Figure 1.
Average branch support analysis across different loci and phylogenetic methods.
Data of single- and combined-loci was analyzed using Bayesian analysis (Bayes), Maximum Likelihood (ML), Neighbor Joining (NJ) and Maximum Parsimony (MP). The average branch support was calculated for well resolved clades (above 50%), resulting from all methods used. Error bars indicate standard error of support values. The average support varied significantly using different methods for single locus analysis, but decreased with the combination of loci.
Figure 2.
Higher content of parsimony informative characters (PIC) is not related to high species resolution.
The percentage of PIC was plotted across the average species resolution calculated over all methods used for single or combined datasets. Error bars show standard error of species resolution among different methods used. trnH-psbA spacer performed poorly compared to matK and rbcL in single locus analysis, while rbcL/matK nearly reach the same resolution percentage as the three-loci combination.
Figure 3.
Observed frequency of uncorrected intra- and intergeneric p-distance.
The frequency of the uncorrected p-distance was analyzed to visualize the “barcoding gap”. Frequency was logged on a scale from 0 to 20% distance, indicating that trnH-psbA is out performing with an average inter-specific p-distance of more than 20%. Inter-generic p-distance shown in darker color and intra-generic p-distance lighter color, blue for trnH-psbA spacer, violet for matK and green for rbcL, respectively.
Figure 4.
Meta tree of all taxa using matK/rbcL.
Combined tree of matK/rbcL loci, branch support values are given in percent. Support values highlighted by the method used: Maximum Likelihood (black), Maximum Parsimony (violet), Neighbor Joining (green) and Bayesian Analysis (turquoise). Taxa that differed in topology along the different methods are shaded in violet.
Figure 5.
Final consensus tree of all barcode loci and methods.
Combined tree of matK/rbcL/trnH-psbA loci, branch support values are given in percent. Support values highlighted by the method used: Maximum Likelihood (black), Maximum Parsimony (violet), Neighbor Joining (green) and Bayesian Analysis (turquoise).