Biology subjects

Policarpo, M.

Publications and source records attributed to Policarpo, M..

13 recordsLinked to original sources

bioRxiv2026

Early origin of sugar sensing in jawed vertebrates

Sweet taste guides animals to consume carbohydrate-rich foods, and many different vertebrate groups, from fish to mammals, rely on sugar-rich fruits or nectar produced by flowering plants (angiosperms). Although the genes encoding T1R2-T1R3, the receptor pair that mammals use to sense sugars, exist in the genomes of many vertebrates, their functions are unclear--and whether sugar sensing arose once early in vertebrate evolution or independently in different lineages after angiosperms evolved is currently unknown. Here, we combined ancestral reconstruction and receptor functional profiling to examine the evolutionary history of T1R taste receptors--including recently-described non-canonical receptors--across all major vertebrate clades. Our results pinpoint the origin of sugar sensing to before the emergence of angiosperms and uncover a myriad of alternative T1R-based sugar-sensing mechanisms, suggesting multiple independent T1R trajectories and revealing uncharted sensory diversity across vertebrates.

evolutionary biology↗

bioRxiv2026

Cell-type Plasticity Supports Behavioral Adaptations at the Water-to-Land Interface

Animals inhabiting aquatic or terrestrial habitats experience different constraints on their physiology and locomotion, and are exposed to fundamentally different sensory environments. Across evolutionary timescales, most species have adapted to live exclusively either in water or on land. Newts are among the vertebrates that defy this rule and split their adult lives between freshwater ponds and terrestrial habitats. In these amphibians, transitions across environments cause remarkable phenotypic plasticity in their body morphology. But whether and how the nervous system and behavior also adapt to these environmental changes remains poorly explored. Here, we establish the Iberian ribbed newt Pleurodeles waltl as a new model to study the neurobiology of environmental plasticity in a vertebrate. We first show that experimental transitions between aquatic and terrestrial laboratory settings recapitulate morphological changes observed in the wild. Furthermore, aquatic and terrestrial newts display plasticity in sensory and motor behaviors, including differences in walking gait and odor responsiveness. In the olfactory system, the transition from water to land involves a profound remodeling of the nasal epithelium, including reversible transcriptomic changes in secretory and support cells, and an increase of neurogenesis. Together, our findings reveal how plasticity of specific cell types in the nervous system supports behavioral adaptations across environments. More broadly, this work establishes newts as a model to study the functional constraints and convergent adaptations that may have shaped the evolution of vertebrate nervous systems in water and on land.

neuroscience↗

bioRxiv2025

Evolutionary dynamics of the vertebrate Wnt gene repertoire

The Wnt gene family plays a central role in vertebrate development, yet its evolutionary dynamics across lineages remain largely unexplored. Here, we present the most comprehensive analysis of Wnt gene evolution in vertebrates to date, leveraging a large-scale comparative genomics approach of 38,886 Wnt gene sequences mined from 1,961 species. We first investigate overall patterns of gene retention, duplication, and loss, and then focus specifically on the impact of whole-genome duplications (WGDs). We uncover striking variation in Wnt gene repertoire sizes, with ray-finned fishes (Actinopterygii) exhibiting the largest repertoires - even after excluding taxa with recent WGDs. Notably, we identify extreme expansions in polyploid cyprinids, including an octoploid hybrid harbouring 99 Wnt genes, the highest number observed. Unexpectedly elevated Wnt copy numbers in diploid species, such as the Antarctic lanternfish (Electrona antarctica) and the brook lamprey (Lethenteron reissneri), point to lineage-specific expansions with potential adaptive significance. Evolutionary rate analyses reveal that certain Wnt clades - especially Wnt8 and Wnt16 - exhibit elevated dN/dS ratios and high birth-death rates, indicative of repeated episodes of relaxed constraint or adaptive diversification. Contrary to our expectations, there was no relationship between developmental expression timing and evolutionary rates, suggesting pleiotropic regulation and functional redundancy of Wnt genes. Altogether, our findings reveal pervasive, lineage-specific remodelling of Wnt gene repertoires, shaped by both genome duplication history and divergent evolutionary trajectories. This work provides a high-resolution framework for understanding the molecular evolution of a key developmental toolkit and highlights candidate genes for future studies of vertebrate eco-morphological diversity.

evolutionary biology↗

bioRxiv2025

The visual system of the longest-living vertebrate, the Greenland shark

The Greenland shark (Somniosus microcephalus) is the longest-living vertebrate and inhabits the extremely dim and cold waters of the Arctic deep sea. This has led to speculations that it may have lost functional vision. Here, we present genomic, transcriptomic, histological and functional evidence that the Greenland shark retains an intact visual system well-adapted for life in dim light. Histology and in vitro opsin expression revealed visual adaptations typical of deep-sea species, including densely packed, elongated rods and a short-wavelength shift in rod visual pigment sensitivity. RNAscope confirmed the presence of essential visual cell types, such as rods, Muller glia, and bipolar, amacrine, and ganglion cells. Moreover, despite being centuries old, the examined specimens showed no signs of retinal degeneration. Using whole genome and retinal RNA-sequencing, we further show that dim-light (rod-based) vision genes are intact and robustly expressed, while many bright-light (cone-based) vision genes have become pseudogenized and/or are no longer expressed. Finally, our data suggest that efficient DNA repair mechanisms may contribute to the long-term preservation of retinal function over centuries in the Greenland shark.

evolutionary biology↗

bioRxiv2024

Strong evidence for multiple horizontal transfers of immune genes between teleost fishes

Horizontal gene transfer (HGT) is less frequent in eukaryotes than in prokaryotes, yet can have strong functional implications and was proposed as causal factor for major adaptations in several eukaryotic lineages. Most cases of eukaryote HGT reported to date are inter-domain transfers and only few studies have investigated eukaryote-to-eukaryote HGTs. Furthermore, the extent to which HGT has contributed to the gene repertoire of some lineages such as vertebrates remains unclear. Here, we performed a large-scale survey of HGT among 242 species of ray-finned fishes. We found strong evidence supporting 18 teleost-to-teleost HGT events that involve 17 different genes in 11 teleost fish orders. The genes involved in these transfers show lower synonymous divergence than expected under vertical transmission, their phylogeny is inconsistent with that of teleost fishes, and high nucleotide similarity on these genes between donor and recipient lineages extends to non-coding regions. The distribution of HGT events in the teleost tree is heterogenous, with eight of the 18 transfers occurring between the same two orders (Osmeriformes and Clupeiformes). Besides the previously reported transfer of an antifreeze protein, most transferred genes play roles in immunity, suggesting that such genes are more likely than others to confer strong selective advantage to the recipient species. Overall, our work shows that teleost-to-teleost HGT has occurred on multiple occasions and it will be worth further quantifying these transfers and evaluating their impact on teleost evolution as more genomes are being sequenced.

evolutionary biology↗

bioRxiv2024

Evolution of the non-visual and visual opsin gene repertoire in ray-finned fishes

Photoreception - the detection of light for image formation (vision) as well as for non-image-forming purposes (circadian regulation, DNA repair) - is critical to the survival of most animals. In vertebrates, photoreception is mediated by opsin proteins, which are classified, according to their function, into visual and non-visual opsins. Here, we provide the most comprehensive study to date on the evolution of the opsin gene family in the largest class of vertebrate, fishes, with a particular focus on the understudied non-visual opsins. Based on an in-depth analysis of 535 high-quality genomes, we document great variation in gene numbers in the different opsin gene subfamilies across ray-finned fishes and show that visual opsins are more prone to duplications and losses than non-visual opsins. We provide compelling evidence that visual and non-visual opsins co-evolve in ray-finned fishes, both in terms of copy numbers and selective pressures acting on their coding sequences, probably in response to the different photic environments they inhabit. Species that live in dim light or all in the dark (such as in caves or the deep sea) convergently reduced their visual and non-visual opsin gene repertoires, while polar species feature accelerated evolution in both. Fishes that rely on electroreception show a reduction in the number of visual and non-visual opsin genes and accelerated evolution of the remaining genes. We further found that genes of the phototransduction cascade co-evolve with opsins. Finally, that non-visual opsins are mainly expressed in testes and ovaries (next to the eyes) supports a function in gamete biology.

evolutionary biology↗

bioRxiv2022

Genetic identification and reiterated captures suggests that the Astyanax mexicanus El Pachon cavefish population is closed and declining

The size of Astyanax mexicanus blind cavefish populations of North-East Mexico is a demographic parameter of great importance for investigating a variety of ecological, evolutionary and conservation issues. However, very few estimates have been obtained. For these mobile animals living in an environment difficult to explore as a whole, methods based on capture-mark-recapture are appropriate, but the feasibility of such approach and the interpretation of the results depend on several assumptions that must be carefully examined. Here, we provide evidence that minimally invasive genetic identification from captures at different time intervals can give insights on cavefish population size dynamics as well as other important demographic parameters of interest. We also provide tools to calibrate sampling and genotyping efforts necessary to reach a given level of precision. Our results suggest that the El Pachon cave population is currently very small, of an order of magnitude of a few hundreds of individuals, and is distributed in a relatively isolated area. The probable decline in population size in the El Pachon cave since the last census in 1971 raises serious conservation issues.

zoology↗

bioRxiv2022

Ancient and nonuniform loss of olfactory receptor expression renders the shark nose a de facto vomeronasal organ

Cartilaginous fishes are renowned for a keen sense of smell, a reputation based on behavioral observations and supported by the presence of large and morphologically complex olfactory organs. At the molecular level, genes belonging to the four families coding for most olfactory receptors in other vertebrates have been identified in a chimera and a shark, but it was unknown whether they actually code for olfactory receptors in these species. Here we describe the evolutionary dynamics of these gene families in cartilaginous fishes using genomes of a chimera, a skate, a sawfish and eight sharks. The number of putative OR, TAAR and V1R/ORA receptors is very low and stable whereas the number of putative V2R/OlfC receptors is higher and much more dynamic. In the catshark Scyliorhinus canicula, we show that many V2R/OlfC receptors are expressed in the olfactory epithelium in the sparsely distributed pattern characteristic for olfactory receptors. In contrast, the other three vertebrate olfactory receptor families are either not expressed (OR) or only represented with a single receptor (V1R/ORA and TAAR). The complete overlap of markers of microvillous olfactory sensory neurons with panneuronal marker HuC in the olfactory organ suggests the same cell type specificity of V2R/OlfC expression as for bony fishes, i.e. in microvillous neurons. The relatively low number of olfactory receptors in cartilaginous fishes compared to bony fishes could be the result of an ancient and constant selection in favor of a high olfactory sensitivity at the expense of a high discrimination capability.

evolutionary biology↗

bioRxiv2022

Evolution of the regulation of developmental gene expression in blind Mexican cavefish

Changes in gene expression regulation during development are considered the main drivers of morphological evolution and diversification. Here, we analysed the embryonic transcriptomes of surface-dwelling and blind cave-adapted morphs of the species Astyanax mexicanus and their reciprocal F1 hybrids at tailbud stage. Comparing gene expression in parents and allelic expression ratios in hybrids, we found that [~]20% of the transcriptome is differentially expressed and that cis-regulatory changes are the main contributors to variations in early developmental gene expression in the two morphs. We provide a list of 108 cis-regulated genes that could contribute to cavefish developmental evolution, and further explore the regulatory mechanisms controlling the cellular and regional expression of rx3, a "master eye gene". Using quantitative embryology approaches after fluorescent in situ hybridisation, cell transplantations and interference with signalling pathways, we show that rx3 cellular levels -controlling optic cell fates-are regulated in cis and in a cell-autonomous manner, whereas the size of rx3 domain -controlling eye size-depends on non-autonomous Wnt signalling. Altogether, we reveal how distinct mechanisms and regulatory modules can regulate developmental gene expression and shape developmental evolution, with negligible contribution of coding mutations.

developmental biology↗

bioRxiv2021

Coevolution of the olfactory organ and its receptor repertoire in ray-finned fishes

Ray-finned fishes (Actinopterygii) perceive their environment through a range of sensory modalities, including olfaction 1,2. Anatomical diversity of the olfactory organ suggests that olfaction is differentially important among species 1,3,4. To explore this topic, we studied the evolutionary dynamics of the four main gene families (OR, TAAR, ORA/VR1 and OlfC/VR2) 5 coding for olfactory receptors in 185 species of ray-finned fishes. The large variation in the number of functional genes, between 28 in the Ocean Sunfish Mola mola and 1317 in the Reedfish Erpetoichthys calabaricus, is the result of parallel expansions and contractions of the four main gene families. Several ancient and independent simplifications of the olfactory organ are associated with massive gene losses. In contrast, polypteriforms, which have a unique and complex olfactory organ, have almost twice as many olfactory receptor genes as any other ray-finned fish. These observations suggest a functional link between morphology of the olfactory organ and richness of the olfactory receptor repertoire. Further, our results demonstrate that the genomic underpinning of olfaction in ray-finned fishes is heterogeneous and presents a dynamic pattern of evolutionary expansions, simplifications and reacquisitions.

evolutionary biology↗

bioRxiv2021

Genomic evidence that blind cavefishes are not wrecks of ancient life

Cavefishes often have modified eyes, from small but otherwise functional, to highly degenerate structures embedded in a connective tissue and covered by skin. Darwin assumed that these animals are wrecks of ancient life, but several genomic studies suggests they are not ancient. The most radical dating shift is for populations of a Mexican cavefish, Astyanax mexicanus, that have been recently estimated to be at the most a few tens of thousands years old. Despite having highly degenerate eyes, the eye-specific genes of A. mexicanus have low levels of decay. Other blind cavefishes we have examined so far are even older, but also can be dated to the Pleistocene. Here, we estimated the age of blindness of two additional fish species by the level of decay of eye-specific genes. Many pseudogenes were identified in the amblyopsid Typhlichthys subterraneus, suggesting that blindness evolved a few million years ago. In contrast, the blind cichlid Lamprologus lethops appears to be a new case of very recent and rapid eye regression, which occurred in deep river water, an environment similar to caves. Genome-wide analyses support the hypothesis that blindness in cavefishes is never very ancient, and ranges from the Early Pliocene to Late Pleistocene. Together with the description of hundreds of cavefish species, our results suggest that surface fishes were able to recurrently and rapidly adapt to caves and similar small dark ecosystems but the resulting highly specialized blind species with a limited distribution may be evolutionary dead-ends in a relatively short time.

evolutionary biology↗

bioRxiv2021

Evolutionary dynamics of the OR gene repertoire in teleost fishes: evidence of an association with changes in olfactory epithelium shape

Teleost fishes perceive their environment through a range of sensory modalities, among which olfaction often plays an important role. Richness of the olfactory repertoire depends on the diversity of receptors coded by homologous genes classified into four families: OR, TAAR, VR1 and VR2. Herein, we focus on the OR gene repertoire. While independent large contractions of the OR gene repertoire associated with ecological transitions have been found in mammals, little is known about the diversity of the OR gene repertoire and its evolution within teleost fishes, a group that includes more than 34,000 living species. We analyzed genomes of 163 species representing diversity in this large group. We found a large range of variation in the number of functional OR genes, from 15 in Syngnathus typhle and Mola mola, to 429 in Mastacembelus armatus. The number of OR genes was higher in species with an extensively folded olfactory epithelium, that is, for example, when a multi-lamellar rosette was present in the olfactory organ. Moreover, the number of lamellae was correlated with the richness of the OR gene repertoire. While a slow and balanced birth-and-death process generally drives evolution of the OR gene repertoire, we inferred several episodes of high rates of gene loss, sometimes followed by large gains in the number of OR genes. These gains coincide with morphological changes of the olfactory organ and suggest a strong functional association between changes in the morphology and the evolution of the OR gene repertoire.

evolutionary biology↗

bioRxiv2020

Contrasted gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals

Evolution sometimes proceeds by loss, especially when structures and genes become dispensable after an environmental shift relaxing functional constraints. Gene decay can serve as a read-out of this evolutionary process. Animals living in the dark are outstanding models, in particular cavefishes as hundreds of species evolved independently during very different periods of time in absence of light. Here, we sought to understand some general principals on the extent and tempo of decay of several gene sets in cavefishes. The analysis of the genomes of two Cuban species belonging to the genus Lucifuga provides evidence for the most massive loss of eye genes reported so far in cavefishes. Comparisons with a recently-evolved cave population of Astyanax mexicanus and three species belonging to the tetraploid Chinese genus Sinocyclocheilus revealed the combined effects of the level of eye regression, time and genome ploidy on the number of eye pseudogenes. In sharp contrast, most circadian clock and pigmentation genes appeared under strong selection. In cavefishes for which complete genomes are available, the limited extent of eye gene decay and the very small number of loss of function (LoF) mutations per pseudogene suggest that eye degeneration is never very ancient, ranging from early to late Pleistocene. This is in sharp contrast with the identification of several eye pseudogenes carrying many LoF mutations in ancient fossorial mammals. Our analyses support the hypothesis that blind fishes cannot thrive more than a few millions of years in cave ecosystems.

evolutionary biology↗