Comparative mitochondrial and phylomitogenomic analyses support the existence of a cryptic species complex in Gonodactylaceus falcatus (Stomatopoda: Gonodactyloidea)

Mantis shrimp (order Stomatopoda) are known for their aggressive nature and powerful raptorial appendages. Among them, the Philippine mantis shrimp Gonodactylaceus falcatus is suspected to comprise a cryptic species complex with 6 primary synonyms. This study aims to explore this complex focusing on G. falcatus ‘sensu stricto’ and three of its primary synonyms: G. insularis, G. mutatus, and G. siamensis. Complete mitochondrial genomes were fully assembled using Illumina sequencing. The AT-rich studied mitogenomes ranged from 15,894 to 16,267 bp in length. Each contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and one control region. Mitochondrial synteny is identical to previously reported stomatopod mitogenomes, except Gonodactylus smithii. In all studied species, 21 of the 22 tRNA genes were predicted to have the typical ‘cloverleaf’ structure: trnS1 either lacked a D-arm or both a D-arm and D-loop. All mitochondrial protein-coding genes experience purifying selection, noting a Ka/Ks value for the G. insularis nad4l gene was not calculated due to the absence of non-synonymous substitutions. AT-rich di- and tri-nucleotide microsatellites were found in all studied control regions while short tandem repeats were detected in all except G. insularis. Phylomitogenomic analysis supports the monophyly of the order Stomatopoda but not the superfamilies Gonodactyloidea, Lysiosquilloidea, and Squilloidea. Furthermore, phylogenomic placement and genetic distances supported the species status of G. insularis and G. mutatus but not G. siamensis. Our study provides genomic resources to continue improving knowledge of cryptic species complexes in the order Stomatopoda.