Fig. 4

(parts a, b, and c). Mitochondrial phylogenomic inference of Sciurini recovered by ML analysis of 232 specimens (Dataset 5). Nodal support from the ML bootstrap pseudo-replicates are indicated at each node along with Bayesian posterior probabilities (BI). White wedges indicate bootstrap values ≤ 50%, grey indicates bootstrap frequencies between 50 and 75%, and black indicates bootstrap frequencies ≥ 75%. For BI, white indicates PP < 0.95, whereas black indicates PP ≥ 0.95. Scale at the bottom represents substitutions per site. Letters A–L identify species groups discussed in the text. Except by putative unnamed species (“species 1–3”), terminals are named with specific epithets following [1, 2], and [24] (see methods for details), accompanied by museum voucher numbers and geographic information (country code and state/department). The first column represents Operacional Taxonomic Units (OTUs), recognized with base on original identifications and monophyly. The second to fourth columns correspond to the status of the delimitation of OTUs by different species delimitation methods: generalized mixed Yule-coalescent models using ultrametric trees generated with strict molecular clock (GMYC 1) and relaxed log-normal clock (GMYC 2); and Bayesian Phylogenetics and Phylogeography (BPP) analyses