Phylogenetic incongruence has frequently been encountered among different molecular markers. Recent progress in molecular phylogenomics has provided detailed and important information for evolutionary biology and taxonomy. Here we focused on the freshwater viviparid snails (Cipangopaludina chinensis chinensis and C. c. laeta) of East Asia. We conducted phylogenetic analyses and divergence time estimation using two mitochondrial markers. We also performed population genetic analyses using genome-wide SNPs. We investigated how and which phylogenetic patterns reflect shell morphology. The results showed these two species could be separated into four major mitochondrial clades, whereas the nuclear clusters supported two groups. The phylogenetic patterns of both mtDNA and nDNA largely reflected the geographical distribution. Shell morphology reflected the phylogenetic clusters based on nDNA. The findings also showed these two species diversified in the Pliocene to early Pleistocene era, and occurred introgressive hybridisation. The results also raise the taxonomic issue of the two species.

Background: Anthropogenic factors potentially affect observed biogeographical patterns in population genetics, but the effects of ancient human activities on the original patterns created by natural processes are unknown. Sinotaia quadrata, a widely distributed freshwater snail species in East Asia, was used to investigate this issue. It is unclear whether S. quadrata in Japan was introduced from China and how different human uses and varying geographic patterns affect the contemporary population genetics between the two regions. Thus, we investigated the demography of S. quadrata and detected its genetic structure in Japan and continental East Asia.Results: Sinotaia quadrata populations first naturally migrated from continental East Asia to Japan, which is associated with the ancient period in Japanese geohistory (about 70,000 years ago). They were then artificially introduced in association with agriculture expansion by human movements in two recent periods (about 8,000 and 1,200 years ago). Populations in different parts of Japan have their own sources. Natural migration in the ancient period and artificial introduction in the recent period suggest that the population distribution is affected by both the geohistory of East Asia and the history of human expansion. In the background of the historical migration and introduction, contemporary populations in the two regions show different genetic patterns. Population divergence levels were significantly correlated with geographical patterns in Japan and significantly correlated with human interventions variables in continental East Asia, suggesting that long‐term geographical isolation is likely the major factor that shaped the contemporary population genetics in Japan, while modern human uses are likely the major factor in continental East Asia.Conclusions: Our preliminary results show a complex demography and unusual genetic patterns in the contemporary populations for a common freshwater snail and are of significance to determine the historical formation and contemporary patterns of biogeography in Japan and continental East Asia.

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.

Invasion of alien species is one of the major environmental problems in the globalised world. Therefore, identifying pathways for the introduction and spread of alien species can help to mitigate their impact on invaded ecosystems. This study focused on the freshwater snail Gyraulus chinensis, which invades Europe from eastern Eurasia, where it is native. It was first recorded in Europe about 50 years ago and has since expanded its distribution. However, its origin and the mechanisms of its spread have not yet been studied. Therefore, we performed molecular identification and estimated its origin and dispersal mechanisms based on a literature review, molecular phylogenetics, and population genetics. We found that the haplotypes of G. chinensis in Europe are closely related to southern East Asia, namely Hong Kong, Taiwan, and the Ryukyu Islands. The results also suggest multiple introductions, mainly due to the diversity of haplotypes detected in European G. chinensis populations. Currently, the distribution and invasion of the species in the outdoor environments are concentrated in southern Europe, probably due to thermal constraints. However, the species has been recorded in many indoor habitats in the northern part of Europe, indicating a high potential for its spread in the warmer world.

The impact of islanding on the genetics of the dominant species, Niviventer confucianus, was analysed using 13 microsatellite markers. All 16 populations are of high genetic diversity with a total of 134 alleles. The average number of effective alleles (Ne) is 6; the average expected heterozygosity (H_E) and polymorphic information content (PIC) are 0.823 and 0.763, respectively. Landscape fragmentation might contribute to weak genetic differentiation among 13 island populations. Values of F_ST simulated by Structure 2.3.4 implied that the 16 populations could be assigned into three clusters, from which we postulated the possible dispersion history. Pairwise F_ST tests showed that genetic differences mainly occurred between small island populations and others. Currently, habitat area appears to be the main factor affecting the genetics of Niviventer confucianus, and not the distances between islands. Hence we suggest that more attention should be paid to habitat area in the future.