Phylogeny and historical demography of Cynops pyrrhogaster (Amphibia: Urodela): Taxonomic relationships and distributional changes associated with climatic oscillations

Tominaga, Akira; Matsui, Masafumi; Yoshikawa, Natsuhiko; Nishikawa, Kanto; Hayashi, Terutake; Misawa, Yasuchika; Tanabe, Shingo; Ota, Hidetoshi

doi:10.1016/j.ympev.2012.10.015

Cited by 40 publications

(35 citation statements)

References 60 publications

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“…Divergence time between the AM/TK and the ON subclades is estimated as 6.07 (3.81-7.75) MYA in the Calibration I and 3.21 (1.77-4.97) MYA in the Calibration II. The estimated times of divergence between the Amami and Okinawa populations in several amphibians falls within the range from the late Miocene to the early Pleistocene (1.7 [1.1-2.4] MYA for two species of the Odorrana narina complex [Matsui et al, 2005b]; 2.3 [1.5-3.2] MYA for two species of the O. ishikawae species group [Matsui et al, 2005b]; 2.4-8.3 MYA for two species of Babina [Tominaga et al, 2014]; 3.3-6.8 MYA for Cynops ensicauda [Tominaga et al, 2010[Tominaga et al, , 2013; and 3.1-18.0 MYA for Echinotriton andersoni [Honda et al, 2012;Kurabayashi et al, 2012]). Most of these estimations are much older than the formations of straits in the Pleistocene (0.12-1.3 MYA; Kizaki and Oshiro, 1980;Ota, 1998;Kimura, 2003), which have separated the Amami and the Okinawa Groups, and should have induced divergence of the terrestrial animals of the Central Ryukyus into two island group elements.…”

Section: Distribution Patterns and Divergence Historymentioning

confidence: 99%

Phylogeny and Differentiation of Wide-Ranging Ryukyu Kajika FrogBuergeria japonica(Amphibia: Rhacophoridae): Geographic Genetic Pattern Not Simply Explained by Vicariance Through Strait Formation

et al. 2015

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To investigate geographic genetic structures and taxonomic relationships among isolated populations of Buergeria japonica, occurring very widely in various habitats of the Ryukyu Archipelago and Taiwan, we conducted phylogenetic and demographic analyses among individuals from various localities, representing their entire distributional ranges. Buergeria japonica is genetically greatly differentiated and comprises three major clades (the Southern Taiwan [ST] clade, the Northern Taiwan + Southern Ryukyu [NT/SR] clade, and the Central + Northern Ryukyu [CR/NR] clade), each of which seems to represent independent species. The first divergence in the species is estimated to have occurred in the middle to late Miocene in areas of current Taiwan, then eastern periphery of the Asian continent. Split of the ST and the remaining clades, and subsequent divergence between the NT/SR and the CR/NR clades in the latter, indicate consecutive south to north vicariant diversifications. However, these vicariances are not always associated with formation of significant barriers such as deep straits. Less but still prominently diverged subclades (the Amami + Tokara [AM/TK] and the Okinawa [ON] subclades) in the CR/NR clade were recognized in spite of the absence of an intervening deep strait. Contrariwise, individuals from Amami and Tokara Groups formed the AM/TK subclade in spite of the presence of the intervening Tokara Gap (a long-standing deep tectonic strait). Furthermore, in the AM/TK subclade, low but definite genetic divergence was found between the Northern Amami + Tokara (NAM/TK) lineage and the Southern Amami (SAM) lineage. Estimated divergence time and gene flow rate within the NAM/TK lineage indicate that this species reached northern Tokara from the south by overseas dispersal over the Tokara Gap long after its formation, but not by more recent artificial transportation. This overseas dispersal would have been facilitated by its more frequent occurrence around coastal habitats than other frogs.

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Section: Distribution Patterns and Divergence Historymentioning

confidence: 99%

Phylogeny and Differentiation of Wide-Ranging Ryukyu Kajika FrogBuergeria japonica(Amphibia: Rhacophoridae): Geographic Genetic Pattern Not Simply Explained by Vicariance Through Strait Formation

et al. 2015

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“…of Tsukuba) and a field ‘Imori-no-Sato’ (Kaizuka/Kamitakai, Toride city, Ibaraki prefecture, Japan; http://imori-net.org/ ) [4] . This population belongs to Kanto group in Northern lineage [12] and is called ‘Toride-Imori’. In this study, sexually mature adult Toride-Imori (total body length: male, ∼9 cm; female, 11–12 cm) which had been reared in the laboratory were used.…”

Section: Methodsmentioning

confidence: 99%

A Transcriptome for the Study of Early Processes of Retinal Regeneration in the Adult Newt, Cynops pyrrhogaster

et al. 2014

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Retinal regeneration in the adult newt is a useful system to uncover essential mechanisms underlying the regeneration of body parts of this animal as well as to find clues to treat retinal disorders such as proliferative vitreoretinopathy. Here, to facilitate the study of early processes of retinal regeneration, we provide a de novo assembly transcriptome and inferred proteome of the Japanese fire bellied newt (Cynops pyrrhogaster), which was obtained from eyeball samples of day 0–14 after surgical removal of the lens and neural retina. This transcriptome (237,120 in silico transcripts) contains most information of cDNAs/ESTs which has been reported in newts (C. pyrrhogaster, Pleurodeles waltl and Notophthalmus viridescence) thus far. On the other hand, de novo assembly transcriptomes reported lately for N. viridescence only covered 16–31% of this transcriptome, suggesting that most constituents of this transcriptome are specific to the regenerating eye tissues of C. pyrrhogaster. A total of 87,102 in silico transcripts of this transcriptome were functionally annotated. Coding sequence prediction in combination with functional annotation revealed that 76,968 in silico transcripts encode protein/peptides recorded in public databases so far, whereas 17,316 might be unique. qPCR and Sanger sequencing demonstrated that this transcriptome contains much information pertaining to genes that are regulated in association with cell reprogramming, cell-cycle re-entry/proliferation, and tissue patterning in an early phase of retinal regeneration. This data also provides important insight for further investigations addressing cellular mechanisms and molecular networks underlying retinal regeneration as well as differences between retinal regeneration and disorders. This transcriptome can be applied to ensuing comprehensive gene screening steps, providing candidate genes, regardless of whether annotated or unique, to uncover essential mechanisms underlying early processes of retinal regeneration.

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“…The Japanese red‐bellied newt, Cynops pyrrhogaster (Boie, 1826), distributed on the mainland of Japan, has long been studied for geographic variations (Hayashi & Matsui, 1988, 1990; Matsui, 1996; Sawada, 1963a,b; Tominaga et al, 2013, 2015). This species is known to be divided into six morphological/behavioral groups based on morphology and mating behavior (Sawada, 1963a,b; Figure 1a) and five allozyme groups by analyses of enzyme protein polymorphisms (Hayashi & Matsui, 1988, 1990; Matsui, 1996; Figure 1b).…”

Section: Introductionmentioning

confidence: 99%

“…This species is known to be divided into six morphological/behavioral groups based on morphology and mating behavior (Sawada, 1963a,b; Figure 1a) and five allozyme groups by analyses of enzyme protein polymorphisms (Hayashi & Matsui, 1988, 1990; Matsui, 1996; Figure 1b). Moreover, this species comprises five mitochondrial DNA (mtDNA) lineages (Tominaga et al, 2013, 2015; Figure 1c).…”

Section: Introductionmentioning

confidence: 99%

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Structure and movement of the hybrid zone between two divergent lineages of the Japanese newtCynops pyrrhogaster(Amphibia: Urodela) in central Japan

Tominaga

Matsui

Matsui³

2021

J. Zool. Syst. Evol. Res.

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The maintenance mechanisms of hybrid zones between two lineages/species and their gene flow dynamics are major topics for speciation studies. Elucidating these dynamics can help us to understand the process of speciation. The newt Cynops pyrrhogaster is distributed on the main islands of Japan and comprises five mitochondrial DNA (mtDNA) lineages. In this study, we surveyed the genetic relationship between two lineages (northern and central) around their boundary. We genotyped 202 individuals from 24 populations using the mitochondrial cytochrome b gene and 12 microsatellite loci. MtDNA analysis revealed that the two lineages were distributed parapatrically to each other without coexistence, whereas the microsatellite analysis indicated the presence of a hybrid zone. The estimated dispersal rates were higher from both parental lineages to the hybrid populations than those in the opposite directions. These data indicate that the hybrid zone is a tension zone, which is maintained by an equilibrium between selection against hybrid individuals and the invasion of both parental individuals from adjacent areas. The two parental lineages are genetically moderately isolated from each other and appear to be biologically independent species. The overall dispersal rate was more pronounced in the south‐to‐north direction. More than 10 individuals having central type of mtDNA retained some genetic characteristics derived from the northern lineage, which can be regarded as genetic footprint of their northern lineage ancestor. These results suggest that the hybrid zone has shifted from south to north, resulting in replacing the range of the northern lineage to that of the central lineage.

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Phylogeny and historical demography of Cynops pyrrhogaster (Amphibia: Urodela): Taxonomic relationships and distributional changes associated with climatic oscillations

Cited by 40 publications

References 60 publications

Phylogeny and Differentiation of Wide-Ranging Ryukyu Kajika FrogBuergeria japonica(Amphibia: Rhacophoridae): Geographic Genetic Pattern Not Simply Explained by Vicariance Through Strait Formation

Phylogeny and Differentiation of Wide-Ranging Ryukyu Kajika FrogBuergeria japonica(Amphibia: Rhacophoridae): Geographic Genetic Pattern Not Simply Explained by Vicariance Through Strait Formation

A Transcriptome for the Study of Early Processes of Retinal Regeneration in the Adult Newt, Cynops pyrrhogaster

Structure and movement of the hybrid zone between two divergent lineages of the Japanese newtCynops pyrrhogaster(Amphibia: Urodela) in central Japan

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