Abstract
The phylogenetic relationships among 26 species of salmonid fishes (family Salmonidae) were studied using the RAG1 gene as phylogenetic marker. No unambiguous relationships between thymalllins, coregonins, and salmonins it was possible to establish. It seems likely, that divergence of these lineages took place during rather short time interval (about 3 to 4 million years). The thymallins are thought to be the first separated lineage. The genera of the subfamily Salmoninae form two distinct monophyletic groups, represented by (1) Brachymystax and Hucho and (2) Salmo, Parahucho, Salvelinus, Parasalmo and Oncorhynchus. Ancestral forms of these two evolutionary lineages could diverge at the Oligocene-Miocene boundary (about 24 million years ago). It is suggested that diversification of the main lineages within the second group was rather rapid, and took place in middle Miocene (about 19–16 million years ago). Moreover, the lineages of Salvelinus, Parasalmo and Oncorhynchus were the latest to diverge. It seems likely that divergence of the Prosopium and Coregonus ancestral lineages occurred during the same time interval.
References
Evolution illuminated: Salmon and Their Relatives, Hendry, A.P. and Stearns, S.C., Eds., New York: Oxford Univ. Press, 2004.
Davidson, W.S., Koop, B.F., Jones, S.J.M., et al., Sequencing the Genome of the Atlantic Salmon (Salmo salar), Genome Biol., 2010, vol. 11, no. 9, p. 403.
López, J.A., Chen, W.-J., and Ort, G., Esociform Phylogeny, Copeia, 2004, no. 3, pp. 449–464.
Chiari, Y., Meijden, A., Madsen, O., et al., Base Composition, Selection, and Phylogenetic Significance of Indels in the Recombination Activating Gene-1 in Vertebrates, Front. Zool., 2009, vol. 6, p. 32.
Posada, D. and Crandall, K.A., MODELTEST: Testing the Model of DNA Substitution, Bioinformatics, 1998, vol. 14, no. 9, pp. 817–818.
Ronquist, F. and Huelsenbeck, J.P., MRBAYES 3: Bayesian Phylogenetic Inference under Mixed Models, Bioinformatics, 2003, vol. 19, no. 12, pp. 1572–1574.
Swofford, D.L., PAUP* Phylogenetic Analysis Using Parsinomy (and Other Methods): Beta Version 10, Sunderland: Sinauer, 2002.
Felsenstein, J., Evolutionary Trees from DNA Sequences: A Maximum Likelihood Approach, J. Mol. Evol., 1981, vol. 17, no. 6, pp. 368–376.
Drummond, A.J. and Rambaut, A., BEAST: Bayesian Evolutionary Analysis by Sampling Trees, BMC Evol. Biol., 2007, vol. 7, no. 1, p. 214.
Eiting, T.P. and Smith, G.R., Miocene Salmon (Oncorhynchus) from Western North America: Gill Raker Evolution Correlated with Plankton Productivity in the Eastern Pacific, Palaeogeogr. Palaeoclimatol. Palaeoecol., 2007, vol. 249, nos. 3–4, pp. 412–424.
Wilson, M.V.H. and Li, G.-Q., Osteology and Systematic Position of the Eocene Salmonid †Eosalmo driftwoodensis Wilson from Western North America, Zool. J. Linn. Soc., 1999, vol. 125, no. 3, pp. 279–311.
Koop, B.F., Schalburg, K.R., Leong, J., et al., A Salmonid EST Genomic Study: Genes, Duplications, Phylogeny and Microarrays, BMC Genomics, 2008, vol. 9, p. 545.
Oakley, T.H. and Phillips, R.B., Phylogeny of Salmonine Fishes Based on Growth Hormone Introns: Atlantic (Salmo) and Pacific (Oncorhynchus) Salmon Are not Sister Taxa, Mol. Phylogenet. Evol., 1999, vol. 11, no. 3, pp. 381–393.
Crespi, B.J. and Fulton, M.J., Molecular Systematics of Salmonidae: Combined Nuclear Data Yields a Robust Phylogeny, Mol. Phylogenet. Evol., 2004, vol. 31, no. 2, pp. 658–679.
Matveev, V. and Okada, N., Retroposons of Salmonoid Fishes (Actinopterygii: Salmonoidei) and Their Evolution, Gene, 2009, vol. 434, nos. 1–2, pp. 16–28.
Phillips, R.B., Matsuoka, M.P., Konkol, N.R., and McKay, S., Molecular Systematics and Evolution of the Growth Hormone Introns in the Salmoninae, Environ. Biol. Fishes, 2004, vol. 69, nos. 1–4, pp. 433–440.
Osinov, A.G. and Lebedev, V.S., Salmonid Fishes (Salmonidae, Salmoniformes): The Systematic Position in the Superorder Protacanthopterygii, the Main Stages of Evolution, and Molecular Dating, Vopr. Ikhtiol., 2004, vol. 44, no. 6, pp. 738–765.
Wilson, W.D. and Turner, T.F., Phylogenetic Analysis of the Pacific Cutthroat Trout (Oncorhynchus clarki ssp.: Salmonidae) Based on Partial mtDNA ND4 Sequences: A Closer Look at the Highly Fragmented Inland Species, Mol. Phylogenet. Evol., 2009, vol. 52, no. 2, pp. 406–415.
Li, J., Xia, R., McDowall, R.M., et al., Phylogenetic Position of the Enigmatic Lepidogalaxias salamandroides with Comment on the Orders of Lower Euteleostean Fishes, Mol. Phylogenet. Evol., 2010, vol. 57, no. 2, pp. 932–936.
Yasuike, M., Jantzen, S., Cooper, G.A., et al., Grayling (Thymallinae) Phylogeny within Salmonids: Complete Mitochondrial DNA Sequences of Thymallus arcticus and Thymallus thymallus, J. Fish. Biol., 2010, vol. 76, pp. 395–400.
Shedko, S.V., Phylogeny of Mitochondrial DNA in Salmonids of the Subfamily Salmoninae: Analysis of the Cytochrome b Gene Sequences, Russ. J. Genet., 2002, vol. 38, no. 3, pp. 277–285.
Osinov, A. and Lebedev, V.S., Genetic Divergence and Phylogeny of the Salmoninae Based on Allozyme Data, J. Fish. Biol., 2000, vol. 57, no. 2, pp. 354–381.
Author information
Authors and Affiliations
Corresponding author
Additional information
Original Russian Text © S.V. Shedko, I.L. Miroshnichenko, G.A. Nemkova, 2012, published in Genetika, 2012, Vol. 48, No. 5, pp. 676–680.
Rights and permissions
About this article
Cite this article
Shedko, S.V., Miroshnichenko, I.L. & Nemkova, G.A. Phylogeny of salmonids (Salmoniformes: Salmonidae) and its molecular dating: Analysis of nuclear RAG1 gene. Russ J Genet 48, 575–579 (2012). https://doi.org/10.1134/S1022795412050201
Received:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S1022795412050201