Uncovering overlooked diversity using molecular phylogenetic approach: A case of Japanese sphaeriid clams (Bivalvia: Sphaeriidae).

Revealing the species and lineage diversity of a taxon is important for many biological studies of wildlife. In recent decades, DNA-based approaches have been widely utilised to elucidate the diversity of taxa, especially those that are difficult to distinguish based on morphological traits. This study focused on freshwater clams (Sphaeriidae) in Japan, a biodiversity hotspot of freshwater molluscs. Molecular phylogenetic approaches, including divergence time estimation, species delimitation, rarefaction, and biogeographic area estimation, were used to reveal the nature of the species diversity and its formation process, which are largely unknown. Our delimitation and rarefaction analyses suggest that Japanese sphaeriid clams consist of at least 18 delimitated lineages. This lineage diversity is relatively high compared to other Japanese freshwater molluscs, and in addition, the majority of the Japanese lineage appears to have high endemicity despite the possibility of long-distance dispersal in sphaeriid clams. Our biogeographical analyses suggest that this diversity may be due to the combination of colonisation, during the period when Japan was connected to the continent, and the relatively recent dispersal. Our results highlight the overlooked biodiversity of Japan and provide a basis for further Japanese sphaeriid research, including conservation perspectives.

Impact of a dam construction on the intertidal environment and free-living nematodes in the Ba Lai, Mekong Estuaries, Vietnam.

The impact of high siltation and accumulation of organic and waste material in the intertidal of the dammed Ba Lai River in Vietnam as part of the Mekong estuarine system was investigated by means of marine free-living nematodes. Nutrients content (nitrate, ammonium, total phosphorus, total nitrogen), total suspended solids, total organic carbon, coliform, bacteria E. coli, pH, dissolved oxygen, total dissolved solids, methane and hydrogen sulfide concentration, and the nematode communities were characterized in sediment at selected stations along the river above and below the dam. Our results found elevated methane concentrations at the upstream side of the dam while hydrogen sulfide concentrations found to be highest in the downstream side of the dam. Furthermore, methane and hydrogen sulfide concentrations were correlated to nematode community characteristics such as trophic composition densities and genera composition. There was a clear difference between the communities above and below the dam. The discontinuous nematode community distribution indicated that the Ba Lai River is impacted by dam construction. Potentially the high deposition and eutrophication could turn the area into a methane-rich area related to predicted impact on nematodes.

Role of ancient lakes in genetic and phenotypic diversification of freshwater snails.

Endemic organisms of ancient lakes have been studied as models to understand processes of speciation and adaptive radiation. However, it remains unclear how ancient lakes play roles in genetic and phenotypic diversity of freshwater mollusks. In the present study, we focus on viviparid freshwater snails in the ancient lakes of East and Southeast Asia (Japan and China) to address this question. Using molecular phylogenetic analyses based on mitochondrial (COI, 16S) and nuclear genes (18S, 28S, H3), we show that patterns of species diversification in viviparid lineages. Colonization to ancient lakes occurred independently in China and Japan at least four times, with subsequent diversification into more than two species within each lake group. Morphological analyses of fossil related viviparids suggest parallel phenotypic evolution occurred in the different lakes and ages. Each lake contained a single lineage which was phenotypically diversified relative to those from other sites. Using genome-wide SNPs obtained by MIG-seq, we also examined the genetic structure of three Japanese viviparids, including two endemic species of ancient Lake Biwa. The results suggest that these two species diversified from the population of the third species living in wetlands surrounding the lake. These findings suggest that rapid diversification of lineages and phenotypic divergence can occur in ancient lakes compared to other habitats. Formation of large lakes probably promotes speciation and phenotypic divergence as a result of adaptation into different microhabitats. High numbers of ancient lakes could be a driver of species diversity in Asian viviparid snails.

Phylogeography of freshwater planorbid snails reveals diversification patterns in Eurasian continental islands.

BACKGROUND: Islands have traditionally been the centre of evolutionary biological research, but the dynamics of immigration and differentiation at continental islands have not been well studied. Therefore, we focused on the Japanese archipelago, the continental islands located at the eastern end of the Eurasian continent. While the Japanese archipelago is characterised by high biodiversity and rich freshwater habitats, the origin and formation mechanisms of its freshwater organisms are not clear. In order to clarify the history of the planorbid gastropod fauna, we conducted phylogenetic analysis, divergence time estimation, ancestral state reconstruction, and lineage diversity estimations. RESULTS: Our analyses revealed the formation process of the planorbid fauna in the Japanese archipelago. Most lineages in the Japanese archipelago have closely related lineages on the continent, and the divergence within the Japanese lineages presumably occurred after the late Pliocene. In addition, each lineage is characterised by different phylogeographical patterns, suggesting that immigration routes from the continent to the Japanese archipelago differ among lineages. Furthermore, a regional lineage diversity plot showed that the present diversity in the Japanese archipelago potentially reflects the differentiation of lineages within the islands after the development of the Japanese archipelago. CONCLUSIONS: Although additional taxon sampling and genetic analysis focused on each lineage are needed, our results suggest that immigration from multiple routes just prior to the development of the Japanese archipelago and subsequent diversification within the islands are major causes of the present-day diversity of the Japanese planorbid fauna.

Intertidal nematode communities in the Mekong estuaries of Vietnam and their potential for biomonitoring.

Nematode communities in eight Mekong estuaries were investigated during the dry season. The aim of the study was to identify the structure and the diversity of the communities in relation to the main environmental characteristics. In each estuary, three to four intertidal sampling stations were identified at regular distances from the mouth to up to 45 km land inward. The nematode communities showed a strong correlation with sediment composition and to a lesser degree with chlorophyll a concentrations. Multivariate analysis resulted in the identification of four types of communities. We identified two types of Desmodora communities in the sandy mouth stations and two types of Parodontophora communities in the silty sand stations. One of the silt associated communities showed a preference for higher chlorophyll a concentrations, resulting in higher densities and higher diversity, mainly of monhysterid species. Because of the strong association between community structure and sediment composition, nematodes are a meaningful tool for monitoring changes in their environment. In case their community deviates from what is expected based on sediment, it may serve as an early warning for disturbance.

Conquest of the deep, old and cold: an exceptional limpet radiation in Lake Baikal.

Lake Baikal is the deepest, oldest and most speciose ancient lake in the world. The lake is characterized by high levels of molluscan species richness and endemicity, including the limpet family Acroloxidae with 25 endemic species. Members of this group generally inhabit the littoral zone, but have been recently found in the abyssal zone at hydrothermal vents and oil-seeps. Here, we use mitochondrial and nuclear data to provide a first molecular phylogeny of the Lake Baikal limpet radiation, and to date the beginning of intra-lacustrine diversification. Divergence time estimates suggest a considerably younger age for the species flock compared with lake age estimates, and the beginning of extensive diversification is possibly related to rapid deepening and cooling during rifting. Phylogenetic relationships and divergence time estimates do not clearly indicate when exactly the abyssal was colonized but suggest a timeframe coincident with the formation of the abyssal in the northern basin (Middle to Late Pleistocene).

Terrestrial predatory leeches of the genus Orobdella (Hirudinea: Erpobdelliformes: Orobdellidae) endemic to the Southern Russian Far East: a new species of the genus from Primorsky Krai, Russia.

A quadrannulate species, Orobdella ganini sp. nov., is described from the Lazovsky Nature Reserve in Primorsky Krai, the Southern Russian Far East, Russia. Morphological features of O. ghilarovi Nakano & Prozorova, 2019 from the reserve are also provided leading to an amendment of the species diagnosis. Maximum likelihood and Bayesian inference phylogenetic analyses, which were performed using nuclear 18S rRNA, 28S rRNA, and histone H3, and mitochondrial cytochrome c oxidase subunit I, tRNACys, tRNAMet, 12S rRNA, tRNAVal, 16S rRNA, tRNALeu and NADH dehydrogenase subunit 1 markers, show that O. ganini sp. nov., O. ghilarovi and two species endemic to Hokkaido, Japan form a clade, with the new species sister to a lineage composed of the two Japanese species. A partial cytochrome c oxidase subunit I sequence obtained from a cocoon found in the Lazovsky Nature Reserve reveals that Orobdella leeches deposit cocoons somewhat similar to those deposited by terrestrial blood-sucking leeches of Haemadipsidae.

A comprehensive phylogeography of the widespread pond snail genus Radix revealed restricted colonization due to niche conservatism.

To clarify the effect of niche conservatism on evolutionary history, we focused on freshwater snails, which have different ecological and phylogenetic properties from previously tested taxa. We conducted a phylogenetic analysis using 750 lymnaeid individuals from 357 sites of eleven Radix species. Then, we estimated the ancestral distribution using the geographic coordinates and colonization routes. In addition, a statistical test of the colonization distances in the latitudinal and longitudinal directions was performed. We also conducted ecological niche modeling for two widely distributed species using climatic data. Ancestral geographic reconstruction estimated the origin of the genus to be around the Indian subcontinental region and showed that latitudinal immigration distances were shorter than longitudinal immigration distances in the diversification process. Ecological niche models suggested that the current distribution was restricted by climate, with annual mean temperature and precipitation of the driest month as particularly strong factors. Niche conservatism to the climate can affect the diversification of freshwater snails.

First molecular examination of Vietnamese mudflat snails in the genus Naranjia Golding, Ponder & Byrne, 2007 (Gastropoda: Amphibolidae).

Maritime ecosystems in Vietnam such as mangroves and mud flats are characterized by high biodiversity. However, elements of its biodiversity remain unclear and highly threatened. In this context, the assessment of rare species is a starting point to develop effective strategies for the conservation of entire ecosystems. In this paper, we report upon cryptic amphibolid gastropods in Vietnamese mangrove forests from the Mekong Delta. The snail fauna in the mangrove forests was previously known from published literature and three museum specimens as three amphibolid species, 'Amphibola' burmana, A. quadrasi, Salinator fragilis and 'S.' quadrasi. We investigated the identities of such snails using molecular and morphological methods. The amphibolids found in this survey were identified to belong to the genus Naranjia, new for Vietnam fauna. In addition, our phylogenetic analyses suggested that the Vietnamese amphibolids were the same species as Naranjia sp. reported from Thailand, and the amphibolids have both genetic and morphological polymorphisms within the population. These findings add to the great biodiversity of Vietnamese mangrove forests and mudflats.

Parallel evolution of passive and active defence in land snails.

Predator-prey interactions are major processes promoting phenotypic evolution. However, it remains unclear how predation causes morphological and behavioural diversity in prey species and how it might lead to speciation. Here, we show that substantial divergence in the phenotypic traits of prey species has occurred among closely related land snails as a result of adaptation to predator attacks. This caused the divergence of defensive strategies into two alternatives: passive defence and active defence. Phenotypic traits of the subarctic Karaftohelix land snail have undergone radiation in northeast Asia, and distinctive morphotypes generally coexist in the same regions. In these land snails, we documented two alternative defence behaviours against predation by malacophagous beetles. Furthermore, the behaviours are potentially associated with differences in shell morphology. In addition, molecular phylogenetic analyses indicated that these alternative strategies against predation arose independently on the islands and on the continent suggesting that anti-predator adaptation is a major cause of phenotypic diversity in these snails. Finally, we suggest the potential speciation of Karaftohelix snails as a result of the divergence of defensive strategies into passive and active behaviours and the possibility of species radiation due to anti-predatory adaptations.

A new member of troglobitic Carychiidae, Koreozospeum nodongense gen. et sp. n. (Gastropoda, Eupulmonata, Ellobioidea) is described from Korea.

A new genus of troglobitic Carychiidae Jeffreys, 1830 is designated from Nodong Cave, North Chungcheong Province, Danyang, South Korea. This remarkable find represents a great range extension and thus, a highly distant distribution of troglobitic Carychiidae in Asia. The Zospeum-like, carychiid snails were recently included, without a formal description, in records documenting Korean malacofauna. The present paper describes Koreozospeum Jochum & Prozorova, gen. n. and illustrates the type species, Koreozospeum nodongense Lee, Prozorova & Jochum, sp. n. using novel Nano-CT images, including a video, internal shell morphology, SEM and SEM-EDX elemental compositional analysis of the shell.