Evolution of the salmonid mitochondrial control region

Comparison of evolutionary rates in the mitochondrial DNA cytochrome b gene and control region and their implications for phylogeny of the Cobitoidea (Teleostei: Cypriniformes)

“…In rat and mouse, Brown et al (1986) found a slower rate of substitution in CR than that of protein-coding genes. A slower rate of substitution in CR was also found in salmonid Wshes (Bernatchez and Danzmann, 1993;Shedlock et al, 1992), and butterXies of the genus Jalmenus (Taylor et al, 1993). Zhu et al (1994) compared relative rates and patterns of sequence evolution in CR and cyt b sequences from diVerent populations and species of freshwater rainbow Wshes of the genus Melanotaenia, and discovered that the overall levels of divergence were similar for these two gene segments but patterns of sequence evolution varied.…”

Phylogenetic relationship of the genus Oncorhynchus species inferred fromnuclear and mitochondrial markers.

“…We used allozyme electrophoresis to clarify the phylogenetic relationship between the Pacific salmon group and the Pacific trout group. Furthermore, we reanalysed published mitochondrial DNA D-loop sequences (Shedlock et al, 1992). Allozymic data and mtDNA data indicated the following consistent results; (1) all Pacific salmons formed a monophyletic cluster, (2) chum salmon and pink salmon were clustered within those Pacific salmons, (3) masu salmon formed a cluster with other Pacific salmons and diverged first in this group.…”

“…The genus Oncorhynchus belongs to the family Salmonidae and have been the subjects of numerous phylogenetic studies using morphology (Hikita, 1962;Smith and Stearley, 1989), allozyme electrophoresis (Utter et al, 1973), restriction fragment length polymorphism [RFLP] of ribosomal RNA genes [rDNA] (Phillips et al, 1992), RFLP of mitochondrial DNA [mtDNA] (Thomas et al, 1986), HindIII fragment (ATPase 6, CO III, tRNA GLY , ND 3, tRNA ARG , and ND 4L) sequences of mtDNA (Thomas and Beckenbach, 1989), D-loop sequences of mtDNA (Shedlock et al, 1992), ATPase 6 and ND 3 sequences of mtDNA (Domanico and Phillips, 1995), and short interspersed repetitive elements [SINEs] (Kido et al, 1991;Murata et al, 1993;Takasaki et al, 1996). These studies are in general agreements that Oncorhynchus had branched into four groups; (1) the Pacific trout group that consists of rainbow trout (O. mykiss; nijimasu) and cutthroat trout (O. clarki), (2) coho salmon (O. kisutch; ginzake) and chinook salmon (O. tschawytscha; masunosuke) of the Pacific salmon group [we call them A-lineage in this paper], (3) pink salmon (O. gorbuscha; karafutomasu), sockeye salmon (O. nerka; benizake), and chum salmon (O. keta; sake) of the Pacific salmon group [we call them B-lineage in this paper], and (4) masu salmon (O. masou; yamame) of the Pacific salmon group (Fig.…”

Mitochondrial COI Gene Sequence Analyses of Puntius ticto and Compared with Seven Species of Genus Puntius of Family Cyprinidae: A Finding for Phylogenetic Positioning and DNA Barcoding as Model Study for Cryptic Species

“…Although a few base substitutions were identified in the Cox1 sequences of the species, short insertions/deletions were more frequent. Similarly, the occurrence of short base insertions and deletions has been observed in the mtDNA sequences of other fish, such as salmonid species [37]. Five DNA sequences of P. ticto were analyzed in the laboratory.…”