Biology subjects

Forni, G.

Publications and source records attributed to Forni, G..

5 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↗

bioRxiv2024

Hepatic iNKT cells facilitate colorectal cancer metastasis by inducing a fibrotic niche in the liver

The liver is an important metastatic organ that contains many innate immune cells, yet little is known about their role in anti-metastatic defense. We investigated how invariant natural killer T (iNKT) cells influence colorectal cancer-derived liver metastasis using different models in immunocompetent mice. We found that hepatic iNKT cells promote metastasis by creating a supportive niche for disseminated cancer cells. Mechanistically, iNKT cells respond to disseminating cancer cells by producing the fibrogenic cytokines IL-4 and IL-13 in a TCR-independent manner. Selective abrogation of IL-4 and IL-13 sensing in hepatic stellate cells prevented their transdifferentiation into extracellular matrix-producing myofibroblasts, which hindered metastatic outgrowth of disseminated cancer cells. This study highlights a novel tumor-promoting axis driven by iNKT cells in the initial stages of metastasis.

immunology↗

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↗

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↗