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.

An extinct vertebrate preserved by its living hybridogenetic descendant

“…allopolyploidisation 29 , 30 ). Unknown lineages underlie the genetic makeup of some polyploid plants 31 and fishes 32 . Such taxa may be more frequent than imagined in vertebrates, especially in amphibians and fishes where these reproductive modes have been well-documented 9 , 33 .…”

Genomic insight into “sky island” species diversification in a mountainous biodiversity hotspot

“…Their isolated origins and distributions in the sky islands could have evolved in a similar manner to E. baimashanicum with hybrid origin, as discussed above. The polyploid species replaced the sympatric progenitors after the origin because of increased colonization abilities (Otto et al, ; Luo et al, ). Therefore, geographic isolation, hybrid speciation, and polyploidization might have together contributed to the fast species diversification of plants in the sky islands.…”

The origin of allotetraploid Lepisorus inaequibasis (Polypodiaceae) and paternal bias in its morphology and abiotic niche

“…Thus, single‐ or low‐copy nuclear markers and chloroplast DNA are used in molecular phylogenetics to detect allopolyploidization events and determine the progenitors of polyploids (Sang, ; Schuettpelz & al., ; Rothfels & al., ). Recent biotic niche studies found that most polyploids inhabited a geographic range between that of the progenitors and had a high degree of niche overlap with their progenitors (Marchant & al., ; Spoelhof & al., ), but significant ecological divergence between allotetraploids and their putative progenitors was detected in other studies (Wu & al., ; Luo & al., ).…”