The origin of cultivated tree peonies, known as the ‘king of flowers' in China for more than 1000 years, has attracted considerable interest, but remained unsolved. Here, we conducted phylogenetic analyses of explicitly sampled traditional cultivars of tree peonies and all wild species from the shrubby section Moutan of the genus Paeonia based on sequences of 14 fast-evolved chloroplast regions and 25 presumably single-copy nuclear markers identified from RNA-seq data. The phylogeny of the wild species inferred from the nuclear markers was fully resolved and largely congruent with morphology and classification. The incongruence between the nuclear and chloroplast trees suggested that there had been gene flow between the wild species. The comparison of nuclear and chloroplast phylogenies including cultivars showed that the cultivated tree peonies originated from homoploid hybridization among five wild species. Since the origin, thousands of cultivated varieties have spread worldwide, whereas four parental species are currently endangered or on the verge of extinction. The documentation of extensive homoploid hybridization involved in tree peony domestication provides new insights into the mechanisms underlying the origins of garden ornamentals and the way of preserving natural genetic resources through domestication.

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In this paper we argue for the specific status of Paeonia suffruticosa Andrews, for the rationality of P. suffruticosa ssp. yinpingmudan D. Y. Hong, K. Y. Pan & Z. W. Xie and its wildness, and for the treatment of P. suffruticosa ssp. atava (Brühl) S. G. Haw & Lauener as a subspecies of P. rockii, P. rockii ssp. atava (Brühl) D. Y. Hong & K. Y. Pan. P. jishanensis T. Hong & W. Z. Zhao is justified as a legitimate name, while P. spontanea (Rehder) T. Hong & W. Z. Zhao is recognized as a superfluous name. Halda's four combinations and two new hybrid names in sect. Moutan DC. were treated as synonymy. As a result, one new combination is made and five new synonyms are proposed here in this paper.

The majority of tetraploid peonies are allopolyploids derived from crosses between phylogenetically distinct diploid lineages. Tetraploid Paeonia obovata was previously considered to be an autopolyploid because it is morphologically indistinguishable from the diploid of the same species. The presence of the Adh2 gene in tetraploid P. obovata but the inability to amplify the Adh2 gene from Chinese diploids of P. obovata , however, suggests that the tetraploid was not an autotetraploid derivative of the geographically adjacent diploid populations in China. The Adh gene phylogenies rather suggest that the tetraploid originated from crosses between two geographical races of diploid P. obovata distributed in China and Japan. The intermediate status of tetraploid P. obovata between auto-and allopolyploidy highlights the need for population genetic analyses of polyploid origins along the continuous range of genomic divergence.Here we present a model that describes the probabilities of polyploid formation and establishment as a function of genomic divergence between diploid progenitors. The probability of polyploid formation ( P f ) is obtained from the multiplication of the probability of production of unreduced gametes ( P g ) and the probability of 'hybridization' ( P h ). P f stays relatively stable when the genomic divergence is low, and then decreases progressively rapidly with the increase of genomic divergence between diploid progenitors. The probability of polyploid establishment ( P e ), which depends on the rate of appearance of stable beneficial gene combinations and the rate of fertility restoration, is positively correlated with the genomic divergence of diploid parents. Multiplication of P f and P e gives an overall probability of polyploid origins ( P o ) that varies continuously along the genomic divergence between diploid progenitors.