Biology subjects

Paul, M. J.

Publications and source records attributed to Paul, M. J..

7 recordsLinked to original sources

bioRxiv2026

What shapes intraspecific genetic diversity in amphibians and reptiles? A comparative macrogenetic study across six biogeographic regions

Aim: Given that much of Earth's biodiversity is contained within species, inferring intraspecific genetic diversity and identifying its ecological correlates is essential for understanding evolutionary processes and informing conservation. Here, we investigate broad-scale variation in species-level mitochondrial genetic diversity and evaluate the relative importance of alternative ecological hypotheses proposed to explain it. Location: Brazilian Atlantic Forest, Iberian Peninsula, northwestern Africa, Arabian Peninsula, Madagascar and Australian Monsoonal Tropics. Taxon: Amphibians and reptiles Methods: We assembled a comprehensive dataset by integrating and manually curating mitochondrial sequences, occurrence records, environmental data and species traits from multiple open-access sources. We used multiple mitochondrial genes to estimate mean nucleotide diversity for each study species and quantified regional variation in genetic diversity. We then used random forests models to evaluate the relative importance of selected variables representing hypotheses related to water-energy availability, topography, historical climatic stability, land-cover characteristics, species geographic characteristics, life-history traits, evolutionary history and conservation status. Results: The final dataset comprised 247 amphibians and 295 reptiles, for which 43 and 52 explanatory variables were evaluated, respectively. Overall, the strongest support was found for hypotheses related to life-history traits, topographic heterogeneity and water-energy availability. In amphibians, higher genetic diversity was associated with smaller body size and greater environmental heterogeneity, particularly broader elevational and precipitation gradients. In reptiles, genetic diversity was primarily associated with life-history traits, with species of smaller body size and lower reproductive output exhibiting higher diversity. Long-term climatic stability showed comparatively little explanatory power for both taxa. Main conclusions: Our comprehensive study demonstrates that integrating extensive manual data curation with comparative macrogenetic analyses provides a robust framework for identifying broad-scale ecological correlates of mitochondrial genetic diversity. These findings improve our understanding of the factors associated with contemporary patterns of genetic diversity and provide a foundation for future conservation assessments in data-limited systems.

evolutionary biology↗

bioRxiv2026

Overcoming data limitations in macrogenetics: assessing and accounting for spatial heterogeneity in sequence data

At large scales, our ability to compare genetic diversity across species is often challenged by the difficulty of extracting range-wide sequence data from online databases. Using mitochondrial DNA from amphibians and reptiles spanning across six regions: Brazilian Atlantic Forest, Iberian Peninsula, northwestern Africa, Arabian Peninsula, Madagascar and Australian Monsoonal Tropics, we develop and implement a framework to overcome common limitations in macrogenetics. We compiled and manually curated a spatially explicit genetic dataset from public repositories, quantified the spatial representativeness of genetic sampling across species' ranges and developed a novel interpolation framework to estimate and map species-specific patterns of intraspecific genetic diversity (ISD) while accounting for heterogeneous spatial sampling. We estimated mean nucleotide diversity across species to produce regional maps for each genetic marker. Our final dataset comprised 182 amphibian and 239 reptile species, encompassing 184 genera from 54 families. Range representativeness of genetic sampling was generally high, despite some variation across study regions. Spatial patterns of ISD revealed geographic heterogeneity, and were consistent across the best-sampled mitochondrial markers. By combining automated and manual georeferencing, quantifying range representativeness, and accounting for bias in spatial interpolations, our pipeline is marker-agnostic and directly applicable to nuclear and genomic data as they become available.

evolutionary biology↗

bioRxiv2024

A composite subunit vaccine confers full protection against Buruli ulcer disease in the mouse footpad model of Mycobacterium ulcerans infection

Buruli ulcer (BU) disease, a neglected necrotizing tropical skin infection caused by Mycobacterium ulcerans, is the third most common mycobacterial disease after tuberculosis and leprosy. Infections mostly occur in remote, rural areas of Central and West Africa, but also in Australia, Japan and Papua New Guinea. There is currently no vaccine against Buruli ulcer disease and all previous attempts using closely related bacteria and subunit proteins have been partially successful only. Here, we tested in mice a composite subunit formulation incorporating the Mycobacterium ulcerans toxin mycolactone as the immunomodulator, and the antigens Ag85A and Polyketide Synthase Enzyme Ketoreductase A (KRA), formulated with Quil-A adjuvant ( Burulivac). Burulivac induced Ag85A and KRA antigen-specific antibodies, T cells and a mixed pro- and anti-inflammatory cytokine responses, which conferred absolute protection against Buruli ulcer disease in the mouse footpad model over a 14-week period of observation. This was superior to both live attenuated mycobacterial vaccines, that is, BCG and an avirulent M. ulcerans strain that lacks the mycolactone toxin (Mu{Delta}). Interleukin 10 was found to be strongly associated with protection. We suggest that Burulivac is a promising vaccine candidate against Buruli ulcer disease that warrants further exploration. Author summaryBuruli ulcer is a neglected tropical disease caused by skin infections by Mycobacterium ulcerans, an organism related to causative pathogens of tuberculosis and leprosy. The disease is endemic to parts of Central and West Africa but is also found in Australia, Japan and some other countries. While mortality is low, morbidity caused by extensive and unsightly ulceration of the skin is high. There currently is no vaccine against Buruli ulcer and all previous attempts to develop one have been unsuccessful. Here we developed a vaccine formulation termed Burulivac that incorporates three M. ulcerans antigens, two of which are proteins and the third the mycolactone toxin, much responsible for the pathology of the BU disease. Our rationale was that in a vaccine setting and using a controlled dose of the toxin, we could calibrate the immune responses to selected antigens, so that they mimic those induced during natural infection. Using an experimental mouse footpad model of infection, we demonstrate that immunisation with Burulivac completely prevented ulceration in the mouse footpad over an extended 14-weeks period of observation, and that this correlated with elevated levels of anti-inflammatory cytokine Interleukin-10. We propose that Burulivac is a promising vaccine candidate that merits further testing and development.

immunology↗

bioRxiv2023

Mesophyll-specific overexpressing of SvHXK6 gene improves water use efficiency without yield loss in C4 Setaria viridis

Hexokinases (HXK) were the first sugar signalling proteins identified in plants and are well known for their feedback regulation of photosynthetic gene expression. In some C3 plants, HXKs have been found to regulate stomatal function. However, the role of HXK in C4 photosynthesis, which is inherently more water use efficient than C3 metabolism, remains poorly understood. Here, we report on the first tissue-specific modification of HXK in a C4 plant. SvHXK6 was expressed in the model C4 grass Setaria viridis under the control of the ZmPEPC promoter (ZmPEPCpro), which directs expression in the leaf mesophyll tissue. Three S. viridis transgenic lines with increased abundance of SvHXK6 transcripts in the leaf tissue showed significant reduction in stomatal conductance with minimal effects on leaf CO2 assimilation rate. Consequently, the transgenic lines had higher leaf-level water use efficiency relative to the control (wild-type and null) plants. Overexpression of SvHXK6 had no effect on shoot biomass or seed yield of the S. viridis plants. Our study shows conserved function of HXK in regulating stomatal conductance in a C4 grass, demonstrating possible widespread utility in improving water use efficiency in C4 as well as C3 species.

plant biology↗

bioRxiv2023

The scheduling of adolescence with Netrin-1 and UNC5C

Dopamine axons are the only axons known to grow during adolescence. Here, using rodent models, we examined how two proteins, Netrin-1 and its receptor, UNC5C, guide dopamine axons towards the prefrontal cortex and shape behaviour. We demonstrate in mice (Mus musculus) that dopamine axons reach the cortex through a transient gradient of Netrin-1 expressing cells - disrupting this gradient reroutes axons away from their target. Using a seasonal model (Siberian hamsters; Phodopus sungorus) we find that mesocortical dopamine development can be regulated by a natural environmental cue (daylength) in a sexually dimorphic manner - delayed in males, but advanced in females. The timings of dopamine axon growth and UNC5C expression are always phase-locked. Adolescence is an ill-defined, transitional period; we pinpoint neurodevelopmental markers underlying this period.

neuroscience↗

bioRxiv2022

The effects of brief heat during early booting on reproductive, developmental and physiological performance in common wheat (Triticum aestivum L.)

Rising temperatures due to climate change threaten agricultural crop productivity. As a cool-season crop wheat is heat sensitive, but often exposed to high temperatures during cultivation. In the current study, a bread wheat panel of spring wheat genotypes, including putatively heat-tolerant Australian and CIMMYT genotypes, was exposed to a 5-day mild (34{degrees}C/28{degrees}C, day/night) or extreme (37{degrees}C/27{degrees}C) heat stress during the sensitive pollen developmental stage. Worsening effects on anther morphology were observed as heat stress increased from mild to extreme. Even under mild heat a significant decrease in pollen viability and grain number per spike from primary spike was observed compared with the control (21{degrees}C/15{degrees}C), with Sunstar and two CIMMYT breeding lines performing well. A heat-specific positive correlation between the two traits indicates the important role of pollen fertility for grain setting. Interestingly, both mild and extreme heat induced development of new tillers after the heat stress, providing an alternative sink for accumulated photosynthates and significantly contributing to the final yield. Measurements of flag leaf maximum potential quantum efficiency of Photosystem II (Fv/Fm) showed an initial inhibition after the heat treatment, followed by a full recovery within a few days. Despite this, model fitting using chlorophyll SPAD measurements showed an earlier onset or faster senescence rate under heat stress. The data presented here provide interesting entry points for further research into pollen fertility, tillering dynamics and leaf senescence under heat. The identified tolerant wheat genotypes can be used to dissect the underlying mechanisms and breed climate-resilient wheat.

plant biology↗

bioRxiv2021

Integration of embryo-endosperm interaction into a holistic and dynamic picture of seed development using a rice mutant with notched-belly grains

The interaction between the embryo and endosperm affects seed development, an essential process in yield formation in crops such as rice. Signals that communicate between embryo and endosperm are largely unknown. Here we use the notched-belly (NB) mutant with impaired communication between embryo and endosperm to evaluate 1) the impact of embryo on developmental staging of the endosperm; 2) signaling pathways emanating from the embryo that regulate endosperm development. Hierachical clustering of mRNA datasets from embryo and endosperm samples collected through development in NB and wild type showed a delaying effect of the embryo on the developmental transition of the endosperm by extending the middle stage. K-means clustering further identified coexpression modules of gene sets specific for embryo and endosperm development. Combined gene expression and biochemical analysis showed that T6P-SnRK1, gibberellin and auxin signalling from the embryo regulate endosperm developmental transition. The data enable us to propose a new seed developmental staging system for rice and the most detailed signature of rice grain formation to date, that will direct genetic strategies for rice yield improvement.

plant biology↗