Evolutionary origin of a tetraploid Allium species on the Qinghai-Tibet Plateau

Minjie Li, Zeyu Zheng, Juncheng Liu, Yongzhi Yang, Guangpeng Ren, Dafu Ru, Shangzhe Zhang, Xin Du, Tao Ma, Richard Milne, Jianquan Liu*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

12 Citations (Scopus)


Extinct taxa may be detectable if they were ancestors to extant hybrid species, which retain their genetic signature. In this study, we combined phylogenomics, population genetics and fluorescence in situ hybridization (GISH and FISH) analyses to trace the origin of the alpine tetraploid Allium tetraploideum (2n = 4x = 32), one of the five known members in the subgenus Cyathophora. We found that A. tetraploideum was an obvious allotetrapoploid derived from ancestors including at least two closely related diploid species, A. farreri and A. cyathophorum, from which it differs by multiple ecological and genomic attributes. However, these two species cannot account for the full genome of A. tetraploideum, indicating that at least one extinct diploid is also involved in its ancestry. Furthermore, A. tetraploideum appears to have arisen via homoploid hybrid speciation (HHS) from two extinct allotetraploid parents, which derived in turn from the aforementioned diploids. Other modes of origin were possible, but all were even more complex and involved additional extinct ancestors. Our study together highlights how some polyploid species might have very complex origins, involving both HHS and polyploid speciation and also extinct ancestors.

Original languageEnglish
Pages (from-to)5780-5795
Number of pages16
JournalMolecular Ecology
Issue number22
Early online date23 Sept 2021
Publication statusPublished - 19 Nov 2021


  • Allotetraploid
  • Extinction
  • Homoploid hybrid speciation
  • In situ hybridization
  • Phylogenomics
  • Population genetics


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