Multi-Sequence Alignment Files
We compared our five complete mtDNA genome sequences to previously published mitochondrial DNA sequences for modern populations of mountain lions in the Western U.S. and Florida. Outside of the complete mtDNA genome sequences newly determined in this study, the majority of available mtDNA sequences are for only part of the mtDNA genome. Specifically, the majority of our analyses are based on analyses of multi-sequence alignments of the 16s rRNA, ATPase8, and NADH dehydrogenase subunit 5 (NAD5) gene regions only. Sequences were aligned using MAFFT version 7 default settings with the E-INS-i iterative refinement method, which is best for a small number of sequences with multiple conserved domains and large gaps, and verified visually.