Intraspecific sequence variation in the mitochondrial genome of rainbow trout (<i>Oncorhynchus mykiss</i>)

Beckenbach, Andrew T.; Thomas, W. Kelley; Sohrabi, Hoda

doi:10.1139/g90-003

Cited by 30 publications

(10 citation statements)

References 7 publications

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“…Recalculation for these groups produced the grand mean K2P = 0.25 ± 0.04% (here and in further text, ± is followed by SE). A similar value was obtained for a 2214-bp mtDNA fragment, treated with restriction endonuclease HindIII in five individuals of Oncorhynchus mykiss from different populations (Beckenbach et al, 1990): mean for p = 0.254 ± 0.025%. Average (arithmetic mean, M) intrapopulation pdistances were: M = 1.38 ± 0.30% and M = 0.89 ± 0.16%, respectively for genes Cyt-b and Co-1 (Table 1; see supplementary Table 1 for more details, Appendix).…”

Section: Intraspecies Differentiation At Dna Markerssupporting

confidence: 76%

Sequence divergence at mitochondrial genes in animals: Applicability of DNA data in genetics of speciation and molecular phylogenetics

Kartavtsev

2011

Marine Genomics

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Section: Intraspecies Differentiation At Dna Markerssupporting

confidence: 76%

Sequence divergence at mitochondrial genes in animals: Applicability of DNA data in genetics of speciation and molecular phylogenetics

Kartavtsev

2011

Marine Genomics

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“…Transition bias in nucleotide substitution is a ubiquitous phenomenon in animal mitochondrial DNA (mtDNA), having been reported in both vertebrate species (Brown and Simpson 1982;Aquadro and Greenberg 1983;Thomas and Bechkenbach 1989;Bechkenbach et al 1990;Edwards and Wilson 1990;Irwin et al 1991) and invertebrate species (DeSalle et al 1987;Satta et al 1987;Thomas et al 1989;Thomas and Wilson 1991). Although the phenomenon of transition bias is poorly understood, two contributing factors have been suggested.…”

Section: Introductionmentioning

confidence: 99%

On transition bias in mitochondrial genes of pocket gophers

1996

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The relative contribution of mutation and purifying selection to transition bias has not been quantitatively assessed in mitochondrial protein genes. The observed transition/transversion (s/v) ratio is (micros Ps)/(microv Pv), where micros and microv denote mutation rate of transitions and transversions, respectively, and Ps and Pv denote fixation probabilities of transitions and transversions, respectively. Because selection against synonymous transitions can be assumed to be roughly equal to that against synonymous transversions, Ps/Pv approximately 1 at fourfold degenerate sites, so that the s/v ratio at fourfold degenerate sites is approximately micros/microv, which is a measure of mutational contribution to transition bias. Similarly, the s/v ratio at nondegenerate sites is also an estimate of micros/microv if we assume that selection against nonsynonymous transitions is roughly equal to that against nonsynonymous transversions. In two mitochondrial genes, cytochrome oxidase subunit I (COI) and cytochrome b (cyt-b) in pocket gophers, the s/v ratio is about two at nondegenerate and fourfold degenerate sites for both the COI and the cyt-b genes. This implies that mutation contribution to transition bias is relatively small. In contrast, the s/v ratio is much greater at twofold degenerate sites, being 48 for COI and 40 for cyt-b. Given that the micros/microv ratio is about 2, the Ps/Pv ratio at twofold degenerate sites must be on the order of 20 or greater. This suggests a great effect of purifying selection on transition bias in mitochondrial protein genes because transitions are synonymous and transversions are nonsynonymous at twofold degenerate sites in mammalian mitochondrial genes. We also found that nonsynonymous mutations at twofold degenerate sites are more neutral than nonsynonymous mutations at nondegenerate sites, and that the COI gene is subject to stronger purifying selection than is the cyt-b gene. A model is presented to integrate the effect of purifying selection, codon bias, DNA repair and GC content on s/v ratio of protein-coding genes.

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“…Few electrophoretically detectable protein polymorphisms have been found in studies of Arctic charr populations in other countries (Child, 1977(Child, , 1984Ferguson, 1981;Kornfield et al, 198 1;Anderson et al, 1983;Hindar et al, 1986;Magnusson & Ferguson, 1987;Partington & Mills, 1988). As mitochondrial (mt) DNA analysis has proved informative for studying the population genetic structure of other salmonid species (Wilson et a/., 1985;Gyllensten &Wilson, 1987;Grewe & Hebert, 1988;Palva et al, 1989;Hovey et al, 1989;Beckenbach et al, 1990;Birt et al, 199 l), this method was chosen to examine the genetic diversity of seven Scottish populations of Arctic charr. Two procedures for analysing mtDNA were utilized:…”

Section: Introductionmentioning

confidence: 99%

Mitochondrial DNA analysis of Scottish populations of Arctic charr, Salvelinus alpinus (L.)

Hartley

Bartlett

Davidson

1992

Journal of Fish Biology

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Mitochondrial DNA analysis of a total of 82 individuals from seven Scottishpopulations of Arctic charr (Sulvelinus alpinus L.) using restriction fragment length polymorphism and direct nucleotide sequencing of the cytochrome b gene revealed little variation within or between populations. One of 19 restriction enzymes showed a polymorphism that was present in three of the seven populations. Only one nucleotide substitution was detected in a 288 base pair segment of the cytochrome b gene examined in 26 fish. Approximately 4% of the mitochondrial genome was surveyed with these complementary procedures.

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Intraspecific sequence variation in the mitochondrial genome of rainbow trout (Oncorhynchus mykiss)

Cited by 30 publications

References 7 publications

Sequence divergence at mitochondrial genes in animals: Applicability of DNA data in genetics of speciation and molecular phylogenetics

Sequence divergence at mitochondrial genes in animals: Applicability of DNA data in genetics of speciation and molecular phylogenetics

On transition bias in mitochondrial genes of pocket gophers

Mitochondrial DNA analysis of Scottish populations of Arctic charr, Salvelinus alpinus (L.)

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