Exploring phylogenetic backbone and deep reticulation of a non-model plant lineage using multi-source genomic data
ID: 613 / 374
Proposed Symposium Title: Exploring phylogenetic backbone and deep reticulation of a non-model plant lineage using multi-source genomic data
Chao Xu1,2, Ze-Tao Jin1,2,3, Hui Wang1,2,4, Si-Yu Xie1,2,5, Xiao-Hua Lin1,2,5, Richard G.J. Hodel6, Yu Zhang1,2,5, Dai-Kun Ma1,2,7, Bing Liu1,2, Guang-Ning Liu2, Shui-Hu Jin4, Liang Zhao5, Jun Wu3, Chen Ren8, De-Yuan Hong1,2, Bin-Bin Liu1,2
Affiliations: 1 State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China 2 China National Botanical Garden, Beijing 100093, China 3 State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China 4 College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China 5 College of Life Sciences & Herbarium of Northwest A&F University, Northwest A&F University, Yangling 727100, China 6 Department of Botany, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, USA 7 University of Chinese Academy of Sciences, Beijing 100049, China 8 Key Laboratory of Plant Resources Conservation and Sustainable Utilization & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
Phylogenetic networks, rather than purely bifurcating trees, more accurately depict the intricate evolutionary dynamics of most lineages, especially those characterized by extensive hybridization and allopolyploidization events. However, the challenges of achieving complete taxon sampling, and limited financial resources for studying non-model plant lineages, have hindered comprehensive and robust estimation of phylogenetic backbones with guidance from networks. The bellflower tribe, Campanuleae, characterized by a reticulate evolutionary history, serves as an ideal model to investigate how to diagnose nested ancient reticulation events. Here, by integrating multiple genomic data sources and a range of phylogenetic inference methods, we produced a robust phylogenetic backbone for the tribe Campanuleae. Our investigation of reticulate evolution indicates that hybridization and allopolyploidization were instrumental in shaping the diversity of the bellflower tribe, particularly during the initial diversification of the subtribe Phytematinae. Additionally, we ascertained that conflicting topologies resulting from distinct genomic datasets and inference methodologies significantly impact downstream estimates of divergence dating, ancestral area construction, and diversification rates. This study offers a universally relevant framework for deciphering how to use network-based phylogenetic structures using various genomic sources and inference methods.