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Map of the Amami Islands. The largest island is AmamiOshima (Oshima), and the second largest one, south of and next to Oshima, is Kakeroma-jima. Black circles show the sampling localities of Babina subaspera, labelled with their three-letter codes and the number of samples in parentheses. Thick lines indicate National Road No. 58, with tunnels shown in dotted lines. Naze area is the centre of human population
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The otton frog (Babina subaspera) is an endangered species endemic to the Amami Islands, Japan. High predation pressure from an introduced carnivore, the mongoose, has caused declines in the frog populations and created a large habitat gap around an urban area. To promote effective conservation, we investigated the genetic status of the species and...
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... as deforestation and road construction in the forests have deteriorated the habitats of these animals (Environment Agency 2000). Furthermore, to control the native venomous pit viper, the mongoose (Herpestes java- nicus), an invasive carnivore, was introduced by humans in 1979 near the centre of the Naze area on Amami-Oshima (hereafter Oshima; Fig. 1). The mongoose rapidly expanded its distribution up to 10 km from the release point by 1990, and more than 20 km by 2004 (Ministry of the Environment 2005). Rather than reducing the viper population, the mon- gooses prey on many native species ( Abe et al. 1999) and have had strong negative impacts on rare vertebrates ( Watari et al. ...
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... (22) AOK (44) FUK (16) KAR (18) YUW (48) UKN (11) KMY (16) 10 km two islands are 2 km apart at their closest point. Oshima, which is 712 km 2 with a human population of 68,000, has several ridges and valleys with rivers ( Fig. 1). Nearly 40,000 people live in Naze City, which is located on the northern part of Oshima (Centered at Naze area; Fig. 1). Because mountainous areas are not suitable for human residence, the urban areas are mostly located along the coastline near large roads. The largest road on Oshima is National Road No. 58, which crosses the island ...
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... (22) AOK (44) FUK (16) KAR (18) YUW (48) UKN (11) KMY (16) 10 km two islands are 2 km apart at their closest point. Oshima, which is 712 km 2 with a human population of 68,000, has several ridges and valleys with rivers ( Fig. 1). Nearly 40,000 people live in Naze City, which is located on the northern part of Oshima (Centered at Naze area; Fig. 1). Because mountainous areas are not suitable for human residence, the urban areas are mostly located along the coastline near large roads. The largest road on Oshima is National Road No. 58, which crosses the island from the north through Naze area to the south (Fig. 1). With the exception of the road and associated human areas, the ...
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... City, which is located on the northern part of Oshima (Centered at Naze area; Fig. 1). Because mountainous areas are not suitable for human residence, the urban areas are mostly located along the coastline near large roads. The largest road on Oshima is National Road No. 58, which crosses the island from the north through Naze area to the south (Fig. 1). With the exception of the road and associated human areas, the mountains are essentially continuous on Oshima. The mongoose was introduced to the centre of Naze area in 1979, and its population subsequently expanded toward the south-west of the island. Kakeroma-jima is only 77.4 km 2 with 1,500 people and consists of continuous ...
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... toes of 175 adult B. subaspera were sampled in 2004-2007 (1 in 2004, 82 in 2005, 73 in 2006, 19 in 2007) in Oshima and Kakeroma-jima. Individuals within close geographical distance were grouped into seven populations ( Fig. 1). Population sample sizes ranged from 11 to 48. DNA was extracted from ethanol-preserved toes using PrepMan Ultra Sample Preparation Reagent (Applied Biosystems). Five microsatellite loci were examined: Bas2011, Bas2037, Bas2044, Bas2051, and Bas2091 (Iwai et al. 2011). The forward primer of each primer set was end-labelled with NED ...
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... Many faunas and floras in freshwater habitats are critically endangered (Abell, 2002;Saunders et al., 2002). In Japan, some freshwater species were investigated for their intraspecific genetic divergence and diversity, and the results were then utilized to develop methods for their conservation (e.g., Uesugi et al., 2007;Iwai and Shoda-Kagaya, 2012; Kitanishi et al., 2013;Urano et al., 2013;Watanabe et al., 2014). Phylogeography and intraspecific phylogeny have been studied for some species of aquatic insects (e.g., Yoshikawa et al., 2001;Suzuki et al., 2002;Hiyori et al., 2004;Sota et al., 2004;Sota and Hayashi, 2007;Suzuki et al., 2014). ...
Dytiscus sharpi is a critically endangered diving beetle endemic to Japan that is distributed in five distant areas today. Information on the population genetics of this species is crucial for its conservation. We investigated the genetic differentiation and divergence of the D. sharpi in seven populations in North and South Hokuriku on the Sea of Japan side, using mitochondrial cytochrome oxidase subunit I (COI) and nuclear Histone 3 and 28S rRNA gene sequences. Although the nuclear markers showed little geographic genetic differentiation, nine COI haplotypes were identified from 31 individuals, and these haplotypes were divided into two distinct networks A and B. The network A consisted of a single haplotype, and network B consisted of eight haplotypes. The populations in North Hokuriku possessed the haplotypes of both networks, whereas those in South Hokuriku possessed only the haplotypes of network B. The genetic diversity was relatively high in South and North Hokuriku. However, populations in South Hokuriku showed low genetic diversity and the isolation-by-distance pattern was observed among the populations, suggesting a restricted gene flow. Phylogenetic analysis including the data from a previous study revealed that the network A was closely related to a haplotype from Kanto, which is on the Pacific side. These results suggested that in the past this species was distributed widely across the Hokuriku area and the fragmentation of its distribution areas is a recent event. These results will contribute to strategies for the preservation of the current genetic diversity of D. sharpi.
... Nuclear markers such as microsatellite markers can be used to show the fine-scale genetic structure and extensive gene flow of local populations (Rogers and Peacock, 2012;Iwai and Shoda-Kagaya, 2012;Dias et al., 2015). Understanding gene flow and genetic structure using nuclear markers is critical for developing conservation approaches in local populations, because such detailed information provides an improved understanding of the effects of barriers or other strong restrictions on movement among breeding sites and allow for better management (Cushman, 2006;Purrenhage et al., 2009;Safner et al., 2011;Sotiropoulos et al., 2013). ...
Habitat fragmentation is one of the major threats to amphibian species. In a previous study, population genetic analyses of the Japanese brown frog Rana japonica were conducted using a mitochondrial DNA (mtDNA) marker in a typical Japanese agricultural landscape (known as satoyama) in Chiba, Japan. This previous study revealed that gene flow was restricted by the roads and cement-walled urban river that divide this site. In the present study, we reanalyzed the genetic structure of the same metapopulation using microsatellite markers in comparison with the mtDNA results and elucidated fine-scale gene flow. The genetic structure derived from the microsatellite clustering analysis was almost identical to that of the mtDNA results, although some important details differed. We recognized boundaries of genetic structure are consistent with the major roads and cement-walled river, however, we also detected gene flow across those artificial barriers. We concluded that the current genetic structure was formed in the past when gene flow was strongly restricted. Gene flow among breeding populations is now being restored by the maintenance of breeding sites, although it is not sufficient to erase the signature of historical isolation.
... For example, the brown anole lizard (Anolis sagrei) lost allelic richness and heterozygosity because of invasive rats (Ruttus spp.) on the Great Exuma Island, Bahamas (Gasc et al. 2010). Such an effect of an invasive predator on the genetic structure of animals on the Amami Oshima Island has been reported (Iwai and Shoda-Kagaya 2012). Amami Oshima Island has many endemic and/or endangered vertebrate species: e.g., Amami jay (Garrulus lidthi), Otton frog (Babina subaspera), Amami tip-nosed frog (Odorrauna amamiensis), Amami Ishikawa's frog (Odorrana splendida), and the Ryukyu long-haired rat (Diplothrix legata). ...
... The Otton frog population has also decreased in size since the mongoose was released, and their population has been fragmented into NI and SL populations. As the results suggest, the NI population is genetically fragmented and has a different genetic structure from the SL population (Iwai and Shoda-Kagaya 2012). ...
... The frog and rabbit cases differ in that all individuals in the NI and SL populations of the frog were strongly assigned to each population by a Bayesian clustering analysis. Moreover, the frog had one dominant haplotype occurred all over the island, which did not suggest genetic fragmentation in a historical timescale (Iwai and Shoda-Kagaya 2012). Therefore, the genetic characteristics of the NI frog population was likely caused by genetic drift after fragmentation by the mongoose (Iwai and Shoda-Kagaya 2012). ...
Invasive carnivores often cause heavy damage to native species on small islands. Endangered Amami rabbit (Pentalagus furnessi) populations have been fragmented into a north-isolated population (NI) and a south-large population (SL) caused by predation pressure from the invasive small Indian mongoose (Herpestes auropunctatus) on Amami Oshima Island in southern Japan. We investigated the genetic structure of these rabbit populations to determine the effects of fragmentation. We collected rabbit feces from most of the Amami Oshima Island habitat and sequenced the mitochondrial DNA (mtDNA) control region along with its 5′-flanking region (312 bp) and genotyped eight microsatellite DNA loci. Genetic diversity was lower in the NI than that in the SL population, and FST values between the two populations were significantly higher than zero in both the mtDNA and microsatellite DNA. Bayesian clustering analyses suggested four ancestral clusters of Amami rabbit, but clear genetic structure was not observed. A partial Mantel test supported isolation-by-distance but not habitat fragmentation. These results suggest that the low genetic diversity in the NI population was caused by the small population size after fragmentation; however, the difference in genetic structure between the two populations was caused by isolation-by-distance and the structure has been maintained.
... This frog has a high academic value because of its unique feature of a pseudothumb that has an appearance of "fifth finger" (Tokita and Iwai 2010;Iwai 2013), but it is now threatened due to habitat degradation and predation pressure from invasive predators (Watari et al. 2008 November 2012]), which indicates its high priority for conservation. Iwai and Shoda-Kagaya (2012) revealed that some populations of Otton Frog are genetically isolated, which means that conservation measures need to be based on the mobility of the species. However, no data about their home range, mobility, or site fidelity have been available despite the importance of this information in planning conservation measures. ...
For the effective conservation of frogs, knowledge about the movement patterns of the target species is essential. However, methods for tracking frogs, such as mark-recapture, spools of thread, and radiotelemetry all have their limitations. to compensate for the constraints of various methods, I combined radiotelemetry and mark-recapture to reveal the home range and movement patterns of an endangered species, the otton frog (Babina subaspera). I tracked five individuals by radiotelemetry for up to 451 days. additionally, I marked 316 individuals in 2010-2012. Radiotelemetry revealed that three females moved among different areas throughout a year (base area, breeding site, and overwintering site), while a male remained at the breeding site during the active season and then migrated to an overwintering area. the minimum convex polygon of the locations was 5,300-30,000 m2. the migration distances from the base area to the breeding site and then to the overwintering area were 150 and 80-250 m, respectively, for females, and the distance from the breeding site to the overwintering area was 200 m for a male. these migration distances agree with the results of the mark-recapture study: more than 95% of the individuals were recaptured within 200 m of the tagging location during the active season. distance between captures did not increase with time, indicating high site-fidelity in this species. the combination of the two different methods to track frogs proved successful and produced reliable information about the movements of this endangered frog, which will contribute greatly to its conservation.
... In addition, another Babina species, B. okinavana is listed as endangered. Prompt measures to conserve these species are awaited, and a recent population genetics study has been performed on B. subaspera using microsatellite markers (Iwai and Shoda-Kagaya, 2012), but no usable mitochondrial genomic marker on these species has been obtained. Since the initial description of genus Babina (Thompson, 1912 ), several taxonomic changes have been made. ...
Genus Babina is a member of Ranidae, a large family of frogs, currently comprising 10 species. Three of them are listed as endangered species. To identify mitochondrial (mt) genes suitable for future population genetic analyses for endangered species, we determined the complete nucleotide sequences of the mt genomes of 3 endangered Japanese Babina frogs, B. holsti, B. okinavana, and B. subaspera and 1 ranid frog Lithobates catesbeianus. The genes of NADH dehydrogenase subunit 5 (nad5) and the control region (CR) were found to have high sequence divergences and to be usable for population genetics studies. At present, no consensus on the phylogenetic position of genus Babina has been reached. To resolve this problem, we performed molecular phylogenetic analyses with the largest dataset used to date (11,345 bp from 2 ribosomal RNA- and 13 protein-encoding genes) in studies dealing with Babina phylogeny. These analyses revealed monophyly of Babina and Odorrana. It is well known that mt gene rearrangements of animals can provide usable phylogenetic information. Thus, we also compared the mt gene arrangements among Babina species and other related genera. Of the surveyed species, only L. catesbeianus manifested typical neobatrachian-type mt gene organization. In the B. okinavana, an additional pseudogene of tRNA-His (trnH) was observed in the CR downstream region. Furthermore, in the B. holsti and B. subaspera, the trnH/nad5 block was translocated from its typical position to the CR downstream region, and the translocated trnH became a pseudogene. The position of the trnH pseudogene is consistent with the translocated trnH position reported in Odorrana. Consequently, the trnH rearrangement seems to be a common ancestry characteristic (synapomorphy) of Babina and Odorrana. Based on the "duplication and deletion" gene rearrangement model, a single genomic duplication event can explain the order of derived mt genes found in Babina and Odorrana.
The China-Vietnam border region is a well-known biodiversity hotspot, harboring a striking diversity of species and endemism. However, the largest part of this region is so far understudied due to restrictions by political boundaries and difficulties in accessibility. Consequently, many species have only been reported from one side of the political boundary, despite the presence of continuous habitat on both sides. In this study, we present our discovery of the frog Nidirana chapaensis in southern Yunnan Province, China. This species was previously known only from Vietnam. All major morphometric characters of these Chinese specimens were found to match with the Vietnamese specimens. In addition, our mitochondrial phylogeny suggests that the Chinese population is monophyletic with respect to topotypic Nidirana chapaensis, with uncorrected pairwise distances of 0.2% at the COI gene fragment analyzed. Therefore, we report Nidirana chapaensis as a new member of amphibian fauna of China, describe the morphological variation of the Chinese population, and provide additional natural history data of this species based on our observation from China.
The Indo-Pacific red lionfish Pterois volitans has spread throughout the western Atlantic causing declines in biomass and diversity of native species at local reefs; worst-case scenarios predict species extinctions and ecosystem phase shifts. While reductions in reef fish population density and recruitment are evident, it is not known whether lionfish are reducing genetic diversity of native species, a major driver of extinction in natural populations. A before-after control-impact experiment was used to determine whether lionfish removals cause an increase in density of native species and genetic diversity in one species, the bicolor damselfish Stegastes partitus. We found that removing lionfish significantly augmented the density of several reef fish species. However, while allelic frequencies in bicolor damselfish recruits changed after removals, genetic diversity did not increase substantially despite a 3-fold increase in recruit density. Responses to lionfish removal differed among native species; rare species with small population sizes may be more susceptible to recruitment failure and diversity loss as a result of lionfish predation than widespread species with large populations.
Since the first documented declines of amphibian species, researchers have learned how nonnative species can depress amphibian populations and lead to local extinctions. Here, we explore the dimensions of invasions in the context of evolutionary history, anthropogenic disturbance, and climate change. Recent studies indicate that the nonnative groups that have most negatively affected amphibians are plants, fishes, and other amphibians. We review current work aimed at determining the direct and indirect effects of nonnative species on amphibian health, genotypes, and native ecosystem structure, as well as research examining invasions from a community level perspective. We also describe synergistic effects between abiotic, biotic, and nonnative factors. Recent studies have documented the intricacies of invasions and how numerous aspects of invasions can interact additively and complementarily to the detriment of the native ecosystem. Understanding the complexity of invasions means considering if and how biological, environmental, and ecological processes within ecosystems are being reshaped as a result of introduced species. Assessing the ecology and ecosystem dynamics of invasions at multiple levels, from the genome to the ecosystem, is paramount to the conservation, restoration, and future research of invaded amphibian ecosystems.
We surveyed the genetic diversity and genetic differentiation of an endangered frog, Babina holsti, endemic to Okinawajima and Tokashikijima Islands of the Ryukyus, to elucidate its divergence history and obtain basic data for its conservation. Genetic differentiation between the two island lineages is moderate (3.1% p-distance in the cyt b gene). This result suggests that the two island lineages have been isolated between the late Pliocene and the middle Pleistocene and have never migrated between the current northern part of Okinawajima and Tokashikijima Islands, which were once connected in the late Pleistocene glacial age. On Okinawajima Island, the southernmost sample was constituted by a unique haplotype, without considerable genetic distance from haplotypes detected from northern samples. This unique haplotype composition in the southernmost sample would have resulted from the restricted gene flow between the southernmost population and the other populations in Okinawajima Island. Furthermore, the absence of genetic diversity within the southernmost sample indicates that this population has recently experienced population size reduction, possibly by predation pressure from an introduced mongoose, which is more abundant in the southern part than in the northern part of the island. Lower genetic diversity in the Tokashikijima sample implies a small effective population size for mitochondrial DNA (mtDNA) in B. holsti on the island. Immediate conservation measures should be taken for the populations from the southernmost range in Okinawajima and Tokashikijima.
