Format: ORAL

Hong-Fan Chen1,2,3, Ryan Andrew Folk4, Ya-Li Wang1,2,3, Wen-Jing Wang1,3, Guo-Jun Shao1, Mei-Yuan Huang1, Xiang-Qin Yu5, Qing-Jun Li1,3, Li Li*,1,3, Jian-Li Zhao*,1,3

1 Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, 650504, Yunnan, China; 2 Institute of International Rivers and Eco-security, Yunnan University, Kunming, 650504, Yunnan, China; 3 Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Kunming, 650504, Yunnan, China; 4 Department of Biological Sciences, Mississippi State University, Mississippi State, 39762, Mississippi, USA; 5 CAS Key Laboratory for Plant Diversity and Biogeography in East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.

How species boundaries are maintained among sympatric closely related species experiencing gene flow is a puzzling question in evolutionary biology. Introgression is commonly reported, but the dynamics of, and gene function in introgression have rarely been explored to probe why frequent introgression does not necessarily destroy species boundaries in sympatry. Here we use seventeen morphological traits and whole-genome resequencing data to investigate introgression in five closely related species in Roscoea that co-occur in a sky island distributional pattern with limited seed and pollen dispersal. Introgression is the cause of phylogenomic discordance between the nuclear and chloroplast genomes. Introgression is largely asymmetrical in intensity and gene function. Introgressive intensity changed over time with a peak at approximately 2-3 Mya. Inferred functions of introgressed genes were related to reproductive processes in only one species pair. Our results suggested that closely related species with incomplete assortment of alleles could coexist despite theoretical predictions, reflecting the semipermeable nature of species boundaries as reproductive isolation is accrued, a key conceptual framework for understanding the conflict between introgression and species fate. Our finding offers novel insights into how related sympatric species boundaries can be upheld in the face of frequent gene flow.