Administration of Forestry, Ho Chi Minh 760000, Viet Nam
    7 Department of Agriculture and Forestry, Oudomxay Province 04000, The Lao People's Democratic Republic

    *Author for correspondence. E‐mail: gaojie@xtbg.org.cn
  • Received:2022-08-23 Accepted:2023-01-11 Online:2023-01-31


Southeast Asia (SEA) has seen strong climatic oscillations and fluctuations in sea levels during the Quaternary. The impact of past climate changes on the evolution and distribution of local flora in SEA is still poorly understood. Here we aim to infer how the Quaternary climate change affects the evolutionary process and range shifts in two pine species. We investigated the population genetic structure and diversity using cytoplasmic DNA markers, and performed ecological niche modeling to reconstruct the species past distribution and to project range shift under future climates. We found substantial gene flow across the continuous distribution of the subtropical Pinus yunnanensis. In contrast, the tropical Pinus kesiya showed a strong population structure in accordance with its disjunct distribution across montane islands in Indochina and the Philippines. A broad hybrid zone of the two species occurs in southern Yunnan. Asymmetric introgression from the two species was detected in this zone with dominant mitochondrial gene flow from P. yunnanensis and chloroplast gene flow from P. kesiya. The observed population structure suggests a typical postglaciation expansion in P. yunnanensis, and a glacial expansion and interglacial contraction in P. kesiya. Ecological niche modeling supports the inferred demographic history and predicts a decrease in range size for P. kesiya under future climates. Our results suggest that tropical pine species in SEA have undergone evolutionary trajectories different from high latitude species related to their Quaternary climate histories. We also illustrate the need for urgent conservation actions in this fragmented landscape.