Reduced genetic variation in the Japanese giant salamander, Andrias japonicus (Amphibia: Caudata)

Matsui, Masafumi; Tominaga, Akira; Liu, Wan-zhao; Tanaka-Ueno, Tomoko

doi:10.1016/j.ympev.2008.07.020

Cited by 38 publications

(32 citation statements)

References 46 publications

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“…Given the low genetic diversity in R. sibiricus , it seems reasonable that the extra digit is a result of inbreeding, rather than a local adaptation to the surrounding environment (e.g., the flat area around the lake at the AKS site). Although some species display a low level of genetic diversity among populations, they display a strong phylogeographic structure [68], [76]–[78]. In our mtDNA study, the geographically adjacent SLBZ, SLBZ1# and SLBZ2# populations showed greater genetic similarity than other populations; e.g., the Hap-2 haplotype was distributed mainly in these three populations (Table 2).…”

Section: Discussionmentioning

confidence: 60%

Extremely Low Genetic Diversity Indicating the Endangered Status of Ranodon sibiricus (Amphibia: Caudata) and Implications for Phylogeography

et al. 2012

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BackgroundThe Siberian salamander (Ranodon sibiricus), distributed in geographically isolated areas of Central Asia, is an ideal alpine species for studies of conservation and phylogeography. However, there are few data regarding the genetic diversity in R. sibiricus populations.Methodology/Principal FindingsWe used two genetic markers (mtDNA and microsatellites) to survey all six populations of R. sibiricus in China. Both of the markers revealed extreme genetic uniformity among these populations. There were only three haplotypes in the mtDNA, and the overall nucleotide diversity in the mtDNA was 0.00064, ranging from 0.00000 to 0.00091 for the six populations. Although we recovered 70 sequences containing microsatellite repeats, there were only two loci that displayed polymorphism. We used the approximate Bayesian computation (ABC) method to study the demographic history of the populations. This analysis suggested that the extant populations diverged from the ancestral population approximately 120 years ago and that the historical population size was much larger than the present population size; i.e., R. sibiricus has experienced dramatic population declines.Conclusion/SignificanceOur findings suggest that the genetic diversity in the R. sibiricus populations is the lowest among all investigated amphibians. We conclude that the isolation of R. sibiricus populations occurred recently and was a result of recent human activity and/or climatic changes. The Pleistocene glaciation oscillations may have facilitated intraspecies genetic homogeneity rather than enhanced divergence. A low genomic evolutionary rate and elevated inbreeding frequency may have also contributed to the low genetic variation observed in this species. Our findings indicate the urgency of implementing a protection plan for this endangered species.

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Section: Discussionmentioning

confidence: 60%

Extremely Low Genetic Diversity Indicating the Endangered Status of Ranodon sibiricus (Amphibia: Caudata) and Implications for Phylogeography

et al. 2012

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“…A maximum likelihood tree was constructed using online tool RAxML (Stamatakis et al 2008) (Figure 1). The phylogenetic analysis result was consistent with the previous research (Matsui et al 2008). …”

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confidence: 92%

Complete mitochondrial genome of a living wild-type Chinese giant salamander Andrias davidianus (Amphibia: Cryptobranchidae) in Huangshan

Yang

Chen

et al. 2016

Mitochondrial DNA Part B

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“…A relatively high level of mtDNA genetic differentiation (1.92% to 4.37%) was observed among the seven clades. The high levels of genetic diversity uncovered in A. davidianus are not unexpected since previous genetic studies of the congeneric A. japonicus and confamilial C. alleganiensis also revealed detectable intraspecific divergence (Matsui, Tominaga, Liu, & Tanaka‐Ueno, ; Sabatino & Routman, ). For instance, Matsui et al () detected that A. japonicus populations were divided into two clades with 1.1% sequence divergence between them.…”

Section: Discussionmentioning

confidence: 63%

“…The high levels of genetic diversity uncovered in A. davidianus are not unexpected since previous genetic studies of the congeneric A. japonicus and confamilial C. alleganiensis also revealed detectable intraspecific divergence (Matsui, Tominaga, Liu, & Tanaka‐Ueno, ; Sabatino & Routman, ). For instance, Matsui et al () detected that A. japonicus populations were divided into two clades with 1.1% sequence divergence between them. Likewise, Sabatino and Routman () found that C. alleganiensis populations in eight reciprocally monophyletic clades had 0.7% to 5.4% sequence divergence between them.…”

Section: Discussionmentioning

confidence: 63%

Phylogeographic patterns and conservation implications of the endangered Chinese giant salamander

Liang

Chen

Wang

et al. 2019

Ecology and Evolution

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Understanding genetic diversity patterns of endangered species is an important premise for biodiversity conservation. The critically endangered salamander Andrias davidianus , endemic to central and southern mainland in China, has suffered from sharp range and population size declines over the past three decades. However, the levels and patterns of genetic diversity of A. davidianus populations in wild remain poorly understood. Herein, we explore the levels and phylogeographic patterns of genetic diversity of wild‐caught A. davidianus using larvae and adult collection with the aid of sequence variation in (a) the mitochondrial DNA (mtDNA) fragments ( n = 320 individuals; 33 localities), (b) 19 whole mtDNA genomes, and (c) nuclear recombinase activating gene 2 ( RAG2 ; n = 88 individuals; 19 localities). Phylogenetic analyses based on mtDNA datasets uncovered seven divergent mitochondrial clades (A–G), which likely originated in association with the uplifting of mountains during the Late Miocene, specific habitat requirements, barriers including mountains and drainages and lower dispersal ability. The distributions of clades were geographic partitioned and confined in neighboring regions. Furthermore, we discovered some mountains, rivers, and provinces harbored more than one clades. RAG2 analyses revealed no obvious geographic patterns among the five alleles detected. Our study depicts a relatively intact distribution map of A. davidianus clades in natural species range and provides important knowledge that can be used to improve monitoring programs and develop a conservation strategy for this critically endangered organism.

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Reduced genetic variation in the Japanese giant salamander, Andrias japonicus (Amphibia: Caudata)

Cited by 38 publications

References 46 publications

Extremely Low Genetic Diversity Indicating the Endangered Status of Ranodon sibiricus (Amphibia: Caudata) and Implications for Phylogeography

Extremely Low Genetic Diversity Indicating the Endangered Status of Ranodon sibiricus (Amphibia: Caudata) and Implications for Phylogeography

Complete mitochondrial genome of a living wild-type Chinese giant salamander Andrias davidianus (Amphibia: Cryptobranchidae) in Huangshan

Phylogeographic patterns and conservation implications of the endangered Chinese giant salamander

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