Testing the utility of DNA barcodes and a preliminary phylogenetic framework for Chinese freshwater mussels (Bivalvia: Unionidae) from the middle and lower Yangtze River

Molecular and morphological evidence reveals a hidden new taxon in the endemic genus Pseudocuneopsis (Bivalvia, Unionidae) from China

A new species of freshwater mussel belonging to the genus Pseudocuneopsis, namely Pseudocuneopsiswuanasp. nov., is diagnosed and described from Guangxi Province, China. This paper provides a detailed shell morphological description, soft-body anatomical characteristics, and partial sequences of mitochondrial COI as DNA barcode data for the novel species. The new species can be distinguished from its congeners (Pseudocuneopsissichuanensis, P.yangshuoensis, and P.capitata) by shell shape, beak position, and surface sculpture. Phylogenetic analyses based on the mitochondrial COI gene reveal that Pseudocuneopsiswuanasp. nov. forms a sister group with P.yangshuoensis and exhibits an interspecific genetic distance of 5.1%. Therefore, we provide robust morphological and molecular evidence to support the validity of this new species.

New species of the genus Pseudocuneopsis Huang, Dai, Chen & Wu, 2022 (Bivalvia, Unionidae) from Guangxi Province, China

A new species of freshwater mussel belonging to the genus Pseudocuneopsis, namely Pseudocuneopsisyangshuoensissp. nov., is diagnosed and described from Guangxi Province, China. This paper provides a detailed morphological description, photograph of the type specimen, and anatomical characteristics along with partial sequences of mitochondrial COI as DNA barcode data for this novel species. The new species can be distinguished from its congeners (Pseudocuneopsissichuanensis and Pseudocuneopsiscapitata) by shell shape, beak position and surface sculpture. The interspecies genetic distance based on the COI barcode between P.yangshuoensissp. nov. and P.sichuanensis is 8%, while it reaches 9% with P.capitata. Therefore, we provide robust morphological and molecular evidence to support the validity of this new species.

A freshwater mussel species reflects a Miocene stream capture between the Mekong Basin and East Asian rivers

Freshwater mussels belonging to the genus Cristaria Schumacher, 1817 (Bivalvia: Unionidae) are widespread from Mongolia to Indochina while the range of one species, C. plicata (Leach, 1814), covers two biogeographic subregions, i.e., East Asian (Amur River to Vietnam) and Sundaland (Mekong River basin). We present here a taxonomic revision of the nominal taxon Anodonta bellua Morelet, 1866 which was described from the Mekong (Lake Tonle-Sap, Cambodia) but is currently considered a synonym of C. plicata. We obtained molecular data for newly collected Cristaria representatives from the Mekong’s tributaries in Laos, which were found as a divergent species-level phylogenetic clade within the genus that is distant from C. plicata. Nevertheless, comparative morphological and morphometric studies did not reveal any significant differences between these two congeners. Our time-calibrated biogeographic modeling reveals that the split between Cristaria bellua (Mekong) and C. clessini (East Asia) probably occurred in the mid-Miocene (15.8 Ma) and may reflect an ancient stream capture between the Mekong Basin and East Asian rivers.

Phylogeny and biogeography of Indochinese freshwater mussels in the genus Pilsbryoconcha Simpson, 1900 (Bivalvia: Unionidae) with descriptions of four new species

The body of knowledge regarding the classification and evolution of freshwater mussels in the family Unionidae (Bivalvia) in Indochina has recently increased. However, the taxonomic revision of all extant taxa in the region is still ongoing. In this study, the genus Pilsbryoconcha was revised based on an integrative analysis of shell morphology, biogeography, and molecular data. Multi-locus phylogeny indicated the availability of eight species within the genus. Four previously recognized species are P. exilis (Lea, 1838), P. schomburgki (Martens, 1860) stat. rev., P. linguaeformis (Morelet, 1875), and P. carinifera (Conrad, 1837), while four other species are described herein as P. acuta sp. nov., P. mekongiana sp. nov., P. kittitati sp. nov., and P. hoikaab sp. nov. In addition, the neotype of P. carinifera is also designated to clarify its long taxonomic ambiguity. Divergent time estimation and historical biogeography analysis revealed that Pilsbryoconcha originated in the area now called the Khorat Plateau around the middle of the Eocene (mean age = 43.12 Mya), before its range was expanded across Indochina through a series of complex geomorphological changes of river systems, which also led to diversification of the genus.

Resolving species-level diversity of Beringiana and Sinanodonta mussels (Bivalvia: Unionidae) in the Japanese archipelago using genome-wide data

Accurate species identification is of primary importance in ecology and evolutionary biology. For a long time, the unionid mussels Beringiana and Sinanodonta have puzzled researchers trying to unravel their diversity because of their poorly discernible morphologies. A recent study conducted species delineation of unionid mussels based on mitochondrial DNA variation, opening up a new avenue to grasp species diversity of the mussels. However, mtDNA-based classification may not align with species boundaries because mtDNA is prone to introgression and incomplete lineage sorting that cause discordance between species affiliation and gene phylogeny. In this study, we evaluated the validity of the mtDNA-based classification of unionid mussels Beringiana and Sinanodonta in Japan using mitochondrial sequence data, double digest restriction site-associated DNA library (ddRAD) sequencing, and morphological data. We found significant inconsistencies in the mitochondrial and nuclear DNA phylogenies, casting doubt on the reliability of the mtDNA-based classification in this group. In addition, nuclear DNA phylogeny revealed that there are at least two unionid lineages hidden in the mtDNA phylogeny. Although molecular dating technique indicates that Beringiana and Sinanodonta diverged >35 million years ago, their shell morphologies are often indistinguishable. Specifically, morphological analyses exhibited the parallel appearance of nearly identical ball-like shell forms in the two genera in Lake Biwa, which further complicates species identification and the morphological evolution of unionid mussels. Our study adds to a growing body of literature that accurate species identification of unionid mussels is difficult when using morphological characters alone. Although mtDNA-based classification is a simple and convenient way to classify unionid mussels, considerable caution is warranted for its application in ecological and evolutionary studies.

DNA barcoding, multilocus phylogeny, and morphometry reveal phenotypic plasticity in the Chinese freshwater mussel Lamprotula caveata (Bivalvia: Unionidae)

Accurate species identification is crucial for developing conservation strategies for freshwater mussels, one of the most imperiled faunas in the world. Traditionally, mussel species description primarily relied on conchological characters. However, shell morphology has great variability, which leads to the complexity of species delimitation. As endemic species to China, Lamprotula caveata was originally described by Heude (1877). Lamprotula quadrangulosus and Lamprotula contritus were considered for synonymization of L. caveata based on shell variants in the early 20th century, which has been long debated due to lack of rigorous molecular analysis. Moreover, great morphological variation caused doubt whether there are cryptic species. In this study, we used a combined phylogenetic and morphometric approach to verify the validity of the synonymization of L. caveata. The results of molecular species delimitation showed that two molecular operational taxonomic units (MOTUs) were identified in Lamprotula spp., including the L. leaii lineage and the complex lineage (L. quadrangulosa, L. cornuumlunae, L. contritus, and L. caveata). Phylogenetic analyses revealed that L. cornuumlunae formed a basal monophyletic clade, whose divergence time was relatively recent (4.26 Ma [95% HPD = 1.91-7.22 Ma]), and L. contritus, L. caveata, and L. quadrangulosa formed a large polytomy group with very shallow branches. In the previous study, we have demonstrated the validity of L. cornuumlunae. The molecular evidences supported that the complex (L. quadrangulosa + L. contritus + L. caveata) was a valid species; L. quadrangulosa and L. contritus were synonyms of L. caveata. In addition, three morphospecies (L. quadrangulosa, L. contritus, and L. caveata) were aggregated without clear differentiation based on shell morphometric analysis. We confirmed multiple phenotypes in L. caveata for species identification and presumed that the phenotypic plasticity was a response to specific habitats. This study clarified the diversity and phylogeny of the Lamprotula group, which is a crucial step for developing new conservation and management strategies for this imperiled group.

New species of the genus Inversidens Haas, 1911 (Unionoida, Unionidae, Gonideinae) from Jiangxi Province, China

We diagnose and describe a new freshwater mussel species of the genus Inversidens, I.rentianensis sp. nov. from Jiangxi Province, China based on morphological characters and molecular data. This paper includes a morphological description and photograph of the holotype, and partial sequences of mitochondrial COI as DNA barcode data.

Aquatic Organisms Research with DNA Barcodes

Since their inception, DNA barcodes have become a powerful tool for understanding the biodiversity and biology of aquatic species, with multiple applications in diverse fields such as food security, fisheries, environmental DNA, conservation, and exotic species detection. Nevertheless, most aquatic ecosystems, from marine to freshwater, are understudied, with many species disappearing due to environmental stress, mostly caused by human activities. Here we highlight the progress that has been made in studying aquatic organisms with DNA barcodes, and encourage its further development in assisting sustainable use of aquatic resources and conservation.

Molecular identification and phylogenetic analysis of the mitogenome of Solenaia oleivora MG

Solenaia oleivora, belongs to Bivalvia, Unionidae, and Gonideinae, is a burrowing bivalve uniquely distributed in China. In this study, the complete mitochondrial genome of S. oleivora MG was sequenced and determined. The complete mitogenome of S. oleivora MG is 16,392 bp in total length, consist of 22 tRNA genes, 13 protein-coding genes (PCGs), and 2 rRNA genes. The overall base composition of the S. oleivora MG mitogenome is 36.90% A, 23.85% T, 27.09% C, and 12.16% G, respectively, exhibits a similar AT bias (60.75%) feature to other invertebrate bivalve mitogenomes. The phylogenetic analysis that S. oleivora MG clustered in genus Solenaia. This result provides useful data to the conservation and sustainable utilization of S. oleivora MG and other invertebrate mussels.

Integrative taxonomy, biogeography and conservation of freshwater mussels (Unionidae) in Russia

Freshwater mussels are ecosystem engineers and keystone species in aquatic environments. Unfortunately, due to dramatic declines this fauna is among the most threatened globally. Here, we clarify the taxonomy and biogeography of Russian Unionidae species based on the most comprehensive multi-locus dataset sampled to date. We revise the distribution and assess the conservation status for each species. This fauna comprises 16 native species from 11 genera and 4 tribes: Anodonta, Pseudanodonta (Anodontini); Amuranodonta, Beringiana, Buldowskia, Cristaria, Sinanodonta (Cristariini); Middendorffinaia, Nodularia, Unio (Unionini); and Lanceolaria (Lanceolariini). No country-level endemic species are known in Russia, except for Buldowskia suifunica that may also occur in China. Sinanodonta woodiana, a non-native species, was introduced from China. Russia comprises the northern parts of Western and Eastern Palearctic subregions. The first subregion with six species encompasses a huge area from the western boundary of Russia to the Lena Basin in Siberia. The second subregion with 10 species covers the Amur Basin, rivers east of the Lena Basin, coastal basins of the Japan Sea, and the North Pacific Islands. The fauna of Russia primarily includes widespread generalist species that are here considered Least Concern (LC). However, Buldowskia suifunica and Sinanodonta lauta have restricted distributions and are assessed here as Vulnerable (VU) and Endangered (EN), respectively.

Analysis of mitochondrial genomes resolves the phylogenetic position of Chinese freshwater mussels (Bivalvia, Unionidae)

The Yangtze River basin is one of the most species-rich regions for freshwater mussels on Earth, but is gravely threatened by anthropogenic activities. However, conservation planning and management of mussel species has been hindered by a number of taxonomic uncertainties. In order to clarify the taxonomic status and phylogenetic position of these species, mitochondrial genomes of four species (Acuticostachinensis, Schistodesmuslampreyanus, Cuneopsisheudei and Cuneopsiscapitatus) were generated and analyzed along with data from 43 other mitogenomes. The complete F-type mitogenomes of A.chinensis, S.lampreyanus, C.heudei, and C.capitatus are 15652 bp, 15855 bp, 15892 bp, and 15844 bp, respectively, and all four F-type mitogenomes have the same pattern of gene arrangement. ML and BI trees based on the mitogenome dataset are completely congruent, and indicate that the included Unionidae belong to three subfamilies with high bootstrap and posterior probabilities, i.e., Unioninae (Aculamprotula, Cuneopsis, Nodularia, and Schistodesmus), Anodontinae (Cristaria, Arconaia, Acuticosta, Lanceolaria, Anemina, and Sinoanodonta), and Gonideinae (Ptychorhynchus, Solenaia, Lamprotula, and Sinohyriopsis). Results also indicate that A.chinensis has affinities with Arconaialanceolata and Lanceolariagrayii and is a member of the subfamily Anodontinae.