J Syst Evol ›› 2022, Vol. 60 ›› Issue (1): 1-15.DOI: 10.1111/jse.12727

• Research Articles •     Next Articles

Plastid and nuclear phylogenomic incongruences and biogeographic implications of Magnolia s.l. (Magnoliaceae)

Shan-Shan Dong1†, Ya-Ling Wang2†, Nian-He Xia3, Yang Liu1, Min Liu4, Lian Lian5, Na Li1, Ling-Fei Li1, Xiao-An Lang1, Yi-Qing Gong1, Lu Chen1, Ernest Wu6, and Shou-Zhou Zhang1*   

  1. 1 Fairylake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen 518004, China
    2 Xi'an Botanical Garden, Xi'an 710061, China
    3 South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
    4 State Key Laboratory of Agricultural Genomics, BGI‐Shenzhen, Shenzhen 518083, China
    5 State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
    6 Department of Biology, University of British Columbia, Vancouver, BC V6T1Z4, Canada

    These authors contributed equally to this work.
    *Author for correspondence. E‐mail: shouzhouz@szbg.ac.cn
  • Received:2020-05-27 Accepted:2020-12-31 Online:2021-01-15 Published:2022-01-01

Abstract: Magnoliaceae, an assemblage of early diverged angiosperms, comprises two subfamilies, speciose Magnolioideae with approximately 300 species in varying numbers of genera and monogeneric Liriodendroideae with two species in Liriodendron L. This family occupies a pivotal phylogenetic position with important insights into the diversification of early angiosperms, and shows intercontinentally disjunct distribution patterns between eastern Asia and the Americas. Widespread morphological homogeneity and slow substitution rates in Magnolia L. s.l. resulted in poorly supported phylogenetic relationships based on morphology or molecular evidence, which hampers our understanding of the genus’ temporal and spacial evolution. Here, based on the newly generated genome skimming data for 48 Magnolia s.l. species, we produced robust Magnolia phylogenies using genome-wide markers from both plastid genomes and single nucleotide polymorphism data. Contrasting the plastid and nuclear phylogenies revealed extensive cytonuclear conflicts in both shallow and deep relationships. ABBA-BABA and PhyloNet analyses suggested hybridization occurred within sect. Yulania, and sect. Magnolia, which is in concordance with the ploidy level of the species in these two sections. Divergence time estimates and biogeographic reconstruction indicated that the timing of the three tropical Magnolia disjunctions coincided with the mid-Eocene cooling climate and/or late Eocene climate deterioration, and two temperate disjunctions occurred much later, possibly during the warm periods of the Miocene, hence supporting the boreotropical flora concept of Magnolia s.l.

Key words: biogeography, hybridization, Magnoliaceae, phylogenomics, plastid