Integrating fossils in a molecular-based phylogeny and testing them as calibration points for divergence time estimates in Menispermaceae  

作　　者：Frederic M.B. JACQUES Wei WANG Rosa Del C. ORTIZ Hong-Lei LI Zhe-Kun ZHOU Zhi-Duan CHEN 

机构地区：[1]Department of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China [2]State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China [3]Missouri Botanical Garden, St. Louis MO 63166-0299, USA [4]Graduate School of the Chinese Academy of Sciences, Beijing 100049, China [5]Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China

出　　处：《Journal of Systematics and Evolution》2011年第1期25-49,共25页植物分类学报（英文版）

基　　金：supported by a 973 grant (no. 2007CB411601);the Chinese Academy of Sciences (grant no. KSCX2-YW-R-136);a Chinese post-doctorate grant (no. 20080431286);a grant from the Key Laboratory, Kunming Institute of Botany(no. 086341121)

摘　　要：The phylogeny of extant Menispermaceae （Ranunculales） is reconstructed based on DNA sequences of two chloroplast genes （rbcL and atpB） from 94 species belonging to 56 genera. Fossilized endocarps represent 34 genera. The positions of these are inferred using 30 morphological characters and the molecular phylogeny as a backbone constraint. Nine of the thirteen nodes that are each dated by a fossil are used as calibration points for the estimates of molecular divergence times. BEAST is used to estimate stem age （121.2 Myr） and crown age （105.4 Myr） for Menispermaceae. This method does not require an input tree topology and can also account for rate heterogeneity among lineages. The sensitivity of these estimates to fossil constraints is then evaluated by a cross-validation procedure. The estimated origin for Menispermaceae is dated to the mid-Jurassic if the customary maximum age of 125 Myr for eudicots is not implemented. All constraints when used alone failed to estimate node ages in some parts of the tree. Fossils from the Palaeocene and Eocene impose strict constraints. Likewise, the use of Prototinomiscium as a dating constraint for Menispermaceae appears to be a conservative approach.The phylogeny of extant Menispermaceae （Ranunculales） is reconstructed based on DNA sequences of two chloroplast genes （rbcL and atpB） from 94 species belonging to 56 genera. Fossilized endocarps represent 34 genera. The positions of these are inferred using 30 morphological characters and the molecular phylogeny as a backbone constraint. Nine of the thirteen nodes that are each dated by a fossil are used as calibration points for the estimates of molecular divergence times. BEAST is used to estimate stem age （121.2 Myr） and crown age （105.4 Myr） for Menispermaceae. This method does not require an input tree topology and can also account for rate heterogeneity among lineages. The sensitivity of these estimates to fossil constraints is then evaluated by a cross-validation procedure. The estimated origin for Menispermaceae is dated to the mid-Jurassic if the customary maximum age of 125 Myr for eudicots is not implemented. All constraints when used alone failed to estimate node ages in some parts of the tree. Fossils from the Palaeocene and Eocene impose strict constraints. Likewise, the use of Prototinomiscium as a dating constraint for Menispermaceae appears to be a conservative approach.

关 键 词：age calibration cross-validation FOSSIL MENISPERMACEAE molecular scaffold phylogeny. 

分 类 号：Q949[生物学—植物学]