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.

Genetic and ecophysiological evidence that hybridization facilitated lineage diversification in yellow Camellia (Theaceae) species: a case study of natural hybridization between C. micrantha and C. flavida

“…However, a recent phylogenomics study revealed a conflicting relationship for C. “ ptilosperma ”, with it found more closely related to C. micrantha in the chloroplast phylogeny, whereas it was genetically closer to C. flavida in the phylogenetic trees constructed with nuclear DNA [ 45 ]. In contrast to C. “ ptilosperma ”, individuals from NG-LR and other populations of C. flavida show consistent relationships in all phylogenies [ 45 ]. Further, earlier it was found that only one chloroplast haplotype was observed in the C. “ ptilosperma ” population and it is genetically distinct from all haplotypes of C. flavida [ 55 ].…”

“…The clean reads thus obtained were further assembled to stacks ( ustacks ), which were used to build a catalog ( cstacks ) for variant calling. In these two steps, two main parameters (M parameter of ustacks , and n parameter of cstacks ) were identical to those suggested previously for use in phylogenomics of yellow camellias [ 45 ], which were determined based on the protocol described by Rochette and Catchen [ 85 ]. All the samples in the population map were matched against the catalog using the sstacks .…”

“…For example, on a single mountain, C. flavida occupies its karst valley while C. perpatua is restricted to its upper slope near to peak. In addition, several interspecific hybridization events have been inferred among the yellow Camellia plants growing in China [ 45 ]. The high richness of species in close proximity to each other, their high degree of habitat specialization, in addition several suspected reticular events together make yellow camellias an excellent model for studying the potential role of hybridization in diversification events in karst regions.…”

“…Karst and non-karst species also differ in their hydraulic traits in correspondence with their distribution patterns [ 28 ]. Despite this, a plant known as Camellia ptilosperma is suspected to have originated via hybridization between C. micrantha and C. flavida based on the inconsistencies in the phylogenies derived from nuclear and chloroplast genomes [ 45 ]. Morphologically similar to C .…”

Genotypic and Phenotypic Diversity of Endemic Golden Camellias Collected from China

“…Lu [20] used chloroplasts and single-copy-sequence molecular techniques to analyze the phylogeography and conservation genetics of Camellia (Theaceae) in southern Guangxi, China. Wei [21] used phylogenetics to calculate the taxonomic information of yellow camellia plants in the Camellia family in China, and they found that the phylogeny of dd-RAD, RNA-sep and the chloroplast genome in the genus Camellia in China was inconsistent. Furthermore, it was also found that certain developmental trees were not separated or had differences, thus making them difficult to distinguish between, and indicating that hybridization and introgression affect the inconsistency between nuclear genes and the organelle genes of the genus Yellow Camellia.…”