Using phylogenomics to untangle the taxonomic incongruence of yellow‐flowered Camellia species (Theaceae) in China

Abstract All yellow Camellia plants in China are threatened, but their classification is contentious. Here, we performed a phylogenetic reconstruction based on nuclear double‐digest restriction site‐associated DNA sequencing (ddRAD), transcriptomes, nuclear ribosomal internal transcribed spacer (nrITS), and the small single‐copy region of the chloroplast genome, in combination with morphological evidence to help resolve taxonomic ambiguity of those rare and threatened species. Conflicting relationships were derived from nuclear and chloroplast sequences. The strong hybridization/introgression signal detected suggests reticulate evolution mainly caused this discordance pattern. The nuclear‐ddRAD and RNA‐seq phylogenies fit better to the yellow camellias' morphology, providing a clear resolution for inferring their relationships in China. Based on present phylogenetic analyses and morphological characters, we propose these taxonomic suggestions: (i) Camellia petelotii and Camellia nitidissima are distinct species; (ii) Camellia ptilosperma , Camellia longruiensis , Camellia longgangensis , and C. longgangensis var. grandis are conspecific with Camellia flavida ; (iii) Camellia multipetala and C. longgangensis var. patens are synonyms of Camellia quinqueloculosa , and C. quinqueloculosa should be recognized as an independent species; (iv) Camellia wumingensis should be formally recognized as an independent species; (v) Camellia longzhouensis is a synonym of Camellia chrysanthoides ; (vi) Camellia xiashiensis and Camellia parvipetala should be treated as synonyms of Camellia micrantha ; (vii) Camellia achrysantha is a good species; (viii) Camellia tunghinensis is an independent species; (ix) species status of Camellia huana is well‐supported; and (x) Camellia pingguoensis var. terminals should be correctly identified to species level as Camellia terminalis . These results provide the basis for the recognition 20 yellow Camellia species in China.