title: Towards a more robust molecular phylogeny of Chinese Apiaceae subfamily Apioideae: additional evidence from nrDNA ITS and cpDNA intron (rpl16 and rps16) sequences.
abstract: China contains some of the world's greatest diversity of Apiaceae (Umbelliferae), with ten endemic genera. Our previous investigation into the phylogenetic relationships of Chinese Apiaceae subfamily Apioideae, based exclusively on nrDNA ITS sequences, revealed several major clades heretofore unrecognized in the subfamily and confirmed the phylogenetic placements of five endemic genera. To further elucidate relationships among Chinese Apioideae, ascertain the phylogenetic placements of the remaining endemic genera, and test hypotheses of relationships proposed in our earlier study, additional taxa were examined for ITS and, for smaller sets of accessions, cpDNA rpl16 and rps16 intron sequence variation. These ITS and cpDNA data matrices comprised 158 and 131 accessions, respectively, with 110 accessions included in the analysis of combined ITS and cpDNA data. Maximum parsimony and Bayesian analyses of partitioned ITS and chloroplast data sets resulted in highly consistent phylogenies, whereas analyses of combined molecular data resulted in trees of greatest resolution and overall branch support. Two major clades identified in our previous study are recognized at the tribal level: Komarovieae J. Zhou & S. R. Downie trib. nov. and Chamaesieae J. Zhou & F. D. Pu trib. nov. The monotypic tribe Chamaesieae represents one of the earliest diverging lineages of subfamily Apioideae in Asia. The Acronema and East Asia clades of previous circumscription are each expanded. Of the five Chinese endemic genera not examined previously, Chaerophyllopsis finds affinity within tribe Scandiceae subtribe Scandicinae, Chuanminshen allies with Changium and Cyclorhiza in tribe Komarovieae, Harrysmithia falls within the Acronema Clade, Melanosciadium embeds in Angelica in tribe Selineae, and Dickinsia is confirmed as a member of Apiaceae subfamily Azorelloideae. The cpDNA-based phylogenies are not sufficiently resolved in their distal portions to elucidate the tribal placement of the endemic genus Nothosmyrnium, whereas the ITS trees strongly indicate an affinity with tribe Pimpinelleae. The affinities of several Chinese endemic species are also addressed. Peucedanum delavayi, for example, is phylogenetically distant from Sinodielsia and Meeboldia, genera with which it has been allied previously, and shows close affinity to three Chinese species of Ligusticum in tribe Selineae. Aside from providing a framework for taxonomic revisions, the phylogenetic structure recovered in this study for subfamily Apioideae will lay the foundation for future investigations of evolutionary patterns of morphological characters and biogeography.
authors.affiliation: Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Zhou
authors.forename: Xun
authors.initials: X
authors.lastname: Gong
authors.forename: Stephen R
authors.initials: SR
authors.lastname: Downie
authors.forename: Hua
authors.initials: H
authors.lastname: Peng
mesh_terms: D019661:Apiaceae / Q000145:classification / Q000235:genetics*; D001499:Bayes Theorem; D002681:China; D002736:Chloroplasts / Q000235:genetics; D018742:DNA, Chloroplast / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D019143:Evolution, Molecular; D017343:Genes, Plant; D007438:Introns; D008957:Models, Genetic; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D018742:DNA, Chloroplast; D018744:DNA, Plant; D021903:DNA, Ribosomal Spacer