Biology subjects

Luchetti, A.

Publications and source records attributed to Luchetti, A..

10 recordsLinked to original sources

bioRxiv2026

Under pressure: Evolutionary trade-offs shape the single visual opsin of deep-sea octopods

Octopods possess remarkable camera-type eyes and specialised image-forming vision that support orientation, prey detection, predator avoidance and visual communication. Unlike vertebrates and arthropods, however, octopod vision is thought to rely mainly on a single rhodopsin (r-opsin1), raising the question of how such a constrained system adapts across contrasting light environments from shallow coastal waters to deep-sea habitats. Using transcriptional profiling of the retina and optic lobe from seven native octopod species of the Gulf of Naples, we show that r-opsin1 is the predominant visual gene across all species and investigate how contrasting photic habitats have shaped its molecular and functional evolution. Although positive selection analyses revealed no general association between habitat depth and r-opsin1 evolution, twelve codons in the deep-mesopelagic Pteroctopus tetracirrhus r-opsin1 showed evidence of positive selection, including two residues located on opposing helices of the retinal-binding pocket. In vitro experiments demonstrated that substituting either I87V and F201N produced a marked bathochromatic shift from the wild-type blue-green spectrum towards red wavelengths, whereas their combination restored the wild-type spectral profile. Other deep-sea octopod r-opsin1 naturally bearing one of these substitutions retained blue-green sensitivity. Reconstructed ancestral proteins similarly maintained blue-green absorption, supporting conservation of this spectral phenotype throughout octopod r-opsin1 evolution. We further show that F201N reduces adiabatic compressibility within the retinal-binding pocket, by co-evolving compensatory sites offering a structural trade-off, favouring pressure adaptation while restraining spectral tuning. Together, our findings support that octopod visual rhodopsin evolution has been shaped by the multiple ecological pressures of contrasting marine environments, illustrated with lineage-specific and habitat-dependent trajectories on a single locus while preserving a conserved visual phenotype.

evolutionary biology↗

bioRxiv2026

Transposable element activity and polymorphisms drive structural variability within and between individual in bivalves

Structural variants (SVs) represent one of the most abundant sources of genetic variation across eukaryotes, with transposable elements (TEs) standing out as primary contributors in their emergence. While the growing availability of chromosome-scale genomes has revealed the central role of SVs in species diversification and adaptation, non-model invertebrates remain critically understudied in this context. Here, we explore how SVs and their interaction with TEs shape genetic diversity at both the individual and population levels. To achieve this, we leverage four high-quality oyster genomes and a large-scale dataset of the Estuarine oyster (Crassostrea ariakensis) collected across a wide range of different temperature and salinity conditions. We explicitly account for strengths and limitations of current SV-calling software, and benchmark our results through simulations. We uncover pervasive within-individual structural variability, with up to 14% of oyster genome basepairs being in an hemizygous state. The strong enrichment of TEs within these SVs is driven by a prevalence of insertions over deletions, reflecting population-level TE activity. Strikingly, both SVs and de novo TE insertions -- driven by the concurrent mobilization of diverse TE families -- segregate among C. ariakensis populations and contribute to genomic differentiation associated with local adaptation to contrasting sea salinity and temperature levels. Our study demonstrates the power of integrating long- and short-read sequencing to recover a high-confidence catalogue of SVs and de novo TE insertions, and provides empirical evidence that structural variation is an active evolutionary force generating potentially adaptive genetic variation in a key lineage of ecologically and economically important bivalves.

evolutionary biology↗

bioRxiv2025

Exploring the evolution of sex determination related genes through a cross-species genomics analysis

The molecular basis of sex determination (SD), while being extensively studied in model organisms, remains poorly understood in many animal groups. Bivalves, a diverse class of molluscs with a variety of reproductive modes, represent an ideal yet challenging clade for investigating SD and the evolution of sexual systems. However, the absence of a comprehensive framework has limited progress in this field, particularly regarding the study of sex-determination related genes (SRGs). In this study, we performed a genome-wide sequence evolutionary analysis of the Dmrt, Sox, and Fox gene families in more than 40 bivalve species. For the first time, we provide an extensive and phylogenetic-aware dataset of these SRGs, and we find support to the hypothesis that Dmrt-1L and Sox-H may act as primary sex-determining genes, by showing their high levels of sequence diversity within the bivalve genomic context. To validate our findings, we studied the same gene families in two well-characterized systems, mammals and Drosophila. In the former, we found that the male sex-determining gene Sry exhibits a pattern of amino acid sequence diversity similar to that of Dmrt-1L and Sox-H in bivalves, consistent with its role of master SD regulator. In contrast, no such pattern was observed among genes of the fruit fly SD cascade, which is controlled by a chromosomic mechanism. Overall, our findings highlight similarities in the sequence evolution of some mammal and bivalve SRGs, possibly driven by a comparable architecture of SD cascades. This work underscores once again the importance of employing a comparative approach when investigating understudied and non-model systems.

evolutionary biology↗

bioRxiv2023

The molecular groundplan of male reproduction is partially preserved in parthenogenetic stick insects.

After the loss of a trait, theory predicts that the molecular machinery underlying its phenotypic expression should decay. Yet, empirical evidence is contrasting. Here, we test the hypotheses that (1) the molecular ground plan of a lost trait could persist due to pleiotropic effects on other traits and (2) that gene co-expression network architecture could constrain individual gene expression. Our testing ground has been the Bacillus stick insect species complex, which contains close relatives that are either bisexual or parthenogenetic. After the identification of genes expressed in male reproductive tissues in a bisexual species, we investigated their gene co-expression network structure in two parthenogenetic species. We found that gene co-expression within the male gonads was preserved in parthenogens. Furthermore, parthenogens did not show relaxed selection on genes upregulated in male gonads in the bisexual species. As these genes were mostly expressed in female gonads, this preservation could be driven by pleiotropic interactions and an ongoing role in female reproduction. Connectivity within the network also played a key role, with highly connected - and more pleiotropic - genes within male gonad also having a gonad-biased expression in parthenogens. Our findings provide novel insight into the mechanisms which could underlie the production of rare males in parthenogenetic lineages; more generally, they provide an example of the cryptic persistence of a lost trait molecular ground plan, driven by gene pleiotropy on other traits and within their co-expression network. SignificanceLoss of traits commonly occurs in diverse lineages of organisms. Here we investigate what happens to genes and regulatory networks associated with these traits, using parthenogenetic insect species as a model. We investigated the fate of genes and gene regulatory networks associated with male gonads in a bisexual species in closely related parthenogens. Rather than showing signs of disuse and decay, they have been partially preserved in parthenogens. More highly pleiotropic genes in male gonads were more likely to have a gonad-biased expression profile in parthenogens. These results highlight the role of pleiotropy in the cryptic persistence of a trait molecular ground plan, despite its phenotypical absence.

evolutionary biology↗

bioRxiv2023

Evolution of alternative reproductive systems in Bacillus stick insects

Reproduction is a key feature of all organisms, yet the way in which it is achieved varies greatly across the tree of life. One striking example of this variation is the stick insect genus Bacillus, in which five different reproductive modes have been described: sex, facultative and obligate parthenogenesis, and two highly unusual reproductive modes: hybridogenesis and androgenesis. Under hybridogenesis, the entire genome from the paternal species is eliminated, and replaced each generation by mating with the corresponding species. Under androgenesis, an egg is fertilized but the developing diploid offspring bear two paternal genomes, and no maternal genome, as a consequence of unknown mechanisms. Here, we re-evaluate previous descriptions of Bacillus lineages and the proposed F1 hybrid ancestries of the hybridogenetic and obligately parthenogenetic lineages (based on allozymes and karyotypes) from Sicily, where all these reproductive modes are found. We generate a chromosome-level genome assembly for a facultative parthenogenetic species (B. rossius) and combine extensive field sampling with RADseq and mtDNA data. We identify and genetically corroborate all previously described species and confirm the ancestry of hybrid lineages. All hybrid lineages have fully retained their F1 hybrid constitution throughout the genome, indicating that the elimination of the paternal genome in hybridogens is always complete and that obligate parthenogenesis in Bacillus hybrid species is not associated with an erosion of heterozygosity as known in other hybrid asexuals. Our results provide a stepping stone towards understanding the transitions between reproductive modes and the proximate mechanisms of genome elimination.

evolutionary biology↗

bioRxiv2021

A Locus Coeruleus- dorsal CA1 dopaminergic circuit modulates memory linking

Individual memories are often linked so that the recall of one triggers the recall of another. For example, contextual memories acquired close in time can be linked, and this is known to depend on temporary increase in excitability that drive the overlap between dorsal CA1 (dCA1) hippocampal ensembles encoding the linked memories. Here, we show that the Locus Coeruleus (LC) cells projecting to dCA1 have a key permissive role in contextual memory linking, without affecting contextual memory formation, and that this effect is mediated by dopamine and not by noradrenaline. Additionally, we found that LC to dCA1 projecting neurons modulate the excitability of dCA1 neurons, and the extent of overlap between dCA1 memory ensembles, as well as the stability of coactivity patterns within these ensembles. This discovery of a neuromodulatory system that specifically affects memory linking without affecting memory formation, reveals a fundamental separation between the brain mechanisms that modulate these two distinct processes.

neuroscience↗

bioRxiv2021

Shared and unique properties of place cells in anterior cingulate cortex and hippocampus

Hippocampal sharp-wave ripples (SWRs) and the associated replay of neuronal sequences are well-established as the primary physiological substrates for memory consolidation. While the local transformations they induce within the hippocampus are well-characterized, their impact on the downstream cortical representations remains unknown. Here, we identify a distinct functional class of neurons in the anterior cingulate cortex "spatial context cells" that emerge through the multi-day integration of discrete hippocampal inputs. Using closed-loop disruption of SWRs and longitudinal calcium imaging, we demonstrate that formation of this global spatial framework depends on SWRs during offline periods. Whereas standard cortical place maps remain intact following SWR disruption, the emergence of spatial context cells is selectively abolished. These cells preferentially express c-Fos, identifying them as constituents of the cortical memory engram, and exhibit broad receptive fields that develop through an experience-dependent process of field convergence. Collectively, these findings establish SWR-mediated replay as a computational bridge transforming high-resolution, fragmented hippocampal spatial codes into generalized, stable cortical schemas. This work reveals a bifurcated consolidation process, identifying SWR-dependent synaptic remodeling as a fundamental mechanism for the ontogeny of remote memory.

neuroscience↗

bioRxiv2020

BASE: a novel workflow to integrate non-ubiquitous genes in genomics analyses for selection.

Inferring the selective forces that different ortholog genes underwent across different lineages can make us understand the evolutionary processes which shaped their extant diversity. The more widespread metric to estimate coding sequences selection regimes across across their sites and species phylogeny is the ratio of nonsynonymous to synonymous substitutions (dN/dS, also known as{omega} ). Nowadays, modern sequencing technologies and the large amount of already available sequence data allow the retrieval of thousands of genes orthology groups across large numbers of species. Nonetheless, the tools available to explore selection regimes are not designed to automatically process all orthogroups and practical usage is often restricted to those consisting of single-copy genes which are ubiquitous across the species considered (i.e. the subset of genes which is shared by all the species considered). This approach limits the scale of the analysis to a fraction of single-copy genes, which can be as lower as an order of magnitude in respect to non-ubiquitous ones (i.e. those which are not present across all the species considered). Here we present a workflow named BASE that - leveraging the CodeML framework - ease the inference and interpretation of selection regimes in the context of comparative genomics. Although a number of bioinformatics tools have already been developed to facilitate this kind of analyses, BASE is the first to be specifically designed to ease the integration of non-ubiquitous genes orthogroups. The workflow - along with all the relevant documentation - is available at github.com/for-giobbe/BASE.

bioinformatics↗

bioRxiv2020

Macroevolutionary Analyses Provide New Evidences of Phasmids Wings Evolution as a Reversible Process.

AO_SCPLOWBSTRACTC_SCPLOWThe concept that complex ancestral traits can never be re-acquired after their loss has grown popular since its initial formulation and its often referred to as Dollos law. Nonetheless, several macroevolutionary evidences - along with molecular ones - suggest instances where complex phenotypes could have been lost throughout a clade evolutionary history and subsequently reverted to their former state in derived lineages. One of the first and most notable rejection of Dollos law is represented by wing evolution in phasmids: this polyneopteran order of insects - which comprises stick and leaf insects - has played a central role in initiating a long-standing debate on the topic. In this study, a novel and comprehensive time-tree - including over 300 Phasmatodea species - is used as a framework for investigating wings evolutionary patterns in the clade. Despite accounting for several possible biases and sources of uncertainty, macroevolutionary analyses consistently support a dynamic and reversible evolution of wings, with multiple transitions to ancestral states taking place after their loss. Our findings suggest that wings and flight are decoupled from Phasmatodea diversification dynamics and that brachyptery is an unstable state, unless when co-opted for non-aerodynamic adaptations. We also explored how different assumptions of wings reversals probability could impact their inference: we found that until reversals are assumed to be over 30 times more unlikely than losses, they are consistently retrieved despite uncertainty in tree and model parameters. Our findings demonstrate that wings evolution can be a reversible and dynamic process in phasmids and contribute to shape our understanding of how complex phenotypes evolve.

evolutionary biology↗

bioRxiv2020

Basal ganglia high-frequency activity is co-modulated with the phase of motor cortical beta and shifted between the subthalamic nucleus and the internal pallidum during sustained motor control

Beta oscillations are readily observed in motor cortex and the basal ganglia, but to which extent they are functionally relevant is unclear. To understand how activity transfer between different nodes of the cortico-basal ganglia network is affected by cortical beta oscillations in different behavioural conditions, we recorded local field potentials and electroencephalography (EEG) activity in a low-force motor control task and during rest in Parkinsons patients undergoing deep brain stimulation (DBS) surgery. The patients received DBS of either the subthalamic nucleus (STN) or the internal globus pallidus (GPi), which allowed us to investigate if STN and GPi broad-band high-frequency activity (HFA; >150 Hz) is co-modulated with the phase of motor cortical beta activity. We found significant modulation patterns in the STN and the GPi, which were inverted while patients performed the task, showing that GPi activity fluctuations likely are crafted by other inputs than the direct excitatory STN afferents. We also found that consistent STN modulation disappeared during rest, showing disengagement in this condition, while GPi modulation was maintained, again evidencing that beta-band activity fluctuations in the GPi can be relatively independent of those in the STN. The difference between HFA modulation patterns in the task and rest recordings suggests a potential functional role of beta phase-locked HFA modulation in controlling sustained contractions. Examination of HFA co-modulation patterns at different sites of the cortico-basal ganglia-thalamo-cortical network under different behavioural conditions may provide a tool with which to define the impact of beta synchronization on network communication.

neuroscience↗