An integrative taxonomic reassessment of the Chinese endemic genus Acuticosta (Bivalvia: Unionidae), with the description of a new genus

Accurate identification and precise classification of freshwater mussel species that are among the most threatened freshwater taxa in the world, play a crucial role in informing conservation and management efforts for these organisms. However, due to the variability in shell morphology, relying solely on shell characteristics for species taxonomy poses significant challenges, thereby impeding effective conservation planning and management. The freshwater mussel genus Ptychorhynchus Simpson, 1900 is one such group in need of study. We integrate molecular phylogeny, shell morphology and soft-body anatomy to examine the classification of Ptychorhynchus denserugata (Haas, 1910) and Ptychorhynchus resupinatus (von Martens, 1902). The COI barcoding data support the clustering of P. denserugata and Nodularia douglasiae within a single clade, and P. denserugata shares the diagnostic feature of the genus Nodularia , i.e. knobs or bumps on the inner mantle surface in the excurrent aperture. Therefore, by integrating molecular data and anatomical characteristics, we confirm that the nominal species P. denserugata syn. nov. is a new synonym for N. douglasiae . The multi-locus (COI + ND1 + 16S rRNA + 18S rRNA + 28S rRNA ) phylogeny and mitochondrial phylogenomics support the transfer of P. resupinatus from Ptychorhynchus to the newly elevated genus Cosmopseudodon stat. rev., as Cosmopseudodon resupinatus stat. rev. that is still considered the designated type species. We also describe a new species based on integrative taxonomy, i.e. Cosmopseudodon wenshanensis sp. nov. The comprehensive understanding of the taxonomy and diversity of the revised Cosmopseudodon species, and shell heteromorphism of N. douglasiae (=P. denserugata syn. nov.), will serve as a crucial foundation for further scientific assessment and conservation strategies pertaining to these taxa. ZooBank: urn:lsid:zoobank.org:pub:E48968B1-DF0F-42AD-8F31-B8C95F23CE57.

The genus Nodularia poses a significant challenge to traditional species classification and identification due to its highly convergent and variable shells, rendering it one of the most intricate groups within the family Unionidae. Fortunately, significant progress has been made by researchers in recent years regarding the species validity and the phylogeny of this group based on molecular data. However, the inadequate exploration of regional constraints and inherent limitations in research methodologies remains a crucial factor contributing to the underestimation of species diversity. In this study, a new species of freshwater mussel from the Qingshui River in Nanning City, Guangxi Province, China, Nodularia guiensissp. nov., is described based on shell morphology, anatomical characters, and molecular phylogenetics. Mitochondrial phylogenomic analyses reveal the following phylogenetic relationships: (((Nodularia hanensis + Nodularia micheloti) + Nodularia dorri) + (Nodularia breviconcha + (Nodularia huana + (Nodularia fusiformans + (Nodularia guiensissp. nov. + ((Nodularia nuxpersicae + Nodularia nipponensis) + (Nodularia dualobtusus + Nodularia douglasiae))))))). The discovery of this new taxon further enhances the diversity level within the genus Nodularia in China and also highlights the necessity for comprehensive surveys of unexplored regions in order to potentially unveil additional new taxa in the future.

Molecules and morphology reveal ‘new’ widespread North American freshwater mussel species (Bivalvia: Unionidae)

Trematode infection affects shell shape and size in Bulinus tropicus.

The two widespread ostracod genera Cypria Zenker, 1854 and Physocypria Vávra, 1897 are traditionally distinguished based on the presence or absence of tubercles on the right valve margin. However, recent research based on soft body parts has uncovered new cryptic genera within Cypria and Physocypria. Following this line of research, a new Cyclocyprididae genus and species, Vizcainocypria viator gen. nov. sp. nov., is here described from individuals collected in rice fields and wetlands of the Iberian Peninsula. Vizcainocypria is compared with Cypria, Physocypria, Dentocypria Savatenalinton, 2017, Keysercypria Karanovic, 2011, Brasilocypria Almeida et al., 2023, and Claudecypria Almeida et al., 2023 based on morphological evidence. Besides the presence or absence of tubercles on the right valve, these genera can be distinguished according to their mandibular palp, second thoracopod, caudal ramus, and male hemipenis. Molecular analyses using mitochondrial (COX1), and nuclear (28S rDNA) genes provide further support for the differentiation of Cypria, Dentocypria, Physocypria and Vizcainocypria gen. nov. The present study highlights the importance of using an integrative taxonomy approach, combining shell and soft-body parts morphology and molecular data, to characterize the rich diversity of freshwater ostracods.

ABSTRACTShell shape varies markedly in freshwater mussels in the order Unionoida. Freshwater mussels belonging to the genus Velesunio (Family Hyriidae) are distributed widely in the rivers and wetlands of Australia, with recent molecular evidence suggesting at least three more species within the genus Velesunio than previously described using shell morphology. This study explored differences in shell morphology between and within two major Australian drainage basins: the Murray–Darling and Lake Eyre. Differences in shell shape among the species were difficult to detect with variability in morphology, showing the greatest difference between drainage basins. For all species, there were significant differences in morphology between rivers within basins; Shells from the Lake Eyre Basin, showed small differences in shell morphology among with greater species level differences in morphology at the site scale in the Murray–Darling Basin. Extreme flow variability of Lake Eyre Basin rivers means they spend considerable time as lentic waterholes. In contrast, the rivers of the Murray–Darling Basin, while still highly variable, spend a far greater time under flowing conditions. Thus, the variability in shell morphology among sites may reflect local hydraulic variability rather than large-scale flow variability.

Freshwater mussels have suffered a severe decline during the last century. Accurate description and identification of species have been an arduous and important task for the conservation of this group. Recently, with the promotion of molecular technology, especially mtDNA, many morphological species have been merged. In the genus Lamprotula, L. caveata, L. cornuumlunae and L. leaii are recognized as valid species. The complete mitogenome of. L. cornuumlunae was firstly sequenced in this study. By comparing mitochondrial genomics and phylogenetic analysis, the results showed that mtDNA cannot distinguish between L. caveata and L. cornuumlunae. We hypothesized that the deficiencies of mtDNA in species delimitation was caused by very recent speciation. Time-calibrated multilocus divergence time estimation revealed that L. caveata and L. cornuumlunae recently diverged in the Neogene Pliocene. This study presents the potential problems of relying on mtDNA sequences for delimiting recently diverged species. We emphasis that mtDNA cannot be used solely or dominantly to understand biodiversity. Instead, it is indeed an effective tool, combined with more data, such as shell morphology, reproductive characters and biogeography, to integrate species concepts.

The high diversity and limited floral information in tropical forests often pose a challenge for species identification. However, over the past decade, DNA barcoding has been employed in tropical forests, including Sumatran forests, to enhance floristic surveys. This technique facilitates the discrimination of morphologically similar species and addresses the limitations of conventional species identification, which relies on short‐lived reproductive structures. This study aimed to evaluate the efficiency of matK, rbcL, and the combination of both chloroplast markers for species identification in Burseraceae by employing genetic distance and species tree inference. In this study, we collected 197 specimens representing 20 species from five genera of Burseraceae. The highest percentage of specimens' identification (36%) at the species level was obtained using matK + rbcL, followed by matK (31%), and rbcL (7%). The matK dataset presented the highest interspecific divergence with a mean of 0.008. In addition, a lack of barcode gap was observed in both markers, suggesting potential limitations of the core barcodes for distinguishing Sumatran species within Burseraceae. The monophyly test confirmed five species as monophyletic using Bayesian species tree inferences for matK. Overall, our results demonstrate that matK outperforms rbcL in species identification of Burseraceae, whereas their combination did not enhance species delimitation. To improve the molecular species assignments of this family, future studies may consider including more DNA markers in conjuction with matK, and broadening the availability of reference sequences for species that have not yet been included in the databases. The outcomes of molecular species identification vary depending on the taxonomic group under investigation. Implementation of phylogenomics for species delimitation and diagnostic marker development is strongly recommended for tropical biodiversity assessments, especially for poorly studied clades.

The cone snails are hyper diverse group of marine gastropods and the shell morphology is the base of primary species identification. Among the Conidae, homoplasy and plasticity of morphological characters are common. Since speciation is positively correlated with peptide complexity in Conidae family, the present study was carried out to ascertain the genetic status of drastically varying phenotypes observed among the targeted Conus species of different environments and to detect cryptic species using mitochondrial and nuclear markers. Morphological parameters were recorded for the phenotypes of the species. Specific differences were observed for shell coloration. Three mitochondrial genes, COI (658bp), 16s rRNA (550bp), 12s rRNA (450bp) and Nuclear H3 gene (350bp) were amplified in five specimens each of varying phenotypes of targeted species. The analysis revealed that the phenotypic variations in C. inscriptus C.amadis and C.malacanus in different environments are not underpinned by the genome, The present study generated species-specific molecular signatures from varying phenotypes of conidae Since speciation is positively correlated with the complexity of conopeptides of the species, the findings provide confirmation of phenotypic variation and will be used for bioprospecting research on the species and also conservation and management of the species in Indian waters.

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.

Ourapteryx is widely distributed in the Palearctic and Oriental regions, with the highest species diversity found in China. As of 2024, 95 described species have been recorded globally; however, no comprehensive revision of this genus has been published. Identifying Ourapteryx species based solely on wing patterns is challenging due to their extreme similarity, often leading to frequent misidentifications and the oversight of cryptic species. In this study, we utilized 68 morphological species, along with 1050 COI sequences, to develop an integrative taxonomy for Ourapteryx. This taxonomy integrates morphological, molecular, distributional, and ecological evidences. Our findings identified nine candidate species (labeled as sp1–sp7, O. horishana and O. brachycerca), increasing the total number of recognized species from 68 to 77. Using this updated checklist, we compared four molecular delimitation methods against the outcomes of morphological taxonomy. The analysis indicated that a 2% threshold produced the highest efficiency. Additionally, we explored the reasons behind morpho‐molecular discordance and the presence of hidden species. Our study underscores the importance and reliability of integrative taxonomy, which relies on multiple lines of evidence for accurate species identification and classification.

Freshwater mussels in the genera Fusconaia, Pleurobema, and Pleuronaia are similar in their external shell morphology, which has made the identification and classification of species within these genera difficult and led to many taxonomic revisions. Large samples (N = 464) of select mussel species in these genera were collected from 2012 through 2014, primarily in the upper Tennessee River basin of Tennessee and Virginia, USA. Mitochondrial ND1 and nuclear ITS1 DNA sequences were analyzed to assess phylogenetic relationships among taxa. Ten species were verified as phylogenetically distinct at ND1, two of which were cryptic and previously unrecognized species. Described herein as Pleurobema parmaleei and Pleuronaia estabrookianus, each species clade was diverged at this gene region by ~3.0% from the respective closest congener. The nuclear ITS1 gene region’s nucleotide-site insertion/deletion (indel) patterns were analyzed as single mutational events rather than as fifth character states or missing data. Most species, including these two, were phylogenetically distinct at the ITS1 region when incorporating indels into analyses, but some estimated interspecific pairwise distances were lower than corresponding intraspecific estimates. Among morphological traits assessed for each species, differences in foot color and gravidity characteristics illustrated differences between phylogenetically recognized species and their closest congeners. Due to the limited known geographical distributions of these two cryptic species, each may require protection under the U.S. Endangered Species Act. While this study collected large sample sizes for each species, many streams in the basin remain unsampled and could potentially contain populations of these species or additional cryptic species.

Assessing shell morphology in freshwater mussels (Mollusca: Bivalvia: Unionidae) from the Maâden River, Tunisia: Insights from geometric morphometrics and shape descriptors

The use of classical taxonomy, with its reliance on the physically observable, is currently waning in the face of increased reliance on molecular phylogenetics. This thesis demonstrates that a pluralistic approach to classical taxonomic practice can lead to increased internal cladistic resolution within a clade, including the recognition of new taxa at all nomenclatural levels. In particular, this thesis has three aims to bring greater resolution to the clade Stromboidea Rafinesque, 1815 (Gastropoda Linne, 1758): 1) to divide the Stromboidea into two distinctive evolutionary crown clades using morphological evidence, thereby reinstating the historical understanding of the internal cladistic relationships that have been lost as a consequence of taxonomic inflation; 2) to complete an α-taxonomic revision of Seraphsidae Gray, 1853 (Stromboidea) based on a pluralist approach to species conception; and 3) to resolve the infrafamilial relationships within Seraphsidae using morphological cladistics. This thesis examined all species hypotheses and their synonymies, and revised these in a pluralist light against the rules that govern precedence and availability. From this information, an annotated synonymy was generated for each taxon, the precedence of names determined, and revised descriptions formulated. Character sets that reflect the synapomorphies within the major subclades of Seraphsidae were coded and a cladogram generated using maximum likelihood within the tnt program with default settings. Four forms of material and evidence were used in this systematic review: 1) the type material for each taxon; 2) physical material; 3) published images; and 4) literary references for specimen localities without illustration. The current morphologically-based classification of Seraphsidae was found to be sound in terms of current species delimitations. Regardless of this, the use of a pluralist approach improved understanding of the internal cladistic relationships within Seraphsidae, which led to higher resolution of the internal cladistic arrangements and taxonomic delimitation. Furthermore, this increased resolution is now reflected in the higher evolutionary contextualisation of the family nomenclature. This thesis included Mauryna de Gregorio, 1880 within Seraphsidae on the grounds that it provides a basal link to the Seraphsidae sister taxa Semiterebellum Cossmann, 1889 and Terebellopsis Leymerie, 1846, both contained within Rostellariidae Gabb, 1868, and all three clades may in time be brought together under one family. It was not possible within the context of this thesis to test the results of the pluralist α-taxonomic findings against phylogenies generated with molecular data. This was due to the high number of extinct taxa within the Seraphsidae. Therefore, it is imperative that further revisions be undertaken with groups of predominantly extant taxa to test the pluralist classical taxonomic methodologies against molecular data, and thereby seek to reverse the trend in the literature whereby classical taxonomy is deemed fundamentally redundant in the face of advances in analysis of molecular data.

DNA barcoding and DNA taxonomy have recently been proposed as solutions to the crisis of taxonomy and received significant attention from scientific journals, grant agencies, natural history museums, and mainstream media. Here, we test two key claims of molecular taxonomy using 1333 mitochondrial COI sequences for 449 species of Diptera. We investigate whether sequences can be used for species identification ("DNA barcoding") and find a relatively low success rate (< 70%) based on tree-based and newly proposed species identification criteria. Misidentifications are due to wide overlap between intra- and interspecific genetic variability, which causes 6.5% of all query sequences to have allospecific or a mixture of allo- and conspecific (3.6%) best-matching barcodes. Even when two COI sequences are identical, there is a 6% chance that they belong to different species. We also find that 21% of all species lack unique barcodes when consensus sequences of all conspecific sequences are used. Lastly, we test whether DNA sequences yield an unambiguous species-level taxonomy when sequence profiles are assembled based on pairwise distance thresholds. We find many sequence triplets for which two of the three pairwise distances remain below the threshold, whereas the third exceeds it; i.e., it is impossible to consistently delimit species based on pairwise distances. Furthermore, for species profiles based on a 3% threshold, only 47% of all profiles are consistent with currently accepted species limits, 20% contain more than one species, and 33% only some sequences from one species; i.e., adopting such a DNA taxonomy would require the redescription of a large proportion of the known species, thus worsening the taxonomic impediment. We conclude with an outlook on the prospects of obtaining complete barcode databases and the future use of DNA sequences in a modern integrative taxonomy.