Molecular phylogeny and taxonomy of roaches (Rutilus, Leuciscidae) in the southern part of the Caspian Sea

Document Type : Research Paper


1 Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran

2 Freshwater Science Group; Dipartimento di Scienze Biologiche, Geologiche ed Ambientali (BiGeA); AlmaMater Studiorum-Università di Bologna, Bologna, Italy

3 Department of Fisheries, Faculty of Natural Resources, University of Guilan, Sowmeh Sara, Guilan, Iran

4 Zoological Museum, Moscow State University, Biological Department, Moscow, Russia



The aims of this study were to testify a phylogenetic hypothesis for the genus Rutilus in the Southern Caspian Sea using sequence variation of mitochondrial and nuclear genes and to define the taxonomic status of phylogenetic clades represented in this region. Phylogenetic analysis was based on the variability of mitochondrial genes cytochrome b and cytochrome c oxidase subunit I and nuclear recombination activating gene 1 and inter-photoreceptor retinoid-binding protein. Compared to previous studies, this phylogenetic analysis included significant material from the South Caspian, both from the collected samples and from GenBank data. As a result, only two species of Rutilus were confirmed in the ichthyofauna of the studied region. The first of them corresponds to R. lacustris, therefore, materials from the South Caspian can be included in genetically identified vouchers of this species to determine its morphological diagnostic features. The second species represented separate sister phylogenetic lineage for the Pontic populations of R. frisii sensu lato. Due to the low genetic distance between the Caspian and Pontic lineages and the strong overlap of their morphological features, but previously proven divergence in separate Pleistocene refugia, the Caspian populations are classified in this study as a subspecies R. frisii kutum.


Abbasi, K, Moradi, M, Mirzajani, A, Nikpour, M, Zahmatkesh, Y, Abdoli, A & Mousavi-Sabet, H 2019, Ichthyo-   
         diversity in the Anzali Wetland and its related rivers in the southern Caspian Sea basin, Iran. Journal of Animal Diversity, 1: 90-135.
Abbasi, K, Valipour, A, Talebi Haghighi, D, Sarpanah, A & Nezami, S 1999, Atlas of Iranian Fishes. Gilan Inland
       Waters. Gilan Fisheries Research Centre, Rasht. 113 p.
Abdolhay, HA, Pourkazemi, M, Rezvani, S, Kamal Abdul Satar, M, Hosseinzadeh Sahafi, H, Siti Khalijah, D & Siti Shapor, S 2010, Morphometrics studies of Mahisefid (Rutilus frisii kutum, Kamensky, 1901) from selected rivers in the southern Caspian Sea. Iranian Journal of Fisheries Sciences, 9: 118.
Abdolhay, HA, Siti Khalijah, D, Rezvani Gilkolahi, S, Pourkazemi, M, Siti Shapor, S & Javanmard, A 2012,            
        Genetic diversity of Mahisefid (Rutilus frisii kutum, Kamensky 1901) in different rivers of the south Caspian
        Sea using PCR-RFLP. Iranian Journal of Fisheries Sciences, 11: 235-251.
Abdoli, A & Naderi, M 2009, Biodiversity of fishes of the southern basin of the Caspian Sea. Abzian Scientific  
        Publication, Tehran, 237 p. [In Persian].
Abdullah, AHJ, Abdullah, SAG & Yaseen, AT 2022, Composition of fish assemblages in the southern part of the     Main Outfall Drains, Southern Iraq. Caspian Journal of Environmental Sciences, 20 [In Press].
Abdurakhmanov, YA 1962, Freshwater fishes of Azerbaijan. Akademiya Nauk AzerbSSR, Baku [In Russian].
Aliabadian, M, Nijman, V, Mahmoudi, A, Naderi, M, Vonk, R & Vences, M 2014, ExcaliBAR: a simple and fast 
        software utility to calculate intra-and interspecific distances from DNA barcodes. Contributions to Zoology, 83: 79-84.
Aljanabi, SM & Martinez, I 1997, Universal and rapid salt-extraction of high-quality genomic DNA for PCR-based techniques. Nucleic Acids Research, 25: 4692-4693.
Berg, LS 1949, Fishes of freshwaters of the USSR and adjacent countries. Pt. 2: 469-925.
Bogutskaya, NG 1998, Subfamily Leuciscinae. In: Annotated check-list of Cyclostomata and fishes of the
        continental waters of Russia: pp. 54-74. 
Bogutskaya, NG & Naseka, AM 2004, Catalogue of Agnathans and fishes of fresh and brackish waters of Russia 
        with comments on nomenclature and taxonomy. KMK Scientific Press Ltd, Moscow [In Russian].
Bogutskaya, NG, Kijashko, PV, Naseka, AM & Orlova, MI 2013, Identification keys for fish and invertebrates. Vol. 1: Fish and Molluscs. KMK Scientific Press Ltd, Moscow [In Russian].
Chakmehdouz Ghasemi, F, Behmanesh, Sh, Yarmohammadi, M & Hasanzadeh, SM 2014, The study of molecular
        and population diversity of Rutilus frisii kutum in Anzali Lagoon and Shirud River by using of molecular  
        genetic method. Journal of Animal Biology, 7: 21-30.
Chakmehdouz Ghasemi, F & Behmanesh, Sh 2015, Gene diversity and phylogeny relation of two species of Rutilus genus in southern part of Caspian Sea based on DNA sequencing of mitochondrial cytochrome b gene. Journal of Aquaculture Development, 9: 19-28.
Chen, WJ, Miya, M, Saitoh, K & Mayden, RL 2008, Phylogenetic utility of two existing and four novel nuclear 
         gene loci in reconstructing Tree of Life of ray-finned fishes: the order Cypriniformes (Ostariophysi) as acase  
        study. Gene, 423: 125-134.
Coad, BW 1980, Environmental change and its impact on the freshwater fishes of Iran. Biological Conservation, 19: 51-80.
Coad, BW 1995, Freshwater Fishes of Iran. Acta Scientiarum Naturalium Academiae Scientiarum Bohemicae. Brno, 29: 1-6.
Coad, BW 2016, Freshwater fishes of Iran. Retrieved from Revised: 14 November 2016.
Darriba, D, Taboada, GL, Doallo, R & Posada, D 2012, JModelTest 2: more models, new heuristics and parallel 
        computing. Nature Methods, 9: 772.
Ermakov, OA, Levina, MA, Titov, SV & Levin, BA 2017, mtDNA-based identification of two widespread roach  
        species (Rutilus, Cyprinidae) characterized by sympatric zone. Inland Water Biology, 10: 112-114.
Esmaeili, HR, Coad, BW, Gholamifard, A, Nazari, N & Teimory, A 2010, Annotated checklist of the freshwater 
        fishes of Iran. Zoosystematica Rossica, 19: 361-386.
Esmaeili, HR, Sayyadzadeh, G, Eagderi, S & Abbasi, K 2017, Checklist of freshwater fishes of Iran. FishTaxa, 3: 1- 95.
Forouhar Vajargah, M, Sattari, M, Imanpour Namin, J & Bibak, M 2020a, Length-weight, length-length 
         relationships and condition factor of Rutilus kutum (Actinopterygii: Cyprinidae) from the southern Caspian
        Sea, Iran. Journal of Animal Diversity, 2: 56-61.
Forouhar Vajargah, M, Sattari, M, Imanpour Namin, J & Bibak, M 2020b, Length-weight relationship and‎ some
        growth parameters of‎ Rutilus kutum (Kaminski, 1901) in‎ the South Caspian Sea. Experimental animal 
        Biology, 9: 11-20.
Forouhar Vajargah, M, Sattari, M, Imanpour Namin, J & Bibak, M 2021, 'Evaluation of Trace Element  
        Contaminations in the Skin Tissue of Rutilus kutum (Kamensky, 1901) from the South of the Caspian  
        Sea', Journal of Advances in Environmental Health Research, 9: 139-148.
Fricke, R, Eschmeyer, WN & Van der Laan, R (eds) 2022, Eschmeyer’s catalog of fishes: genera, species, 
        version accessed 4 January 2022.
Gharibkhani, M, Pourkazemi, M, Azizzadeh, L, Fallah, BF & Tatina, M 2011, The study on the phylogeny of five 
         species of Caspian Sea cyprinids inferred from mitochondrial cytochrome b gene. Journal of Animal Biology, 3: 33-40
Ghojoghi, F, Eagderi, S & Nasri, M 2018, Body shape comparison of kutum fish Rutilus kutum (Kamensky, 1901)
         from southern Caspian Sea using geometric morphometric methods. Journal of Aquaculture Development, 12: 63-73.
Huelsenbeck, JP & Ronquist, FR 2001, MrBayes: Bayesian inference of phylogeny. Bioinformatics, 17: 754-755.
Jorfipour, M, Keivany, Y, Paykan-Heyrati, F, Ghafoori, Z 2022, Feeding indices of Planiliza abu (Heckel 1843) in Karun River, Southwestern Iran. Caspian Journal of Environmental Sciences, 20: 693-700
Jouladeh-Roudbar, A, Vatandoust, S, Eagderi, S, Jafari-Kenari, S & Mousavi-Sabet, H 2015, Freshwater fishes of Iran; an updated checklist. AACL Bioflux, 8: 855-909.
Jouladeh-Roudbar, A, Ghanavi, HR & Doadrio, I 2020, Ichthyofauna from Iranian freshwater: annotated checklist, diagnosis, taxonomy, distribution and conservation assessment. Zoological Studies, 59: 21.
Jurajda, P & Pavlov, I 2016, Rediscovery of Rutilus virgo in the River Dyje, Czech Republic. Folia Zoologica, 65: 8-100.
Kashiri, H, Shabani, A, Gorgin, S, Rezaii, M & Jabale, AR 2018, Microsatellite DNA marker analysis of genetic
        variation in wild and hatchery populations of Caspian Kutum (Rutilus kutum). Turkish Journal of Fisheries and Aquatic Sciences, 18: 1101-1111.
Kavan, LS, Gilkolaei, SR, Vossoughi, G, Fatemi, SMR, Safari, R & Jamili, S 2009, Population genetic study of
        Rutilus frisii kutum (Kamansky 1901) from the Caspian Sea; Iran and Azerbaijan regions, using microsatellite 
        markers. Journal of Fisheries and Aquatic Science, 4: 316-322.
Keivany, Y, Nasri, M, Abbasi, K & Abdoli, A 2016, Fishes of Iran. Atlas of inland water. Department of
        Environment, Tehran, Iran.
Ketmaier, V, Bianco, PG & Durand, JD 2008, Molecular systematics, phylogeny and biogeography of roaches
        (Rutilus, Teleostei, Cyprinidae). Molecular Phylogenetics and Evolution, 49: 362-367.
Kotlik, P, Markova, S, Choleva, L, Bogutskaya, NG, Ekmekçi, FG & Ivanova, PP 2008, Divergence with gene flow between Ponto-Caspian refugia in an anadromous cyprinid Rutilus frisii revealed by multiple gene 
        phylogeography. Molecular Ecology, 17: 1076-1088.
Kottelat, M 1997, European freshwater fishes. An heuristic checklist of the freshwater fishes of Europe (exclusive of former USSR), with an introduction for non-systematics and comments on nomenclature and conservation. Biologia, Bratislava, 52: 1-271.
Kottelat, M & Freyhof, J 2007, Handbook of European freshwater fishes. Kottelat, Cornol, Switzerland and Freyhof, Berlin, Germany.
Kuljanishvili, T, Epitashvili, G, Freyhof, J, Japoshvili, B, Kalous, L, Levin, B, Mustafayev, N, Ibrahimov, S,
         Pipoyan, S and Mumladze, L 2020, Checklist of the freshwater fishes of Armenia, Azerbaijan and Georgia.  
        Journal of Applied Ichthyology, 36: 4501-514.
Larmuseau, MHD, Freyhof, J, Volckaert, FAM & Van Houdt, JKJ 2009, Matrilinear phylogeography and 
        demographical patterns of Rutilus rutilus: implications for taxonomy and conservation. Journal of Fish 
        Biology, 75: 332-353.
Levin, BA, Simonov, EP, Ermakov, OA, Levina, MA, Interesova, EA, Kovalchuk, OM, Malinina, Y, Mamilov, NS, Mustafayev, NJ, Pilin, DV, Pozdeev, IV, Prostakov, NI, Roubenyan, HR, Titov, SV & Vekhov, DA 2017, Phylogeny and phylogeography of the roaches, genus Rutilus (Cyprinidae), at the Eastern part of its range as inferred from mtDNA analysis. Hydrobiologia, 788: 33-46.
Miller, MA, Pfeiffer, W & Schwartz, T 2010, Creating the CIPRES Science Gateway for inference of large
         phylogenetic trees. In ‘Proceedings of the Gateway Computing Environments Workshop (GCE), New Orleans, LA. pp. 1-8.
Mirzajani, A, Hamidian, AH, Abbasi, K & Karami, M 2016, Distribution and abundance of fish in the southwest of Caspian Sea coastal waters. Russian Journal of Marine Biology, 42: 178-189.
Naseka, NM & Bogutskaya, NG 2009, Fishes of the Caspian Sea: zoogeography and updated check-list.
        Zoosystematica Rossica, 18: 295-317.
Parin, NV, Evseenko, SA & Vasil’Eva, ED 2014, Fishes of Russian seas: annotated catalogue. KMK Scientific
        Press, Moscow, 53, p.733.
Perea, S, Böhme, M, Zupančič, P, Freyhof, J, Šanda, R, Özuluğ, M, Abdoli, A & Doadrio, I 2010, Phylogenetic
        relationships and biogeographical patterns in Circum-Mediterranean subfamily Leuciscinae (Teleostei,
        Cyprinidae) inferred from both mitochondrial and nuclear data. BMC Evolutionary Biology, 10: 265.
Pourshabanan, A, Yazdani-Moghaddam, F, Aliabadian, M, Ghasemzadeh, F & Mousavi-Sabet, H 2020,
         Investigation of species diversity of the Minnows (Cypriniformes: Leuciscinae) in the Caspian Sea basin, Iran using molecular approach. Journal of Applied Ichthyological Research, 8 (5) [In Persian].
Pourshabanan, A, Yazdani-Moghaddam, F, Ghassemzadeh, F, Mousavi-Sabet, H, Rossi, G & Aliabadian, M 2021a, Morpho-species of the genus Leuciscus Cuvier, 1816 (Teleostei: Leuciscinae) from Iran revisited using molecular approaches. Zoology in the Middle East, 67: 126-132.
Pourshabanan, A, Yazdani-Moghaddam, F, Aliabadian, M, Ghasemzadeh, F & Mousavi-Sabet, H 2021b, Molecular Phylogeny of the subfamily Leuciscinae in Iran with emphasis on the genera Leuciscus, Squalius and Petroleuciscus (Actinopterygii: Leuciscidae). PhD Dissertation, Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran [In Persian].
Rashidi, Z, Khara, H & Mousavi-Sabet, H 2012, Hematological profile of the mature Rutilus frisii kutum
        (Cyprinidae) migrated to the Tajan River in the southern Caspian Sea. World Journal of Fish and Marine 
        Sciences, 4: 665-671.
Safari, R 2016, Population structure of Rutilus frisii kutum in Iranian coastline of the Caspian Sea using 
        microsatellite markers. Environmental Resources Research, 4: 65-74.
Sattari, M, Namin, JI, Bibak, M, Vajargah, MF, Hedayati, A, Khosravi, A & Mazareiy, MH 2019a, Morphological
        comparison of western and eastern populations of Caspian kutum, Rutilus kutum (Kamensky, 1901) 
        (Cyprinidae) in the southern Caspian Sea. International Journal of Aquatic Biology, 6: 242-247.
Sattari, M, Imanpour, J, Bibak, M, Forouhar Vajargah, M & Khosravi, A 2019b, Investigation of metal element
        concentrations in tissue of Rutilus frisii in the Southwest Caspian Sea. Iranian Scientific Fisheries Journal, 28: 149-161.
Sattari, M, Namin, JI, Bibak, M, Vajargah, MF, Bakhshalizadeh, S & Faggio, C 2019c, Determination of trace   
         element accumulation in gonads of Rutilus kutum (Kamensky, 1901) from the south Caspian Sea trace element contaminations in gonads. Proceedings of the National Academy of Sciences, India Section B: Biological Sciences, 1-8.
Sattari, M, Bibak, M & Forouhar Vajargah, M 2020, Evaluation of trace elements contaminations in muscles of  
        Rutilus kutum (Pisces: Cyprinidae) from the Southern shores of the Caspian Sea. Environmental Health
        Engineering and Management Journal, 7: 89-96.
Schönhuth, S, Vukić, J, Šanda, R, Yang, L & Mayden, RL 2018, Phylogenetic relationships and classification of the Holarctic family Leuciscidae (Cypriniformes: Cyprinoidei). Molecular Phylogenetics and Evolution, 127: 781-799.
Stamatakis, A 2006, RAxML-VI-HPC: Maximum Likelihood-based phylogenetic analyses with thousands of taxa 
       and mixed models. Bioinformatics, 22: 2688-2690.
Tsoumani, M, Georgiadis, A, Giantsis, IA, Leonardos, I & Apostolidis, AP 2014, Phylogenetic relationships among southern Balkan Rutilus species inferred from cytochrome b sequence analysis: Micro-geographic resolution and taxonomic implications. Biochemical Systematics and Ecology, 54: 172-178.
Vajargah, MF, Hedayati, A, Yalsuyi, AM, Abarghoei, S, Gerami, MH & Farsani, HG 2014, Acute toxicity of  
        butachlor to Caspian kutum (Rutilus frisii Kutum Kamensky, 1991). Journal of Environmental Treatment  
        Techniques, 2:155-157.
Vajargah, MF, Sattari, M, Namin, JI & Bibak, M 2021, Predicting the Trace Element Levels in Caspian Kutum 
         (Rutilus kutum) from South of the Caspian Sea Based on Locality, Season and Fish Tissue. Biological Trace 
        Element Research, 1-10.
Vasil’eva, ED & Luzhnyak, VA 2013, Fishes of the basin of the Azov Sea. SSC RAS Publishers, Rostov-on-Don 
        [In Russian].
Yang, T, Meng, W, Zhang, R, Gao, T, Cai, L, Hai, S & Zhou, Q 2016, DNA barcoding of fishes in Irtysh River 
        China. Russian Journal of Genetics, 52: 969-976.