Molecular species identification of Rockskipper (Pisces: Blenniidae) from Porok Beach (Yogyakarta, Indonesia) based on 16S rRNA and COI genes

Abstract

Rockskipper belongs to the species-rich family of Blenniidae (Combtooth blenny) and is known for its cryptic and species complexes presence. Identifying cryptic species based solely on morphological features is challenging due to their similar morphological characteristics. As a result, molecular genetic techniques based on two partial mtDNA genes, COI and 16S rRNA, were employed to identify fish accurately. This study aimed to evaluate the effectiveness of COI and 16S rRNA gene for the identification of Rockskipper fish and investigate the genetic relationship between species of Rockskipper from Porok Beach. The result revealed that the thirteen Rockskipper samples from Porok Beach that belong to six species (E. vermiculatus, E. striatus, I. lineatus, I. dussumieri, I. edentulus, and B. caudolineata) with more than 99% similarity. In contrast, the 16S analysis identified five species. A Bayesian phylogenetic tree demonstrated that six species of Rockskipper from Porok Beach are genetically distinct and separated into two clusters. We also found that two samples (RS-9 and RS-10) form a monophyletic group with B. caudolineata with maximum bootstrap (NJ and ML: 100%) and posterior probability (1.00). We hypothesized that B. caudolineata is a species complex with at least two lineages: one was genetically closer to RS-8, and another was more closely related to RS-9 and RS-10. Both the COI and 16S rRNA genes were found to be capable of delineating species and revealing genetic variation among Rockskipper samples in this study. However, our findings demonstrated that the COI gene is a more accurate and reliable marker for identifying Rockskipper species from Porok Beach, Gunungkidul, Yogyakarta, Indonesia.