The Natural History Museum of Bern (German: Naturhistorisches Museum Bern) is a museum in Bern, Switzerland. In its teaching and research it cooperates closely with the University of Bern. It is visited by around 131,000 people yearly.
Cypriniformes, the most species-rich order of freshwater fishes (~5,000 species), represents a key lineage for understanding vertebrate diversification in freshwater ecosystems. This clade includes several highly miniaturized and understudied lineages whose phylogenetic placements have long remained contentious. Here, we present the first phylogenomic analysis of Cypriniformes with complete family-level representation and broad genus-level coverage, encompassing 316 species comprising approximately 30% of all described genera. Our dataset integrates 257 newly assembled genomes with publicly available resources and analyzes multiple sets of genome-wide markers using both concatenation-based and coalescent-aware approaches. The general concordance among analytical frameworks indicates that the backbone topology of Cypriniformes is now established, allowing clear identification between well-supported clades and regions of persistent conflict. Our results strengthen the evolutionary relationships of several miniaturized lineages, while identifying recalcitrant relationships shaped by both biological processes and model artefacts that can yield superficially similar patterns of phylogenetic conflict. Our study substantially expands genomic representation and establishes a phylogenomic foundation for future comparative, developmental, and evolutionary research in this freshwater radiation. ### Competing Interest Statement The authors have declared no competing interest. Swiss National Science Foundation, 310030_185120 Basler Stiftung für Biologische Forschung TAMU HATCH, TEX09452-1
Out of the Oriental Clivina lobata-species group, the following three new species are described and illustrated: Clivina caputquadrata sp. n., C. omnicarinata sp. n., and C. dentata sp. n. The species Clivina advena Putzeys, 1867 is resurrected to species status from synonymy with C. sabulosa MacLeay, 1825, and a lectotype is designated.
Abstract Miniaturization, the reduction of adult body size to an extreme degree, has evolved repeatedly across vertebrates. Yet its genomic underpinnings remain poorly understood. Cypriniformes, the most species-rich order of freshwater fishes, contains multiple miniaturized lineages that have evolved contrasting developmental processes. Proportioned dwarfs are tiny-bodied but otherwise morphologically similar to larger relatives, while progenetic miniatures exhibit developmental truncation thus retaining larval-like anatomical features into adulthood. Using a new time-calibrated phylogeny of 309 cypriniform species and comparative genomic analyses of 33 high-quality genome assemblies, we investigated the evolutionary history and genomic correlates of miniaturization across this order. Ancestral state reconstruction revealed multiple independent origins of both miniature types, with transitions predominantly unidirectional and non-randomly distributed across the phylogeny. The origins of the two types of miniatures differed in their timing. Progenetic miniatures arose predominantly as early as the Eocene while proportioned dwarfs arose mainly within the Miocene period. Genome size variation across Cypriniformes has been overwhelmingly driven by polyploidy. However, progenetic miniatures but not proportioned dwarfs showed consistent genome size reduction. Comparative genomic analyses revealed that all three independently-evolved progenetic miniature lineages share convergent signatures of repeat loss alongside genome-wide intron shortening, patterns absent in proportioned dwarfs. Our study provides the broadest evidence to date that progenetic miniaturization, despite independent origins, is underpinned by predictable structural genomic changes, revealing a fundamental link between developmental truncation and genome architecture in vertebrates.
Finding live individuals of the minute, subterranean snail genus, Iberozospeum Jochum, Kneub & uuml;hler, Prieto & Neubert, 2022 is a serendipitous, challenging endeavor. Its diversity has largely been described from caves explored in the Spanish, Cantabrian-Pyrenean part of its range, but only rarely from the French side of the western Pyrenees. Recent exploration has thus targeted cave systems in the D & eacute;partment Pyr & eacute;n & eacute;es-Atlantiques to reveal iberozospeid diversity on the southwest, French Pyrenean side. In this study, four live populations were discovered in four different French caves and subjected to integrative taxonomic study, incorporating new genetic data and 3D X-ray microscopic imagery. We show that the new individuals are genetically and morphologically most similar to I. bellesi (Gittenberger, 1973) and consequently, assign them to this species. 3D X-ray image data of type material ofI. bellesi and that of individuals within this study are presented. The new genetic data is presented within the latest phylogenetic reconstruction of Iberozospeum while the prevalence of thriving, live populations ofI. bellesi is confirmed in multiple caves for the first time in France.
Abstract The acidic blackwaters of Southeast Asia’s peat-swamp forests represent some of the most extreme freshwater environments on Earth. Despite their very low pH values, limited nutrients, and hypoxic conditions, these blackwater habitats harbor a remarkable diversity of freshwater fishes, including multiple lineages that have independently adapted to these extreme conditions and, in some cases, exhibiting extreme body miniaturization. These replicate evolutionary lineages therefore provide a powerful comparative framework to investigate adaptation to extreme environments and the genomic basis of miniaturization. Here, we present high-quality, annotated reference genomes for four cypriniform species endemic to these peat-swamp forest ecosystems: Paedocypris sp., Sundadanio atomus , Boraras brigittae , and Rasbora kalochroma . The first two are progenetic miniatures, including Paedocypris , comprising the smallest known fish, while B. brigittae represents a proportioned dwarf and R. kalochroma a non-miniature taxon. Genome sizes ranged from 401-1,290 Mb and heterozygosity from 0.34-1.7%. All genome assemblies achieved pseudo-chromosome-level contiguity, high k-mer completeness (>99%), and high BUSCO completeness (94.5-98.9%). Repeat analyses revealed lineage-specific differences in transposable element landscapes and abundances, while gene annotation identified notable intron length reduction in progenetic miniatures.
