title: Diversification of mitochondrial genome of Daphnia galeata (Cladocera, Crustacea): Comparison with phylogenetic consideration of the complete sequences of clones isolated from five lakes in Japan.
abstract: To characterize genetic diversity and gene flow among Daphnia galeata populations, the complete nucleotide (nt) sequences of the mitochondrial (mt) DNAs of D. galeata clones isolated from five lakes in Japan (Lakes Shirakaba, Suwa, Kizaki, Kasumigaura, and Biwa) were determined. Comparison of non-synonymous (amino acid altering) substitution rates with synonymous substitution rates of D. galeata mt protein-coding genes demonstrated that ATPase8 and COI genes were the most and least susceptible, respectively, to the evolutional forces selecting the aa substitutions. Several non-synonymous substitutions were found in ATPase8 and ATPase6 even in the comparison that no synonymous substitution was found. Comparison of the total number of nt variations among the mt DNAs suggested the phylogenetic relationship ((((Shirakaba/Suwa, Kizaki), Kasumigaura), Biwa), D. pulex). Maximum-likelihood analysis using the total nt sequences of mt protein-coding genes confirmed this relationship with bootstrap values higher than 98%. All the mtDNAs of the analyzed Japanese D. galeata clones contained a control region of essentially the same structure that is distinct from those of the previously reported European Daphnia species of the D. longispina complex. The two control regions of different structures spread among mtDNAs of the Japanese and European Daphnia species, respectively, probably after the divergence of the Japanese D. galeata under different selection pressures associated with their habitats.
authors.affiliation: School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan. Electronic address: shinichi@ls.toyaku.ac.jp.
authors.forename: Shin-Ichi
authors.initials: SI
authors.lastname: Tokishita
authors.affiliation: School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Shibuya
authors.affiliation: School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.
authors.forename: Taku
authors.initials: T
authors.lastname: Kobayashi
authors.affiliation: Department of Environmental Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan.
authors.forename: Masaki
authors.initials: M
authors.lastname: Sakamoto
authors.affiliation: Department of Environmental Sciences, Faculty of Science, Shinshu University, Matsumoto Asahi 3-1-1, Nagano 390-8621, Japan.
authors.forename: Jin-Yong
authors.initials: JY
authors.lastname: Ha
authors.affiliation: School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.
authors.forename: Shin-Ichi
authors.initials: SI
authors.lastname: Yokobori
authors.affiliation: School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.
authors.forename: Hideo
authors.initials: H
authors.lastname: Yamagata
authors.affiliation: Suwa Hydrobiological Station, Shinshu University, 5-2-4 Kogandori, Suwa, Nagano 392-0027, Japan.
authors.forename: Takayuki
authors.initials: T
authors.lastname: Hanazato
mesh_terms: D000818:Animals; D060829:Arthropod Proteins / Q000235:genetics; D001483:Base Sequence; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics*; D003621:Daphnia / Q000145:classification / Q000235:genetics*; D023061:Gene Order; D050259:Genes, Mitochondrial / Q000235:genetics; D014644:Genetic Variation; D054629:Genome, Mitochondrial / Q000235:genetics*; D007564:Japan; D060106:Lakes / Q000469:parasitology; D024101:Mitochondrial Proteins / Q000235:genetics; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity
chemical_list: D060829:Arthropod Proteins; D004272:DNA, Mitochondrial; D024101:Mitochondrial Proteins
keywords: Control region; Daphnia galeata; Mitochondrial DNA; Phylogenetic tree; Positive selection; ka/ks ratio