title: Phylogenomic analyses of large-scale nuclear genes provide new insights into the evolutionary relationships within the rosids.
abstract: The Rosids is one of the largest groups of flowering plants, with 140 families and ∼70,000 species. Previous phylogenetic studies of the rosids have primarily utilized organelle genes that likely differ in evolutionary histories from nuclear genes. To better understand the evolutionary history of rosids, it is necessary to investigate their phylogenetic relationships using nuclear genes. Here, we employed large-scale phylogenomic datasets composed of nuclear genes, including 891 clusters of putative orthologous genes. Combined with comprehensive taxon sampling covering 63 species representing 14 out of the 17 orders, we reconstructed the rosids phylogeny with coalescence and concatenation methods, yielding similar tree topologies from all datasets. However, these topologies did not agree on the placement of Zygophyllales. Through comprehensive analyses, we found that missing data and gene tree heterogeneity were potential factors that may mislead concatenation methods, in particular, large amounts of missing data under high gene tree heterogeneity. Our results provided new insights into the deep phylogenetic relationships of the rosids, and demonstrated that coalescence methods may effectively resolve the phylogenetic relationships of the rosids with missing data under high gene tree heterogeneity.
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Zhao
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
authors.forename: Xia
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA.
authors.forename: Ning
authors.initials: N
authors.lastname: Zhang
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
authors.forename: Shu-Dong
authors.initials: SD
authors.lastname: Zhang
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
authors.forename: Ting-Shuang
authors.initials: TS
authors.lastname: Yi
authors.affiliation: Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200032, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Ma
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China. Electronic address: guozhenhua@mail.kib.ac.cn.
authors.forename: Zhen-Hua
authors.initials: ZH
authors.lastname: Guo
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China. Electronic address: dzl@mail.kib.ac.cn.
authors.forename: De-Zhu
authors.initials: DZ
authors.lastname: Li
mesh_terms: D005075:Biological Evolution; D017343:Genes, Plant; D019684:Magnoliopsida / Q000145:classification* / Q000235:genetics; D010802:Phylogeny
keywords: Coalescence; Gene tree; Nuclear genes; Rosids phylogenomics; Species tree