Biology subjects

Joyce, D.

Publications and source records attributed to Joyce, D..

8 recordsLinked to original sources

bioRxiv2026

Genome-wide chromatin accessibility during early embryogenesis in a generalist cichlid fish

Background Lake Malawi's haplochromine cichlids are one of the most rapid and species-rich vertebrate adaptive radiations known, generating hundreds of species within < 1 million years, yet how regulatory regions shape their embryonic development remains poorly understood. Astatotilapia calliptera, a generalist riverine lineage and proxy for the ancestral stock that seeded this radiation, offers a developmental chromatin baseline against which regulatory divergence in specialised lineages can be compared. Results We generated genome-wide ATAC-seq profiles of A. calliptera embryos across three developmental stages (3, 7 and 12 days post-fertilisation, dpf), identifying 550,876-701,889 accessible chromatin peaks per stage. Accessible chromatin was enriched at gene promoters and at both highly conserved and accelerated conserved noncoding elements at every stage. The functional repertoire of accessible-promoter genes shifted across development, from early patterning at 3 dpf to the broadest regulatory repertoire at 7 dpf, and an increasingly neural- and locomotory-behaviour-enriched repertoire by 12 dpf, coinciding with post-hatching motor maturation. Differential accessibility showed that chromatin opening, rather than closing, dominates the earliest transitions (3 vs 7 and 3 vs 12 dpf), driven mostly by general metabolic genes, whereas the smaller, later 7 vs 12 dpf transition combined targeted gains at tissue-remodelling and apoptosis genes with losses at genes governing early neural and retinal patterning; almost all of these losses (96%) were at promoters that had opened between 3 and 7 dpf, indicating transient rather than sustained opening. Transcription factor (TF) footprinting identified stage-specific regulatory activity among developmentally important TFs, while the broader TF-promoter network remained topologically stable across all three stages, built around conserved hub regulators of core neural and sensory patterning genes e.g., SOX2, FOXG1, PTF1A, SOX10. This suggests that wiring is established early and largely maintained, following the hourglass model, with developmental progression driven by changes in activity of this conserved programme. Conclusions Together, these findings establish the first embryonic epigenomic resource for A. calliptera, revealing a developmental chromatin landscape of broad early opening and progressive functional specialisation, and providing a comparative framework for understanding how regulatory evolution has shaped Lake Malawi cichlid diversification.

genomics↗

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↗

bioRxiv2025

Serotonin inhibits sexual receptivity in female cichlid fish

Serotonin is involved in multiple diverse and complex biological processes. Selective serotonin reuptake inhibitors (SSRIs) are often used to test this, and fluoxetine, a commonly detected SSRI in aquatic ecosystems from pharmaceutical pollution, has been found to disrupt important behaviours and functions in organisms exposed to the antidepressant. Increased serotonin generally has an inhibitory effect on sexual behaviour and decreased serotonin has a facilitatory effect, however in the few existing studies on fish, either no effect or the opposite effect have been reported in females, with most studies focusing on male behaviour. The present research aims to examine the role of the serotonin pathway in female sexual receptivity in the cichlid fish Nyassachromis cf. microcephalus. The sexual dimorphism and lekking system of this species, where male-male competition is aggressive and female choice is important, make them an important and interesting evolutionary system. Serotonin levels were modulated using fluoxetine and after a three-week exposure to their respective treatments (control - 0{micro}g/L, low ecologically relevant dose - 0.54{micro}g/L, high dose - 5.4{micro}g/L), female sexual receptivity to male courtship was measured in a simulated lek mating arena where multiple males were presented simultaneously. Sexual receptivity was inhibited in females exposed to a high dose of fluoxetine. This behaviour change due to a disruption of the serotonin pathway could affect sexual selection in the long term, and in the short term highlights the potential for pollution to affect aquatic life by directly altering mating behaviour. Highlights- Disrupting the serotonin pathway reduces sexual receptivity in female cichlid fish - The inhibitory effect of fluoxetine on female receptivity is dose-dependent - The serotonin pathway could be important in the evolution of male mating strategies - SSRI pollution could cause behaviour changes that amplify freshwater biodiversity loss

animal behavior and cognition↗

bioRxiv2024

Who Grows There? A Course-based Undergraduate Research Experience to explore the human microbiome through 16S DNA metabarcoding

We describe a two week Course-based Undergraduate Research Experience (CURE) to introduce students to next-generation DNA sequencing, molecular biology methods and a bioinformatic workflow. The CURE is designed to take students with little to no technical and bioinformatic experience through key steps of the protocol through scaffolded laboratory and computational practicals. Our students extract and amplify human microbiome DNA using 16S ribosomal RNA specific primers, then construct a sequencing library for Oxford Nanopore based sequencing. They taxonomically assign the sequencing reads, and determine the ecological community composition using relevant software packages. Our students were able to successfully prepare sequencing libraries and analyse the data to produce relevant figures, demonstrating they met the learning objectives of the CURE. Students identified that they had developed higher level learning as defined by Blooms taxonomy, and that their confidence in practical work significantly increased as a result of doing the CURE. We share recommendations for implementation of the CURE in undergraduate curricula, and adaptations of the methods for use in schools outreach. Our CURE successfully provides training for students in genetic analysis in an enjoyable and relatively time and cost efficient manner, preparing them for future research or careers in modern molecular biology techniques.

scientific communication and education↗

bioRxiv2024

Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes

East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. Orthology inference revealed an expansion of piwil1 genes in Lake Malawi cichlids, likely driven by PiggyBac TEs. The expanded piwil1 copies have signatures of positive selection and retain amino acid residues essential for catalytic activity. Furthermore, the gonads of African cichlids express a Piwi-interacting RNA (piRNA) pathway that target TEs. We define the genomic sites of piRNA production in African cichlids and find divergence in closely related species, in line with fast evolution of piRNA-producing loci. Our findings suggest dynamic co-evolution of TEs and host silencing pathways in the African cichlid radiations. We propose that this co-evolution has contributed to cichlid genomic diversity.

evolutionary biology↗

bioRxiv2024

High-resolution single particle imaging at 100-200 keV with the Gatan Alpine direct electron detector.

Developments in direct electron detector technology have played a pivotal role in enabling high-resolution structural studies by cryo-EM at 200 and 300 keV. Yet, theory and recent experiments indicate advantages to imaging at 100 keV, energies for which the current detectors have not been optimized. In this study, we evaluated the Gatan Alpine detector, designed for operation at 100 and 200 keV. Compared to the Gatan K3, Alpine demonstrated a significant DQE improvement at these voltages, specifically a ~4-fold improvement at Nyquist at 100 keV. In single-particle cryo-EM experiments, Alpine datasets yielded better than 2 [A] resolution reconstructions of apoferritin at 120 and 200 keV on a ThermoFisher Scientific (TFS) Glacios microscope. We also achieved a ~3.2 [A] resolution reconstruction for a 115 kDa asymmetric protein complex, proving its effectiveness with complex biological samples. In-depth analysis revealed that Alpine reconstructions are comparable to K3 reconstructions at 200 keV, and remarkably, reconstruction from Alpine at 120 keV on a TFS Glacios surpassed all but the 300 keV data from a TFS Titan Krios with GIF/K3. Additionally, we show Alpines capability for high-resolution data acquisition and screening on lower-end systems by obtaining ~3 [A] resolution reconstructions of apoferritin and aldolase at 100 keV and detailed 2D averages of a 55 kDa sample using a side-entry cryo holder. Overall, we show that Gatan Alpine performs well with the standard 200 keV imaging systems and may potentially capture the benefits of lower accelerating voltages, possibly bringing smaller sized particles within the scope of cryo-EM.

biophysics↗

bioRxiv2022

Territorial aggression in male bower-building cichlids Nyassachromis cf. microcephalus is disrupted by exposure to environmental concentrations of fluoxetine

Selective serotonin reuptake inhibitors (SSRIs) are commonly prescribed drugs for treating human depression, but the role of serotonin--often called the happy chemical--is complex, associated with the regulation of appetite, anxiety, aggression, and more. With such psychoactive pharmaceuticals being increasingly detected in aquatic environments and their effects on non-target species an uncertainty, this study seeks to investigate how inhibiting the serotonin pathway with the SSRI fluoxetine affects territorial aggression, using the cichlid fish Nyassachromis cf. microcephalus as a model. Males of this sand-dwelling Lake Malawi species build bowers to attract females within a lekking system, where male-male competition is intense. Being aggressive in defending against intruders would serve to maximise mating opportunities and reproductive success for the territory holding male. However, after a one-week exposure to fluoxetine at environmentally relevant concentrations, a decline in aggression was observed in the male cichlids. This implies the serotonergic system plays an important role in modulating aggression and therefore sexual selection in cichlid fishes, and that environmental pollution has the potential to disrupt these behaviours.

animal behavior and cognition↗

bioRxiv2022

oca2 targeting using CRISPR/Cas9 in the Malawi cichlid Astatotilapia calliptera

Identifying genetic loci underlying trait variation provides insights into the mechanisms of diversification, but demonstrating causality and characterising the role of genetic loci requires testing candidate gene function, often in non-model species. Here we establish CRISPR/Cas9 editing in Astatotilapia calliptera, a generalist cichlid of the remarkably diverse Lake Malawi radiation. By targeting the gene oca2 required for melanin synthesis in other vertebrate species, we show efficient editing and germline transmission. Gene edits include indels in the coding region, likely a result of non-homologous end joining, and a large deletion in the 3' UTR due to homology-directed repair. We find that oca2 knock-out A. calliptera lack melanin, which may be useful for developmental imaging in embryos and studying colour pattern formation in adults. As A. calliptera resembles the presumed generalist ancestor of the Lake Malawi cichlids radiation, establishing genome editing in this species will facilitate investigating speciation, adaptation and trait diversification in this textbook radiation.

developmental biology↗