Mitochondrial DNA differentiation in the Japanese brown frog Rana japonica as revealed by restriction endonuclease analysis.

Sumida, Masayuki

doi:10.1266/ggs.72.79

Cited by 7 publications

(6 citation statements)

References 49 publications

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“…The fact that the sequence divergences of the northwestern Akita population from the six eastern populations averaged 3.07%, but 11.59% from the five western populations, supports the idea that the mtDNA of the Akita population was derived from that of the eastern populations, as was already suggested by mtDNA RFLP analysis (Sumida, 1997b). On the other hand, the sequence divergences were 8.44~9.93% (x ¯ = 9.24%) between the northwestern Nakajo and Izumozaki populations and the six eastern populations, 8.20~9.99% (x¯ = 9.18%) between the former and the five western populations, and 8.97~9.98% (x ¯ = 9.47%) between the former and the northwestern Akita population.…”

Section: Discussionsupporting

confidence: 78%

“…1). These frogs were screened from among 78, of which the mtDNA was analyzed by the RFLP method (Sumida, 1997b), and covered all mtDNA RFLP haplotypes. MtDNA was extracted from the livers or ovaries of each frog according to the method reported by Sumida (1997a), which was modified from that of Yonekawa et al (1980).…”

Section: Mtdna Sourcesmentioning

confidence: 99%

“…Extensive intraspecific crossing experiments among 20 populations from Honshu and Kyushu revealed that three groups of popula-tions, the eastern, western, and northwestern groups, were reproductively isolated from each other by incomplete male hybrid sterility (Sumida, 1996). By the mtDNA RFLP analysis of 16 populations, Sumida (1997b) showed a distinct divergence between the eastern and western groups of R. japonica. On the basis of the results of allozyme analysis, crossing experiments and mtDNA RFLP analysis, he suggested that the eastern and western groups of R. japonica have experienced secondary contact, and that introgression has occurred in the northwestern populations of Honshu.…”

Section: Introductionmentioning

confidence: 99%

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Intraspecific Differentiation in the Japanese Brown Frog Rana japonica Inferred from Mitochondrial DNA Sequences of the CytochromebGene

Sumida

Ogata

1998

Zoological Science

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Intraspecific differentiation of the Japanese brown frog Rana japonica was investigated by analyzing nucleotide sequences of the mitochondrial cytochrome b (cyt b) gene in order to clarify phylogenetic relationships among three population groups known to exist in this species. The nucleotide sequences of 447 base pair (bp) segments were determined by the PCR-direct sequencing method on 31 individuals from 14 populations of R. japonica from Honshu, and phylogenetic trees were constructed by the UPGMA and NJ methods using Rana catesbeiana as an outgroup. A sequence alignment provided 92 variable sites (15 corresponded to the first codon position, three to the second, and 74 to the third), and 19 haplotypes were identified from 31 frogs. The sequence divergences were 0.22~2.50% (x¯ = 0.65%) within populations, 0.22~12.02% (x ¯ = 7.34%) between populations, and 23.59~27.89% (x¯ = 26.19%) between R. japonica and R. catesbeiana. Although many nucleotide substitutions were silent mutations, 12 amino acid replacements were found to occur within R. japonica. A high frequency of transitions relative to transversions was observed within R. japonica. The present nucleotide sequence data showed that the eastern and western groups of R. japonica was considerably differentiated to each other, and that the Akita population of the northwestern group was evidently derived from the eastern group, but the Nakajo and Izumozaki populations of the northwestern group diverged considerably from each of the eastern and the western groups.

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Section: Discussionsupporting

confidence: 78%

Section: Mtdna Sourcesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Intraspecific Differentiation in the Japanese Brown Frog Rana japonica Inferred from Mitochondrial DNA Sequences of the CytochromebGene

Sumida

Ogata

1998

Zoological Science

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“…The mtDNA data are extrinsic to the organ-Fishes Cutthroat trout, 2 ssp., Gyllensten et al (1985b) isms under analysis, and so the lack of support does Amphibia not falsify the nuclear DNA based phylogeny. Addi-Rana, 2 ssp., Sumida (1997b) tionally, the opportunity for introgression between lat-Xenopus, 4 ssp., Carr et al (1987) eralis and nigroviridis suggests that the mtDNA results may not reflect species relationships. Given this, the…”

Section: Taxonomic Commentmentioning

confidence: 99%

Palm‐Pitviper (Bothriechis) Phylogeny, mtDNA, and Consilience

2001

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The phylogeny of the neotropical palm-pitviper genuswith Ophryachus as the sister lineage. Crother et al. Bothriechis has been previously inferred from morphol- (1992) inferred the phylogeny of Bothriechis with alloogy and allozymes. These nuclear-based data sets were zymes and morphology and found the two data sets found to be congruent and also consilient with the geo-to be congruent (Fig. 2). They (Crother et al., 1992) also logic history of the region. We present mtDNA sequence detailed the historical biogeography of Bothriechis and data as an additional data set in the inference of the models of the vicariant history of Middle America Bothriechis phylogeny and analyze it separately and com-and determined these to be entirely consilient with bined with previous data. The mtDNA phylogeny is their phylogenetic hypotheses of Bothriechis relationincongruent with the nuclear data sets. Based on a numships. Werman (1997) found that lactate dehydrogeber of factors, we hypothesize that the incongruence is nase phenotypes corroborated his hypothesis of a modue to both mtDNA introgression and lineage sorting.nophyletic Bothriechis. Gutberlet (1998) employed We argue that mtDNA represents extrinsic data and as morphological data in a phylogenetic study of Middle such should be used as a consilient data set. ᭧ 2001 The American pitvipers and his phylogeny corroborated Willi Hennig Society Werman's (1992, 1997) hypothesis, with the placement of Ophryachus as sister to a monophyletic Bothriechis. Most recently, Parkinson (1999) used 12S and 16S Palm-Pitviper Phylogeny 357 mtDNA an ideal choice in which to frame a consilient test (T. W. Taggart et al., submitted for publication). The purpose of this study was to infer a mtDNA phylogeny of Bothriechis and to employ it in a consilient fashion to test the previous nuclear-based phylogeny. METHODSWhole genomic DNA, including the mtDNA, was extracted from muscle and liver using a standard phenol-chloroform protocol. One specimen each of Bothriechis bicolor (Bb), B. marchi (Bm), B. rowleyi (Br), and B. aurifer (Ba); two specimens each of B. lateralis (Bl) and Ophryacus undulatus (Ou); and three specimens of B. schlegelii (Bs) were used. Sources of tissues and/ or DNAs are given in the Appendix. The 12S sequence for B. nigroviridis (Bn) was from Parkinson (1999) and was included in the alignment and subsequent analysis. FIG. 2. The morphology-and allozyme-based phylogeny inferred by Crother et al. (1992).TABLE 6-Continued

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“…melanotos, Christidis et al (1996) CONCLUSIONS "Subspecies" Insecta Apis mellifera, 3 ssp., Heliconius erato, 14 ssp., Brower (1996) The hypothesis generated by the mtDNA lineages H. melpomene, 13 ssp., Brower (1996) was not consilient with the nuclear DNA-derived hy-H. cydno, 3 ssp., Brower (1996) pothesis. Addi-Rana, 2 ssp., Sumida (1997b) tionally, the opportunity for introgression between lat-Xenopus, 4 ssp., Carr et al (1987) eralis and nigroviridis suggests that the mtDNA results may not reflect species relationships. Addi-Rana, 2 ssp., Sumida (1997b) tionally, the opportunity for introgression between lat-Xenopus, 4 ssp., Carr et al (1987) eralis and nigroviridis suggests that the mtDNA results may not reflect species relationships.…”

Section: Taxonomic Commentmentioning

confidence: 99%