Biology subjects

Sudasinghe, H.

Publications and source records attributed to Sudasinghe, H..

5 recordsLinked to original sources

bioRxiv2026

Convergent genome streamlining accompanies independent miniaturization in the world's smallest fishes

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.

evolutionary biology↗

bioRxiv2026

Disentangling site-specific and shared local adaptation in a classic system of repeated evolution

Repeated divergence across contrasting habitats is widely used to infer natural selection and adaptation. However, such inferences remain inherently correlative and capture only adaptation shared among populations from the same habitat type, thereby missing site-specific adaptation unique to individual populations. Field transplant experiments test adaptation more directly by measuring fitness in nature, but they are typically limited to pairwise reciprocal exchanges between populations and therefore cannot separate shared habitat-level and unique site-specific adaptation. Here we extend the typical transplant framework to include multiple populations from both within and across habitat types, allowing fitness variation to be partitioned into shared habitat-level and unique site-specific components. We apply this framework to lake-stream stickleback, a classic system for studying adaptation via repeated divergence. Specifically, we transplanted laboratory-reared fish from a panmictic lake population and four independent stream populations across one lake and two stream sites. Stream fish outperformed lake fish in streams and vice versa, demonstrating adaptive lake-stream divergence. However, at both stream sites, local stream fish also outperformed foreign stream fish. Strikingly, this site-specific advantage was twice as large as the advantage of foreign stream fish over lake fish, reflecting the fitness benefit of shared stream adaptation. These results show that most fitness-relevant evolutionary variation in this system is unique to individual populations and therefore invisible to approaches that rely on repeated evolution to infer adaptation. More broadly, our work underscores the importance of ecological scale for understanding adaptation and evolutionary predictability. Significance statementRepeated evolutionary responses to similar environments commonly serve as evidence for adaptation. However, such comparative approaches do not directly measure fitness or resolve whether variation among populations from the same nominal habitat reflects adaptation to site-specific conditions. Using laboratory-raised lake and stream stickleback transplanted both within and across habitat types, we separated the fitness effects of shared adaptation to the same nominal habitat and site-specific adaptation unique to individual populations. Site-specific adaptation explained two-thirds of the total fitness variation, exceeding the contribution of adaptation shared among populations from the same habitat type. Our study highlights that natural selection generates fitness-relevant divergence at finer ecological scales than comparative approaches can resolve, underscoring the irreplaceable value of field experiments for understanding evolution.

evolutionary biology↗

bioRxiv2026

Reference genomes of four miniature and non-miniature cypriniform fishes inhabiting acidic peat-swamp forest blackwaters of Southeast Asia

The acidic blackwaters of Southeast Asias 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.

genomics↗

bioRxiv2026

Phylogenomics of Cypriniformes, the most diverse order of freshwater fishes: consensus, challenges and limitations

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.

evolutionary biology↗

bioRxiv2025

Integrative Species Delimitation in a Speciation Continuum: Phylogenomics, Cryptic Diversity, Diversification and Historical Biogeography of Sinocyclocheilus Cavefish

The transition from structured populations to distinct species often unfolds along a speciation continuum. However, empirically dissecting this continuum poses challenges for species delimitation, particularly in rapid radiations marked by recent divergence, incomplete lineage sorting, and gene flow. The species-rich Sinocyclocheilus cavefish radiation of Southwest China, an emerging evolutionary multi-species model system, shows a notable mismatch between its high morphological diversity and the limited divergence observed in commonly used mitochondrial DNA markers. This pattern suggests that true species richness may be underestimated. Yet, comprehensive genome-wide approaches to resolve species boundaries in this group are still lacking. To address this, we combine phylogenomics, coalescent-based species delimitation, population genetics, and historical biogeography, using both genome-wide RAD-seq and multi-locus Sanger data (including nuclear and mitochondrial DNA). Our phylogenomic analyses resolve major clades and reveal substantial cryptic diversity, well beyond what was detected by earlier markers. Species delimitation based on RAD-seq genomic data identifies several cryptic evolutionary lineages. We recover a dynamic divergence history shaped by isolation and episodic connectivity. Biogeographic reconstruction supports a mid-Miocene origin following a major vicariance event, with subsequent founder-event dispersals into subterranean habitats. This long history of fragmentation is further complicated by reticulation and ancestral polymorphism, and is reflected in present-day patterns of restricted gene flow across river valleys. These results highlight the utility of integrative genomic approaches in resolving species boundaries and uncovering the evolutionary processes that underlie high diversity in large and complex radiations.

evolutionary biology↗