Biology subjects

Robinson-Rechavi, M.

Publications and source records attributed to Robinson-Rechavi, M..

At least 19 recordsLinked to original sources

bioRxiv2026

The Molecular Programme of the Biphasic Isopod Moult: A Transcriptomic Chimera

Isopods are an order of crustaceans characterised by a biphasic moulting pattern, in which the posterior cuticle is shed before the anterior cuticle, with an intramoult period of up to a few days between the two. In order to understand how this unusual moulting pattern is regulated, we carried out a transcriptomic analysis covering three distantly related terrestrial isopod species. We analysed the transcriptomic profile of four body regions: the front legs, the hind legs, the thorax and the head, at different phases of the moulting cycle in the three species. We describe a conserved cyclic pattern in the transcriptomic profiles corresponding to the phases of the moulting cycle. The genes driving this conserved pattern provide a catalogue of the central players of the moulting process and are prime candidates for future experimental work. Furthermore, we show that during the intramoult phase, the posterior limbs display a transcriptomic profile more similar to the postmoult phase, indicating that at this phase, the animal is functionally a transcriptomic chimera, with the anterior and posterior halves experiencing radically different molecular environments, with disjunct regulatory programmes active in each half.

evolutionary biology↗

bioRxiv2026

An evolvable and functionally partitioned network underlies developmental remodelling in teleosts

Comparative embryology has revealed that early animal development is based on highly conserved genetic programs. Beyond embryogenesis however, animals undergo remarkably diverse post-embryonic developmental transitions such as metamorphosis. Whether these transitions are also organised into conserved genetic programs remains largely unexplored. To identify conserved genetic programs underlying post-embryonic development, we examine metamorphic remodelling in five teleost fishes, spanning 200 million years of evolution. By integrating comparative co-expression networks, evolutionary genomics, phylogenetic modelling, and functional data in zebrafish, we uncovered a conserved post-embryonic developmental network. This conserved network comprises components involved in core cellular processes, and involved in development and physiology, both of which are under the control of thyroid hormone during metamorphosis. Despite evolutionary conservation at the coding sequence level, this network exhibits significant turnover in gene family copy number following the teleost-specific whole-genome duplication as well as lineage-specific expansions and contractions. The variation in gene copy numbers is associated with macroevolutionary variation in a number of ecological and morphological traits, including swimming performance, and trophic level. Cross-species tissue expression, zebrafish single-cell transcriptomics, and zebrafish perturbation phenotypes placed the implicated genes in biological contexts relevant to these traits. Together, our results provide evidence of an ancient, functionally partitioned post-embryonic developmental network that has diversified throughout teleost evolution. The heterochronic variation in network function, changes in endocrine activity, and gene-family turnover provide potential routes through which a shared developmental architecture contributed to the evolution of phenotypic diversity in teleosts.

evolutionary biology↗

bioRxiv2026

A developmental chimera: co-option of appendage, secretory and myogenic programs underlies spider venom gland evolution

The evolutionary emergence of complex organs requires the integration of distinct developmental modules, yet the mechanisms bridging divergent tissue programs into unified functional units remain poorly understood. Animal venom systems, combining high-output secretory epithelia with muscular delivery systems, a provide an exceptional model for studying this modular integration. Here, we show that the venom gland of the spider Parasteatoda tepidariorum is a developmental chimera built by the hierarchical co-option of three ancestral programs. The appendage-patterning gene Distal-less establishes the primary spatial coordinate system for gland development. Downstream, the transcription factor sage maintains secretory epithelium identity; its loss causes downregulation of key venom-processing enzymes and triggers a dramatic phenotypic reversion to a neuronal state. This neural upregulation, accompanied by the downregulation of Notch ligands (delta and jagged), reveals that sage actively represses a latent neural program to maintain secretory fate. Crucially, the myogenic factor sum-1 governs the surrounding muscle layer to drive paracrine crosstalk (Wnt) and sustain lipid metabolism. Knockdown of sum-1 downregulates wntless and fatty acid anabolism genes, alongside the abnormal accumulation of lipid droplets in the secretory epithelium. Ultimately, our findings demonstrate how a complex organ is assembled by fusing an appendicular address, a repressed neuroglandular program, and a myogenic metabolic driver. This modular architecture illustrates a fundamental principle in evolutionary developmental biology: novelty can arise by harnessing the physiological and metabolic capacities of adjacent tissues to fuel the physiological demands of a newly emerged organ. Significance statementHow novel organs evolve by integrating distinct developmental modules remains a fundamental question in biology. Using the spider venom gland as a model, we show that this complex organ is a developmental chimera built by recruiting three ancestral tissue programs. The appendage-selector gene Distal-less (Dll) establishes the glands primary proximal-distal structural axis. Downstream, the transcription factor sage maintains secretory epithelial identity by actively repressing a default neural program. Concurrently, the myogenic regulator sum-1 sustains epithelial lipid metabolism through paracrine Wnt signaling. These findings establish a mosaic model of organogenesis, demonstrating that radical evolutionary innovation can arise by forging morphogenetic and metabolic partnerships that harness adjacent tissues to fuel newly emerged structures.

evolutionary biology↗

bioRxiv2026

Patterns of molecular conservation along tooth development are only partly shaped by evolutionary pressures on tooth

Although it is well established that certain stages of development are molecularly more conserved than others, the reasons for this phenomenon remain largely unknown. We study molecular conservation in the development of an organ, the molar, by comparing the temporal profiles of expression in mice and hamsters. We find that the cause of conservation of expression and of coding sequences changes over molar development. Gene expression levels display a classical increase of divergence as development progresses. In terms of genes expressed, the composition of early and late stages is better conserved and enriched in pleiotropic genes, yet each stage mobilizes different sets of pleiotropic genes, cell division for bud growth and secretion for tooth mineralization. Moreover similar patterns of higher divergence of gene sets and of coding sequences at mid development, are caused by different biological phenomena, in that case heterochronies and blood colonisation respectively. In conclusion, the patterns of molecular conservation in developing molars are shaped by a combination of processes intrinsic to the teeth, and by negative and positive selection on functions which are mostly extrinsic to the teeth. This is likely translatable to explain molecular conservation patterns in many other biological systems. AUTHOR SUMMARYFor species to evolve different adaptations to different life styles, their anatomy has to evolve correspondingly. This in turn implies evolution of the embryonic development of anatomical structures. Notably, tooth shape can evolve rapidly as an adaptation to different diets. Mice and hamsters are closely related rodents who yet differ in the shape of their molars, and thus in their development. In this study, we investigated why the genes active in molar development are more or less similar between the two species from early tooth bud to fully formed embryo molar. We found that early and late molar development were slow evolving, while mid-development was evolving faster. But surprisingly, this was in part due not to tooth evolution, but to the involvement of genes which are active in other processes in the body. For example an influx of immune cells also brings fast evolving immune genes. This helps us understand better the complexity of causes of apparently simple evolutionary patterns.

evolutionary biology↗

bioRxiv2026

scFAIR Consortium: a decentralized hub for single-cell RNA-Seq data standardization and unification

The rapid accumulation of single-cell RNA-Seq (scRNA-seq) data across multiple repositories presents major challenges for data accessibility, integration, and reproducibility. While primary repositories provide raw data, they rarely include structured cell-type annotations or descriptions of analytical workflows, limiting the ability to reuse and integrate datasets in a FAIR (Findable, Accessible, Interoperable, Reusable) manner. Here we present scFAIR, a consortium of single-cell data resources that has developed a unified metadata schema and common curation framework to improve the FAIRness of scRNA-seq data. Building on and extending the CZ CELLxGENE Discover metadata schema, the scFAIR consortium has been instrumental in driving key schema improvements, including the expansion of supported organisms, richer biological context, and structured reporting of computational workflows. To provide unified access to decentralized datasets, the consortium developed the sc-fair.org portal, which currently aggregates 2,346 datasets across partner resources through ontology-aware semantic search. We demonstrate the practical value of FAIR-compliant datasets through a cross-species validation between human and mouse Allen Brain Atlases, showing that standardized ontology annotations enable reliable annotation transfer across species, with 90% of neuronal clusters receiving an exact or equivalent label. Together, the scFAIR schema, validator, and portal constitute a community-driven framework that advances single-cell data standardization and lays the foundation for reproducible, large-scale integration of single-cell datasets.

bioinformatics↗

bioRxiv2026

Advances in protein function prediction from the fifth CAFA challenge

The Critical Assessment of Functional Annotation (CAFA) is a long-standing community effort to independently assess computational methods for protein function prediction, to highlight well-performing methodologies, to identify bottlenecks in the field, and to provide a forum for the dissemination of results and exchange of ideas. In its fifth round (CAFA5) of triennial challenges, a partnership with Kaggle Inc. facilitated participation from a large community of data scientists and computational biologists through a competitive prospective challenge on the crowdsourcing platform. In this work, we present an in-depth analysis of the submitted predictions and report improvements in accuracy over all methods from the previous CAFA challenges. We further introduce a new evaluation setting for proteins with pre-existing (incomplete) annotations and identify the need for methods that better leverage existing annotations to predict those that will be discovered later. Finally, we characterize the prospective evaluation framework by examining performance on a strict set of unpublished annotations and across intermediate database releases. Our results indicate that recent developments in the field, such as the availability of protein language models and accurately predicted 3D structures, as well as the growth of experimental annotations through biocuration, have all contributed to performance improvements. 1

bioinformatics↗

bioRxiv2026

TaxonMatch: taxonomic integration and tree construction from heterogeneous biological databases

Integrating taxonomic data across heterogeneous biological databases remains a major challenge in biodiversity research due to non-standardized nomenclature, incomplete synonym annotation, and inconsistencies in taxonomic hierarchies. These issues limit interoperability between key resources such as the Global Biodiversity Information Facility (GBIF), the National Center for Biotechnology Information (NCBI), and citizen science platforms such as iNaturalist. Here, we present TaxonMatch, a scalable and reproducible framework for taxonomic reconciliation and cross-database integration. The workflow combines string-based candidate generation using TF-IDF vectorization, supervised machine learning for match classification, and lineage-aware synonym resolution to align taxonomic entities across multiple sources. By integrating both declared and implicit equivalences, TaxonMatch resolves typographical variation, synonymy, and structural inconsistencies in taxonomic data. The framework produces a unified taxonomic structure in which equivalent entities are reconciled while preserving source-specific identifiers, provenance information, and hierarchical relationships. We evaluate its robustness across multiple classifiers and demonstrate its effectiveness in resolving ambiguous taxonomic cases that are not handled by traditional matching approaches. We illustrate the applicability of TaxonMatch through three use cases: the construction of a unified arthropod taxonomy integrating GBIF, NCBI, and iNaturalist data; the identification of closest extant relatives of fossil taxa with molecular information; and the integration of genomic resources with conservation data from the IUCN Red List. These applications highlight the ability of the workflow to support the integration of ecological, genomic, and paleontological datasets. TaxonMatch provides a flexible and generalizable solution for taxonomic data integration, enabling the construction of coherent and interoperable biodiversity datasets for downstream analyses in ecology, evolution, and conservation biology.

evolutionary biology↗

bioRxiv2026

Morphological characterization of moulting in the Atlantic horseshoecrab Limulus polyphemus: phylogenetic conservation amongchelicerates and evolutionary convergence of ecdysis linked to headshield patterns

Arthropods must periodically moult their exoskeleton to permit growth, a conserved developmental process whose morphological and behavioural execution varies widely among lineages. Horseshoe crabs (Limulidae) are members of Xiphosura, a chelicerate lineage with a fossil record extending as far back as the Ordovician and provide a valuable comparative framework for studying the evolution of moulting strategies in Arthropoda. Despite their importance, detailed morphological characterization of moulting in horseshoe crabs remains scarce, limiting developmental studies and broader comparative analyses. Here, we provide a detailed morphological characterization of the moulting process in the Atlantic horseshoe crab Limulus polyphemus. Morphological changes in specific anatomical structures, including the anterior margin of the prosoma, lateral spines and dorsal spinous process of the opisthosoma, were observed during the moulting process. By tracking these morphological markers, such as retraction of the epidermis from the cuticle and degree of corrugation of the epidermis, we were able to identify individuals in the early and late pre-moult stage, predict the onset of ecdysis, and distinguish post-moult and intermoult stages. We compare ecdysis patterns in L. polyphemus with other arthropod taxa, both extant and fossil. We find that, despite differences in behavioural execution, ecdysis in L. polyphemus shares features with other chelicerates, and that both phylogenetic signal and convergent patterns are evident across Arthropoda. This study offers a robust, non-invasive method for determining moult stages in juvenile horseshoe crabs and provides insights into the diversity and constraints of ecdysis in Arthropoda.

evolutionary biology↗

bioRxiv2026

Moulting in Pancrustacea is characterised by both deeplyconserved and recently evolved gene modules

Arthropods such as insects and crustaceans, which together form the monophyletic group Pancrustacea, possess a rigid chitinous exoskeleton that must be periodically shed through moulting to allow growth and morphological change. Although moulting is a deeply conserved developmental process across Arthropoda, our understanding of its molecular mechanisms is still largely derived from insect model species. Lineage-specific innovations and losses of moulting related genes raise fundamental questions on the extent of its conservation outside non-insect arthropods. Here, we investigate the evolutionary conservation of moulting gene expression across five representative pancrustacean species using publicly available transcriptomic datasets. Changes in gene expression during moulting are characterized by both deeply conserved and lineage-specific gene modules. Temporal gene expression analyses reveal that these lineage-specific signatures are not uniformly distributed across the moulting process: the middle transitional phase is more lineage-specific, thereby exhibiting an inverse hourglass pattern. This is likely due to life-history specific processes, development of the cuticle and specialized structures of the exoskeleton. Overall, this study provides evidence for both the evolutionary conservation and divergence of this key post-embryonic developmental process and highlights the modular architecture of the moulting programme.

evolutionary biology↗

bioRxiv2026

The highly heterozygous European amphioxus (Branchiostoma lanceolatum) at the edge of panmixia

Amphioxus (Cephalochordata) are small marine chordates that have broad ecological ranges, yet as adults form local settlements and exhibit limited mobility. Genomic surveys of two amphioxus species have suggested that they rank among the most genetically diverse metazoans. Here, we present the first accurate assessment of genomic diversity in the European amphioxus (Branchiostoma lanceolatum) and investigate the processes underlying this diversity. We leverage whole-genome sequencing data from multiple individuals sampled at two geographically distant Atlantic and Mediterranean locations. Consistent with previous estimates in other amphioxus species, we measure exceptionally high genomic diversity, with an average heterozygosity of 2.73% in B. lanceolatum. Despite the large geographic separation between sampling sites, population differentiation is minimal, indicating extensive gene flow among distant adult settlements. Phylogenetic analyses combined with population genetic simulations confirm that this elevated genomic diversity is primarily driven by a large effective population size. Although adult amphioxus have limited mobility, our results indicate that long-distance larval dispersal mediated by ocean currents is sufficient to generate a near-panmictic population structure across their broad ecological range. Author SummaryAmphioxus are small marine animals that are close relatives of vertebrates. Although they appear simple and are very similar among species, previous studies have suggested that their genome may be more diverse than expected. In this study, we accurately measured genetic diversity across the entire genome of European amphioxus collected from the Atlantic Ocean and the Mediterranean Sea. We found that this species exhibits a genetic diversity among the highest reported in animals. Despite being collected from far-apart locations, individuals are genetically very similar. This suggests that amphioxus populations are strongly interconnected. While adults move very little, their larvae drift with ocean currents, enabling them to travel long distances before settling. This widespread mixing helps to maintain a single, large, interconnected population. Our results demonstrate that even species that appear simple and sedentary can exhibit extraordinary genetic diversity when they have large populations and effective long-distance dispersal mechanisms. Understanding how such diversity is generated and maintained is essential for comprehending evolution and marine biodiversity.

evolutionary biology↗

bioRxiv2025

Evolutionary dynamics of the arthropod moulting machinery

Exoskeletons define arthropods, providing support for segmented bodies and appendages while protecting against environmental stress and predation. Although ubiquitous, this evolutionarily variable feature has enabled arthropods to occupy diverse lifestyles and ecological niches, contributing to their unrivalled diversity. Because the chitinous cuticle is rigid, exoskeletons must be periodically shed and replaced as animals grow. Arthropods therefore develop through discrete moults, with conserved phases that progress from pre-moult preparation to ecdysis and post-moult maturation. These are tightly regulated developmental transitions controlled by a molecular toolkit comprising neuropeptides, hormone-synthesising enzymes, receptors, and the early, fate, and late gene sets that activate and execute the moulting process. Although genetic studies in model species have identified many components, major knowledge gaps remain, especially in non-insect arthropods. Advances in genome sequencing now enable comparative genomic analyses across diverse, previously understudied arthropod lineages to begin to address these gaps. We present a comprehensive comparative genomic survey of arthropods, sampling all four subphyla: Chelicerata, Myriapoda, Crustacea, and Hexapoda. Orthology inference and gene copy-number analyses contrast stable and dynamic components of the moulting machinery across the phylum. Ancestral state reconstructions and phylogenetic reconciliations reveal gene duplication and loss dynamics and the evolutionary histories of key moulting gene families. The inclusion of newly generated myriapod genomes addresses a major taxonomic gap and enables inferences of gene repertoire changes in the Mandibulata ancestor. The broad taxonomic representation enables a phylum-wide assessment to systematically evaluate, refine, and revise current understanding of the evolutionary dynamics of the entire moulting genetic toolkit.

evolutionary biology↗

bioRxiv2025

RegEvol: detection of directional selection in regulatory sequences through phenotypic predictions and phenotype-to-fitness functions

Regulatory DNA controls when and where genes are expressed, making it a key driver of phenotypic evolution. Yet detecting selection in non-coding regions remains difficult, as most approaches rely on sequence conservation or changes in substitution rate rather than molecular effects. RegEvol bridges this gap by linking machine learning-based predictions of transcription factor binding to explicit evolutionary models. It uses the distribution of predicted mutational effects to infer fitness functions under different evolutionary scenarios including random drift, stabilising selection, and directional selection. Through maximum-likelihood estimation, it identifies the regime that best explains observed changes along a lineage from an ancestral sequence. When substitution numbers are limited, such as along short evolutionary branches, likelihood differences can be aggregated across sets of regulatory elements to increase statistical power. RegEvol corrects biases that affected previous tests based on machine learning of transcription factor binding, while remaining conservative across different levels of divergence. Applied to over 3 million Drosophila melanogaster regulatory regions, we identify 5.1% under directional selection, enriched near reproductive and immune genes. Applying the aggregation strategy to human CTCF binding across tissues reveals enrichment of directional signals in nervous and male reproductive systems. The framework is readily applicable to experimentally detected regulatory elements with alignable ancestral sequences and is flexible to future advances in understanding regulatory function, providing a powerful basis for investigating adaptation in non-coding regions.

evolutionary biology↗

bioRxiv2025

Inverse hourglass pattern of conservation in rodent molar development.

Although it is well established that certain stages of development are more conserved than others, the reasons for this phenomenon remain largely unknown. We study molecular conservation in the development of an organ, the molar, by comparing the temporal profiles of expression in mice and hamsters. We find that molar development is characterized by a rarely observed pattern of conservation of expression level and coding sequences forming an inverse hourglass, with more conservation at the beginning and end of morphogenesis than at intermediate stages. As the development of the rodent molar is well described, we were able to link this pattern to the properties of the expressed genes and the activity of different developmental processes. Early and late stages mobilize different sets of pleiotropic genes, cell division for bud growth and secretion for tooth mineralization. The particularities of dental morphogenesis and homeostasis, with the degradation of certain tissues at the end of development and the hosting of immune cells, as well as heterochronies linked to adaptations, also probably contribute to the pattern. Our study of the different actors explains the inverted hourglass of molars by a combination of processes intrinsic to the teeth, and by negative and positive selection which is mostly extrinsic to the teeth. This is likely translatable to explain molecular conservation patterns in many other biological systems.

evolutionary biology↗

bioRxiv2024

Inter-individual gene expression variability implies stable regulation of brain-biased genes across organs

Phenotypic variation among individuals provides the raw material for evolution, and gene expression is a key mediator between genetic and phenotypic variation. As for phenotypes, the range of gene expression is limited and biased by evolutionary and developmental constraints. Observed expression variability due to biomolecular stochasticity and cell-to-cell heterogeneity has been well-studied in isogenic populations of unicellular organisms. However, for multicellular organisms with a diversity of cells and tissues sharing the same genetic background, the interplay between expression variability, gene and organ function, and gene regulation remains an open question. Here, we use highly multiplexed 3-end bulk RNA sequencing to generate transcriptome profiles spanning at least nine organs in outbred individuals of three ray-finned fish species: zebrafish, Northern pike, and spotted gar. Per organ, we quantify individual-to-individual gene expression variability independent of mean expression level. Lowly variable genes are enriched in cellular housekeeping functions whereas highly variable genes are enriched in stimulus-response functions. Furthermore, highly variable genes evolve under weaker purifying selection at the protein-coding sequence, indicating that intra-species expression variability predicts inter-species protein sequence divergence. Genes that are broadly expressed across organs are both highly expressed and lowly variable, whereas organ-biased genes are typically highly variable within their top organ. Among organ-biased genes, patterns of expression variance are dependent on the top organ. Specifically, brain- and gonads-biased genes have lowly variable expression across different organs, suggesting stabilizing selection. These patterns suggest that gene regulatory mechanisms evolve under organ-specific selective pressures.

evolutionary biology↗

bioRxiv2024

Evolution of venom production in marine predatory snails

Venom-secreting glands are highly specialised organs evolved throughout the entire animal kingdom to synthetise and secrete toxins for predation and defence. Venom is extensively studied for its toxin components and application potential; yet, how animals become venomous remains poorly understood. Venom systems therefore offer a unique opportunity to understand the molecular mechanisms underlying functional innovation. Here, we conducted a multi-species multi-tissue comparative transcriptomics analysis of 12 marine predatory gastropods, including species with venom glands and species with homologous non-venom producing glands, to examine how specialised functions evolve through gene expression changes. We found that while the venom gland specialised for the mass production of toxins, its homologous glands retained the ancestral digestive functions. The functional divergence and specialisation of the venom gland was achieved through a redistribution of its ancestral digestive functions to other organs, specifically the oesophagus. This entailed concerted expression changes and accelerated transcriptome evolution across the entire digestive system. The increase in venom gland secretory capacity was achieved through the modulation of an ancient secretory machinery, particularly genes involved in endoplasmic reticulum stress and unfolded protein response. This study shifts the focus from the well-explored evolution of toxins to the lesser-known evolution of the organ and mechanisms responsible for venom production. As such, it contributes to elucidating the molecular mechanisms underlying organ evolution at a fine evolutionary scale, highlighting the specific events that lead to functional divergence.

evolutionary biology↗

bioRxiv2024

Moult cycle and setal development of the Atlantic ditch shrimp Palaemon varians Leach, 1814

The Atlantic ditch shrimp Palaemon varians Leach, 1814 is a common estuarine and brackish water species on Northern Atlantic coasts. Palaemon varians is an appealing model organism for studying arthropod developmental processes, such as moulting (ecdysis). Detailed morphological information on its moult cycle is still lacking, hence we have characterised the changes in the setal features corresponding to the moult stages of P. varians grown under laboratory conditions. The stages of the moult cycle were differentiated and described using microscopic analysis of the setae in the uropods of P. varians based on Drachs classification system. Moult stages were defined as early and late post-moult (A and B), inter-moult (C), early-, mid- and late pre-moult (D0, D1, and D2), as well as ecdysis stage (E), the actual shedding of the exuvia. Average moult cycle duration was 8.7 days, where pre-moult accounted for the longest duration of 4.4 days on average. This study provides a morphological reference for determining the moult stage of P. varians without the use of invasive techniques, and thus it is well suited for repetitive observations of an individual to track the entire moulting process.

developmental biology↗

bioRxiv2024

Estimates of molecular convergence reveal pleiotropic genes underlying adaptive variation across teleost fish

Molecular convergence, where specific non-synonymous changes in protein-coding genes lead to identical amino acid substitutions across multiple lineages, provides strong evidence of adaptive evolution. Detecting this signal across diverse taxa can reveal broad evolutionary mechanisms that may not be apparent when studying individual lineages. In this study, we search for convergent substitutions in the most speciose group of vertebrates, teleost fishes. Using an unsupervised approach, we detected convergence in 89 protein-coding genes across 143 chromosomal-level genomes. To assess their functional implications, we integrate data on protein properties, gene expression across species and tissues, single-cell RNA sequencing of zebrafish embryonic development, and gene perturbation experiments in zebrafish. The convergent genes were associated with diverse processes including embryonic development, tissue morphogenesis, metabolism, and responses to hormones and heat stress. The convergent substitutions altered amino acid properties, with some occurring at functionally critical sites. Notably, only one-third of these genes were tissue-specific, while the majority were expressed across multiple tissues and cell types. Genetic perturbation data further showed that the convergent genes can affect multiple structures across diverse tissues. These results highlight the pleiotropic nature of the convergent genes. Using an evolutionary modeling approach, we show that adaptive variation tends to accumulate in genes with intermediate pleiotropy, enabling organisms to overcome selective pressures during ecological shifts. Although traditionally considered a source of constraint, we argue that adaptation via genes with intermediate pleiotropy might be particularly advantageous following periods of ecological shifts, and can potentially lead to the evolution of convergent phenotypes.

evolutionary biology↗

bioRxiv2023

Phylogenetic modeling provides evidence for sudden shifts in expression after small-scale duplication in vertebrates and strong support for the ortholog conjecture

Gene duplication is a potential source of innovation, but the evolutionary dynamics of functional change are still poorly understood. Under the debated "ortholog conjecture", most functional change and innovation is assumed to follow duplication. Testing the ortholog conjecture allows to better understand and characterize the way in which gene function evolves. Most models of functional evolution assume continuous change, an assumption which we challenge here. We have applied a Levy model of evolutionary trait jumps to the evolution of gene expression in vertebrates, with a special focus on duplication in teleost fishes. We show for the first time that trait jumps strongly affects paralogs, in addition to other modes of functional evolution. We find that at least 25% of teleost fish small-scale duplicates follow a rapid evolutionary rate shift model for both expression level and tissue-specificity, much more than after speciations. However, genome-wide duplicates (ohnologs) do not support such a trait jump model, and thus follow a different evolutionary dynamic. While there is some evidence for more positive selection at the protein-coding level after duplication, it is not strongly linked to jumps in expression. Finally, both small-scale paralogs and ohnologs strongly support the ortholog conjecture by contrasting speciation branches pre- and post-duplication to the duplication branches themselves, with trait jumps explaining much of the higher phylogenetic independent contrasts between small-scale paralogs. Significance statementThe debate on the ortholog conjecture, i.e. that gene function changes little between orthologs but changes frequently between paralogs, provides a framework to understand better the evolution of gene function. Here we add two pieces to the puzzle: a novel way to use phylogenetic contrasts to test the ortholog conjecture, by comparing not only duplication to speciation, but speciation according to whether they were preceded by a duplication; and a model of jumps rather than continuous change of gene function. We tested these on vertebrates, with emphasis on teleost fishes, distinguishing small-scale duplications and whole-genome duplication; in all cases we support strongly the ortholog conjecture. We find that trait jumps strongly affect small-scale paralogs but not genome duplication paralogs, providing an exciting new model for gene function evolution.

evolutionary biology↗