Cyt b gene tree of the genus Thomasomys and close outgroups. The tree was inferred by maximum likelihood (ML) using a nucleotide substitution model (GTR+F+G4); it contains 222 terminals belonging to 36 named species of Thomasomys, including the two new species here described (indicated with black arrows), it also contains at least 20 putative new species of Thomasomys, and 20 outgroups of the genera Rhipidomys, Chilomys and Rhagomys. Nodal support statistics for the analyses in IQ-Tree are from: ultrafast bootstrap approximation (UF), SH-like approximate likelihood ratio test (aL), and the aBayes test (aB). White sections of the circles indicate UF and aL bootstrap frequencies <75% and aB posterior probabilities <0.95, whereas black sections of the circles indicate UF and aL bootstrap frequencies ~75% and aB posterior probabilities ~0.95. Insets represent differences in topology and branch lengths of three ML approaches. Inset A: Collapsed gene tree of the main figure. Inset B: Collapsed gene tree inferred with a codon substitution model. Inset C: Collapsed gene tree estimated with the RAxML tree with the CAT approximation; black circles represent bootstrap values ~75%. Terminals are labeled with GenBank accession number, museum voucher number and scientific name—in case that the species have not been described, the sequences are indicated with ‘sp’ and a geographical proxy—‘ONT’ indicates that the sequence was obtained with MinION Oxford Nanopore Technologies.