Phylogenetic and genetic variation of common mudskippers (Periophthalmus kalolo Lesson, 1831) from the southern coast of Java, Indonesia inferred from the COI mitochondrial gene

The common mudskipper (Periophthalmus kalolo Lesson, 1831) belongs to a group of fish species that exhibit amphibious lifestyles during specific daily periods. However, identifying this species poses a challenge due to its morphological similarities with other mudskipper species. These similarities have occasionally caused misidentifications of mudskippers. In Indonesia, previous studies have examined the genetic variation of common mudskippers, but these investigations have been limited to a few specific areas, particularly along the southern coast of Java. As a result, the available data remain fragmented, and no comprehensive genetic population analysis of common mudskippers on the southern coast of Java has been conducted. Therefore, our study aimed to establish DNA barcodes of COI mtDNA and explore the genetic variation and relationship among these common mudskipper populations from the southern coast of Java. We collected nine specimens from two populations, Cilacap Mangrove Forest and Kondang Bandung Beach, and supplemented our dataset with 38 previously collected COI sequences of common mudskippers from three different populations from the southern coast of Java (Pasir Mendit Beach, Bogowonto Lagoon, and Baros Beach). The study revealed that 47 common mudskippers from five different populations are separated into three genetically distinct clades (A, B, and C). These clades display genetic divergences ranging from 0.97% to 1.91%. Each clade exhibits high levels of haplotype diversity but relatively low nucleotide diversity, suggesting a previous bottleneck in population followed by a fast expansion. However, the phylogeny, haplotype network, and principal coordinate analysis indicate overlapping populations with no geographic separation within these clades. This suggests the potential occurrence of gene flow among these populations, which might have been facilitated by past geological events. These results enhance our understanding of common mudskipper biodiversity in Indonesia. Further studies involving common mudskipper populations from various geographical sites in Indonesia are required to further enrich our understanding of the variation and evolution of this species.