Molecular Phylogeny

Saitoh K. 2021. Conservation issues partly solved on "Suigenzenitanago" (Rhodeus smithii complex) impaired by the taxonomic confusion. Ichthyol Res 68:322-324.

Igarashi Y, Zhang H, Tan E, Sekino M, Yoshitake K, Kinoshita S, Mitsuyama S, Yoshinaga T, Chow S, Kurogi H, Shinoda A, Han Y-S, Wakiya R, Mochioka N, Yamamoto T, Kuwada H, Kaji Y, Suzuki Y, Gojobori T, Kobayashi T, Saitoh K, Watabe S, Asakawa S. 2018. Whole-genome sequencing of 84 Japanese eels reveals evidence against panmixia and support for sympatric speciation. Genes 9:474.

Saitoh K. 2019. Reconciliation of taxonomy with laboratory fish research communities. Ichthyol Res 66:192-197.

Saitoh K. 2018. Clupeiformes and Ostariophysi: their evolutionary relationships, pp64-67. In: Jpn Soc Ichthyol (ed). The Encyclopedia of Ichthyology, Maruzen, Tokyo.

Nakamura Y, Yasuike M, Mekuchi M, Iwasaki Y, Ojima N, Fujiwara A, Chow S, Saitoh K. 2017. Rhodopsin gene copies in Japanese eel originated in a teleost-specific genome duplication. Zool Lett 3:18.

Tajima N, Saitoh K, Sato S, Maruyama F, Ichinomiya M, Yoshikawa S, Kurokawa K, Ohta H, Tabata S, Kuwata A, Sato N. 2016. Sequencing and analysis of the complete organellar genomes of Parmales, a closely related group to Bacillariophyta (diatoms). Curr Genet 62:887-896.

Yang L, Sado T, Hirt MV, Pasco-Viel E, Arunachalam M, Li J, Wang X, Freyhof J, Saitoh K, Simons AM, Miya M, He S, Mayden RL. 2015. Phylogeny and polyploidy: resolving the classification of cyprinine fishes (Teleostei: Cypriniformes). Mol Phylogenet Evol 85:97-116.

Kartavtsev YP, Sharina SN, Saitoh K, Imoto JM, Hanzawa N, Redin AD. 2016. Phylogenetic relationships of Russian far eastern flatfish (Pleuronectiformes, Pleuronectidae) based on two mitochondrial gene sequences, Co-1 and Cyt-b, with inferences in order phylogeny using complete mitogenome data. Mitochondrial DNA 27:667-678.

Saitoh K. 2014. Interrelationships and classification of fishes of the family Cyprinidae. Aquabiology 210:116-124.

Nishikawa T, Oohara I, Saitoh K, Shigenobu Y, Hasegawa N, Kanamori M, Baba K, Turon X, Bishop JDD. 2014. Molecular and morphological discrimination between an invasive ascidian, Ascidiella aspersa and its congener A. scabra (Urochordata: Ascidiacea). Zool Sci 31:180-185.

Nakamura Y, Mori K, Saitoh K, Oshima K, Mekuchi M, Sugaya T, Shigenobu Y, Ojima N, Muta S, Fujiwara A, Yasuike M, Oohara I, Hirakawa H, Chowdhury VS, Kobayashi T, Nakajima K, Sano M, Wada T, Tashiro K, Ikeo K, Hattori M, Kuhara S, Gojobori T, Inouye K. 2013. Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna. Proc Natl Acad Sci USA 110:11061-11066.

Tang KL, Agnew MK, Hirt MV, Lumbantobing DN, Raley ME, Sado T, Teoh V-H, Yang L, Harris PM, He S, Miya M, Saitoh K, Simons AM, Wood RM, Mayden RL. 2013. Limits and phylogenetic relationships of East Asian fishes Oxygastrinae (Teleostei: Cypriniformes: Cyprinidae). Zootaxa 3681:101-135.

Imoto JM, Saitoh K, Sasaki T, Yonezawa T, Adachi J, Kartavtsev YP, Miya M, Nishida M, Hanzawa N. 2013. Phylogeny and biogeography of highly diverged freshwater fish species (Leuciscinae, Cyprinidae, Teleostei) inferred from mitochondrial genome analysis. Gene 514:112-124.

Kuwata A, Ichinomiya M, Yoshikawa S, Ohki K, Kamiya M, Takaichi S, Kawachi M, Saitoh K, Sato N, Sawada K. 2012. Parmales, an insight into diatom ancestry? J Phycol 48:S11-S12.

Yang L, Arunachalam M, Sado T, Levin BA, Golubtsov AS, Freyhof J, Friel JP, Chen WJ, Vincent Hirt M, Manickam R, Agnew MK, Simons AM, Saitoh K, Miya M, Mayden RL, He S. 2012. Molecular phylogeny of the cyprinid tribe Labeonini (Teleostei: Cypriniformes). Mol Phylogenet Evol 65:362-379.

Nakatani M, Miya M, Mabuchi K, Saitoh K, Nishida M. 2011. Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation. BMC Evol Biol 11:177.

Tang KL, Agnew MK, Chen W-J, Hirt MV, Raley ME, Sado T, Schneider LM, Yang L, Bart HL, He SP, Liu H, Miya M, Saitoh K, Simons AM, Wood RM, Mayden RL. 2011. Phylogeny of the gudgeons (Teleostei: Cyprinidae: Gobioninae). Mol Phylogenet Evol 61:103-124.

Saitoh K, Sado T, Doosey MH, Bart HLJr, Inoue JG, Nishida M, Mayden RL, Miya M. 2011. Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi). Zool J Linn Soc 161:633-662.

Yang L, Mayden RL, Sado T, He SP, Saitoh K, Miya M. 2010. Molecular phylogeny of the fishes traditionally referred to Cyprinini sensu stricto (Teleostei: Cypriniformes). Zool Scr 39:527-550.

Tang KL, Agnew MK, Chen W-J, Hirt MV, Sado T, Schneider LM, Freyhof J, Sulaiman Z, Swartz E, Vidthayanon C, Miya M, Saitoh K, Simons AM, Wood RM, Mayden RL. 2010. Systematics of the subfamily Danioninae (Teleostei: Cypriniformes: Cyprinidae). Mol Phylogenet Evol 57:189-214.

Saitoh K, Chen W-J, Mayden RL. 2010. Extensive hybridization and tetrapolyploidy in spined loach fish. Mol Phylogenet Evol 56:1001-1010.

Doosey MH, Bart HLJr, Saitoh K, Miya M. 2010. Phylogenetic relationships of catostomid fishes (Actinopterygii: Cypriniformes) based on mitochondrial ND4/ND5 gene sequences. Mol Phylogenet Evol 54:1028-1034.

Mayden RL, Chen W-J, Bart HL, Doosey MH, Simons AM, Tang KL, Wood RM, Agnew MK, Yang L, Hirt MV, Clements MD, Saitoh K, Sado T, Miya M, Nishida M. 2009. Reconstructing the phylogenetic relationships of the earth's most diverse clade of freshwater fishes – order Cypriniformes (Actinopterygii: Ostariophysi): A case study using multiple nuclear loci and the mitochondrial genome. Mol Phylogenet Evol 51:500-514.

Chen W-J, Miya M, Saitoh K, Mayden RL. 2008. Phylogenetic utility of two existing and four novel nuclear loci in reconstructing tree of life of ray-finned fishes: the order Cypriniformes (Ostariophysi) as a case study. Gene 423:125-134.

Mayden RL, Tang KL, Wood RM, Chen W-J, Agnew M, Conway KW, Yang L, Simons AM, Bart HL, Harris PM, Li J, Wang Z, Saitoh K, He S, Liu H, Chen Y, Nishida M, Miya M. 2008. Inferring the tree of life of the order Cypriniformes, the earth's most diverse clade of freshwater fishes: Implications of varied taxon and character sampling. J Syst Evol 46:424-438.

Mayden RL, Tang KL, Conway KW, Freyhof J, Chamberlain J, Haskins M, Schneider L, Sudkamp M, Wood RM, Agnew M, Bufalino A, Sulaiman Z, Miya M, Saitoh K, He S. 2007. Phylogenetic relationships of Danio within the order Cypriniformes: A framework for comparative and evolutionary studies of a model species. J Exp Zool 308B:642-654.

Lavoue S, Miya M, Saitoh K, Ishiguro NB, Nishida M. 2007. Phylogenetic relationships among anchovies, sardines, herrings and their relatives (Clupeiformes), inferred from whole mitogenome sequences. Mol Phylogenet Evol 43:1096-1105.

Saitoh K, Sado T, Mayden RL, Hanzawa N, Nakamura K, Nishida M, Miya M. 2006. Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): The first evidence toward resolution of higher-level relationships of the world's largest freshwater fish clade based on 59 whole mitogenome sequences. J Mol Evol 63:826-841.

Miya M, Saitoh K, Wood R, Nishida M, Mayden RL. 2006. New primers for amplifying and sequencing the mitochondrial ND4/ND5 gene region of the Cypriniformes (Actinopterygii: Ostariophysi). Ichthyol Res 53:75-81.

Saitoh K, Muraoka D. 2006. Undaria mitochondrial large subunit ribosomal DNAs (Phaeophyceae, Alariaceae): Structural properties and use for phylogenetic analysis. Phycol Res 54:149-153.

Lavoue S, Miya M, Inoue JG, Saitoh K, Ishiguro NB, Nishida M. 2005. Molecular systematics of the gonorynchiform fishes (Teleostei) based on whole mitogenome sequences: Implications for higher-level relationships within the Otocephala. Mol Phylogenet Evol 37:165-177.

Saitoh K, Miya M, Inoue JG, Ishiguro NB, Nishida M. 2003. Mitochondrial genomics of ostariophysan fishes: Perspectives on phylogeny and biogeography. J Mol Evol 56:464-472.

Saitoh K, Kobayashi T, Asahida T, Hayashizaki K, Yokoyama Y, Toyohara H, Yamashita Y. 2001. Sequence and structure of Japanese flounder (Paralichthys olivaceus) mitochondrial genome. Bull Tohoku Natl Fish Res Inst 64:1-36.

Saitoh K, Kobayashi T, Ueshima R, Numachi K. 2000. Analyses of mitochondrial and satellite DNAs on spined loaches of the genus Cobitis from Japan have revealed relationships among populations of three diploid-tetraploid complexes. Folia Zool 49(S1):9-16.

Saitoh K, Hayashizaki K, Yokoyama Y, Asahida T, Toyohara H, Yamashita Y. 2000. Complete nucleotide sequence of Japanese flounder (Paralichthys olivaceus) mitochondrial genome: structural properties and cue for resolving teleostean relationships. J Hered 91:271-278.