Mitogenomic analysis of Palaeopsylla remota and Frontopsylla elata elata with implications for the phylogeny of Siphonaptera

Fleas are among the most prevalent hematophagous ectoparasites found on mammals and have the ability to spread various pathogens. This study presents the first sequencing and analysis of the mitochondrial genomes of Palaeopsylla remota and Frontopsylla elata elata , alongside a comparative examination using mitochondrial genomic data from other flea species. Multiple aspects were investigated, including nucleotide composition, tRNA secondary structures, codon usage bias, nucleotide diversity, selective pressure, phylogenetic relationships, and divergence time estimation. Both species possess a typical mitochondrial genome comprising 37 genes and one control region, showing a pronounced A+T bias. Non-canonical G-U and U-U pairings were identified in some tRNA genes. ENC-plot and PR2-plot analyses indicated that natural selection is the main factor shaping codon usage bias in these two fleas. Within Siphonaptera, nucleotide diversity and selection pressure analyses revealed that the cox1 gene exhibited the lowest values for both Pi and Ka/Ks. Phylogenetic reconstructions based on BI and ML methods using PCG123 and PCG12 datasets consistently supported the monophyly of the superfamily Ceratophylloidea and the family Pulicidae, whereas the families Ceratophyllidae, Leptopsyllidae, and Ctenophthalmidae displayed paraphyletic associations. Divergence time estimates suggest that the most recent common ancestor of extant fleas dates back to the Cretaceous period, with significant radiation events occurring after the K-Pg boundary. This study expands the mitochondrial genomic resources for fleas and offers new insights into their evolutionary history and phylogenetic relationships.