Figure 1.
Sample location map showing South East Asia, Australia, New Guinea and the western Pacific region.
The middle pane is a more detailed view of New Guinea (comprising Papua, a province of Indonesia, and Papua New Guinea) and the bottom pane is a map of Papua New Guinea showing some major features, including the provinces, mentioned in the text. Note that given the scales involved the sample positions are approximate.
Table 1.
Sample identification history.
Table 2.
Primers used to amplify short fragments of the D-loop region.
Figure 2.
Sequence coverage in the dataset.
A total of 217 samples are represented with an aligned sequence length of up to 1216A represents samples with the full 1216 bp of D-loop and COI. B represents the museum samples with D-loop and a 152 bp fragment of COI sequence. This 152 bp fragment falls at the 5′ end but within the 655 bp COI amplicon. C represents samples with only COI sequences and D represents samples with only D-loop sequences.
Figure 3.
ML tree for D-loop based on 192 taxa with sequence lengths of 560 bp. In this figure and in Figures 4, 5, and 6, nominal species names are used and monophyletic species are indicated by blue triangles that are named on the tree, while polyphyletic or paraphyletic species are colour coded as indicated in the key.
The boxes labelled A, B, C, and D are shown enlarged on the right of the figure and, as discussed in the text, they are used in this and subsequent figures to emphasise changes in relative positions and species make-up of clusters. Bootstrap support of ≥70% and Bayesian posterior probabilities ≥0.80 are shown as symbols in the order RAxML/PHYML/MrBayes.
Figure 4.
ML tree for COI based on 162 taxa with sequence lengths of 655 bp.
As explained in the caption for Fig. 3, monophyletic species are named on the tree while other species are colour coded. Note the changed positions and species make-up shown in the boxes and see further discussion of this in the text. Bootstrap support of ≥70% and Bayesian posterior probabilities ≥0.80 are shown as symbols in the order RAxML/PHYML/MrBayes.
Figure 5.
ML tree for COI based on 195 taxa with sequence lengths of either 655 bp.
As explained in the caption for Fig. 3, monophyletic species are named on the tree while other species are colour coded. Note the changed positions and species make-up shown in the boxes and see further discussion of this in the text. Bootstrap support of ≥70% is shown as symbols in the order RAxML/PHYML.
Figure 6.
ML tree for COI based on 195 taxa with sequence lengths of 152 bp.
As explained in the caption for Fig. 3, monophyletic species are named on the tree while other species are colour coded. Note the changed positions and species make-up shown in the boxes and see further discussion of this in the text. Bootstrap support of ≥70% is shown as symbols in the order RAxML/PHYML.
Table 3.
The presence of monophyletic species across the trees compared with nominal species designations.