Nucleotide Diversity Analysis of F. binodulus Mitochondrial Genome

Nucleotide diversity of the 21 Lucanid mitochondrial genomes was calculated based on the method proposed by Nei and Li (Nei and Li 1979) using the perl script, one of analysis tools implemented in the GenomeArchive; http://www.genoomearchive.info/ (Park and Xi 2018, Park et al., in preparation). Window size and step size of sliding-window method were set as 500 and 200 bp, respectively. Genomic positions of each windows were compared with gene annotations of the mitochondrial genome.

All available 88 Scarabaeoid mitochondrial sequences including the 21 Lucanids mitochondrial genomes that contained all 13 protein-coding gene (PCGs) were retrieved from NCBI and sequences of each PCGs were extracted. Multiple sequence alignments for each PCG sequence for two datasets (21 Lucanids mitochondrial genomes and 88 Scarabaeiod mitochondrial genomes) were conducted with MAFFT v7.450 (Katoh and Standley 2013). Nucleotide diversity for each alignment was calculated based on Nei and Li (1979) using the perl script without sliding-window option.