Biology subjects

Fernando, D.

Publications and source records attributed to Fernando, D..

14 recordsLinked to original sources

bioRxiv2026

Why are fishers retaining manta and devil ray bycatch?

Increasing fishing pressure, including from small-scale fisheries, has caused declines in more than one-third of all elasmobranch species. Tackling conservation issues in small-scale fisheries requires interdisciplinary approaches due to the coastal community's interdependence on marine resources. To support inclusive policy change and fisher engagement, an understanding of the motivations driving fishers' operational choices (i.e., the retention of elasmobranch bycatch) is needed. We assess the motivational drivers behind bycatch retention of one of the slowest-growing and most vulnerable elasmobranch groups, manta and devil rays (collectively, mobulids), through a case study in India, their largest fishery in the world. We conducted a best-worst scaling survey in the fishery-intensive states of Tamil Nadu and Andhra Pradesh, which make significant contributions to mobulid landings on India's east coast. Our results suggest that fishers exhibit varied motivations for retaining mobulid bycatch across states. Financial motivation to sell mobulids for additional revenue was the most important motivator for bycatch retention in both states. In Tamil Nadu, the top three motivators were all financially driven, whereas in Andhra Pradesh, the top three motivators included both financial and non-financial attributes, such as nutritional importance and storage optimisation. As the first socio-economic study of mobulid fisheries in India, we show that motivations underlying bycatch retention decisions vary geographically and may be influenced by cultural differences between states and the socio-economic characteristics of decision makers. Based on identified fisher motivations, we provide context-specific recommendations to align conservation strategies with the values fishers derive from the mobulid fishery and encourage participation in conservation. These include subsidies for net repair to encourage mobulid release; promotion of a minimum price measure for sustainably sourced alternative species; quality improvement of target species; and increased awareness of national and international regulatory obligations (e.g., CITES, CMS, IOTC).

ecology↗

bioRxiv2026

No single measure is enough: Recovery of the Critically Endangered Mobula mobular requires integrated maximum bycatch mitigation and nursery area protection.

As anthropogenic threats have intensified over the past 500 years, we find ourselves in the midst of a sixth mass extinction, with continued losses of biodiversity threatening ecosystem stability. This biodiversity loss has caused species extinctions across taxa, and placed several others at high risk of functional extinction. These disturbance-driven impacts represent one of the most acute biodiversity crises facing global marine systems. Species exhibiting slow life histories characteristically have low resilience to disturbance. Here, we assess the risk of functional extinction and identify policy pathways for population recovery of the slow-living, Critically Endangered elasmobranch, the spinetail devil ray (Mobula mobular). We develop a stochastic, state-structured Integral Projection Model (IPM) parameterised with demographic data collected from fishery landings data in India, the world's largest mobulid fishery, and supplemented with data on vital rates from published literature. Using the IPM, we estimate that the population is declining at approximately 12% annually, experiencing substantial limiting pressure from fisheries overexploitation and failing to approach its biological maximum growth potential. Our results indicate that populations of M. mobular will be at high risk of functional extinction if 'business as usual' harvest scenario persists for another decade. We further show that long-term population recovery is only possible if survival increases significantly across all size classes, especially among large reproductive females, alongside a concurrent increase in fecundity. We conclude that no single policy measure is sufficient to recover population of M. mobular along the southeastern coast of India. Instead, combined protection through maximum bycatch mitigation and protection of nursery areas in no-take zones will be required for population recovery. This research demonstrates that recovery of overexploited populations often requires integrated resource management across life stages, and that the Critically Endangered M. mobular warrants urgent conservation action to avoid functional extinction.

ecology↗

bioRxiv2026

DENcode: A model for haplotype-informed transmission probability of dengue virus

Dengue virus transmission networks are often only partially resolved, due to gaps in sampling, unobserved mosquito-mediated transmission, and using methods (phylogenetics) that describe evolutionary relatedness but not explicit, probabilistic transmission links between individual infections. We developed DENcode, a framework to estimate the relative likelihood of vector-mediated transmission between pairs of dengue cases by combining a temperature- and time-modulated epidemiological kernel, which captures the extrinsic incubation period and human infectiousness, with a phylogenetically informed genetic similarity kernel derived from patristic distances between viral haplotypes or consensus sequences. Validation with a real-life dataset of 90 dengue infections sampled from Colombo, Sri Lanka between 2017 - 2020 and sequenced to resolve within-host haplotypes, DENcode estimates were stable across 100 Monte Carlo iterations, yielding narrow credible intervals (median width <0.001) and consistent top-ranked transmission pairs. Sensitivity analyses using ablation experiments showed that removing either the genetic or epidemiological component substantially altered the distribution of linkage probabilities, indicating that both contribute meaningfully to the inferred transmission structure. Serotype-specific transmission networks constructed from pairwise linkage probabilities from DENcode were analysed using degree- and path-based centrality measures at probability thresholds of 0.1 and 0.5, revealing relative importance of cases to disease transmission within the community. Haplotype-derived networks were more informative than consensus-based networks (x 3.6 and x 1.6 times more edges for DENV2 and 3 respectively). DENcode is a robust framework to explore dengue transmission within a community that provides an output of network of transmission probabilities informed by pathogen genetic similarity and clinical epidemiological parameters. Author summaryTracing epidemics of dengue in setting where dengue transmission happens continuously poses many challenges especially with limited availability of genomic surveillance. Here we introduce a model that uses genomic data together with time and location data to calculate a probability of two cases of dengue being related to each other. Using data from the Colombo dengue study, from 2017 to 2020, Sri Lanka, we evaluated the model. We used haplotype level sequences that correspond to the viral variation within the human host and consensus level sequences that average the data from a single human host into a single sequence. We constructed transmission probability networks for each dengue serotype and were able to identify patients who played key roles in the corresponding networks. We were able to show that this model is robust and will be a valuable tool in the context of dengue control.

bioinformatics↗

bioRxiv2025

Between- and within-host mutation of dengue virus

RNA viruses exhibit high mutation rates due to error-prone polymerases, leading to a diverse pool of viral haplotypes (also referred to as quasi-species) within infected hosts. While haplotypes have been well studied in chronic infections like HIV and HCV, diversity remains under-explored in acute infections like dengue (DENV), which are constrained by a short viremic phase. This study aimed to characterise the mutation hotspots in DENV genomes at both consensus and haplotype levels. Near full length DENV genomes were sequenced using Oxford Nanopore Technology (ONT) from the plasma of Sri Lankan patients with dengue fever recruited between 2017 -2020. Consensus sequences were mapped with Minimap-2, and haplotypes were reconstructed with Nano-Q, a tool designed for estimation of RNA virus haplotypes and their relative abundance. The genomic variability of DENV genomes was assessed by calculating Shannon Entropy (SE). Codons undergoing diversifying selection were identified with three phylogenetics-based algorithms (FEL, MEME, FUBAR) implemented within the Datamonkey suite. From 150 samples tested, both consensus and haplotype sequences were characterised in 90 samples (DENV1: 8, DENV2: 51, DENV3: 31). The genomic variability of consensus sequences measured by SE was higher in DENV2 compared to DENV3, and the reverse was true for haplotypes. At the consensus level, the NS2A gene had the greatest number of mutable sites when adjusted for gene length across all serotypes, while at the haplotype level the NS1 gene had the same. Overall, the haplotypes sequences revealed more sites with high mutability and codons under diversifying selection than those visible at consensus level. This provides proof-in-principle that in acute RNA viruses also have high mutability in haplotypes, which may be inapparent with a consensus-level analysis.

bioinformatics↗

bioRxiv2025

Establishing a DNA reference library for the identification of elasmobranchs in the Indian Ocean using Oxford Nanopore Sequencing

Elasmobranchs, comprising sharks and rays, are among the most threatened species globally. The first elasmobranchs were added to the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) in 2002. Since then, the number of species listed has increased to 151, highlighting the urgent conservation challenges faced by these species. In Sri Lanka, where over 100 species have been recorded, the demand for elasmobranch products drives significant export and import activities, complicating conservation efforts. Accurate species identification is crucial for fisheries monitoring, trade regulation, and conservation management. However, relying solely on morphological characteristics is challenging, especially since key identifying features are unavailable in certain derivatives like meat and oil in market samples. This study aims to develop a robust DNA reference library for elasmobranch species in Sri Lanka and to showcase the application of Oxford Nanopore Technology (ONT) as a reliable tool for fisheries monitoring and conservation. Using DNA barcoding and ONT sequencing, we analysed 49 elasmobranch species, focusing on the Cytochrome Oxidase I (COI) and 12S ribosomal ribonucleic acid (rRNA) genes to develop a DNA reference library. The creation of reliable barcode reference libraries is essential for effective species identification in biomonitoring because it facilitates the assessment of population trends and the effectiveness of fishing and trade regulations. We conducted a phylogenetic analysis to assess the robustness of reference sequences in species discrimination. All DNA reference sequences are publicly accessible through GenBank. This study enhances the capacity to monitor and regulate the elasmobranch trade in Sri Lanka and beyond.

genetics↗

bioRxiv2025

Hidden Diversity of Threatened Sharks and Rays in the Global Meat Trade

International wildlife trade is a major source of biodiversity loss, yet many species lie hidden within aggregated data that conceals trade impacts. We overcome this problem for the largest vertebrate wildlife trade globally - shark and ray meat - comprising 438 538 mt yr-1 across more than 150 species, 76% of which are Threatened. Revealed trade contains greater quantities of skates (+10%), hammerheads (+8%), and smoothhounds, dogfishes & tope (+5%), and fewer pelagic sharks (-38%) than previously known. Shorttail yellownose skate, smoothound, silky, mako, and blue sharks are the most underreported meat species, due to aggregated landings from China, Argentina, Japan, and Indonesia, demonstrating international trade in shark and ray meat as a diverse, pervasive, and previously hidden source of fishing mortality for many threatened species.

ecology↗

bioRxiv2024

Population structure and genetic diversity of the Critically Endangered bowmouth guitarfish (Rhina ancylostomus) in the Northwest Indian Ocean

The bowmouth guitarfish (Rhina ancylostomus) is a unique and understudied species of wedgefish with a distribution spanning the Indo-Pacific Oceans. Due to targeted and bycatch fisheries, this species is experiencing serious declines across its range. It is now considered among the most threatened species of elasmobranch. Despite this, species-specific management is limited, particularly around primary fishing hotspots. This is in part due to knowing very little about fundamental population processes. Here, we combine mitochondrial and single nucleotide polymorphism (SNP) data to carry out the first genetic assessment of R. ancylostomus across the Northwest Indian Ocean. We detect genetic differentiation across the northwest range, shaped by both oceanographic barriers and intrinsic dispersal constraints, and uncover a cline in genetic variation from east to west. These findings emphasise the importance of maintaining habitat connectivity while also identifying regions that may require heightened protection. In doing so, our study provides a critical baseline for conservation planning of R. ancylostomus and highlights the value of genomic data in elasmobranch conservation.

evolutionary biology↗

bioRxiv2024

Development of a qPCR assay and a LAMP assay for Verticillium longisporum detection and a triplex qPCR assay for simultaneous detection of V. longisporum, Leptosphaeria biglobosa and L. maculans from canola samples

Verticillium wilt, Verticillium stem striping, and Verticillium stripe, are common disease names that all denote infection caused by Verticillium longisporum, on canola, or other Brassica crops. In this study, a quantitative PCR (qPCR) assay and a loop-mediated isothermal amplification (LAMP) assay were developed for the detection of V. longisporum from canola stem samples. Both assays are specific to V. longisporum at the species level and ubiquitous at the strain level. The low limit for positive detection of the two assays is 1 pg fungal DNA in a 20-{micro} L reaction or 1,400 fungal cells in 100-mg plant tissue. The qPCR assay was combined with the duplex qPCR assay for the two blackleg pathogens, Leptosphaeria biglobosa and L. maculans to constitute a triplex qPCR system for simultaneous detection of all three pathogens. The usefulness of this triplex qPCR system was verified on canola samples collected from various locations in Alberta, Canada. Using this triplex qPCR system, V. longisporum was detected from one sample, while the two blackleg pathogens were detected at higher frequencies. Since it is sometimes difficult to differentiate Verticillium stripe and blackleg on Alberta canola samples based on visual symptoms, the triplex qPCR system is an important tool for the detection of V. longisporum, especially when its presence is masked or obscured by symptoms of blackleg.

microbiology↗

bioRxiv2023

Comparative population genomics of manta rays has global implications for management

Understanding population connectivity and genetic diversity is of fundamental importance to conservation. However, in globally threatened marine megafauna, challenges remain due to their elusive nature and wide-ranging distributions. As overexploitation continues to threaten biodiversity across the globe, such knowledge gaps compromise both the suitability and effectiveness of management actions. Here, we use a comparative framework to investigate genetic differentiation and diversity of manta rays, one of the most iconic yet vulnerable groups of elasmobranchs on the planet. Despite their recent divergence, we show how oceanic manta rays (Mobula birostris) display significantly higher heterozygosity than reef manta rays (Mobula alfredi) and that M. birostris populations display higher connectivity worldwide. Through inferring modes of colonisation, we reveal how both contemporary and historical forces have likely influenced these patterns, with important implications for population management. Our findings highlight the potential for fisheries to disrupt population dynamics at both local and global scales and therefore have direct relevance for international conservation of marine species.

evolutionary biology↗

bioRxiv2022

Loss of EED in the oocyte causes initial fetal growth restriction followed by placental hyperplasia and offspring overgrowth

Germline epigenetic programming, including genomic imprinting, substantially influences offspring development. Polycomb Repressive Complex 2 (PRC2) plays an important role in Histone 3 Lysine 27 trimethylation (H3K27me3)-dependent imprinting, loss of which leads to placental hyperplasia in mammalian offspring generated by somatic cell nuclear transfer (SCNT). In this study, we show that offspring from mouse oocytes lacking the Polycomb protein Embryonic Ectoderm Development (EED) were initially growth restricted, characterised by low blastocyst cell counts and substantial mid-gestational developmental delay. This initial developmental delay was followed by striking late-gestational placental hyperplasia, fetal catch-up growth and extended gestational length that culminated in offspring overgrowth. This involved remodelling of the placenta, including expansion of fetal and maternal tissues and conspicuous expansion of the glycogen enriched cell population in the junctional zone that was associated with a delay in parturition. Despite this remodelling and offspring catchup growth, fetal/placental weight ratio and fetal blood glucose levels were low indicating low placental efficiency. Genome-wide analyses identified extensive transcriptional dysregulation in affected placentas, including a range of imprinted and non-imprinted genes and increased expression of the H3K27me3-imprinted gene Slc38a4, which regulates transport of essential amino acids in the placenta. Our data provide an explanation for apparently opposing observations of growth restriction and overgrowth of offspring derived from Eed-null oocytes and demonstrate that PRC2-dependent programming in the oocyte regulates fetal and placental growth and developmental outcomes.

developmental biology↗

bioRxiv2021

Tissue-specific mRNA profiling of the Brassica napus-Sclerotinia sclerotiorum interaction uncovers novel regulators of plant immunity

White mold in Brassica napus (canola) is caused by the fungal pathogen Sclerotinia sclerotiorum and is responsible for significant losses in crop yield across the globe. With advances in high-throughput transcriptomics, our understanding of the B. napus defense response to S. sclerotiorum is becoming clearer; however, the response of individual tissue layers directly at the site of infection has yet to be explored. Using laser microdissection coupled with RNA sequencing, we profiled the epidermis, mesophyll and vascular leaf tissue layers in response to S. sclerotiorum. This strategy increases the number of genes detected compared to whole-leaf assessments and provides unprecedented information on tissue-specific gene expression networks in response to pathogen attack. Our findings provide novel insight into the conserved and specific roles of ontogenetically distinct leaf tissue layers in response to infection. Using bioinformatics tools, we identified several defense genes that might coordinate plant immunity responses shared across different tissue layers within the leaf. These genes were functionally characterized by challenging T-DNA insertion lines of Arabidopsis with necrotrophic, hemi-biotrophic, and biotrophic pathogens, ultimately converging on the PR5-like RECEPTOR KINASE (PRK5). Together, these data provide insight on the complexity of the B. napus defense response directly at the site of infection. HighlightLaser microdissection coupled RNA sequencing of the B. napus - S. sclerotiorum interaction identifies candidate genes predicted to guide plant immunity against pathogen attack.

plant biology↗

bioRxiv2019

Geldanamycin inhibits Jumonji histone lysine demethylase KDM4 and targets chimeric transcription factor PAX3-FOXO1

Histone lysine demethylases (KDMs) are emerging as therapeutic targets in cancer. Development of potent KDM inhibitors may provide additional options for epigenomics-oriented therapies. Using a Time-Resolved Fluorescence Resonance Energy Transfer (TR-FRET) functional demethylation assay, in combination with a high-content immunofluorescence imaging phenotypic screen, Matrix-Assisted Laser Desorption/Ionization-Fourier Transform Ion Cyclotron Resonance mass spectrometry (MALDI-FTICR MS) and Amplified Luminescent Proximity Homogeneous Assay (ALPHA), we identified geldanamycin, an inhibitor of heat shock protein 90 (Hsp90), as a novel inhibitor of JmjC-domain containing demethylases such as KDM4B. We further found that geldanamycin can destabilize the PAX3-FOXO1 fusion oncoprotein, an Hsp90 client, which is a driver of clinically unfavorable alveolar rhabdomyosarcoma (aRMS). We then hypothesized that dual inhibition of PAX3-FOXO1 and epigenetic modifiers of aRMS would have synergistic antitumor activity. We repurposed the geldanamycin analog 17-DMAG to target aRMS and found that 17-DMAG significantly delays tumor growth, extends survival in xenograft mouse models, and inhibits expression of PAX3-FOXO1 targets and multiple oncogenic pathways including MYC, E2F and NOTCH. In addition, the combination of 17-DMAG with conventional chemotherapy or the bromodomain inhibitor JQ1 significantly enhances therapeutic efficacy. In summary, we have identified geldanamycin and 17-DMAG as dual KDM/Hsp90 inhibitors and 17-DMAG is efficacious against PAX3-FOXO1-driven rhabdomyosarcoma.

cancer biology↗

bioRxiv2019

Investigation of the quorum-sensing regulon of the biocontrol bacterium Pseudomonas chlororaphis strain PA23

Pseudomonas chlororaphis strain PA23 is a biocontrol agent capable of protecting canola from stem rot disease caused by the fungal pathogen Sclerotinia sclerotiorum. PA23 produces several of inhibitory compounds that are under control of a complex regulatory network. Included in this cascade is the PhzRI quorum sensing (QS) system, which plays an essential role in PA23 biocontrol. The focus of the current study was to employ RNA sequencing to explore the spectrum of PA23 genes under QS control. Transcriptomic profiling revealed 545 differentially expressed genes (365 downregulated; 180 upregulated) in the phzR mutant and 534 genes (382 downregulated; 152 upregulated) in the AHL-deficient PA23-6863. In both strains, decreased expression of phenazine, pyrrolnitrin, and exoprotease biosynthetic genes was observed. We have previously reported that QS activates expression of these genes and their encoded products. In addition, elevated siderophore and decreased chitinase gene expression was observed in the QS-deficient stains, which was confirmed by phenotypic analysis. Inspection of the promoter regions revealed the presence of "phz-box" sequences in only 58 of the 807 differentially expressed genes, suggesting that much of the QS regulon is indirectly regulated. Consistent with this notion, 41 transcriptional regulators displayed altered expression in one or both of the QS-deficient strains. Collectively, our findings indicate that QS governs expression of approximately 13% of the PA23 genome affecting diverse functions ranging from secondary metabolite production to general metabolism. To the best of our knowledge, this represents the first global transcriptomic analysis of the QS regulon of a biocontrol pseudomonad.

microbiology↗

bioRxiv2018

Phylogenomics and species delimitation of mobulid rays reveals cryptic diversity and a new species of manta ray

Practical biodiversity conservation relies on delineation of biologically meaningful units, particularly with respect to global conventions and regulatory frameworks. Traditional approaches have typically relied on morphological observation, resulting in artificially broad delineations and non-optimal species units for conservation. More recently, species delimitation methods have been revolutionised with High-Throughput Sequencing approaches, allowing study of diversity within species radiations using genome-wide data. The highly mobile elasmobranchs, manta and devil rays (Mobula spp.), are threatened globally by targeted and bycatch fishing pressures resulting in recent protection under several global conventions. However, a lack of global data, morphological similarities, a succession of recent taxonomic changes and ineffectual traceability measures combine to impede development and implementation of a coherent and enforceable conservation strategy. Here, we generate genome-wide Single Nucleotide Polymorphism (SNP) data from among the most globally and taxonomically representative set of mobulid tissues. The resulting phylogeny and delimitation of species units represents the most comprehensive assessment of mobulid diversity with molecular data to date. We find a mismatch between current species classifications, and optimal species units for effective conservation. Specifically, we find robust evidence for an undescribed species of manta ray in the Gulf of Mexico and show that species recently synonymised are reproductively isolated. Further resolution is achieved at the population level, where cryptic diversity is detected in geographically distinct populations, and indicates potential for future traceability work determining regional location of catch. We estimate the optimal species tree and uncover substantial incomplete lineage sorting, where standing variation in extinct ancestral populations is identified as a driver of phylogenetic uncertainty, with further conservation implications. Our study provides a framework for molecular genetic species delimitation that is relevant to wide-ranging taxa of conservation concern, and highlights the potential for genomic data to support effective management, conservation and law enforcement strategies.

genomics↗