植物的物种形成、生物多样性对气候变化的生态响应和进化适应。主要应用生物信息学、现代群体遗传学（Population Genetics）和系统发育（Phylogenetics）的理论与方法对自然植物类群开展组学水平的大数据（Big Data）研究，分析遗传变异的结构和地理分布模式（Pattern），挖掘变异模式产生的遗传机制（Mechanism），模拟和揭示植物的物种形成过程（Process），探讨古气候变化/高山隆升对植物多样性的影响（Effects）。 

第一作者论文 

1) Sun Yongshuai, Li, L., Li, L., Zou, J.B., Liu, J.* Distributional dynamics and interspecific gene flow in Picea likiangensis and P. wilsonii triggered by climate change on the Qinghai-Tibet Plateau. Journal of Biogeography. 2015, 42: 475-484.  

2) Sun, Yongshuai, Abbott, R.J., Li, L., Li, L., Zou, J., Liu, J.* Evolutionary history of Purple cone spruce (Picea purpurea) in the Qinghai–Tibet Plateau: homoploid hybrid origin and Pleistocene expansion. Molecular Ecology. 2014. 23: 343–359.  

3)Wan, D#., Sun, Yongshuai#, Zhang, X., Bai, X., Wang, J., Wang, A.*, Milne, R. Multiple ITS Copies Reveal Extensive Hybridization within Rheum (Polygonaceae), a Genus That Has Undergone Rapid Radiation. PLoS One. 2014, 9: e89769. (co-first author)  

4)Sun, Yongshuai, Wang, A., Wan, D., Wang, Q., Liu, J.* Rapid radiation of Rheum (Polygonaceae) and parallel evolution of morphological traits. Molecular Phylogenetics and Evolution. 2012, 63: 150–158.  

5)Sun, Yongshuai, Ikeda, H., Wang, Y., Liu, J.* Phylogeography of Potentilla fruticosa (Rosaceae) in the Qinghai–Tibetan Plateau revisited: A reappraisal and new insights. Plant Ecology & Diversity. 2010, 3: 249–257.  

通讯作者论文 

1)Ru, D., Mao, K., Zhang, L., Wang, X., Lu, Z., Sun, Yongshuai*. Genomic evidence for polyphyletic origins and inter-lineage gene flow within complex taxa: a case study of Picea brachytyla in the Qinghai-Tibet Plateau. Molecular Ecology. 2016, 25: 2373–2386.  

2)Bi, H., Yue, W., Wang, X., Zou, J., Li, L., Liu, J., Sun, Yongshuai*. Late Pleistocene climate change promoted divergence between Picea asperata and P. crassifolia on the Qinghai-Tibet Plateau through recent bottlenecks. Ecology and Evolution. 2016, 6: 4435–4444.  

3)Wang, X., Li, Y., Liang, Q., Zhang, L., Wang, Q., Hu, H., Sun, Yongshuai*. Contrasting responses to Pleistocene climate changes: A case study of two sister species Allium cyathophorum and A. spicata (Amaryllidaceae) distributed in the eastern and western Qinghai-Tibet Plateau. Ecology and Evolution. 2015, 5: 1513–1524.  

4)Tian, B., Ji, M., Zhang, Y., Fu, Y., Yu, D., Sun, Yongshuai*. The Advance on Homoploid Hybrid Speciation. Journal of Yunnan Agricultural University. 2014, 29: 586-590.  

其它参与发表论文 

1)China Plant BOL Group, Li, D., Gao, L., Li, H., Wang, H., Ge, X., Liu, J., Chen, Z., Zhou, S., Chen, S., Yang, J., Fu, C., Zeng, C., Yan, H., Zhu, Y., Sun, Yongshuai, Chen, S., Zhao, L., Wang, K., Yang, T., Duan, G. Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. Proceedings of the National Academy of Sciences USA. 2011, 108: 19641–19646. 

2)Li, L., Abbott, R. J., Liu, B., Sun, Yongshuai, Li, L., Zou, J., Wang, X., Miehe, G., Liu, J. Pliocene intraspecific divergence and Plio-Pleistocene range expansions within Picea likiangensis (Lijiang spruce), a dominant forest tree of the Qinghai-Tibet Plateau. Molecular Ecology. 2013, 22: 5237–5255.  

3)Wu, L., Cui, X., Milne, R.I., Sun, Yongshuai, Liu, J. Multiple autopolyploidizations and range expansion of Allium przewalskianum Regel. (Alliaceae) in the Qinghai–Tibetan Plateau. Molecular Ecology. 2010, 19: 1691–1704.  

4)Zou, J., Sun, Yonghuai, Li, L., Wang, G., Yue, W., Lu, Z., Wang, Q., Liu, J. Population genetic evidence for speciation pattern and gene flow between Picea wilsonii, P. morrisonicola and P. neoveitchii. Annals of botany. 2013, 112: 1829–1844.  

5)Li, L., Sun, Yongshuai, Zou, J., Yue, W., Wang, X., Liu, J. Origin and speciation of Picea schrenkiana and P. smithiana in the Center Asian Highlands and Himalayas. Plant Molecular Biology Reporter. 2015, 33: 661-672.  

6)Liu, J., Sun, Yongshuai, Ge, X., Gao, L., Qiu, Y. Phylogeographic studies of plants in China: advances in the past and directions in the future. Journal of Systematics and Evolution. 2012, 50: 267–275.  

7)Wang, X., Shi, D., Wang, X., Wang, J., Sun, Yongshuai Liu, J. Evolutionary Migration of the Disjunct Salt Cress Eutrema salsugineum (= Thellungiella salsuginea, Brassicaceae) between Asia and North America. PLoS One. 2015, 10: e0124010.  

8)Hu, H., Al-Shehbaz, I.A., Sun, Yongshuai, Hao, G., Wang, Q. Liu, J. Species delimitation in Orychophragmus (Brassicaceae) based on chloroplast and nuclear DNA barcodes. Taxon. 2015, 64: 714-726.