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
MartÃnez-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.