Phylogenetic analyses
The Bayesian phylogram derived from the cox1 data set (Figure S1) recovered the putative species E. ruidum sp. 1 and E. ruidum sp. 2 each as monophyletic (PP= 1.0 in both cases). The specimens assigned to E. ruidum spp. 3–4 and 2x3 on the other hand appeared intermingled in a single clade (PP= 1.0). Ectatomma ruidum sp. 1 was sister to the remaining taxa, but with low support (PP= 0.87). Most of the internal relationships within E. ruidumsp. 1, formed by specimens from southern Mexico, Guatemala, Honduras, Nicaragua, Costa Rica, Colombia, Venezuela and the Lesser Antilles, were unresolved. In contrast, E. ruidum sp. 2 had an evident geographic structure, being composed of four main, significantly-supported subclades. One of these clades contained specimens from Ecuador (PP= 1.0), a second specimens from the remaining South and Central American localities (PP = 0.87), a third specimens from Quintana Roo in southeast Mexico (PP = 0.99), and the fourth contained specimens from southeast, central, and northeast Mexico (PP= 0.66).
The cox1 haplotype network showed that the E. ruidumhaplotypes are grouped into three main haplogroups, which are separated from each other by 17 to 20 mutational steps (Figure 2D). Two of these haplogroups are each represented by specimens assigned to E. ruidum spp. 1 and 2, whereas the remaining one had members of E. ruidum spp. 3, 4 and 2x3. Moreover, the haplogroup with specimens ofE. ruidum sp. 2 was divided into various geographically structured clusters.
The phylogenetic analyses with the 3RAD data set yielded well resolved, highly supported topologies. All the topologies derived from the ML, Exabayes and SVDquartets’ analyses recovered four main clades with significant support (Figures 2B, S2). One of these clades contained members of E. ruidum sp. 1, which was sister to a second clade represented by the specimens of E. ruidum sp. 2. These two taxa were sister to the two remaining main clades, one of which contained four of the five specimens of E. ruidum sp. 3 and the two specimens of E. ruidum sp. 4, and the remaining one the specimen assigned to E. ruidum sp. 2x3 from a locality near Pinotepa Nacional, Oaxaca, and the specimen of E. ruidum sp. 3 from Guerrero, Mexico. The main clade formed by samples assigned to E. ruidum sp. 2 was further divided into two subclades. One was exclusively composed of specimens distributed from southeast (Yucatan and Chiapas) to northeast (Tamaulipas) Mexico (E. ruidum sp. 2A), whereas the second was comprised of specimens from Central America, including Quintana Roo in southeast Mexico, and South America (E. ruidum sp. 2B).
Most of the UCE analyses carried out with the ML, Exabayes and species tree methods recovered the above four clades with the same relationships among them mostly with strong support (Figure 2C, Supplementary Material S2). However, in contrast to most of the 3RAD topologies, the ML phylograms based on the 90, 95 and 100% occupancy matrices recoveredE. ruidum sp. 1 as sister to the clade formed by E. ruidumsp. 3, 4 and 2x3 (BTP= 100).