Molecular phylogenetic affinities of some subtidal gobies (Teleostei: Gobiidae) from Qeshm Island

Document Type : Research articles


Department of Biology, Faculty of Science, University of Sistan and Baluchestan, Zahedan, Iran


Typical gobies are small in size and usually found as marine fishes. They inhabit on or whitin the substrates holes, and are mostly invisible. The present study identified two goby genera including Valenciennea and Gobiodon in Qeshm Island for the first time. Nuclear rhodopsin gene was sequenced in four goby species including G. citrinus, V. puellaris, V. sexguttata, as well as V. strigata. Furthermore, nuclear rhodopsin and mitochondrial cytochrome oxidase subunit I (COI) sequences of 38 Gobiidae species from GenBank were used to obtain a representative data-set in order to assess the phylogenetic position of the new samples and to compare the resultant tree with other related molecular reconstructions. Our phylogenetic tree was composed of two Clades. Clade 1 involved two genera including Gobiodon and Paragobiodon and Clade 2 involved three genera, including Valenciennea, Signigobius and Amblygobius. While, Valenciennea and Signigobius species were nested within Sub-Clade X, only Amblygobius species was nested within Sub-Clade Y. This study examined the phylogenetic relationships of four goby species using Rhodopsin and COI, as new markers. Our results on molecular phylogenetic analysis were in agreement with those of other studies using different molecular markers and morphological examinations.


Agorreta, A., San Mauro, D., Schliewen, U., Van Tassell, J.L., Kovačić, M., Zardoya, R., Rüber, L., 2013. Molecular phylogenetics of Gobioidei and phylogenetic placement of European gobies. Molecular Phylogenetic Evolution 69(3), 619-633.
Bishop, J.M., 2003. History and current checklist of Kuwait's ichthyofauna. Journal of Arid Environments 54(1), 237-256.
Blegvad, H., Løppenthin, B., 1944. Fishes of the Iranian Gulf. Danish Scientific Investigations in Iran. Einar Munksgaard Copenhagen, 247 p.
Bosaghzadeh, F., Ghanbarifardi, M., Pehpuri, A., Maddahi, H., 2015. Intertidal ichthyofauna of the Persian Gulf and Makran Sea with a new record from the Persian Gulf. The Third Iranian Conference of Ichthyology, Shiraz University, 6-7 May 2015.
Duchene, D., Klanten, S.O., Munday, P.L., Herler, J., van Herwerden, L., 2013. Phylogenetic evidence for recent diversification of obligate coral-dwelling gobies compared with their host corals. Molecular Phylogenetic Evolution 69(1), 123-132.
Eagderi, S., Fricke, R., Esmaeili, H.R., Jalili, P., 2019. Annotated checklist of the fishes of the Persian Gulf: Diversity and conservation status. Iranian Journal of Ichthyology 6, 1-171.
Felsenstein, J., 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17(6), 368-376.
Fricke, R., Eschmeyer, W.N., Fong, J.D., 2020. Species by family/subfamily in Eschmeyer's Catalog of Fishes, Online Version, Updated 2 March 2020.
Ghanbarifardi, M., Malek, M., 2007. Permanent intertidal fish from the Persian Gulf and Gulf of Oman, Iran. Iranian Journal of Animal Biosystematics 3(1), 1-14.
Ghanbarifardi, M., Malek, M., 2009. Distribution, diversity, and abundance of rocky intertidal fishes in the Persian Gulf and Gulf of Oman, Iran. Marine Biology Research 5(5), 496-502.
Ghanbarifardi, M., Lagzian, M., 2019. Molecular phylogeny of some gobies (Teleostei, Gobiidae) from Iranian water bodies with a new record. Russian Journal of Marine Biology 45, 385-392.
Harold, A.S., Winterbottom, R., Munday, P.L., Chapman, R.W., 2008. Phylogenetic relationships of Indo-Pacific coral gobies of the genus Gobiodon (Teleostei: Gobiidae), based on morphological and molecular data. Bulletin of Marine Science 82(1), 119-136.
Herler, J., Bogorodsky, S.V., Suzuki, T., 2013. Four new species of coral gobies (Teleostei: Gobiidae: Gobiodon), with comments on their relationships within the genus. Zootaxa 3709(4), 301-329.
Hoese, D.F., Allen, G.R., 1977. Signigobius biocellatus, a new genus and species of sand-dwelling coral reef gobiid fish from the western tropical Pacific. Japanese Journal of Ichthyology 23(4), 199-207.
Hoese, D.F., Larson, H.K., 1994. Revision of the Indo-Pacific gobiid fish genus Valenciennea, with descriptions of seven new species. Indo-Pacific Fishes, 23, 1-71.
Huelsenbeck, J.P., Ronquist, F., Nielsen, R., Bollback, J.P. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294(5550), 2310-2314.
Jones, D.A., 1986. A field guide to the sea shores of Kuwait and the Persian Gulf. University of Kuwait pp.1-192.
Katoh, K., Standley, D.M., 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology Evolution 30(4), 772-780.
Kovačić, M., Bogorodsky, S.V., Mal, A.O., Alpermann, T.J., 2018. First record of Valenciennea parva (Teleostei: Perciformes, Gobiidae) for the Red Sea, with a key to Red Sea species of the genus. Marine Biodiversity 48(2), 1229-1236.
Kovačić, M., Sadeghi, R., Esmaeili, H.R., 2020. New species of Silhouettea (Teleostei: Gobiidae) from Qeshm Island, Iran and the DNA barcoding of the Persian Gulf and Oman Sea gobies. Zootaxa 4750(1), 49-66.
Kuronuma, K., Abe, Y., 1972. Fishes of Kuwait. Kuwait Institute for Scientific Research. Safat Kuwait, 323 p.
Lanfear, R., Frandsen, P.B., Wright, A.M., Senfeld, T., Calcott, B., 2016. Partition Finder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Molecular Biology Evolution 34(3), 772-773.
Polgar, G., Ghanbarifardi, M., Milli, S., Agorreta, A., Aliabadian, M., Esmaeili, H.R., Khang, T.F., 2017. Ecomorphological adaptation in three mudskippers (Teleostei: Gobioidei: Gobiidae) from the Persian Gulf and the Gulf of Oman. Hydrobiologia 795(1), 91-111.
Rahimian, H., Pehpuri, A., 2006. Intertidal Fishes of Qeshm Island the Persian Gulf. I. Gobiidae (Pisces: Perciformes). Journal of Science (University of Tehran) 334, 69-76.
Randall, J.E., 1995. Coastal fishes of Oman. University of Hawaii Press , 439 pp.
Ronquist, F., Teslenko, M., Van Der Mark, P., Ayres, D.L., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M.A., Huelsenbeck, J.P., 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61(3), 539-542.
Sadeghi, R., Esmaeili, H.R., Fricke, R., Larson, H., 2017. New geographical record and morphological features of the Indo Pacific tropical sand goby, Favonigobius reichei (Bleeker, 1854) from Iranian coast of the Makran Sea (Teleostei, Gobiidae). Check List 13, 641-645.
Sadeghi, R., Esmaeili, H.R., 2019a. Cocos Frillgoby, Bathygobius cocosensis (Bleeker, 1854): an additional fish element for the Iranian marine waters (Teleostei: Gobiidae). International Journal of Aquatic Biology 7(3), 117-122.
Sadeghi, R., Esmaeili, H.R., 2019b. First documentation of an uncommon goby genus and species, Palutrus scapulopunctatus (de Beaufort, 1912) from the Persian Gulf (Teleostei: Gobiidae). Iranian Journal of Ichthyology 6(3), 143-149.
Sadeghi, R., Ebrahimi, M., Esmaeili, H.R., 2019a. Tessellate goby, Coryogalops tessellatus Randall, 1994 (Teleostei: Gobiidae), an additional fish element for the Iranian marine waters. FishTaxa 4(2), 25-30.
Sadeghi, R., Esmaeili, H.R., Riazi, M., Taherizadeh, M.R., Safaie, M., 2019b. Lagoon shrimp goby, Cryptocentrus cyanotaenia (Bleeker, 1853) (Teleostei: Gobiidae), an additional fish element for the Iranian waters. Iranian Journal of Ichthyology 6(2), 98-105.
Stamatakis, A., 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9), 1312-1313.
Suzuki, T., Senou, H., Randall, J.E., 2016. Valenciennea yanoi, a new gobiid fish from the Ryukyu Islands, Japan (Teleostei: Gobiidae). Journal of the Ocean Science Foundation 21, 1-9.
Thacker, C.E., 2011. Systematics of Gobiidae. In: Patzner, R.A., Van Tassell, J.L., Kovacˇic´, M., Kapoor, B.G. (Eds.). The Biology of Gobies, Science Publishers. Enfield NH. pp: 129-136.
Thacker, C.E., Roje, D.M., 2011. Phylogeny of Gobiidae and identification of gobiid lineages. Systematics and Biodiversity 9(4), 329-347.