Intraspecific Differentiation in the Japanese Brown Frog Rana japonica Inferred from Mitochondrial DNA Sequences of the Cytochrome<i>b</i>Gene

Sumida, Masayuki; Ogata, Mitsuaki

doi:10.2108/zsj.15.989

Cited by 15 publications

(4 citation statements)

References 41 publications

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“…Clades A1 and A2, distributed in the Tohoku region, shrank their ranges into refugia and expanded after the glacial period. Some amphibians with overlapping distribution with toads also diverged in the Tohoku region ( Sumida & Ogata, 1998 ; Yoshikawa et al, 2008 ; Aoki, Matsui & Nishikawa, 2013 ; Tominaga et al, 2013 ; Yoshikawa & Matsui, 2014 ; Matsui et al, 2020 ). Although divergence times did not coincide, the maintenance of genetic structures within the Tohoku region suggests the presence of multiple refugia for amphibians in this region.…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity and demography of Bufo japonicus and B. torrenticola (Amphibia: Anura: Bufonidae) influenced by the Quaternary climate

Fukutani

Matsui

Tran

et al. 2022

PeerJ

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The Quaternary climate affected the present species richness and geographic distribution patterns of amphibians by limiting their activities during the glacial period. The present study examined the phylogenetic relationships of Japanese toads (Bufo japonicus and B. torrenticola) and the demography of each lineage from the past to the present based on mitochondrial sequences and ecological niche models. Japanese toads are a monophyletic group with two main clades (clades A and B). Clade A represents B. j. formosus, including three clades (clades A1, A2, and A3). Clade B contains three clades, two of which corresponded to B. j. japonicus (clades B1 and B2) and the other to B. torrenticola. Clade B2 and B. torrenticola made a sister group, and, thus, B. j. japonicus is paraphyletic. Clades A and B diverged in the late Miocene 5.7 million years ago (Mya) during the period when the Japanese archipelago was constructed. The earliest divergence between the three clades of clade A was estimated at 1.8 Mya. Clades A1 and A2 may have diverged at 0.8 Mya, resulting from the isolation in the multiple different refugia; however, the effects of the glacial climate on the divergence events of clade A3 are unclear. Divergences within clade B occurred from the late Pliocene to the early Pleistocene (3.2–2.2 Mya). Niche similarity between the parapatric clade in clade B (clades B1 and B2) indicated their allopatric divergence. It was suggested that niche segregation between B. japonicus and B. torrenticola contributed to a rapid adaptation of B. torrenticola for lotic breeding. All clade of Japanese toads retreated to each refugium at a low elevation in the glacial period, and effective population sizes increased to construct the current populations after the Last Glacial Maximum. Furthermore, we highlight the areas of climate stability from the last glacial maximum to the present that have served as the refugia of Japanese toads and, thus, affected their present distribution patterns.

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Section: Discussionmentioning

confidence: 99%

Genetic diversity and demography of Bufo japonicus and B. torrenticola (Amphibia: Anura: Bufonidae) influenced by the Quaternary climate

Fukutani

Matsui

Tran

et al. 2022

PeerJ

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“…Generally, in the mt DNA of most water frog species the amount of species-speci c sites, which can be considered as apomorphic characters, is very low (Plötner and Ohst, 2001). Besides the recognition of speci c substitutions the degree of sequence divergence is an important and often an even more appropriate parameter to separate species, especially when closely related species are studied (e.g., Lydeard et al, 1995;Shaffer and McKnight,1996;Sumida and Ogata, 1998;Armbruster and Bernhard, 2000). It is assumed that more than 7 substitutions in the ND3 gene (D2.4% sequence divergence) and 3 substitutions in the III.…”

Section: Discussionmentioning

confidence: 99%

Divergence in mitochondrial DNA of Near Eastern water frogs with special reference to the systematic status of Cypriote and Anatolian populations (Anura, Ranidae)

Ohst¹,

Böhme²,

Schreiber³

et al. 2001

Amphib Reptilia

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Water frogs from Anatolia, Syria, Jordan, and central Asia (Turkmenistan, Uzbekistan, Kazakhstan) were compared on the basis of the complete mitochondrial (mt) ND3 gene (340 bp), two anking mt t-RNA gene fragments (26 bp), and a 374 bp fragment of the mt 12S rRNA gene. A total of 27 haplotypes were found among the investigated individuals. Anatolian water frogs differed from Syrian and Jordanian Rana bedriagae by 2.2-3.4% of the analysed sites. The observed divergence (2.8-4.1%) between the Cypriote water frogs and frogs from the surrounding mainland (southern Turkey, west Syria) was in the same range as between R. bedriagae and European R. ridibunda (3.1-3.9%). These results suggest that neither the Cypriote nor the Anatolian water frogs represent R. bedriagae. Furthermore, maximum parsimony and neighbour-joinin g trees showed a clear subdivision of Asian water frogs into three Anatolian lineages, two central Asian lineages, a Cypriote lineage and the bedriagae lineage. In all trees the Cypriote lineage branches off rst and a clade formed by two Anatolian lineages is placed as the sister group of water frogs from Turkmenistan and Uzbekistan, whereas the phylogeneti c positions of R. bedriagae, the Ceyhan lineage, the Kazakhstan lineage and R. ridibunda remain unclear.

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“…We sequenced the 16S rRNA and 12S rRNA of mitochondrial genes from our 21 samples. Fragments of the two genes were amplified using the primer pairs designed for ranid frogs (Sumida & Ogata 1998;Sumida et al 2000). PCR amplification reactions were performed in a 30 volume reaction with the following cycling conditions: an initial denaturing step at 95°C for 4 min; 35 cycles of denaturing at 95°C for 40 s, annealing at 55°C (for 16S rRNA) or 53°C (for 12S rRNA) for 40 s and extending at 72°C for 60 s, and a final extending step of 72°C for 10 min.…”

Section: Methodsmentioning

confidence: 99%

A new species of the genus Odorrana (Amphibia: Ranidae) and the first record of Odorrana bacboensis from China

Wang

Lau²,

Yang³

et al. 2015

Zootaxa

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A new species of the genus Odorrana (Amphibia: Ranidae) and the first record of Odorrana bacboensis from China AbstractThe genus Odorrana currently contains at least 56 recognized species that inhabits montane streams in subtropical and tropical Asia. Twenty new species have been described in the last decade, indicating the potential cryptic species diversity of this genus. We collected several specimens of Odorrana species from Southern China from 2007 to 2014, and on the basis of a combined morphological characters and phylogenetic analysis, we described the new species Odorrana fengkaiensis sp. nov. herein. The new species is very similar to O. hainanensis and O. bacboensis, but can be consistently separated by morphology, and allopatric distribution. It is further reciprocally monophyletic to O. hainanensis in a mitochondrial gene trees with an average genetic divergence of 2.1% (1.9%-2.4%). The new species inhabits in lowland broad streams, rivers, pools and near the riparian areas, but its general ecology remains poorly known. The new species is characterized by its body length of adult females approximately twice as long as adult males (SVL 77.8-111.9 mm in females, 37.4-51.8 mm in males); eye large in males, eye diameter 1.01-1.16 times as long as snout length; tympanum of males large and distinct, extremely close to the eye, 0.7-1.4 mm in tympanum-eye distance; dorsolateral folds absent; dorsal skin shagreened, with several large tubercles in males; flanks with tubercles and scattered larger pustules, 8-10 of which usually arranged in a dorsolateral row; ventral skin smooth, with spines in adult males during the breeding season; the tibio-tarsal articulation stretched forward beyond the tip of snout; relative finger lengths: II < I < IV < III; dorsum brown with irregularly reticulated green markings in males and young females, uniformly brown in some old adult females; males with velvety nuptial pad on thumb, paired gular pouches; mature oocytes almost purely black in life, showed dark grey animal pole and olive vegetative pole in preservative. In addition, we found O. bacboensis, a new country record from China, indicating a range extension from north-central Vietnam to southeast Yunnan and adjacent area in Guangxi.

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

Cited by 15 publications

References 41 publications

Genetic diversity and demography of Bufo japonicus and B. torrenticola (Amphibia: Anura: Bufonidae) influenced by the Quaternary climate

Genetic diversity and demography of Bufo japonicus and B. torrenticola (Amphibia: Anura: Bufonidae) influenced by the Quaternary climate

Divergence in mitochondrial DNA of Near Eastern water frogs with special reference to the systematic status of Cypriote and Anatolian populations (Anura, Ranidae)

A new species of the genus Odorrana (Amphibia: Ranidae) and the first record of Odorrana bacboensis from China

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