title: Multilocus species tree analyses resolve the ancient radiation of the subtribe Zizaniinae (Poaceae).
abstract: The phylogeny of the subtribe Zizaniinae of rice tribe (Oryzeae) has not been well resolved, particularly for the monotypic Hygroryza whose systematic position was inconsistent in previous studies. Here, we used the concatenation approach and coalescent-based species tree methods to reconstruct the phylogeny of Zizaniinae based on sequences of 14 nuclear single-copy loci and concatenated chloroplast fragments. Despite the low resolution of the tree from concatenated data and substantial topological incongruence of individual gene trees, the species trees inferred from three coalescent-based methods were fully concordant and highly supported. Importantly, the genus Hygroryza was consistently recovered with strong support by all coalescent-based methods. Further various phylogenetic analyses indicated that incomplete lineage sorting was the most likely process that generated pervasive discordance among individual gene trees, although hybridization and introgression cannot be excluded completely. Our species tree inferences based on multilocus data successfully resolved the phylogenetic relationships of the Zizaniinae lineages and confirmed that ancient rapid radiation has taken place in the diversification history of Zizaniinae. This study demonstrates that coalescent-based species tree approaches outperformed the concatenation method and could effectively decipher ancient rapid radiations as long as well resolved individual gene trees were sufficiently sampled.
authors: College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China.
authors: Liang
authors: L
authors: Tang
authors: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China.
authors: Xin-hui
authors: XH
authors: Zou
authors: Department of Biology, Emory University, Atlanta, GA 30322, USA.
authors: Lin-bin
authors: LB
authors: Zhang
authors: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China. Electronic address: gesong@ibcas.ac.cn.
authors: Song
authors: S
authors: Ge
mesh_terms: D001499:Bayes Theorem; D005075:Biological Evolution; D002467:Cell Nucleus / Q000235:genetics; D018742:DNA, Chloroplast / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D016013:Likelihood Functions; D008957:Models, Genetic; D010802:Phylogeny; D006109:Poaceae / Q000145:classification*; D017422:Sequence Analysis, DNA
chemical_list: D018742:DNA, Chloroplast; D018744:DNA, Plant
keywords: Ancient rapid radiation; Incomplete lineage sorting; Multilocus data; Species tree; Zizaniinae