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Historically, the thick‐shelled river mussel (Unio crassus agg. complex) was considered a single, widespread species across Europe. However, recent phylogenetic taxonomic revisions have delineated 12 species from this complex, including Unio crassus (s. str. Philipsson in Retzius, 1788) and Unio nanus (Lamarck, 1819 stat. rev.), which exhibit substantial range overlap and broad European distributions. Understanding their fine‐scale genetic diversity, population structure, and potential for recent or ancient hybridization is critical for effective conservation planning. This study investigated the genetic diversity and structure of U. crassus and U. nanus across Europe, examining the influence of glacial disturbance history and host‐fish associations. Using mitochondrial (COI) and nuclear (microsatellite) markers on 60 populations, we revealed a discordance between mitochondrial and nuclear structuring, suggesting ancient introgression. Crucially, no evidence of recent hybridization was detected between U. crassus and U. nanus. We found significantly higher nuclear genetic diversity in U. crassus compared to U. nanus. Our findings indicate an older Black Sea–Caspian Sea divergence and ancient introgression between U. nanus and U. crassus, as well as distinct postglacial colonization routes: a Western route for U. nanus and an Eastern route for U. crassus, converging in a secondary contact zone. Our results highlight the strong influence of host‐fish associations and glacial history in shaping the genetic patterns of these mussels, underscoring the need to incorporate intraspecific genetic diversity into conservation strategies. As shell morphology proved unreliable for species identification, we recommend DNA barcoding for reliable species recognition and suggest further research into host‐fish preferences to improve conservation efforts. This paper presents novel findings on the genetic diversity of the recently described thick‐shelled river mussel complex, combining nuclear, mitochondrial, and morphometric markers in relation to European host‐fish colonization patterns. In particular, we identified currently unknown contact zones across their European distribution and found pronounced differences in the genetic diversity among the different species within the U. crassus complex.

Aim: The indirect consequences of biotic homogenization, the process of a gradual increase in the similarity of regional biotas driven by the combined effects of species invasions and extinctions, are still poorly understood. In this study, we aimed to assess the ability of a native affiliate species to maintain its host resources under the condition of biotic homogenization of host communities. Location: Central (Vltava River Basin, Czech Republic) and western (Douro River Basin, Portugal) Europe. Methods: We tested the ability of non-native species to serve as an alternative partner in local host—affiliate relationships. We used a European freshwater mussel, Anodonta anatina, which is considered to be a host generalist of native fish species, and compared the compatibility of its glochidia with native versus non-native fishes in two distinct European regions. Subsequently, we projected the obtained host compatibility data into the recent progress of biotic homogenization and estimated the degree of host dilution. Results: We found significant differences in the ability of A. anatina glochidia to parasitize the native and non-native fish species in both the central and peripheral parts of the mussel's distribution range. As a result, the increasing presence of non-native species within fish communities across Europe likely significantly decreases the availability of the mussel's host. Biotic homogenization of host communities may interfere with general life history traits (host specificity) of their local affiliate species. Main conclusions: This study demonstrates that the mixing of regional biotas may lead to an excessive loss of host availability even for host generalists, such as the freshwater mussel A. anatina, with potentially broad consequences for their population dynamics. Conservation strategies of endangered affiliate species need to incorporate the biogeographical context of host—affiliate relationships and particularly the consequences of biotic homogenization.

Bivalves are ubiquitous members of freshwater ecosystems and responsible for important functions and services. The present paper revises freshwater bivalve diversity, conservation status and threats at the global scale and discusses future research needs and management actions. The diversity patterns are uneven across the globe with hotspots in the interior basin in the United States of America (USA), Central America, Indian subcontinent and Southeast Asia. Freshwater bivalves are affected by multiple threats that vary across the globe; however, pollution and natural system (habitat) modifications being consistently found as the most impacting. Freshwater bivalves are among the most threatened groups in the world with 40% of the species being near threatened, threatened or extinct, and among them the order Unionida is the most endangered. We suggest that global cooperation between scientists, managers, politicians and general public, and application of new technologies (new generation sequencing and remote sensing, among others) will strengthen the quality of studies on the natural history and conservation of freshwater bivalves. Finally, we introduce the articles published in this special issue of Hydrobiologia under the scope of the Second International Meeting on Biology and Conservation of Freshwater Bivalves held in 2015 in Buffalo, New York, USA.

The first animal mitochondrial genomes to be sequenced were of several vertebrates and model organisms, and the consistency of genomic features found has led to a 'textbook description'. However, a more broad phylogenetic sampling of complete animal mitochondrial genomes has found many cases where these features do not exist, and the phylum Mollusca is especially replete with these exceptions. The characterization of full mollusc mitogenomes required considerable effort involving challenging molecular biology, but has created an enormous catalogue of surprising deviations from that textbook description, including wide variation in size, radical genome rearrangements, gene duplications and losses, the introduction of novel genes, and a complex system of inheritance dubbed 'doubly uniparental inheritance'. Here, we review the extraordinary variation in architecture, molecular functioning and intergenerational transmission of molluscan mitochondrial genomes. Such features represent a great potential for the discovery of biological history, processes and functions that are novel for animal mitochondrial genomes. This provides a model system for studying the evolution and the manifold roles that mitochondria play in organismal physiology, and many ways that the study of mitochondrial genomes are useful for phylogeny and population biology. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.

Molluscs are among the most diverse and widespread animal groups in freshwater habitats. Unfortunately, like most freshwater taxa, they are decreasing dramatically and are now among the most threatened animals on Earth, with many species already extinct or on the brink of extinction. Here, we review our current knowledge on the biodiversity and conservation of freshwater molluscs using the concept of knowledge shortfalls. We focus on seven previously proposed key shortfalls to review and analyse existing knowledge gaps relating to (1) taxonomy, the Linnean Shortfall; (2) distribution, the Wallacean Shortfall; (3) abundance and population dynamics, the Prestonian Shortfall: (4) evolution, the Darwinian Shortfall; (5) abiotic tolerances, the Hutchinsonian Shortfall; (6) traits, the Raunkiaeran Shortfall; and (7) biotic interactions, the Eltonian Shortfall. In addition, we address a new shortfall, which relates to the application and effectiveness of conservation measures, including assessments, methods, funding, and policies, the Ostromian Shortfall. Based on our review, we provide recommendations and suggest pathways to overcome these existing shortfalls. This work also introduces the articles in this special issue of Hydrobiologia, which represent key contributions to the First International Freshwater Mollusk Conservation Society Meeting held in Verbania, Italy, in 2018.

Mollusca is the second most species-rich phylum within the metazoans, displaying critical economic, ecological and scientific importance. Yet, they are still largely underrepresented with respect to genomic resources. The emergence of next-generation sequencing technologies has revolutionized deep-scale genomic characterization of non-model organisms, and molluscs are slowly entering this transformative era. Here, we provide a historical contextualization of the Genome Revolution in molluscs with a tour de force revision of key research trends observed over the past decade. Omic approaches such as RAD-seq, transcriptome, mitogenome and whole-genome sequencing represent the most significant resources produced for this phylum. Importantly, the molecular mechanisms underscoring multiple biological novelties and adaptations observed in molluscs are starting to be unravelled. In contrast, compared to other metazoan lineages the genomic resources currently available for this lineage still lag far behind. We put forward that to fully grasp the evolutionary and adaptive roads of this tantalizing group of organisms crucially depends on the full embracement of high-throughput sequencing (HTS) technologies in the near future.

Freshwater ecosystems are the most vulnerable worldwide and freshwater bivalves rank amongst the most threatened animals in the world. Surveying and monitoring freshwater bivalves are difficult tasks: they are difficult to find, hard to identify (taxonomic expertise is needed), and working underwater is technically challenging. It is therefore crucial to find more efficient methods to survey and monitor these species. Here, we present the first metabarcoding approach for freshwater bivalves and compare environmental DNA (eDNA) and traditional surveys. We describe two sets of primers (for Unionida and Venerida) developed for freshwater bivalves eDNA metabarcoding. These primers have been tested in the field, with about 300 studied sites. Results were compared to freshwater bivalves’ surveys using traditional methods, with eDNA always detecting more species than traditional surveys, especially when Sphaerids were taken into account. While our study initially focused on Western Palearctic freshwater bivalve species, our primers were confronted in silico with available sequences and have proven to be effective at a global scale. The results show that eDNA metabarcoding, with our developed primers, is a remarkable tool allowing for non-invasive surveys, detection of rare and inconspicuous species, absence data and overall freshwater bivalves routine monitoring.

Recent research efforts have significantly advanced our knowledge on Asian freshwater mussel (Bivalvia: Unionidae) diversity and distribution. Here we provide a modern consensus of the diversity, biogeography and conservation of Unionida in the region comprising East and Southeast Asia (excluding Wallacea) and Asian Russia. A data review confirmed the presence of 228 native and 3 non-native Unionida (98% Unionidae, 2% Margaritiferidae), rendering the region a global hotspot of freshwater mussel diversity. Species richness was highest in China (particularly Yangtze basin) in absolute numbers and Cambodia when correcting for country area, and decreased gradually towards the south and steeply towards the north and east. Six of the seven unionid subfamilies are native to the region, with species richness peaking in Southeast Asia for Rectidentinae, Gonideinae, Parreysiinae and Modellnaiinae, China for Anodontinae and Unioninae, and Asian Russia for Margaritiferidae. Conservation status and data collected after 1980 were not available for 61 and 24% of species, respectively. Dams, deforestation and pollution are likely the major threats to mussels in the region, though data in this respect are scarce. The Philippines, Laos, Indonesia, Myanmar and Malaysia are among the countries with the poorest data availability and urgently require research.

Challenges in freshwater organism conservation in West Africa are worsened by significant knowledge gaps, even for charismatic species like crocodiles. This study addresses these gaps by assessing crocodile diversity, distribution, and conservation threats in Guinea-Bissau, where existing data is outdated. We used visual surveys, inquiries, molecular barcoding, camera trapping, and bibliographic reviews to investigate crocodile populations. Notably, we found evidence suggesting the Nile crocodile ( Crocodylus niloticus ), previously thought extinct in West Africa since about 200 years, may persist in Guinea-Bissau’s Cacheu region. We also confirmed the presence of the West African crocodile ( Crocodylus suchus ) in major river basins and coastal lagoons, including the Bijagós Archipelago, and the West African dwarf crocodile ( Osteolaemus cf. tetraspis ) in the southern mainland and the Bijagós Archipelago. Habitat loss and deliberate killings were identified as major threats. Standardized surveys and genetic sampling are essential to assess population size, connectivity, and genetic diversity, informing evolutionary studies and conservation planning. Conservation efforts should prioritize habitat protection through community-managed reserves and restoration initiatives. Additionally, engaging local communities to raise awareness and develop conflict mitigation strategies is crucial, particularly in areas with human-crocodile interactions.

An important population of the critically endangered pearl mussel Margaritifera margaritifera (Linnaeus, 1758) was surveyed at the edge of its southern distribution (River Paiva, Portugal). Although an earlier study suggested that this population had a very low number of individuals (<500), a narrow distribution, and was mainly comprised by old specimens our data contradict these findings. Our assessment estimated a population with probably more than 5,000 individuals distributed across 80 km of the river length. From the 32 sites surveyed, 19 contained M. margaritifera with higher abundances verified in the middle and upper parts of the river (a maximum of 78 ind. per 100 m of river stretch was recorded). The pearl mussels showed a clear preference for areas near the banks, in shallow water, sandier and gravel sediments, and a high degree of riparian vegetation cover. The population structure was skewed with a very high percentage of large (and old) animals but 3.7 % of the individuals collected were juveniles (<60 mm in length); therefore, this population can be considered functional. Environmental characterization indicated that this river is still in excellent or good condition although some areas showed deterioration due to discharge of domestic effluents. The main conservation requirements of M. margaritifera in the River Paiva include maintaining the water quality (and if possible stopping the discharge of domestic effluents), increasing riparian vegetation cover, removing several weirs to increase connectivity, and increasing trout density.