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_dataset
ITS matrix from Brassicaceae dataset
ITS.nex
phyA_Brassicaceae_dataset
phyA matrix from Brassicaceae dataset
phyA.nex
chs_Brassicaceae_dataset
chs matrix from Brassicaceae dataset
chs.nex
ndhF_Brassicaceae_dataset
ndhF matrix from Brassicaceae dataset
ndhF.nex
rbcL_Brassicaceae_dataset
rbcL matrix from Brassicaceae dataset
rbcL.nex
matK_Brassicaceae_dataset
matK matrix from Brassicaceae dataset
matK.nex
trnLF_Brassicaceae_dataset
trnLF matrix from Brassicaceae dataset
trnLF.nex
nad4_Brassicaceae_dataset
nad4 matrix from Brassicaceae dataset
nad4.nex
fossil_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.xml
secondary_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 calibration
secondary_calibration.xml
ML_RAxML_bestTree_Brassicaceae_dataset
Maximum likelihood tree obtained using the Brassicaceae dataset (supermatrix approach) under RAxML 8.1.11
ML_RAxML_bestTree.tre
fossil_calibration_MCCT_Brassicaceae_dataset
Maximum clade credibility tree obtained in BEASTv2.2 using the Brassicaceae dataset (supermatrix approach) and the "four Brassicales fossil scheme" for calibration.
fossil_calibration_MCCT.tre
secondary_calibration_MCCT_Brassicaceae_dataset
Maximum clade credibility tree obtained in BEASTv2.2 using the Brassicaceae dataset (supermatrix approach) and the "secondary calibration scheme" for calibration.
secondary_calibration_MCCT.tre
ITS_CES_dataset
ITS matrix from CES (Cremolobeae, Eudemeae, Schizopetaleae) dataset
cITS_CES(BEAST).nex
trnLF_CES_dataset
trnLF matrix from CES (Cremolobeae, Eudemeae, Schizopetaleae) dataset
ctrnLF_CES(BEAST).nex
trnH_CES_dataset
trnH matrix from CES (Cremolobeae, Eudemeae, Schizopetaleae) dataset
ctrnH_CES(BEAST).nex
rps16_CES_dataset
rps16 matrix from CES (Cremolobeae, Eudemeae, Schizopetaleae) dataset
crps16_CES(BEAST).nex
CES_analyses(BEASTv2.2)
XML file for running the analyses with the CES dataset (Cremolobeae, Eudemeae, Schizopetaleae) in BEASTv2.2 (Bouckaert et al., 2014).
CES.xml
ML_RAxML_bestTree_CES_dataset
Maximum likelihood tree obtained using the CES (Cremolobeae, Eudemeae, Schizopetaleae) dataset in RAxML 8.1.11 (Stamatakis, 2006)
CES_RAxML_bestTree.tre
MCCT_CES_dataset
Maximum clade credibility tree obtained in BEASTv2.2 analyses using the CES (Cremolobeae, Eudemeae, Schizopetaleae) dataset.
CES_MCCT.tre
1000_trees_CES_dataset
1000 posterior trees from the BEASTv2.2 analyses using the CES (Cremolobeae, Eudemeae, Schizopetaleae) dataset.
CES_1000_trees.tre
Materials&Methods
Materials & Methods for data analyses