Phylogeography of Oxyeleotris marmorata (Marble Goby) reveals a novel cytochrome c oxidase subunit I (COI) haplotype from borneo

¹ Department of Biology, Faculty of Sciences and Technology, Universitas Airlangga. Jl. Dr. Ir. H. Soekarno, Mulyorejo, Surabaya, East Java 60115, Indonesia
² Advanced Tropical Biodiversity, Genomics, and Conservation Research Group, Faculty of Science and Technology, Universitas Airlangga. Jl. Dr. Ir. H. Soekarno, Mulyorejo, Surabaya, East Java 60115, Indonesia
³ Department of Biology, Faculty of Mathematics and Natural Science, Universitas Mulawarman, Jl. Barong Tongkok No. 4, Samarinda, East Kalimantan 75242, Indonesia
⁴ Freshwater Aquaculture Research Center, National Research and Innovation Agency, Jl. Raya Jakarta - Bogor KM 46, Cibinong 16911, Indonesia
⁵ Study Program of Aquaculture, Department of Health and Life Sciences, Faculty of Health, Medicine, and Life Sciences, Universitas Airlangga, Jl. Wijaya Kusuma No.113, Banyuwangi, East Java 68425, Indonesia
⁶ Department Of Aquatic Resources Management, Faculty of Marine Science and Fisheries, Udayana University, Jl. Raya Kampus Unud, Jimbaran, Badung, Bali 80361, Indonesia
⁷ Department of Marine Biology, Pukyong National University, Yongso-ro 45, Nam-Gu, Busan 48513, Republic of Korea
⁸ Aquatic Ecology and Evolution Group, Department of Biology, University of Konstanz, Germany

^* Corresponding author: This email address is being protected from spambots. You need JavaScript enabled to view it.

Abstract

The marble goby (Oxyeleotris marmorata) is an ecologically and economically important freshwater fish distributed in Southeast Asia, yet its phylogeographic patterns remain insufficiently understood. In this study, we investigated the genetic variation of marble goby populations using mitochondrial cytochrome oxidase subunit I (COI) gene sequences. Specimens were collected from the Brantas River in East Java and the Mahakam River in East Kalimantan, and additional sequence data were integrated from the GenBank database to broaden the geographic coverage. A total of 32 samples were analyzed, revealing a maximum of seven nucleotide differences among sequences, with overall similarity ranging from 98.46% to 100%. The haplotype accumulation curve reached an asymptote at approximately seven haplotypes, indicating a limited but distinct level of genetic variation within the sampled population. Two major genetic clusters were revealed: a well-supported monophyletic Java clade dominated by a single haplotype, and a diverse mainland Southeast Asian clade characterized by unique, region-specific haplotypes with limited sharing, suggesting long-term isolation. A novel Bornean haplotype was identified, clustering closely with the mainland lineage. Overall nucleotide diversity was low (π = 0.0032), indicating reduced genetic variation and raising concerns about the species’ vulnerability. These findings highlight strong regional structuring, limited gene flow among populations, and the potential conservation significance of maintaining genetic diversity in O. marmorata.