Phylogeography reveals an ancient cryptic radiation in East-Asian tree frogs (Hyla japonica group) and complex relationships between continental and island lineages

Background

In contrast to the Western Palearctic and Nearctic biogeographic regions, the phylogeography of Eastern-Palearctic terrestrial vertebrates has received relatively little attention. In East Asia, tectonic events, along with Pleistocene climatic conditions, likely affected species distribution and diversity, especially through their impact on sea levels and the consequent opening and closing of land-bridges between Eurasia and the Japanese Archipelago. To better understand these effects, we sequenced mitochondrial and nuclear markers to determine phylogeographic patterns in East-Asian tree frogs, with a particular focus on the widespread H. japonica.

Results

We document several cryptic lineages within the currently recognized H. japonica populations, including two main clades of Late Miocene divergence (~5 Mya). One occurs on the northeastern Japanese Archipelago (Honshu and Hokkaido) and the Russian Far-East islands (Kunashir and Sakhalin), and the second one inhabits the remaining range, comprising southwestern Japan, the Korean Peninsula, Transiberian China, Russia and Mongolia. Each clade further features strong allopatric Plio-Pleistocene subdivisions (~2-3 Mya), especially among continental and southwestern Japanese tree frog populations. Combined with paleo-climate-based distribution models, the molecular data allowed the identification of Pleistocene glacial refugia and continental routes of postglacial recolonization. Phylogenetic reconstructions further supported genetic homogeneity between the Korean H. suweonensis and Chinese H. immaculata, suggesting the former to be a relic population of the latter that arose when the Yellow Sea formed, at the end of the last glaciation.

Conclusions

Patterns of divergence and diversity were likely triggered by Miocene tectonic activities and Quaternary climatic fluctuations (including glaciations), causing the formation and disappearance of land-bridges between the Japanese islands and the continent. Overall, this resulted in a ring-like diversification of H. japonica around the Sea of Japan. Our findings urge for important taxonomic revisions in East-Asian tree frogs. First, they support the synonymy of H. suweonensis (Kuramoto, 1980) and H. immaculata (Boettger, 1888). Second, the nominal H. japonica (Günther, 1859) represents at least two species: an eastern (new taxon A) on the northern Japanese and Russian Far East islands, and a southwestern species (n. t. B) on southern Japanese islands and possibly also forming continental populations. Third, these continental tree frogs may also represent an additional entity, previously described as H. stepheni Boulenger, 1888 (senior synonym of H. ussuriensis Nikolskii, 1918). A complete revision of this group requires further taxonomic and nomenclatural analyses, especially since it remains unclear to which taxon the species-epitheton japonica corresponds to.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0814-x) contains supplementary material, which is available to authorized users.

Shifts in sensitivity of amphibian metamorphosis to endocrine disruption: the common frog (Rana temporaria) as a case study

Effective conservation actions require knowledge on the sensitivity of species to pollution and other anthropogenic stressors. Many of these stressors are endocrine disruptors (EDs) that can impair the hypothalamus-pituitary-thyroid axis and thus alter thyroid hormone (TH) levels with physiological consequences to wildlife. Due to their specific habitat requirements, amphibians are often sentinels of environmental degradation. We investigated how altered TH levels affected the bioenergetics of growth and development (i.e. age, size, metabolism, cardiac function and energy stores) before, during and after metamorphosis in the European common frog (Rana temporaria). We also determined how ontogenetic stage affected susceptibility to endocrine disruption and estimated juvenile performance. TH levels significantly affected growth and energetics at all developmental stages. Tadpoles and froglets exposed to high TH levels were significantly younger, smaller and lighter at all stages compared to those in control and low TH groups, indicating increased developmental and reduced growth rates. Across all ontogenetic stages tested, physiological consequences were rapidly observed after exposure to EDs. High TH increased heart rate by an average of 86% and reduced energy stores (fat content) by 33% compared to controls. Effects of exposure were smallest after the completion of metamorphosis. Our results demonstrate that both morphological and physiological traits of the European common frog are strongly impacted by endocrine disruption and that ontogenetic stage modulates the sensitivity of this species to endocrine disruption. Since endocrine disruption during metamorphosis can impair the physiological stress response in later life stages, long-term studies examining carry-over effects will be an important contribution to the conservation physiology of amphibians.

Bioaccumulation of DDT and other organochlorine pesticides in amphibians from two conservation areas within malaria risk regions of South Africa

The threat to wildlife from chemical exposure exists regardless of the presence of conservation boundaries. An issue exacerbated by the use of environmentally persistent insecticides for vector control and long-range transport of legacy persistent organic pollutants. In this comparative study between two important conservation regions in South Africa, Kruger National Park (KNP) and Ndumo Game Reserve (NGR), we assessed organochlorine pesticide (OCP) accumulation in several anuran species collected from within the conservation regions. The two conservation regions differ in size and subsequent proximity of collection sites to OCP input sources. Detectable concentrations of OCPs were present in ∼ half the frogs analysed from KNP and ∼all frogs from NGR and total OCP loads were similar between regions, where measured in the same species. The OCP profiles in KNP frogs were representative of legacy pesticides likely introduced via long-range transport, whereas NGR profiles showed influence of current use of DDT consistent with close proximity to sources. This indicates amphibians can accumulate OCPs within conservation regions and that the exposure of non-target organisms inside conservation regions to current use pesticides has a strong association with proximity to sources. These results serve to inform conservation management decision making with regard to the non-target organism effects of chemical interventions such as vector control pesticide use in and around conservation regions.

Captivity-Induced Changes in the Skin Microbial Communities of Hellbenders (Cryptobranchus alleganiensis)

Variation in environmental conditions can result in disparate associations between hosts and microbial symbionts. As such, it is imperative to evaluate how environmental variables (e.g., habitat quality) can influence host-associated microbiome composition. Within wildlife conservation programs, captive conditions can negatively influence the establishment and maintenance of "wild-type" microbiotas within a host. Alternative microbial communities can result in the proliferation of disease among captive stock or upon reintroduction. Hellbenders (Cryptobranchus alleganiensis) are a threatened salamander for which extensive captive management is currently employed. Using metabarcoding, we characterized the skin microbiota of wild and captive hellbenders from two subspecies in the state of Missouri, the eastern (C. a. alleganiensis) and the Ozark hellbender (C. a. bishopi). Both subspecies in our study included wild adults and captive juveniles that were collected from the wild as eggs. Our objectives were to investigate differences in the skin microbial communities' richness/diversity, composition, and functional profiles of microbes between wild and captive individuals. Captive eastern hellbenders possessed richer communities than wild cohorts, whereas the opposite pattern was observed within the Ozark subspecies. We found significant microbial community structure between wild and captive populations of both subspecies. Microbiota structure translated into differences in the predicted metagenome of wild and captive individuals as well. As such, we can expect captive hellbenders to experience alternative microbial structure and function upon reintroduction into the wild. Our study provides a baseline for the effect of captivity on the skin microbial communities of hellbenders, and highlights the need to incorporate microbiota management in current captive-rearing programs.

Widespread occurrence of the antifungal cutaneous bacterium Janthinobacterium lividum on Andean water frogs threatened by fungal disease

Amphibian diversity has declined due to the infectious disease chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd). Coexistence between amphibian hosts and this pathogen in some locations is attributed to the presence of the cutaneous bacterium Janthinobacterium lividum (Jliv). This microbe inhibits the growth of Bd on the host, reduces morbidity, and improves survival. Andean water frogs in the genus Telmatobius seem to be particularly vulnerable to the disease yet populations of T. intermedius and T. marmoratus persist in southern and central Peru. We investigated the presence of Jliv on these 2 frog species and assessed the relationship of Jliv presence with prevalence and intensity of Bd infection. By sampling 125 frogs from 7 streams (3323-3950 m a.s.l.) and 27 from a city market, we found spatial variation in the mutualism among populations (range 0-40% proportion of Jliv-positives). Overall, 57% of frogs were infected with Bd, 12.5% of frogs hosted both Jliv and Bd, while 7.2% hosted just Jliv. We found that the probability of an individual being infected with Bd was independent of the presence of Jliv; however, we did detect a protective effect of Jliv with respect to intensity of infection. The extent of Jliv distribution in the high Andes stands in stark contrast to the rarity of Jliv on frogs in lower elevation cloud forest biomes.

First report of Euryhelmis parasites (Trematoda, Heterophyidae) in Africa: conservation implications for endemic amphibians

In this study, we report, through molecular identification, the first African records of a digenean trematode parasite of the genus Euryhelmis. We recovered metacercariae encysted in an anuran, the endemic Moroccan painted frog (Discoglossus scovazzi), and a vulnerable caudate, the North African fire salamander (Salamandra algira), from four localities in North Africa (Morocco). Our records go back to the past century and have been confirmed in successive fieldwork seasons thereafter. Metacercarial stages of these parasites require amphibians as the last intermediate host, but the exact identity of the primary hosts and predators of the infected animals in Africa remain unknown. Our searches with basic local alignment search tool (BLAST) from Genbank revealed that hosts were infected by parasites of Euryhelmis costaricensis, which showed almost the same genetic identity (with only one substitution) to previous reports from Costa Rica and Japan, suggesting a recent introduction in Morocco. We proceed to discuss the likely role of introduced mustelids as the potential definitive hosts of trematode adults. Under this assumption, we conclude that the infestation of Discoglossus scovazzi and Salamandra algira might pose a risk to these threatened species.

Potential hotspots of amphibian roadkill risk in Spain

We test a forecasting strategy to identify potential hotspots of amphibian roadkill, combining the spatial distribution of amphibians, their relative risk of collision with vehicles and data on road density in Spain. We extracted a large dataset from studies reporting road casualties of 39 European amphibian species and then estimated the 'relative roadkill risk' of species as the frequency of occurrence of casualties for each amphibian and standardized by the range of distribution of the species in Europe. Using a map with the spatial distribution of Spanish amphibians at a spatial resolution of 10 × 10 Km squares, we estimated the 'cumulative relative risk of roadkill' for each amphibian assemblage as the sum of risk estimates previously calculated for each species. We also calculated the total length of roads in each square (road density). Finally, combining all layers of information, we elaborated a forecasting map highlighting the potential amphibian roadkill risk across Spain. Our findings are relevant to suggest areas that should be focused on at more detailed spatial scales. Additionally, we found that the frequency of roadkill was unrelated to the evolutionary distinctiveness score and conservation status of amphibian species, while was positively correlated with their distribution range.

Water quality limitations for tadpoles of the Wood Frog in the northern Great Plains, Canada

Some wetlands in the northern Great Plains support hundreds to thousands of late-stage tadpoles providing important sources of recruitment to the Wood Frog (Lithobates sylvaticus) population while many other wetlands produce none. Relationships between water quality and late-stage tadpole abundance were determined to identify the water quality parameters associated with tadpole abundance. Water samples were collected, and late-stage tadpole abundances were assessed once each year in late June for 12 years in 26 wetlands. Catch or abundance was the number of tadpoles captured in 30 min with a dip-net. The catch of tadpoles was variable both among wetlands and over the long-term for individual wetlands, and ranged from 0 to several hundred individuals. Wood Frog tadpoles were especially sensitive to sodium and chloride concentrations. At Cl concentrations less than 5 mg/L, occupancy for late-stage tadpoles was 84%, and declined by about 8% for each 5 mg/L increase in Cl to 40.1 mg/L Cl, the maximum concentration associated with the detection of tadpoles. Optimal water quality for late-stage Wood Frog tadpoles included low concentrations of Na [Formula: see text] = 8.1 mg/L), and Cl [Formula: see text] = 4.2 mg/L) relative to total dissolved solids and other ions, and high concentrations of phosphorus. In a landscape where ion concentrations in wetlands can range over 3 orders of magnitude, water quality analyses suggest that abundant Wood Frog tadpole populations occur in wetlands dominated by snow-melt runoff with its characteristic low ion concentrations. The present study highlights the importance to amphibian conservation of the water quality environment of tadpole habitat.

A quantitative approach to ranking management actions for an endangered pool-breeding amphibian

Management of vulnerable amphibian populations requires a better understanding of the habitat factors that will make the greatest difference in their preservation. We set out to develop a predictive model of amphibian abundance based on habitat characteristics that may influence their survival and persistence. Our study system was the Sonoma County California tiger salamander (Ambystoma californiense; SCTS), an amphibian threatened by habitat loss and fragmentation. In 2019, 298 ponds (almost every breeding pond in this federally endangered Distinct Population Segment) were surveyed to determine SCTS larval densities, a proxy for population well-being. We used model selection to identify which factors of pool morphology, the surrounding pool neighborhood, and terrestrial upland habitat best predict variation in larval densities. Our best model showed a significant positive relationship between larval SCTS densities and three variables: pool depth, number of breeding pools within 500 m of a focal pool, and amount of suitable and accessible upland habitat within 1500 m of a pool. To further refine this model, we then examined interactions and non-linearities using a generalized additive model. Based on this refined model, we simulated a variety of management scenarios to identify which management practices would most increase larval densities across the endangered Distinct Population Segment and where on the landscape employing each mitigation action would yield the greatest return. This provides the basis for a county-wide Habitat Conservation Plan for SCTS, and highlights habitat characteristics likely critical to the conservation of other pond-breeding amphibians.

The phenotypic variability in Rana temporaria decreases in response to drying habitats

In this study, we evaluated the diversity of skin coloration as a proxy for phenotypic diversity. The European common frog (Rana temporaria) populations from the Southern slope of central Pyrenees lie at the limit of the species distribution in latitude and altitude. We analysed the relationship of skin color typology with different environmental variables and found a large decrease in skin type variety in frogs developing in temporary water bodies when compared to those developing in permanent water bodies. Our results show that our method can be used as a non-invasive way to study phenotypic diversity and suggest that adaptation to an early metamorphosis in a rapidly-drying habitat can have negative effects on adult phenotypic diversity. In light of these results, we argue that access to permanent water bodies is important to prevent loss of diversity in anuran populations and reduce their vulnerability to environmental impacts as well as pathogens.

Reclamation history and land use types across multiple spatial scales shape anuran communities in the coastal land reclamation region

Land reclamation is a widely adopted method for managing land shortage and promoting coastal economic development globally. However, its impacts on biodiversity vary based on distinct reclamation histories and land use management strategies in different regions. This study aims to examine the effects of reclamation history and land use types at different spatial scales on anuran communities in coastal reclaimed land, which are an important taxon in the coastal ecosystem. We used visual and acoustic encounter methods to survey anurans in 2016 and 2017 across 20 1-km radius coastal land reclamation landscapes with different reclamation histories (10, 20, and 60 y after reclamation) in Nanhui Dongtan of Shanghai, an important coastal land reclamation region along the Yangtze River Estuary. Landscape variables (farmlands, woodlands, and impermeable surface covers, and the landscape Shannon diversity index) at four different spatial scales (250 m, 500 m, 750 m and 1000 m) and water salinity in each landscape were measured. Our findings reveal differences in anuran communities between study sites with 10, 20, and 60 years of reclamation history. Abundances of the ornamented pygmy frog (Microhyla fissipes) and Beijing gold-striped pond frog (Pelophylax plancyi) in landscapes with a 10-year reclamation history were significantly lower compared to those with histories of 20 and 60 years. Zhoushan toad (Bufo gargarizans) abundance was significantly negatively related to farmland cover at the 1000 m scale and impermeable surface cover at the 250 m scale; Hong Kong rice-paddy frog (Fejervarya multistriata) abundance was significantly positively related to farmland cover at the 1000 m scale; ornamented pygmy frog abundance was positively related to farmland cover at the 1000 m scale; and Beijing gold-striped pond frog abundance was significantly positively and negatively related to the landscape Shannon diversity index at the 1000 m scale and to water salinity, respectively. Amphibians quickly migrated and colonized coastal reclaimed land from older natural lands. However, two anuran species with specific habitat requirements tended to avoid areas with shorter reclamation histories. The single-species models revealed different responses to various land uses at the various scales, which indicated that land use management was important to amphibian conservation in coastal reclamation regions.

Widespread occurrence of the amphibian chytrid panzootic lineage in Uruguay is constrained by climate

The amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) causes chytridiomycosis, a disease among the main causes of amphibian declines worldwide. However, Bd studies on Neotropical amphibians from temperate areas are scarce. We present a comprehensive survey of Bd in Uruguay, in temperate central eastern South America, carried out between 2006 and 2014. Skin swabs of 535 specimens of 21 native and exotic frogs were tested by PCR. We used individual-level data to examine the relationship between infection, climatic variables, and their effects on body condition and the number of prey items found in stomach contents. Infection was widespread in free-ranging anurans with an overall prevalence of 41.9%, detected in 15 native species, wild American bullfrogs Aquarana catesbeiana, and captive specimens of Ceratophrys ornata and Xenopus laevis. Three haplotypes of the Bd ITS region were identified in native amphibians, all belonging to the global panzootic lineage (BdGPL), of which only one was present in exotic hosts. Despite high infection frequencies in different anurans, we found no evidence of morbidity or mortality attributable to chytridiomycosis, and we observed no discernible impact on body condition or consumed prey. Climatic conditions at the time of our surveys suggested that the chance of infection is associated with monthly mean temperature, mean humidity, and total precipitation. Temperatures below 21°C combined with moderate humidity and pronounced rainfall may increase the likelihood of infection. Multiple haplotypes of BdGPL combined with high frequencies of infection suggest an enzootic pattern in native species, underscoring the need for continued monitoring.