Table 1.
Calibration scheme from Andújar et al. 2012 [16].
Table 2.
Calibration strategy of this study.
Fig 1.
Ultrametric time-calibrated phylogenetic tree obtained with BEAST2 for nd5 data in Carabus.
Green symbols depict calibration points employed (see Table 2 for details). Red symbols depict cladogenetic events whose age distributions (see Table 3) were utilized in subsequent analyses.
Fig 2.
Violin plots of different TMRCA in relation to individual calibration points.
The plots depict the mean (white dots), standard deviation (sd; black bars), 2*sd (black line), and density distribution (grey shape) of a clade’s age as obtained from the calibration analyses in Fig 1 for each major clade in relation to exclusion of individual calibration points. The x-axis denotes (letter) and depicts (icon) the respectively excluded calibration points in the respective analysis.
Table 3.
Comparison of secondary calibration points derived in this study and in Andújar et al. [16] to calibrate the molecular phylogenies of the single (left) and combined datasets (right) in Carabus.
Fig 3.
Violin plots of different TMRCA in relation to individual calibration points when root dating is omitted.
The plots depict mean (white dots), standard deviation (sd; black bars), 2*sd (black line), and density distribution (grey shape) of a clade’s age as obtained from the calibration analyses in Fig 1 for each major clade in relation to exclusion of individual calibration points. The x-axis denotes (letter) and depicts (icon) the respectively excluded calibration points in the respective analysis.
Table 4.
Estimates of the molecular age of the MRCA of Carabus according to gene or gene set.
Fig 4.
Ultrametric time-calibrated trees for combined DNA markers (MIT-NUC dataset) of Carabidae in this study (A) and Andújar et al. [16] (B).
Analyses were conducted with BEAST2 and followed the approach of Andújar et al. [16] applying an uncorrelated log-normal relaxed clock. All mitochondrial data sets were included under a 2P codon partition scheme with site models and clock models unlinked. Posterior probabilities are given. Grey bars represent the 95% confidence intervals for node ages in Ma. The vertical brown bar shows the 95% HPD interval for the split between Carabus and Calosoma, while the vertical grey bar in the inset represents the same in the study of Andújar and coworkers.
Fig 5.
Ultrametric time-calibrated trees obtained with BEAST2 for each individual (left) and combined datasets (right) of the Carabus ingroup data set.
Red clades and letters A, B, and C, are given for the individual gene trees when clades were supported by PPs of more than 0.8, and for the latter for the concatenated data sets. They are equivalent to the dated clades given in Table 3. Grey bars indicated the 95% HPD for the respective nodes, with the TMRCA bar being superposed for the respective phylogeny. T denotes the TMRCA of Carabus.