Phylogeography, codon usage, and DNA barcoding of lesser short nosed fruit bat (Cynopterus brachyotis Muller, 1838) populations in Indonesia

Fruit bat (Pteropodidae) is one of the mammals that is common in environments and widely distributed from subtropical to tropical Asia. Whereas the information on phylogeography of fruit bat Cynopterus brachyotis is still limited. From this situation, this paper aims to assess the phylogeography, codon usage, and DNA barcoding of C. brachyotis populations in Indonesia. Phylogeography was developed based on 657 bp of the mtDNA COI gene for all bat individuals and Bayesian inference to construct the phylogeny tree. The C. brachyotis populations in Indonesia are different to the populations from the Asias continent. The results show that C. brachyotis populations in Indonesia were divided into 3 distinct clades. A putative geographical barrier, recent, and rapid range expansion in the Sunda lineage associated with changes in sea levels, possibly coupled with related ecological differences, may have driven population divergence, allopatric, and sympatric speciation. Codon usage and high frequency were also contributing to the dispersal of C. brachyotis forming a distinct population.