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

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.

Automated summary

Through studying the population genetic structure and diversity of two pine species, it is found that tropical pine species and subtropical pine species have different evolutionary processes and distribution ranges under the influence of past climate change in SEA. The subtropical Pinus yunnanensis shows significant gene flow, while the tropical Pinus kesiya exhibits strong population structure. There is a wide hybrid zone between the two species in southern Yunnan. Predictions indicate that the range of Pinus kesiya will decrease under future climate change. This study highlights the different evolutionary trajectories of pine species in SEA compared to high latitude species, emphasizing the urgent need for conservation efforts in this fragmented landscape.