Genetic Diversity of the Pearse’s Mudskipper Periophthalmus novemradiatus (Perciformes: Gobiidae) and Characterization of its Complete Mitochondrial Genome Min Pau Tan 1,2,3 & Han Ming Gan 4 & Mohd Hamzah Nabilsyafiq 1 & Abd. Ghaffar Mazlan 5 & Tun Nurul Aimi Mat Jaafar 1 & Mohd Nor Siti Azizah 2 & Muhd Danish-Daniel 1,2 & Yeong Yik Sung 2 Received: 9 May 2019 /Revised: 6 December 2019 / # Springer Nature Switzerland AG 2020 Abstract Present study provides a first characterization of the complete mitochondrial DNA (mtDNA) genome of the Pearse’ s mudskipper Periophthalmus novemradiatus and describes its population genetics based on mtDNA cytochrome c oxidase subunit 1 (co1) gene. The whole mitogenome of P. novemradiatus is the fourth representative for its genus that consists of 23 formally described species to date. Eighty samples from six localities in Setiu Wetlands, Terengganu, Malaysia were sequenced at partial co1 gene region and analyzed, revealing an overall moderate haplotype diversity (h = 0.613) and low nucleotide diversity (π = 0.20%). Moreover, both the neutrality tests and mismatch distribution analyses of co1 suggest that the mudskipper populations might experience a genetic bottleneck or founder event followed by rapid expansion and accumulation of mutations dating approxi- mately 46,251 years ago. Hap01 was the most dominant (61.13%) haplotype that present at all sampling locations, while five haplotypes were respectively observed in two to four locations, and nine haplotypes were singleton. This supports the close relationship of P. novemradiatus in Setiu Wetlands, as also corroborated in the population pairwise F ST and genetic distance analyses. Interestingly, genetic propinquity with P. novemradiatus at Java and Bali, Indonesia (the only available sequences in GenBank) was also apparent, suggesting a common source of origin or long range dispersal ability of its planktonic larvae (> 1600 km). The lack of phylogeographic structure suggests there is no evidence of a barrier to gene flow between the South China Sea and Java/ Bali Sea and such pattern is most likely driven by ecological and environmental factor. Preservation of all the P. novemradiatus habitats in Setiu Wetlands is highly recommended because they each possess unique haplotypes present only at the respective location. Keywords Mitochondrial DNA . co1 . Genetic diversity . Mudskipper . Population structure . Periophthalmus Introduction Mudskippers of the genus Periophthalmus (Family: Gobiidae; Subfamily: Oxudercinae) are amphibious fishes that exhibit unique adaptation by living out of water for some part of their daily life cycle (Itoki et al., 2012; Kuciel, 2013). They are commonly found in mangrove ecosystems and mudflats, rel- atively small in size and are generally important as indicator species of environmental pollution (Bu-Olayan and Thomas, 2008; Shirani et al., 2012; Ansari et al., 2014). Twenty three species are recognized in genus Periophthalmus (Froese and Pauly, 2019) distributed in tropical, sub-tropical and temperate areas (Murdy, 1989; Jaafar and Larson, 2008; Jaafar et al., 2009). Still little is known about this genus, especially the Pearse’ s mudskipper P. novemradiatus that can be found in tropical countries such as India, Myanmar, Thailand, the Philippines and Malaysia (Murdy, 1989). * Min Pau Tan mptan@umt.edu.my 1 School of Fisheries and Aquaculture Sciences, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia 2 Institute of Marine Biotechnology (IMB), Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia 3 Institut Biodiversiti Tropika dan Pembangunan Lestari (BIO-D Tropika), Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia 4 Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3220, Australia 5 Institute of Oceanography and Environment (INOS), Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia Thalassas: An International Journal of Marine Sciences https://doi.org/10.1007/s41208-019-00189-5