Genetic data.
DNA sequences from the mitochondrial gene cytb and the nuclear genes Intron 7 of the beta fibrinogen (Fgb-I7) and Interphotoreceptor retinoid-binding protein (IRBP) were obtained from collected specimens and tissue loans from mammal collections (Fig. 1). Wild-caught specimens followed the Guidelines approved by the American Society of Mammologists (Sikes et al. 2016). Genomic DNA extraction, primer information, and PCR procedures for the cytb and Fgb-I7 genes, as well as sequencing protocols for the amplified PCR products of each gene, are provided in Martínez-Borrego et al. (2022a). Approximately 1140 pb of cytb were amplified in 47 individuals ofR. mexicanus while a 608 bp fragment of Fgb-I7 was amplified in 58 individuals. For the IRBP gene, the amplification protocol was only successful in 3 individuals using primers A1 (Stanhope et al. 1992) and B2 (Wickliffe et al. 2003) and the PCR conditions described in Almendra et al. (2018). In individuals for whom other tissues were unavailable, a skin DNA extraction protocol was implemented with modifications from Rogers et al. (2011). Skin DNA amplification was performed using Illustra PuReTaq Ready-To-Go PCR Beads and a series of primer pairs as follows: L14724 (Irwin et al. 1991) and H15149 (Kocher et al. 1989) for cytb; B17 and Bfib (Wickliffe et al. 2003) for Fgb-I7.
Sequences were edited using Codon Code Aligner v.8.0.2 (CodonCode Corporation, Dedham, MA, USA) and aligned against a reference in UGENE v.1.32.0 (Okonechnikov et al. 2012) using the MUSCLE method. Eleven species of the genusReithrodontomys were employed as outgroups, representing the distinct species groups defined by Hooper (1952): 5 from the R. mexicanus group, 3 from the R. tenuirostris group, 2 from theR. megalotis group, and 1 from the R. fulvescens group. The final dataset comprised 109 sequences for cytb, 68 for Fgb-I7, and 26 for IRBP. The concatenated dataset was only available for cytb + Fgb-I7 (68 sequences, 1750 bp long) and cytb + IRBP (24, 2064 bp long) because very few individuals presented genetic information for all loci. The information on the sequences generated in this study and those downloaded from GenBank is included in Appendix 1.