The mitochondrial genome of Huaaristarchorum (Heude, 1889) (Gastropoda, Cerithioidea, Semisulcospiridae) and its phylogenetic implications

Research on complete mitochondrial genomes can help in understanding the molecular evolution and phylogenetic relationships of various species. In this study, the complete mitogenome of Huaaristarchorum was characterized to supplement the limited mitogenomic information on the genus Hua. Three distinct assembly methods, GetOrganelle, NovoPlasty and SPAdes, were used to ensure reliable assembly. The 15,691 bp mitogenome contains 37 genes and an AT-rich region. Notably, the cytochrome c oxidase subunit I (COX1) gene, commonly used for species identification, appears to be slow-evolving and less variable, which may suggest the inclusion of rapidly evolving genes (NADH dehydrogenase subunit 6 [ND6] or NADH dehydrogenase subunit 2 [ND2]) as markers in diagnostic, detection, and population genetic studies of Cerithioidea. Moreover, we identified the unreliability of annotations (e.g., the absence of annotations for NADH dehydrogenase subunit 4L [ND4L] in NC_037771) and potential misidentifications (NC_023364) in public databases, which indicate that data from public databases should be manually curated in future research. Phylogenetic analyses of Cerithioidea based on different datasets generated identical trees using maximum likelihood and Bayesian inference methods. The results confirm that Semisulcospiridae is closely related to Pleuroceridae. The sequences of Semisulcospiridae clustered into three clades, of which H.aristarchorum is one; H.aristarchorum is sister to the other two clades. The findings of this study will contribute to a better understanding of the characteristics of the H.aristarchorum mitogenome and the phylogenetic relationships of Semisulcospiridae. The inclusion of further mitochondrial genome sequences will improve knowledge of the phylogeny and origin of Cerithioidea.

Systematic revision of the Japanese freshwater snail

Semisulcospira is a freshwater snail genus highly divergent in the ancient Lake Biwa, Japan, with a history of ~4 million years. Although the shell morphology, karyotype and molecular phylogeny of the genus have been well studied, the systematic status of several non-monophyletic species remains uncertain. In this study, we have evaluated the taxonomic accounts of the species previously identified as Semisulcospira decipiens, S. habei and relatives. We examined the genetic relationships using genome-wide SNP data and elucidated morphological variation among these using Random Forest classification. Morphological relationships between the name-bearing type of S. decipiens and the newly collected specimens were also evaluated. Morphological characteristics effectively discriminated between the nine genetic clusters, and the correlation among morphology and substrates was elucidated. We revised taxonomic accounts of S. decipiens, S. habei, S. arenicola, S. nakasekoae and S. ourensis and synonymised S. multigranosa, S. habei yamaguchi, S. dilatata under S. decipiens and S. fluvialis under S. nakasekoae. We also described two new species, Semisulcospira elongata sp. nov. and Semisulcospira cryptica sp. nov., and redefined two phylogroups of the lacustrine species as the Semisulcospira niponica-group and the Semisulcospira nakasekoae-group. Traits of the species examined exhibiting intraspecific variation in the different substrates and flow velocity may indicate the morphological and trophic adaptations. The habitat-related variation has certainly caused the taxonomic confusion of the lacustrine species. Lake drainage contributes to increasing the species diversity of the genus, generating ecological isolation between the riverine and lacustrine habitats. ZooBank: urn:lsid:zoobank.org:pub:A83B99F4-8709-4295-86B3-A6C595D65DA0

Diversification in ancient Lake Biwa: integrative taxonomy reveals overlooked species diversity of the Japanese freshwater snail genus Semisulcospira (Mollusca: Semisulcospiridae)

The freshwater snail genus Semisulcospira has adaptively radiated in the ancient Lake Biwa, Japan. Although significant geographical variations have been known in the shell morphology of Semisulcospira niponica, their systematics remain uncertain. We evaluated the systematic status of the geographical variations in S. niponica and its congenerics S. biwae and S. fuscata through morphological and genetic investigations. Genome-wide snp s were used to estimate their genetic relationships. Random Forest algorithms explored the morphological variation of the shells of the name-bearing types and newly collected specimens. Our results detected five genetic clusters and revealed the consistency of adult shell morphology with genetic relationships, reinforcing the robustness of shell morphology-based species delimitation of the genus. The present systematics synonymized S. biwae under S. niponica. The five genetic clusters corresponded to the two described species, S. niponica and S. fuscata, and three new species, Semisulcospira watanabei sp. nov., Semisulcospira nakanoi sp. nov., and Semisulcospira salebrosa sp. nov. discovered among the geographical variations of S. niponica. The observed similarities in substrate preference and differences in distribution patterns among species suggest that the diversification of the genus was accelerated by geographical isolation after the initial ecological niche differentiation. We suggest that the distributions of Semisulcospira species may have been influenced by competitive exclusion among them, and that multiple speciation events have occurred in similar patterns.

Ancient drainage networks mediated a large-scale genetic introgression in the East Asian freshwater snails

Biogeography and genetic variation of freshwater organisms are influenced not only by current freshwater connections but also by past drainage networks. The Seto Inland Sea is a shallow enclosed sea in Japan, but geological evidence showed that a large freshwater drainage had intermittently appeared in this area between the late Pliocene and Pleistocene. Here, we demonstrated that this paleodrainage greatly affected the genetic variation of the East Asian freshwater snails, Semisulcospira spp. We found that the mtDNA haplotypes originated in the Lake Biwa endemic Semisulcospira species at the upstream side of the paleodrainage were frequently observed in the riverine Semisulcospira species at its downstream side. The genome-wide DNA and morphological analyses consistently showed that there was no clear evidence of nuclear introgression between the Lake Biwa endemics and riverine species. These results suggest that the large paleodrainage had facilitated mitochondrial introgression and had broadly spread the introgressed mtDNA haplotypes to its downstream region around the Seto Inland Sea. Our study highlights the role of paleodrainages in shaping the genetic variation of freshwater organisms.

Comparative analysis of complete mitochondrial genomes with Cerithioidea and molecular phylogeny of the freshwater snail, Semisulcospira gottschei (Caenogastropoda, Cerithioidea)

In this study, we determined the complete mitochondrial genome (mt genome) of Semisulcospira gottschei for the first time and then compared it with the mt genome of species belonging to Cerithioidea. The mt genome consists of 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and non-coding region with a total length of 16,101 bp. The type of constitutive genes and the direction of the coding strand which appeared in the mt genome were the same as the ones observed in Cerithioidea except for the tRNA-Q and tRNA-R positions. The S. gottschei mt genome had a non-coding region with an AT-rich loop between tRNA-F and tRNA-C regions. In regard to molecular phylogeny, two types of analysis were performed to confirm the introgressive hybridization of S. gottschei and to identify the phylogenetic location among the species in Caenogastropoda. As a result, S. gottschei used in this study belonged to the same clade as other non-introgressed S. gottschei. As for the molecular phylogenic analysis of species belonging to Caenogastropoda, S. gottschei was found to be the closest to S. coreana taxonomically and to be included in Cerithioidea.

Assessing the diversity of Western North American Juga (Semisulcospiridae, Gastropoda)

Juga is a genus of freshwater gastropods distributed in Pacific and Interior drainages of the Pacific Northwest from central California to northern Washington. The current classification has relied heavily on features of the shell, which vary within and across drainages, and often intergrade without sharp distinctions between species. The only previous molecular analysis included limited population sampling, which did not allow robust assessment of intra- versus interspecific levels of genetic diversity, and concluded almost every sampled population to be a distinct OTU. We assembled a multilocus mitochondrial (COI, 16S) and nuclear gene (ITS1) dataset for ∼100 populations collected across the range of the genus. We generated primary species hypotheses using ABGD with best-fit model-corrected distances and further explored our data, both individual gene partitions and concatenated datasets, using a diversity of phylogenetic and species delimitation methods (Bayesian inference, maximum likelihood estimation, StarBEAST2, bGMYC, bPTP, BP&P). Our secondary species delimitation hypotheses, based primarily on the criterion of reciprocal monophyly, and informed by a combination of geography and morphology, support the interpretation that Juga comprises a mixture of geographically widespread species and narrow range endemics. As might be expected in taxa with low vagility and poor dispersal capacities, analysis of molecular variance (AMOVA) revealed highly structured populations with up to 80% of the observed genetic variance explained by variation between populations. Analyses with bGMYC, bPTP, and BP&P appeared sensitive to this genetic structure and returned highly dissected species hypotheses that are likely oversplit. The species diversity of Juga is concluded to be lower than presently recognized, and the systematics to require extensive revision. Features of the teleoconch considered significant in species-level and subgeneric classification were found to be variable within some species, sometimes at a single site. Of a number of potentially new species identified in non-peer reviewed reports and field guides, only one was supported as a distinct OTU.

Comparative morpho-anatomy and mitochondrial phylogeny of Semisulcospiridae in Yunnan, south-western China, with description of four new species (Gastropoda: Cerithioidea)

The taxonomic history of Chinese semisulcospirids is confusing. Originally placed in Melania by late 19th century authors, species have subsequently been dispersed into four different genera, i.e. Semisulcospira Böttger, 1886, Senckenbergia Yen, 1939, Hua Chen, 1943, and Namrutua Abbott, 1948; however, these placements were not conducted within a phylogenetic context. Based on examination of newly collected samples from the Chinese provinces Yunnan, Guizhou, Jiangxi, Anhui and Chongqing, we revised the systematics of the Chinese Semisulcospiridae based on comparative anatomy and mitochondrial phylogenetics. We have examined shell, radular, and reproductive features and employed Bayesian and Maximum Likelihood analyses of partial sequences of mitochondrial genes cytochromec oxidaseI and 16S rRNA to resolve the phylogenetic relationships. The results revealed that Semisulcospiridae is represented by three genera in China, which differ in their reproductive strategy, including Semisulcospira, which is viviparous and contains three species (S. ningpoensis, S. gredleri, and S. pleuroceroides); Hua, which is oviparous and contains 11 species; and Koreoleptoxis, which is oviparous and contains one species. Namrutua and Senckenbergia are identified here as junior subjective synonyms of Semisulcospira. All taxa recognised herein formed well differentiated clades in three mitochondrial phylogeny, and could be reliably distinguished by differences in shell shape and sculpture. Four new species of Hua are described from Yunnan Province. This is the first comprehensive study to review the taxonomy of semisulcospirids in China. These species are sensitive to water quality, and economic development and infrastructure expansion have negatively impacted many populations. We fear that some species may have disappeared before being investigated or described scientifically. Therefore, this research will hopefully inspire further studies and surveys to foster our understanding of freshwater gastropod diversity in China. http://zoobank.org/urn:lsid:zoobank.org:pub:EF2147FD-9EEE-4922-90DC-76651EF9E6AE