Genetic and phylogenetic structure of Hynobius quelpaertensis, an endangered endemic salamander species on the Korean Peninsula

Genetic Diversity and Population Structure of the Endangered Salamander Hynobius yiwuensis Inferred from Mitochondrial DNA Sequences

Understanding the genetic diversity patterns of endangered species is crucial for biodiversity conservation. The endangered salamander Hynobius yiwuensis, endemic to the mainland and Zhoushan Island in Zhejiang, China, has suffered from sharp population declines due to habitat loss. However, the levels and patterns of genetic diversity, differentiation, and population structure of H. yiwuensis remain poorly understood. Here, we explored the genetic diversity and phylogeography of H. yiwuensis based on partial mtDNA sequences (Cytb and CO1) through 111 individuals collected from seven localities. Relatively high overall haplotype diversity (h = 0.965) and low nucleotide diversity (π = 0.013) were detected. Our results, through phylogenetic trees and haplotype network analyses, revealed two divergent haplogroups, mainland and island, and the estimated divergence time indicated they diverged ~2.44 million years ago, which coincided with the period when Zhoushan Island became separated from the mainland.

Differentiated historical demography and ecological niche forming present distribution and genetic structure in coexisting two salamanders (Amphibia, Urodela, Hynobiidae) in a small island, Japan

Background

The climatic oscillations in the Quaternary period considerably shaped the distribution and population genetic structure of organisms. Studies on the historical dynamics of distribution and demography not only reflect the current geographic distribution but also allow us to understand the adaption and genetic differentiation of species. However, the process and factors affecting the present distribution and genetic structure of many taxa are still poorly understood, especially for endemic organisms to small islands.

Methods

Here, we integrated population genetic and ecological niche modelling approaches to investigate the historical distribution and demographic dynamics of two co-existing salamanders on Tsushima Island, Japan: the true H. tsuensis (Group A), and Hynobius sp. (Group B). We also examined the hypothesis on the equivalency and similarity of niches of these groups by identity and background tests for ecological niche space.

Results

Our result showed that Group A is considered to have undergone a recent population expansion after the Last Glacial Maximum while it is unlikely to have occurred in Group B. The highest suitability was predicted for Group A in southern Tsushima Island, whereas the northern part of Tsushima Island was the potential distribution of Group B. The results also suggested a restricted range of both salamanders during the Last Interglacial and Last Glacial Maximum, and recent expansion in Mid-Holocene. The genetic landscape-shape interpolation analysis and historical suitable area of ecological niche modelling were consistent, and suggested refugia used during glacial ages in southern part for Group A, and in northern part of Tsushima Island for Group B. Additionally, we found evidence of nonequivalence for the ecological niche of the two groups of the salamanders, although our test could not show either niche divergence or conservatism based on the background tests. The environmental predictors affecting the potential distribution of each group also showed distinctiveness, leading to differences in selecting suitable areas. Finally, the combination of population genetics and ecological modeling has revealed the differential demographic/historical response between coexisting two salamanders on a small island.

The Asian plethodontid salamander preserves historical genetic imprints of recent northern expansion

The Korean Peninsula, located at the southern tip of Northeast Asia, has never been covered by ice sheets and was a temperate refugium during the Pleistocene. Karsenia koreana, the sole Asian plethodontid salamander species, occurs only on the southern half of the Korean Peninsula and is thought to have found various climatic refugia. Despite its phylogenetic and biogeographic importance, no population-level genetic analysis has been performed on this species. Here we study the population genetic structure of K. koreana using mitochondrial and microsatellite loci to understand the recent historical dispersion process that shaped its current distribution. Overall, the genetic distance between populations correlated well with the spatial distance, and the genetic structure among populations showed signs of a unilateral northward expansion from a southernmost refugium population. Given the distinct genetic structure formed among the populations, the level of historical gene flow among populations appears to have been very low. As the estimated effective population size of K. koreana was also small, these results suggest that the small, restricted populations of K. koreana are extremely vulnerable to environmental changes that may require high levels of genetic diversity to cope with. Thus, special management strategies are needed to preserve these remnant populations.

Disentangling the Impacts of Speciation, Sympatry and the Island Effect on the Morphology of Seven Hynobius sp. Salamanders

Closely related individuals from different areas can see their morphologies change based on differences between clades, but also ecological variables such as the island effect or sympatry. This is the case of salamanders, which have adapted to a broad range of ecological niches, ranging from underground dwellers in xeric landscape to tropical arboreal habitats. On the Korean Peninsula, salamanders from the Hynobius clade are widespread on the mainland and islands, with several partially sympatric clades and candidate species. Currently, seven lineages have been identified based on mtDNA, four of them matching named species and three others for which the species status remains untested. While the morphology of Korean Hynobius is known to be variable between genetically segregated clades, we hypothesise that (1) the candidate species are morphologically different, and that (2) the island effect and (3) the sympatric status have significant impacts on the morphology of individuals within the genus. Here we measured 329 Hynobius salamanders from all seven clades, in areas of sympatry and allopatry, and on islands and on the mainland (Graphical Abstract A). We determined that the island effect had a significant impact on the morphology of the genus, with mainland individuals generally displaying a broader range of morphology than islandic individuals (Graphical Abstract B). We also determined that sympatry had an impact on morphology, with the sizes of individuals from clades in sympatric areas diverging from each other (Graphical Abstract C). Finally, we demonstrated that all seven clades have significantly different morphologies, and we described the three candidate species that had already been isolated based on mtDNA and microsatellite data: Hynobius notialis sp. nov., Hynobius geojeensis sp. nov. and Hynobius perplicatus sp. nov. We conclude that looking at morphology alone would be misleading about the true diversity of Hynobius species, and species in general, because of the island and patry effects.

Identification of the taxonomic status of Scinax nebulosus and Scinax constrictus (Scinaxinae, Anura) based on molecular markers

The validation of many anuran species is based on a strictly descriptive, morphological analysis of a small number of specimens with a limited geographic distribution. The Scinax Wagler, 1830 genus is a controversial group with many doubtful taxa and taxonomic uncertainties, due a high number of cryptic species. One example is the pair of species Scinax constrictus and Scinax nebulosus, which share a similar morphology. Scinax constrictus is restricted to the Brazilian Cerrado savanna, while S. nebulosus is widely distributed throughout northern South America. Despite the validation of many anuran species, discriminations based only on morphological traits is quite difficult due to the high conservative morphology of some groups. In this context, the present study uses mitochondrial and nuclear genes to provide a more consistent diagnosis and test the validity of S. constrictus as a distinct species from S. nebulosus, as well as evaluate the position of these taxa within the Scinax genus. The topologies obtained herein uphold the monophyletic status of Scinax based on all molecular markers assessed in this study, in all analytical approaches, with high levels of statistical support.