Phylogeny

Purpose: Create a phylogenetic tree of the rodent species to calculate the pairwise genetic distances between rodents.

To calculate pairwise phylogenetic distance for the rodent species in our network, we first downloaded cytochrome b sequences for the rodent species from GenBank (Sayers et al. 2022). We included sequences with at least the first 801 base pairs of cytochrome b (maximum length= 1160 bp) which resulted in sufficient sequences for 42 of the 50 rodent species.Using Geneious Prime 2023.0.4 (https://www.geneious.com), we imported the 42 sequences from GenBank and aligned them using the MUSCLE algorithm. Cutting down to only the first 801 bp of the aligned sequences, we constructed a maximum-likelihood phylogenetic tree with PhyML 3.0 (1000 replications) and obtained patristic distances from the distance matrix option.

Sayers, E. W., E. E. Bolton, J. R. Brister, K. Canese, J. Chan, D. C. Comeau, R. Connor, et al. 2022. “Database Resources of the National Center for Biotechnology Information.” Journal Article. Nucleic Acids Res 50 (D1): D20–d26. https://doi.org/10.1093/nar/gkab1112.