Phylogeographic and population insights of the Asian common toad (Bufo gargarizans) in Korea and China: population isolation and expansions as response to the ice ages

Range-Wide Phylogeography and Ecological Niche Modeling Provide Insights into the Evolutionary History of the Mongolian Racerunner (Eremias argus) in Northeast Asia

The Mongolian racerunner, Eremias argus, is a small lizard endemic to Northeast Asia that can serve as an excellent model for investigating how geography and past climate change have jointly influenced the evolution of biodiversity in this region. To elucidate the processes underlying its diversification and demography, we reconstructed the range-wide phylogeographic pattern and evolutionary trajectory, using phylogenetic, population genetic, landscape genetic, Bayesian phylogeographic reconstruction and ecological niche modeling approaches. Phylogenetic analyses of the mtDNA cyt b gene revealed eight lineages that were unbounded by geographic region. The genetic structure of E. argus was mainly determined by geographic distance. Divergence dating indicated that E. argus and E. brenchleyi diverged during the Mid-Pliocene Warm Period. E. argus was estimated to have coalesced at~0.4351 Ma (Marine Isotope Stage 19). Bayesian phylogeographic diffusion analysis revealed out-of-Inner Mongolia and rapid colonization events from the end of the Last Interglacial to the Last Glacial Maximum, which is consistent with the expanded suitable range of the Last Glacial Maximum. Pre-Last Glacial Maximum growth of population is presented for most lineages of E. argus. The Glacial Maximum contraction model and the previous multiple glacial refugia hypotheses are rejected. This may be due to an increase in the amount of climatically favorable habitats in Northeast Asia. Furthermore, E. argus barbouri most likely represents an invalid taxon. The present study is the first to report a range-wide phylogeography of reptiles over such a large region in Northeast Asia. Our results make a significant contribution towards understanding the biogeography of the entire Northeast Asia.

Impacts of Quaternary glaciation, geological history and geography on animal species history in continental East Asia: A phylogeographic review

Continental East Asia has a mild Pleistocene climate and a complex recent geological history. Phylogeographic studies of animals over the last 30 years have produced several distinctive patterns. Glaciation refugia are numerous and are not restricted to any particular regions. Most of them are localized and species-specific, although several large refugia, for example the mountains of SW China, are shared by multiple species and have refugia-within-refugia. Furthermore, postglaciation range expansion events vary greatly in time, scale and direction. Large-scale south-to-north post-LGM expansions are few and mostly occurred in the northern regions. Additionally, several unique geographic features, including the three-step terrain of China and the northern arid belt, have significant impacts on many species histories. Overall, the impacts of Pleistocene glaciations, particularly the LGM, on species history vary drastically from nondetectable to significant. The impacts are the least for species from the southwestern region and are most dominant for species from the north. Geological events play a more significant role in shaping species history than Pleistocene climatic changes. Phylogeographic patterns among animals species are highly consistent with those of plants. Future phylogeographic endeavour in East Asia should be hypothesis-driven and seek processes that underlie common patterns. The wide use of genomic data allow accurate estimates of historical population processes and exploration of older history beyond the Pleistocene.

Genetic diversity and demography of Bufo japonicus and B. torrenticola (Amphibia: Anura: Bufonidae) influenced by the Quaternary climate

The Quaternary climate affected the present species richness and geographic distribution patterns of amphibians by limiting their activities during the glacial period. The present study examined the phylogenetic relationships of Japanese toads (Bufo japonicus and B. torrenticola) and the demography of each lineage from the past to the present based on mitochondrial sequences and ecological niche models. Japanese toads are a monophyletic group with two main clades (clades A and B). Clade A represents B. j. formosus, including three clades (clades A1, A2, and A3). Clade B contains three clades, two of which corresponded to B. j. japonicus (clades B1 and B2) and the other to B. torrenticola. Clade B2 and B. torrenticola made a sister group, and, thus, B. j. japonicus is paraphyletic. Clades A and B diverged in the late Miocene 5.7 million years ago (Mya) during the period when the Japanese archipelago was constructed. The earliest divergence between the three clades of clade A was estimated at 1.8 Mya. Clades A1 and A2 may have diverged at 0.8 Mya, resulting from the isolation in the multiple different refugia; however, the effects of the glacial climate on the divergence events of clade A3 are unclear. Divergences within clade B occurred from the late Pliocene to the early Pleistocene (3.2-2.2 Mya). Niche similarity between the parapatric clade in clade B (clades B1 and B2) indicated their allopatric divergence. It was suggested that niche segregation between B. japonicus and B. torrenticola contributed to a rapid adaptation of B. torrenticola for lotic breeding. All clade of Japanese toads retreated to each refugium at a low elevation in the glacial period, and effective population sizes increased to construct the current populations after the Last Glacial Maximum. Furthermore, we highlight the areas of climate stability from the last glacial maximum to the present that have served as the refugia of Japanese toads and, thus, affected their present distribution patterns.

From Gondwana to the Yellow Sea, evolutionary diversifications of true toads Bufo sp. in the Eastern Palearctic and a revisit of species boundaries for Asian lineages

Taxa with vast distribution ranges often display unresolved phylogeographic structures and unclear taxonomic boundaries resulting in hidden diversity. This hypothesis-driven study reveals the evolutionary history of Bufonidae, covering the phylogeographic patterns found in Holarctic bufonids from the West Gondwana to the phylogenetic taxonomy of Asiatic true toads in the Eastern Palearctic. We used an integrative approach relying on fossilized birth-death calibrations, population dynamics, gene-flow, species distribution, and species delimitation modeling to resolve the biogeography of the clade and highlight cryptic lineages. We verified the near-simultaneous Miocene radiations within Western and Eastern Palearctic Bufo, c. 14.49-10.00 Mya, temporally matching with the maximum dust outflows in Central Asian deserts. Contrary to earlier studies, we demonstrated that the combined impacts of long dispersal and ice-age refugia equally contributed to the current genetic structure of Bufo in East Asia. Our findings reveal a climate-driven adaptation in septentrional Eastern Asian Bufo, explaining its range shifts toward northern latitudes. We resolve species boundaries within the Eastern Palearctic Bufo, and redefine the taxonomic and conservation units of the northeastern species: B. sachalinensis and its subspecies.

Diversity, distribution and molecular species delimitation in frogs and toads from the Eastern Palaearctic

Biodiversity analyses can greatly benefit from coherent species delimitation schemes and up-to-date distribution data. In this article, we have made the daring attempt to delimit and map described and undescribed lineages of anuran amphibians in the Eastern Palaearctic (EP) region in its broad sense. Through a literature review, we have evaluated the species status considering reproductive isolation and genetic divergence, combined with an extensive occurrence dataset (nearly 85k localities). Altogether 274 native species from 46 genera and ten families were retrieved, plus eight additional species introduced from other realms. Independent hotspots of species richness were concentrated in southern Tibet (Medog County), the circum-Sichuan Basin region, Taiwan, the Korean Peninsula and the main Japanese islands. Phylogeographic breaks responsible for recent in situ speciation events were shared around the Sichuan Mountains, across Honshu and between the Ryukyu Island groups, but not across shallow water bodies like the Yellow Sea and the Taiwan Strait. Anuran compositions suggested to restrict the zoogeographical limits of the EP to East Asia. In a rapidly evolving field, our study provides a checkpoint to appreciate patterns of species diversity in the EP under a single, spatially explicit, species delimitation framework that integrates phylogeographic data in taxonomic research.

Phylogeographic study of the Bufo gargarizans species complex, with emphasis on Northeast Asia

We conduct a phylogeographic and population genetic study of the Asiatic toad (Bufo gargarizans) to understand its evolutionary history, and the influence of geology and climate. A total of 292 individuals from 94 locations were genotyped for two mitochondrial loci (cytb, ND2) and five nuclear introns (Sox9-2, Rho-3, CCNB2-3, UCH-2, and DBI-2), and we performed a suite of phylogenetic, population genetic, and divergence dating analyses. The phylogenetic trees constructed using mitochondrial loci inferred B. gargarizans being divided into two major groups: China mainland and Northeast Asia (Northeast China, Russia, and Korean Peninsula). As with previous studies of this species, we recover population genetic structure not tied to geographic region. Additionally, we discover a new genetic clade restricted to Northeast Asia that points towards the Korean Peninsula being a glacial refugium during the Pleistocene. The weak phylogeographic pattern of B. gargarizans is likely the result of multiple biological, anthropogenic, and historical factors – robust dispersal abilities as a consequence of physiological adaptations, human translocation, geologic activity, and glacial cycles of the Pleistocene. We highlight the complex geologic and climatic history of Northeast Asia and encourage further research to understand its impact on the biodiversity in the region.

A simple PCR-RFLP method for identification and detection of medicinal toad and its crude drug even with serious degradation of DNA

The secretions of the venom glands, dry skin and whole body of several Bufo species have been used as traditional medicines in East Asia to treat heart failure and cancer. Due to the highly similar morphological features of Bufo species and their derived commercial crude drugs, along with the high similarity of chemical composition of the secretions of venom glands, it is very challenging to identify the medicinal toads and the related crude drugs. The cyt-b sequences provide useful information to authenticate medicinal Bufo species. Based on the cyt-b sequences, a simple PCR-RFLP method was established for the identification of the medicinally used Bufo species as well as their derived crude drugs. The 23 specimens from three medicinally used Bufo species, B. bufo gargarizans (Bbg), B. melanostictus (Bm) and B. raddei (Br), were clearly divided into 3 groups according to the sequences of amplified cyt-b regions, which could be digested by specific restriction enzymes NcoI, EcoRV and BstXI, respectively. Then the specific PCR-RFLP method was further used to identify 9 samples of commercial crude drugs even with serious degradation of DNA, and all nine samples were identified as B. bufo gargarizans. The method is suitable for identification of medicinally used Bufo species and the related crude drugs.

Update on Distribution and Conservation Status of Amphibians in the Democratic People's Republic of Korea: Conclusions Based on Field Surveys, Environmental Modelling, Molecular Analyses and Call Properties

Determining the range, status, ecology and behaviour of species from areas where surveys and samplings are uncommon or difficult to conduct is a challenge, such as in the Democratic People's Republic of Korea (DPR Korea). Here, we used genetic samples, field surveys, call recordings, photographic identification and a literature review to estimate the presence, range and status of amphibians in the DPR Korea. From our combined results and based on the IUCN Red List categories and criteria, we were able to estimate the national threat levels for most species. Our results demonstrated the presence of 18 native species and the suspected presence of Karsenia koreana and two Onychodactylus species. We reported the first record for Rana uenoi in the vicinity of Pyongyang using molecular tools and similarly confirmed the presence of Dryophytes japonicus at the same location. Based on distribution and modelling, we can expect the contact zone between species within the Rana and Onychodactylus genera to be located along the Changbai Massif, a mountain range that marks a shift in ecoregions and acts as a barrier to dispersion. The species richness was higher in the lowlands and at lower latitudes, with such areas populated by up to 11 species, while more northern regions were characterised by species richness of about half of that value. The combination of ecological models and known threats resulted in the recommendation of ten species as threatened at the national level following the IUCN Red List categories and criteria. This high number of threatened species was anticipated based on the high threat level to amphibians in bordering nations and globally. While the ecology of species in the DPR Korea is still understudied, we argue that species relying on agricultural wetlands such as rice paddies are not under imminent threat due to the enduring presence of extensive agricultural landscapes with low rates of chemical use and mechanisation. The maintenance of such landscapes is a clear benefit to amphibian species, in contrast to more industrialised agricultural landscapes in neighbouring nations. In comparison, the status of species dependent on forested habitats is unclear and threat levels are likely to be higher because of deforestation, as in neighbouring nations.

Impact of the Miocene orogenesis on Kaloula spp. radiation and implication of local refugia on genetic diversification

The phylogeography of the Kaloula genus in East Asia is still poorly understood. One of the difficulties is the absence of fossils to corroborate molecular dating estimates. Here, we examined the mitochondrial structure of Kaloula spp. in East Asia and focused on the impact of glaciations on the northernmost species: Kaloula borealis. We determined the phylogenetic relationships, molecular dating, and genetic connectivity assessments within the genus from 1211 bp of concatenated mitochondrial 12S and 16S. The relaxed clock analyses reveal the emergence of Kaloula spp. common ancestor in East and Southeast Asia between the Eocene and Oligocene, c. 38.47 Ma (24.69-53.65). The genetic diversification of lineages then increased on the East Asian Mainland during the Lower Miocene, c. 20.10 (8.73-30.65), most likely originating from the vicariance and radiation triggered by the orogeny of the Qinghai-Tibetan Plateau. Later, the dispersal towards the North East Asian Mainland during the Upper Miocene drove the population diversification of K. borealis c. 9.01 Ma (3.66-15.29). Finally, the central mainland population became isolated following orogenesis events and diverged into K. rugifera during the Pliocene, c. 3.06 Ma (0.02-10.90). The combination of population genetic and barrier analyses revealed a significant genetic isolation between populations of Kaloula spp. matching with the massive Qinling-Daba Mountain chain located in south-central China. Finally, we highlight a young divergence within the Eastern Mainland population of K. borealis, possibly attributed to refugia in south eastern China from which populations later expanded.

Biogeographical patterns of amphibians and reptiles in the northernmost coastal montane complex of South America

We examine, for the first time, biogeographic patterns in a series of tropical montane coastal systems in northern South America. We use amphibians and reptiles, which constitute the most critical communities based upon the prevalence of endemic taxa, to assess the region's biodiversity. The montane coastal system spans an east-west distance of 925 km. It includes peaks ranging from 549 m to 2765 m above sea level and encompasses the montane complexes of northern Venezuela (including Isla de Margarita), an outlier at Santa Marta (Colombia), and ranges on the islands Trinidad and Tobago. The area supports 14 family level amphibian clades and 23 family level reptile clades. Fieldwork, museum specimen surveys, and a literature review suggest that biodiversity decreases at higher elevations. Here we examine the biogeographic patterns in the region to assess the role of the montane systems as possible refugia. We also look at the possible island and sky island effects using data from altitudes >200 m. At lower elevations, we tabulated 294 species, comprising 112 amphibians and 182 reptiles. About 45% of these taxa are endemic or exclusive to different sub-regions. At mid-elevation montane cloud forests, we find a much-reduced biodiversity with a total of 125 species (66 amphibians and 59 reptiles) exclusive or restricted to the region, and few species shared between systems. We find that biogeographical patterns follow a natural topographic disposition above 200 m in elevations. At the lower elevation cut off, there are 118 species (26 amphibians and 92 reptiles) shared among two or more of the studied mountain systems, suggesting a common origin and dispersal events, despite what seem to be topographic barriers. Biogeographical relationships support a topographic disposition of the region with close associations between the islands of Trinidad and Tobago, the Paria Range and the Turimiquire Massif, and close associations between the Sierra Nevada de Santa Marta and the Sierra de San Luis. Overall, the biogeographic relationships between amphibians and reptiles are similar. Species diversity in the eastern Caribbean region is less rich than in the west. This study includes the first herpetological surveys at the two easternmost mountains (Cerro La Cerbatana and Campeare) belonging to the Paria Range biogeographic unit, and aims to contribute to a better understanding of the rich biodiversity of the region.

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.

Recommendations for IUCN Red List Conservation Status of the “Dryophytes immaculatus Group” in North East Asia

Threat assessment is important to prioritize species conservation projects and planning. The taxonomic resolution regarding the status of the “Dryophytes immaculatus group” and the description of a new species in the Republic of Korea resulted in a shift in ranges and population sizes. Thus, reviewing the IUCN Red List status of the three species from the group: D. immaculatus, D. suweonensis and D. flaviventris and recommending an update is needed. While the three species have similar ecological requirements and are distributed around the Yellow Sea, they are under contrasting anthropological pressure and threats. Here, based on the literature available, I have applied all IUCN Red List criterion and tested the fit of each species in each criteria to recommend listing under the appropriate threat level. This resulted in the recommendation of the following categories: Near Threatened for D. immaculatus, Endangered following the criteria C2a(i)b for D. suweonensis and Critically Endangered following the criteria E for D. flaviventris. All three species are declining, mostly because of landscape changes as a result of human activities, but the differences in range, population dynamics and already extirpated subpopulations result in different threat levels for each species. Dryophytes flaviventris is under the highest threat category mostly because of its limited range segregated into two subpopulations; and several known extirpated subpopulations. Immediate actions for the conservation of this species are required. Dryophytes suweonensis is present in both the Republic of Korea and the Democratic Republic of Korea (DPR Korea) and is under lower ecological pressure in DPR Korea. Dryophytes immaculatus is present in the People’s Republic of China, over a very large range despite a marked decline. I recommend joint efforts for the conservation of these species.

Comparative Morphology of the Lungs and Skin of two Anura, Pelophylax nigromaculatus and Bufo gargarizans

The lungs and skin are important respiratory organs in Anura, but the pulmonary structure of amphibians remains unclear due to the lack of a suitable procedure. This study improved the procedure used for fixing lungs tissues and used light microscopy, transmission electron microscopy and scanning electron microscopy to reveal the differences in the lung and skin morphologies between Pelophylax nigromaculatus (P. nigromaculatus) and Bufo gargarizans (B. gargarizans). In P. nigromaculatus and B. gargarizans, the cystic lungs comprise a continuous outer pulmonary wall on which primary, secondary, and tertiary septa attach, and a number of regular lattices form from raised capillaries and the pulmonary epithelium on the surfaces of the pulmonary wall and septa. Each lattice in P. nigromaculatus consists of several elliptical sheets and flat bottom, and the septa are distributed with denser sheets and have a larger stretching range than the pulmonary wall. The lattice in B. gargarizans consists of thick folds and an uneven bottom with several thin folds, and the septa have more developed thick and thin folds than the pulmonary wall. However, the density of the pulmonary microvilli, the area of a single capillary, the thicknesses of the blood-air barrier, pulmonary wall and septum, and the lung/body weight percentage obtained for B. gargarizans were higher than those found for P. nigromaculatus. In P. nigromaculatus, the dorsal skin has dense capillaries and a ring surface structure with mucus layer on the stratum corneum, and the ventral skin is slightly keratinized. In B. gargarizans, the stratum corneum in both the dorsal and ventral skins is completely keratinized. A fine ultrastructure analysis of P. nigromaculatus and B. gargarizans revealed that the pulmonary septa are more developed than the pulmonary walls, which means that the septa have a stronger respiratory function. The more developed lungs are helpful for the adaptation of B. gargarizans to drought environments, whereas P. nigromaculatus has to rely on more vigorous skin respiration to adapt to a humid environment.

Impact of the Mid-Pleistocene Revolution and Anthropogenic Factors on the Dispersion of Asian Black-Spined Toads (Duttaphrynus melanostictus)

Divergence-time estimation critically improves the understanding of biogeography processes underlying the distribution of species, especially when fossil data is not available. We hypothesise that the Asian black-spined toad, Duttaphrynus melanostictus, expanded into the Eastern Indomalaya following the Quaternary glaciations with the subsequent colonisation of new landscapes during the Last Glacial Maximum. Divergence dating inferred from 364 sequences of mitochondrial tRNAGly ND3 supported the emergence of a common ancestor to the three D. melanostictus clades around 1.85 (±0.77) Ma, matching with the Lower to Mid-Pleistocene transition. Duttaphrynus melanostictus then dispersed into Southeast Asia from the central Indo-Pacific and became isolated in the Southern Sundaic and Wallacea regions 1.43 (±0.10) Ma through vicariance as a result of sea level oscillations. The clade on the Southeast Asian mainland then colonised the peninsula from Myanmar to Vietnam and expanded towards Southeastern China at the end of the Mid-Pleistocene Revolution 0.84 (±0.32) Ma. Population dynamics further highlight an expansion of the Southeast Asian mainland population towards Taiwan, the Northeastern edge of the species' range after the last interglacial, and during the emergence of the Holocene human settlements around 7000 BP. Thus, the current divergence of D. melanostictus into three segregated clades was mostly shaped by Quaternary glaciations, followed by natural dispersion events over land bridges and accelerated by anthropogenic activities.

Yellow sea mediated segregation between North East Asian Dryophytes species

While comparatively few amphibian species have been described on the North East Asian mainland in the last decades, several species have been the subject of taxonomical debates in relation to the Yellow sea. Here, we sampled Dryophytes sp. treefrogs from the Republic of Korea, the Democratic People's Republic of Korea and the People's Republic of China to clarify the status of this clade around the Yellow sea and determine the impact of sea level change on treefrogs' phylogenetic relationships. Based on genetics, call properties, adult morphology, tadpole morphology and niche modelling, we determined the segregated status species of D. suweonensis and D. immaculatus. We then proceeded to describe a new treefrog species, D. flaviventris sp. nov., from the central lowlands of the Republic of Korea. The new species is geographically segregated from D. suweonensis by the Chilgap mountain range and known to occur only in the area of Buyeo, Nonsan and Iksan in the Republic of Korea. While the Yellow sea is the principal element to the current isolation of the three clades, the paleorivers of the Yellow sea basin are likely to have been the major factor for the divergences within this clade. We recommend conducting rapid conservation assessments as these species are present on very narrow and declining ranges.

High mortality in Bufo gargarizans eggs associated with an undescribed Saprolegnia ferax strain in the Republic of Korea

Pathogenic water molds have a significant impact on many species, especially amphibians. The genus Saprolegnia is a pathogenic oomycete restricted to aquatic and moist habitats, and its presence is strongly linked to the abundance of amphibians and fishes. We investigated the influence of Saprolegnia presence on egg mortality and egg occurrence under varying environmental conditions in the Asiatic toad Bufo gargarizans at 27 breeding sites in the Republic of Korea. We then assessed the impact of Saprolegnia on the presence of B. gargarizans at the 27 sites surveyed weekly during the B. gargarizans breeding season for 3 consecutive years. We used molecular tools to identify the water molds as belonging to an undescribed S. ferax strain. We demonstrated that the presence of S. ferax was positively associated with higher water conductivity and ponds. In addition, while S. ferax prevalence was associated with a reduction in B. gargarizans breeding activity and breeding success, we could not determine its impact on the subsequent breeding seasons. Our study highlights the potential negative effects of Saprolegnia on amphibian reproduction, although additional research is necessary to determine the relationship between Saprolegnia, its hosts and the impacts of habitat loss on amphibians.

Patterns of morphological variation in the Schlegel’s Japanese gecko (Gekko japonicus) across populations in China, Japan, and Korea

Background

Studies of morphological variation within and among populations provide an opportunity to understand local adaptation and potential patterns of gene flow. To study the evolutionary divergence patterns of Schlegel’s Japanese gecko (Gekko japonicus) across its distribution, we analyzed data for 15 morphological characters of 324 individuals across 11 populations (2 in China, 4 in Japan, and 5 in Korea).

Results

Among-population morphological variation was smaller than within-population variation, which was primarily explained by variation in axilla-groin length, number of infralabials, number of scansors on toe IV, and head-related variables such as head height and width. The population discrimination power was 32.4% and in cluster analysis, populations from the three countries tended to intermix in two major groups.

Conclusion

Our results indicate that morphological differentiation among the studied populations is scarce, suggesting short history for some populations after their establishment, frequent migration of individuals among the populations, and/or local morphological differentiation in similar urban habitats. Nevertheless, we detected interesting phenetic patterns that may predict consistent linkage of particular populations that are independent of national borders. Additional sampling across the range and inclusion of genetic data could give further clue for the historical relationship among Chinese, Japanese, and Korean populations of G. japonicus.

Investigation of the validity of two Bayesian ancestral state reconstruction models for estimating Salmonella transmission during outbreaks

Ancestral state reconstruction models use genetic data to characterize a group of organisms’ common ancestor. These models have been applied to salmonellosis outbreaks to estimate the number of transmissions between different animal species that share similar geographical locations, with animal host as the state. However, as far as we are aware, no studies have validated these models for outbreak analysis. In this study, salmonellosis outbreaks were simulated using a stochastic Susceptible-Infected-Recovered model, and the host population and transmission parameters of these simulated outbreaks were estimated using Bayesian ancestral state reconstruction models (discrete trait analysis (DTA) and structured coalescent (SC)). These models were unable to accurately estimate the number of transmissions between the host populations or the amount of time spent in each host population. The DTA model was inaccurate because it assumed the number of isolates sampled from each host population was proportional to the number of individuals infected within each host population. The SC model was inaccurate possibly because it assumed that each host population's effective population size was constant over the course of the simulated outbreaks. This study highlights the need for phylodynamic models that can take into consideration factors that influence the characteristics and behavior of outbreaks, e.g. changing effective population sizes, variation in infectious periods, intra-population transmissions, and disproportionate sampling of infected individuals.

Biogeography of Korea's top predator, the yellow-throated Marten: evolutionary history and population dynamics

BACKGROUND

Peninsulas often harvest high genetic diversity through repeated southward migrations of species during glacial maxima. Studies addressing within-species evolutionary responses to climate fluctuations in northeast Asia are limited compared to other regions of the world, and more so in the Korean Peninsula. In this study, we conducted the first population-level study of the yellow-throated marten, Martes flavigula, from the Korean Peninsula, Russian, Taiwanese and Chinese localities in a biogeographic framework using mitochondrial (cyt-b, nd2, cr) and nuclear gene sequencing (ghr).

RESULTS

Bayesian analyses revealed a rather young population, with a split from the most recent common ancestor at around 125 kya. Martes flavigula likely colonized the Korean Peninsula from Mainland China through the Yellow Sea twice, ca. 60 kya and 20 kya. Korean martens diversified during the Late Pleistocene with at least two dispersal events out of Korea, towards the southwest to Taiwan (ca. 80 kya) and towards the North into Russia and eastern China; most likely after the Last Glacial Maxima (ca. 20 kya). We argue that the lack of population structure and mixed populations is possibly a consequence of the high dispersal capability of the species. The Bayesian skyline plot revealed a population decline within the last 5000 years, suggesting potential negative biotic and anthropogenic effects in the area. We find that local populations are not genetically differentiated, therefore no perceptible population structure within Korea was found.

CONCLUSIONS

The topography and geography of the Korean Peninsula has played a pivotal role in its colonization. Connections between the Korean Peninsula and the Mainland through sea-level drops of the Yellow Sea at times of glacial maxima and the high dispersal capability of M. flavigula adds to the lack of geographical structure in this species and the paraphyly of Korean lineages.