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The Japanese freshwater crab Geothelphusa dehaani species complex is distributed widely across the Japanese Archipelago. Despite its suggested high genetic and morphological diversity, key aspects such as nuclear DNA (nuDNA) population structure and relationship between body color patterns and genetic populations remain unclear. To address these gaps, this study analyzed genome-wide single nucleotide polymorphisms (SNPs) in nuDNA and mitochondrial DNA (mtDNA) cytochrome oxidase subunit 1 (COI) markers in samples from Hokkaido to the Tokara Islands, Japan. ADMIXTURE analysis identified five distinct populations with significant geographic boundaries. These populations exhibited unique geographical patterns, spanning across islands and enclave distribution, indicating that G . dehaani populations have been shaped by complex factors, including sea level changes and volcanic activity. Regional body color variations partially aligned with SNP clades. Further, combining body color with collection locality data could help identify the specimen populations. Contrasting patterns between mtDNA and nuDNA suggest historical gene flow and introgression, emphasizing the need for caution when interpreting earlier phylogenetic studies based on combined mtDNA and nuDNA sequences. Our findings provide a foundational baseline for future research into the taxonomy, phylogeny, and population dynamics of the G . dehaani species complex, advancing our understanding of its evolutionary history.

Quaternary climatic cycles strongly affected the genetic diversification and ranges of organisms, shaping current genetic structures and distribution patterns. Urodeles provide ideal examples for exploring these dynamics over time and across space. In this study, we integrated a phylogeographic approach and ensemble species distribution modeling (eSDM) to infer the historical demography and distribution patterns of the Vietnam warty newt, Paramesotriton deloustali . Mitochondrial data revealed two groups, West and East, which diverged approximately 1.92 million years ago (Mya). Diversification was likely driven by change in the climate during early stages of the Pleistocene, with increasing monsoon and drought intensities. Biogeographic analysis indicated that the newt’s current distribution formed as a result of vicariance events. In addition, the two groups occupy distinct ecological niches. Demographic reconstruction showed signs of expansion in the effective population sizes of the two major groups beginning around 0.11 and 0.15 Mya, respectively. However, eSDM showed fluctuating predicted distributions during the last interglacial, last glacial maximum, mid-Holocene, and present. Mountain systems in northern Vietnam are likely to have served as climatic refuges and to have played a crucial role in safeguarding species from the effects of climate change.

[This corrects the article DOI: 10.1371/journal.pone.0305228.].

The Japanese fire-belly newt, Cynops pyrrhogaster, is a near threatened species that is conservation dependent. Here, we examine feeding habits across the year within a genetically divergent intraspecific lineages of this species (the Central Lineage) to provide information to support future insitu and ex-situ conservation activities. Stomach contents from newts were collected in a paddy field habitat, Kyoto City, central Honshu, Japan for two consecutive years. Throughout the year, dipteran aquatic larvae were the most important food source both for males and females, although terrestrial invertebrates were also important prey for the newts. During periods of low prey availability shed skin could also be a relatively valuable source of food. Sympatric frogs and newts appear to target different prey and this may facilitate their co-existence. Our study provides new information on suitable prey items for the Central Lineage of C. pyrrhogaster both in its natural habitat and in captivity.

Competition within and among species can play a key role in structuring the assemblages of anuran tadpoles. Previous studies have reported that tadpoles of the invasive cane toad ( Rhinella marina ) are more strongly disadvantaged by the presence of native frog tadpoles than by the same number of conspecific toad tadpoles. That effect might arise from a lack of coevolution of the invasive toad with its competitors; and/or from a generalized superiority of frog tadpoles over toad tadpoles. To clarify those possibilities, we conducted experimental trials using the larvae of a native rather than invasive toad ( Bufo japonicus formosus in Japan) exposed to larvae of native anurans (the sympatric frogs Rana japonica and Rana ornativentris and the parapatric toad Bufo japonicus japonicus ). In intraspecific competition trials, higher densities of B. j. formosus prolonged the larval period and reduced size at metamorphosis, but did not affect survival. In interspecific competition trials, the effects of the other anuran species on B. j. formosus were similar to the effects of the same number of conspecific larvae. This similarity in impact of interspecific versus intraspecific competition argues against any overall competitive superiority of frog larvae over toad larvae. Instead, the vulnerability of larval cane toads to frog tadpoles may result from a lack of coevolutionary history.

Hybridization following secondary contact may produce different outcomes depending on the extent to which genetic diversity and reproductive barriers have accumulated during isolation. The Japanese toad, Bufo japonicus , is distributed on the main islands of Japan. In the present study, we applied multiplexed inter-simple sequence repeat genotyping by sequencing to achieve the fine-scale resolution of the genetic cluster in B. j. japonicus and B. j. formosus . We also elucidated hybridization patterns and gene flow degrees across contact zones between the clusters identified. Using SNP data, we found four genetic clusters in B. j. japonicus and B. j. formosus and three contact zones of the cluster pairs among these four clusters. The two oldest diverged lineages, B. j. japonicus and B. j. formosus , formed a narrow contact zone consistent with species distinctiveness. Therefore, we recommend that these two subspecies be elevated to the species level. In contrast, the less diverged pairs of two clusters in B. j. japonicus and B. j. formosus , respectively, admixed over a hundred kilometers, suggesting that they have not yet developed strong reproductive isolation and need to be treated as conspecifics. These results will contribute to resolving taxonomic confusion in Japanese toads.

The genus Andrias includes the largest extant salamanders, and is comprised of one Japanese species A . japonicus and four Chinese species. The fossil record of the giant salamander is incomplete and modern giant salamanders are not differentiated osteologically among species, making it difficult to identify bones at the species level. In this study, we re-examined a fossil series of giant salamander discovered from a cave on Shikoku Island, Japan. We obtained ancient DNA from the fossil and confirmed that the partial sequence of mitochondrial DNA was identical to that of extant A . japonicus . These remains were dated to the Late Pleistocene, however, the result of carbon-14 dating in this study estimated the age as more recent, approximately 3,500–4,100 years ago. Currently, there is a small population of A . japonicus in Shikoku, but it is far removed from the fossil discovery area. Our findings suggest that wild A . japonicus in western Shikoku may have been extirpated very recently.

A Bornean megophryid, Leptobrachella gracilis (Günther, 1872), the type species of now synonymized genus Leptolalax, proved to contain two different call types that differ in various aspects of advertisement calls including pulse repetition rate and dominant frequency. Genetic analyses of mtDNA and nuDNA of these two types (slow- and fast-call) co-occurring at the type locality, Matang, Sarawak, revealed them to be heterospecific with no evidence of gene exchange. The female holotype of L. gracilis is estimated to belong to the slow-call type based on morphological similarities. We therefore describe the fast-call type as a new species, Leptolalax sarawakensis sp. nov.

Studying the relationships between predators and their prey is generally complex but provides valuable knowledge into the process of evolution. The clay model method is a technique that has been widely used to assess prey-predator interaction. In the study, we used clay models of the Vietnam warty newt (Paramesotriton deloustali) to evaluate its predator pressures in Tam Dao National Park (NP), northern Vietnam. We also employed camera traps to detect specific predators of the newt in nature. Our camera trap results showed that northern treeshrew (Tupaia belangeri), rats (Rattus sp.), and greater coucal (Centropus sinensis) are predators of the newt in Tam Dao NP. For the clay model experiment observed attacks on the head of clay models were triple those expected by chance, indicating that predators perceived the clay model as actual prey items. The proportions on the models predated upon differed in three habitat types: broadleaf evergreen forests, mixed broadleaf evergreen and bamboo forests, and bamboo forests. We also detected that the attacks on the models were mainly made by mammals. Attack rates at nighttime were three times higher than during the daytime.

A genetic sex identification method was applied to the Japanese Giant Salamander and its hybrids with the introduced Chinese Giant Salamander. This method detects female-specific sequences on the W chromosome by PCR, using specific primers originally designed for the Chinese Giant Salamander. We improved the method for application to the Japanese Giant Salamander and the hybrids. We then applied our new technique to examine the sex ratio of hybrid larvae collected from one breeding nest in the wild. The sex ratio was equal between sexes at this site, suggesting that their sex is determined by chromosomal combination.