title: Three genome-based phylogeny of Cupressaceae s.l.: further evidence for the evolution of gymnosperms and Southern Hemisphere biogeography.
abstract: Phylogenetic information is essential to interpret the evolution of species. While DNA sequences from different genomes have been widely utilized in phylogenetic reconstruction, it is still difficult to use nuclear genes to reconstruct phylogenies of plant groups with large genomes and complex gene families, such as gymnosperms. Here, we use two single-copy nuclear genes, together with chloroplast and mitochondrial genes, to reconstruct the phylogeny of the ecologically-important conifer family Cupressaceae s.l., based on a complete sampling of its 32 genera. The different gene trees generated are highly congruent in topology, supporting the basal position of Cunninghamia and the seven-subfamily classification, and the estimated divergence times based on different datasets correspond well with each other and with the oldest fossil record. These results imply that we have obtained the species phylogeny of Cupressaceae s.l. In addition, possible origins of all three polyploid conifers were investigated, and a hybrid origin was suggested for Cupressus, Fitzroya and Sequoia. Moreover, we found that the biogeographic history of Cupressaceae s.l. is associated with the separation between Laurasia and Gondwana and the further break-up of the latter. Our study also provides new evidence for the gymnosperm phylogeny.
authors.affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
authors.forename: Zu-Yu
authors.initials: ZY
authors.lastname: Yang
authors.forename: Jin-Hua
authors.initials: JH
authors.lastname: Ran
authors.forename: Xiao-Quan
authors.initials: XQ
authors.lastname: Wang
mesh_terms: D005075:Biological Evolution; D002467:Cell Nucleus / Q000235:genetics; D029779:Cupressaceae / Q000145:classification* / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D005580:Fossils; D061125:Genes, Chloroplast; D050259:Genes, Mitochondrial; D017343:Genes, Plant; D018745:Genome, Plant; D016013:Likelihood Functions; D010802:Phylogeny; D058974:Phylogeography; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant