Phylogenomic Analyses Reveal an Allopolyploid Origin of Core Didymocarpinae (Gesneriaceae) Followed by Rapid Radiation

Author:

Yang Lihua1,Harris A J1,Wen Fang2,Li Zheng3,Feng Chao1,Kong Hanghui1ORCID,Kang Ming1ORCID

Affiliation:

1. Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou 510650 , China

2. Guangxi Institute of Botany, Guangxi Zhang Autonomous Region and the Chinese Academy of Sciences , 541006 Guilin , China

3. Department of Ecology and Evolutionary Biology, University of Arizona , 1041 E. Lowell St., Tucson, AZ 85721 , USA

Abstract

Abstract Allopolyploid plants have long been regarded as possessing genetic advantages under certain circumstances due to the combined effects of their hybrid origins and duplicated genomes. However, the evolutionary consequences of allopolyploidy in lineage diversification remain to be fully understood. Here, we investigate the evolutionary consequences of allopolyploidy using 138 transcriptomic sequences of Gesneriaceae, including 124 newly sequenced, focusing particularly on the largest subtribe Didymocarpinae. We estimated the phylogeny of Gesneriaceae using concatenated and coalescent-based methods based on five different nuclear matrices and 27 plastid genes, focusing on relationships among major clades. To better understand the evolutionary affinities in this family, we applied a range of approaches to characterize the extent and cause of phylogenetic incongruence. We found that extensive conflicts between nuclear and chloroplast genomes and among nuclear genes were caused by both incomplete lineage sorting (ILS) and reticulation, and we found evidence of widespread ancient hybridization and introgression. Using the most highly supported phylogenomic framework, we revealed multiple bursts of gene duplication throughout the evolutionary history of Gesneriaceae. By incorporating molecular dating and analyses of diversification dynamics, our study shows that an ancient allopolyploidization event occurred around the Oligocene–Miocene boundary, which may have driven the rapid radiation of core Didymocarpinae.

Funder

Chinese Academy of Sciences

National Natural Science Foundation of China

South China Botanical Garden

Publisher

Oxford University Press (OUP)

Subject

Genetics,Ecology, Evolution, Behavior and Systematics

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