title: Chasing ghosts: allopolyploid origin of Oxyria sinensis (Polygonaceae) from its only diploid congener and an unknown ancestor.
abstract: Reconstructing the origin of a polyploid species is particularly challenging when an ancestor has become extinct. Under such circumstances, the extinct donor of a genome found in the polyploid may be treated as a 'ghost' species in that its prior existence is recognized through the presence of its genome in the polyploid. In this study, we aimed to determine the polyploid origin of Oxyria sinensis (2n = 40) for which only one congeneric species is known, that is diploid O. digyna (2n = 14). Genomic in situ hybridization (GISH), transcriptome, phylogenetic and demographic analyses, and ecological niche modelling were conducted for this purpose. GISH revealed that O. sinensis comprised 14 chromosomes from O. digyna and 26 chromosomes from an unknown ancestor. Transcriptome analysis indicated that following divergence from O. digyna, involving genome duplication around 12 million years ago (Ma), a second genome duplication occurred approximately 6 Ma to give rise to O. sinensis. Oxyria sinensis was shown to contain homologous gene sequences divergent from those present in O. digyna in addition to a set that clustered with those in O. digyna. Coalescent simulations indicated that O. sinensis expanded its distribution approximately 6-7 Ma, possibly following the second polyploidization event, whereas O. digyna expanded its range much later. It was also indicated that the distributions of both species contracted and re-expanded during the Pleistocene climatic oscillations. Ecological niche modelling similarly suggested that both species experienced changes in their distributional ranges in response to Quaternary climatic changes. The extinction of the unknown 'ghost' tetraploid species implicated in the origin of O. sinensis could have resulted from superior adaptation of O. sinensis to repeated climatic changes in the region where it now occurs.
authors.affiliation: MOE Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Luo
authors.affiliation: MOE Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu, China.|State Key Laboratory of Grassland Agro-Ecosystem, College of Life Science, Lanzhou University, Lanzhou, China.
authors.forename: Quanjun
authors.identifier: http://orcid.org/0000-0001-6922-2144
authors.initials: Q
authors.lastname: Hu
authors.affiliation: MOE Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu, China.
authors.forename: Pingping
authors.initials: P
authors.lastname: Zhou
authors.affiliation: MOE Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu, China.
authors.forename: Dan
authors.initials: D
authors.lastname: Zhang
authors.affiliation: MOE Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu, China.|Research Center for Medicine and Biology, Zunyi Medical University, Zunyi, China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Wang
authors.affiliation: School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Abbott
authors.affiliation: MOE Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu, China.|State Key Laboratory of Grassland Agro-Ecosystem, College of Life Science, Lanzhou University, Lanzhou, China.
authors.forename: Jianquan
authors.identifier: http://orcid.org/0000-0003-4277-9772
authors.initials: J
authors.lastname: Liu
mesh_terms: D005075:Biological Evolution; D004171:Diploidy; D017753:Ecosystem; D018745:Genome, Plant; D017403:In Situ Hybridization; D010802:Phylogeny; D019664:Polygonaceae / Q000235:genetics*; D011123:Polyploidy; D059467:Transcriptome
keywords: 
  Oxyria
  ; GISH; allopolyploid speciation; demographic history; ghost species; transcriptome