Biology subjects

Di-Palma, F.

Publications and source records attributed to Di-Palma, F..

5 recordsLinked to original sources

bioRxiv2025

Evolution of chromatin accessibility associated with traits of cichlid phenotypic diversity

The radiations of cichlid fishes in East African Lakes Victoria, Malawi, and Tanganyika showcase a remarkable example of rapid adaptive speciation, with over 2000 species evolving diverse morphological and ecological adaptations within the last few million years. Understanding the molecular basis of this phenotypic diversity remains a key challenge. Building on prior evidence of gene regulatory network (GRN) rewiring underpinning adaptive traits, we profiled chromatin accessibility (ATAC-seq) and matched transcriptomes across forebrain, retina, liver, and testis tissues in five representative cichlid species using optimised protocols. We show extensive divergence in chromatin accessibility corresponding to phylogenetic lineages and tissue identity, with many regulatory regions exhibiting accelerated nucleotide evolution. Transcription factor binding site (TFBS) variation correlates with both chromatin accessibility and differential gene expression, particularly in genes linked to sensory systems. Building on this, we reconstructed tissue- and species-specific GRNs and show that motif-supported network inference reveals pervasive but tissue-dependent rewiring, with the strongest candidate edges concentrated among accessible, highly expressed genes linked to adaptive traits. By integrating TF footprinting with regulatory motif turnover analyses, we demonstrate that dynamic nucleotide changes are associated with GRN rewiring, concordant with ecological niche and lineage-specific adaptations. Our findings highlight that regulatory variation at conserved and novel TFBSs associates with genes linked to phenotypic innovation across radiating and non-radiating East African cichlids. This study provides foundational epigenomic evidence linking GRN divergence to key mechanisms facilitating rapid adaptive diversification in this iconic vertebrate radiation.

evolutionary biology↗

bioRxiv2019

A Galaxy-based training resource for single-cell RNA-seq quality control and analyses.

BackgroundIt is not a trivial step to move from single-cell RNA-seq (scRNA-seq) data production to data analysis. There is a lack of intuitive training materials and easy-to-use analysis tools, and researchers can find it difficult to master the basics of scRNA-seq quality control and analysis.\n\nResultsWe have developed a range of easy-to-use scripts, together with their corresponding Galaxy wrappers, that make scRNA-seq training and analysis accessible to researchers previously daunted by the prospect of scRNA-seq analysis. The simple command-line tools and the point-and-click nature of Galaxy makes it easy to assess, visualise, and quality control scRNA-seq data.\n\nConclusionWe have developed a suite of scRNA-seq tools that can be used for both training and more in-depth analyses.

bioinformatics↗

bioRxiv2018

Evolution of regulatory networks controlling adaptive traits in cichlids

Seminal studies of vertebrate protein evolution speculated that gene regulatory changes can drive anatomical innovations. However, very little is still known about gene regulatory network (GRN) evolution associated with phenotypic effect across ecologically-diverse species. Using a novel approach to reconstruct GRNs in vertebrate species, we aimed to study GRN evolution in representative species of the most striking example of an adaptive radiation, the East African cichlids. We previously demonstrated how the explosive phenotypic diversification of East African cichlids is attributed to diverse molecular mechanisms, including accelerated regulatory sequence evolution and gene expression divergence. To investigate these mechanisms across species at a genome-wide scale, our novel network-based approach identifies ancestral and extant gene co-expression modules along a phylogeny, and by integrating associated regulators, predicts candidate regulatory regions implicated in traits under selection in cichlids. As a case study, we present data from a well-studied adaptive trait - the visual system - for which we report striking cases of network rewiring for visual opsin genes, identify discrete regulatory variants, and investigate the plausibility of their association with cichlid visual system evolution. In regulatory regions of visual opsin genes, in vitro assays confirm that transcription factor binding site mutations disrupt regulatory edges across species, and segregate according to lake species phylogeny and ecology, suggesting GRN rewiring in radiating cichlids. Our approach revealed numerous novel potential candidate regulatory regions across cichlid genomes with no prior association, as well as those with previously reported associations to known adaptive evolutionary traits, thus providing proof of concept.

evolutionary biology↗

bioRxiv2018

Analysis of structural variants in four African cichlids highlights an association with developmental and immune related genes

African Lakes Cichlids are one of the most impressive example of adaptive radiation. Independently in Lake Victoria, Tanganyika, and Malawi, several hundreds of species arose within the last 10 million to 100,000 years. Whereas most analyses in Cichlids focused on nucleotide substitutions across species to investigate the genetic bases of this explosive radiation, to date, no study has investigated the contribution of structural variants (SVs) to speciation events (through a reduction of gene flow) and adaptation to different ecological niches. Here, we annotate and characterize the repertoires and evolutionary potential of different SV classes (deletion, duplication, inversion, insertions and translocations) in five Cichlid species (Haplochromis burtoni, Metriaclima zebra, Neolamprologus brichardi, Pundamilia nyererei and Oreochromis niloticus). We investigate the patterns of gain/loss across the phylogeny for each SV type enabling the identification of both lineage specific events and a set of conserved SVs, common to all four species in the radiation. Both deletion and inversion events show a significant overlap with SINE elements, while inversions additionally show a limited, but significant association with DNA transposons. Inverted regions are enriched for genes regulating behaviour, or involved in skeletal and visual system development. We also find that duplicated regions show enrichment for genes associated with \"antigen processing and presentation\" (GO:0019882) and other immune related categories. Altogether, we provide the first, comprehensive overview of rearrangement evolution in East African Cichlids, and some initial insights into their possible contribution to adaptation.

evolutionary biology↗

bioRxiv2018

Genomic architecture and introgression shape a butterfly radiation

We here pioneer a low-cost assembly strategy for 20 Heliconiini genomes to characterize the evolutionary history of the rapidly radiating genus Heliconius. A bifurcating tree provides a poor fit to the data, and we therefore explore a reticulate phylogeny for Heliconius. We probe the genomic architecture of gene flow, and develop a new method to distinguish incomplete lineage sorting from introgression. We find that most loci with non-canonical histories arose through introgression, and are strongly underrepresented in regions of low recombination and high gene density. This is expected if introgressed alleles are more likely to be purged in such regions due to tighter linkage with incompatibility loci. Finally, we identify a hitherto unrecognized inversion, and show it is a convergent structural rearrangement that captures a known color pattern switch locus within the genus. Our multi-genome assembly approach enables an improved understanding of adaptive radiation.

evolutionary biology↗