Data from: Diversification patterns in the CES clade (Brassicaceae tribes Cremolobeae, Eudemeae, Schizopetaleae) in Andean South America

Dated molecular phylogenetic trees show that the Andean uplift had a major impact on South American biodiversity. For many Andean groups, accelerated diversification (radiation) has been documented. However, not all Andean lineages appear to have diversified following the model of rapid radiation, particularly in the central and southern Andes. Here, we investigated the diversification patterns for the largest South American-endemic lineage of Brassicaceae, composed of tribes Cremolobeae, Eudemeae and Schizopetaleae (CES clade). Species of this group inhabit nearly all Andean biomes and adjacent areas including the Atacama–Sechura desert, the Chilean Matorral and the Patagonian Steppe. First, we studied diversification times and historical biogeography of the CES clade. Second, we analysed diversification rates through time, lineages and associated life forms. Results demonstrate that early diversification of the CES clade occurred in the early to mid-Miocene (c. 12–19 Mya) and involved the central Andes, the southern Andes and the Patagonian Steppe, and the Atacama–Sechura desert. The Chilean Matorral and northern Andes were colonized subsequently in the early Pliocene (4–5 Mya). Diversification of the CES clade was recovered as a gradual process without any evidence for rate shifts or rapid radiation, in contrast to many other Andean groups analysed so far. Diversification time/rates and biogeographical patterns obtained for the CES clade are discussed and compared with patterns and conclusions reported for other Andean plant lineages.ITS_Brassicaceae_datasetITS matrix from Brassicaceae datasetITS.nexphyA_Brassicaceae_datasetphyA matrix from Brassicaceae datasetphyA.nexchs_Brassicaceae_datasetchs matrix from Brassicaceae datasetchs.nexndhF_Brassicaceae_datasetndhF matrix from Brassicaceae datasetndhF.nexrbcL_Brassicaceae_datasetrbcL matrix from Brassicaceae datasetrbcL.nexmatK_Brassicaceae_datasetmatK matrix from Brassicaceae datasetmatK.nextrnLF_Brassicaceae_datasettrnLF matrix from Brassicaceae datasettrnLF.nexnad4_Brassicaceae_datasetnad4 matrix from Brassicaceae datasetnad4.nexfossil_calibration_analyses(BEASTv2.2)XML file for running the analyses with the Brassicaceae dataset (supermatrix approach) in BEASTv2.2 (Bouckaert et al., 2014) using the four Brassicales fossil scheme for calibration.fossil_calibration.xmlsecondary_calibration_analyses(BEASTv2.2)XML file for running the analyses with the Brassicaceae dataset (supermatrix approach) in BEASTv2.2 (Bouckaert et al., 2014) using the three secondary calibration scheme for calibrationsecondary_calibration.xmlML_RAxML_bestTree_Brassicaceae_datasetMaximum likelihood tree obtained using the Brassicaceae dataset (supermatrix approach) under RAxML 8.1.11ML_RAxML_bestTree.trefossil_calibration_MCCT_Brassicaceae_datasetMaximum clade credibility tree obtained in BEASTv2.2 using the Brassicaceae dataset (supermatrix approach) and the "four Brassicales fossil scheme" for calibration.fossil_calibration_MCCT.tresecondary_calibration_MCCT_Brassicaceae_datasetMaximum clade credibility tree obtained in BEASTv2.2 using the Brassicaceae dataset (supermatrix approach) and the "secondary calibration scheme" for calibration.secondary_calibration_MCCT.treITS_CES_datasetITS matrix from CES (Cremolobeae, Eudemeae, Schizopetaleae) datasetcITS_CES(BEAST).nextrnLF_CES_datasettrnLF matrix from CES (Cremolobeae, Eudemeae, Schizopetaleae) datasetctrnLF_CES(BEAST).nextrnH_CES_datasettrnH matrix from CES (Cremolobeae, Eudemeae, Schizopetaleae) datasetctrnH_CES(BEAST).nexrps16_CES_datasetrps16 matrix from CES (Cremolobeae, Eudemeae, Schizopetaleae) datasetcrps16_CES(BEAST).nexCES_analyses(BEASTv2.2)XML file for running the analyses with the CES dataset (Cremolobeae, Eudemeae, Schizopetaleae) in BEASTv2.2 (Bouckaert et al., 2014).CES.xmlML_RAxML_bestTree_CES_datasetMaximum likelihood tree obtained using the CES (Cremolobeae, Eudemeae, Schizopetaleae) dataset in RAxML 8.1.11 (Stamatakis, 2006)CES_RAxML_bestTree.treMCCT_CES_datasetMaximum clade credibility tree obtained in BEASTv2.2 analyses using the CES (Cremolobeae, Eudemeae, Schizopetaleae) dataset.CES_MCCT.tre1000_trees_CES_dataset1000 posterior trees from the BEASTv2.2 analyses using the CES (Cremolobeae, Eudemeae, Schizopetaleae) dataset.CES_1000_trees.treMaterials&MethodsMaterials & Methods for data analyse