SUPPLEMENTARY FIGURES : FIGURE S1. Tree topology derived from the best scoring phylogram of the Maximum Likelihood (ML) analysis with the combined dataset. The support values for the two phylogenetic reconstruction approaches, Bayesian Inference (BI) and ML, are given at each node. All individuals with corresponding assumed putative species status and clade information are provided.
FIGURE S2. Left: the best scoring Maximum Likelihood (ML) tree topology retrieved with the mtDNA dataset. Right: barplots representing the different species delimitation results based on the single locus mtDNA dataset. Grey blocks indicate species that were not supported by that specific method, or two or more groups were not significantly different from each other. The white punctuation without an outline represents putative species boundaries. The “star” represents A. orientalis, “triangle” A. tristis, “circle” A. lineatus, “square” A. grayi, and “diamond” A. litoralis.
FIGURE S3. STACEY maximum clade credibility SMC-tree with similarity matrix and minimal cluster from the total evidence dataset comprising all five gene loci. Different colour schemes represent robustness of posterior probability (PP) support. The “red line frame” represents the minimal cluster suggested by the STACEY analysis, the “black line frame” represents the proposed putative species assumption. The squares in the similarity matrix represent posterior probability values (white = 0, represents lowest similarity, whilst, black = 1, represents highest similarity) for pairwise individuals that belong to the same minimal cluster. The corresponding proposed putative species scheme is provided at the top and right of the matrix.
FIGURE S4. Heat map showing the 16S-based pairwise distance matrix of the Acontinae, with pairwise comparison of the BEAST fossil dating total evidence gene trees. Color gradients, top left, represent the range of 16S pairwise distances, with their corresponding frequencies. Pairwise groups with similar colors represent close relatives, and vice versa. The “barcoding gap” computed with the p-distances matrix for visualizing the gap between interspecific and intraspecific pairwise distance distributions is marked with a red line.
FIGURE S5. Heat map showing the Cyt-b-based pairwise distance matrix of the Acontinae, with pairwise comparison of the BEAST fossil dating total evidence gene trees. Color gradients, top left, represent the range of Cyt-b pairwise distances, with their corresponding frequencies. Pairwise groups with similar colors represent close relatives, and vice versa. The “barcoding gap” computed with the p-distances matrix for visualizing the gap between interspecific and intraspecific pairwise distance distributions is marked with a red line.
SUPPLEMENTARY TABLES: TABLE S1. All samples used in this study, together with corresponding detailed locality information, coordinates, labels used in analyses, species, clades and NCBI GenBank accession numbers of all genes. Note: "-" indicates sequence not available, "?" indicates unknown information. All GenBank accession numbers in bold are the new sequences generated from this study. TABLE S2. The outgroup sequences with their NCBI GeneBank accession numbers used in the phylogenetic reconstruction and fossil calibration dating analyses. " - " indicates sequence not available. TABLE S3. Optimal partition scheme, substitution model, likelihood score (-InL), Gamma shape, proportion of estimated invariant and Homogeneity Test results of the four partitions. TABLE S4. Average uncorrected pairwise distances of the 16S gene of all putative Acontinae species based on our proposed species scheme. TABLE S5. Average uncorrected pairwise distances of the Cyt-b gene of all putative Acontinae species based on our proposed species scheme.