Biology subjects

Ord, J.

Publications and source records attributed to Ord, J..

5 recordsLinked to original sources

bioRxiv2026

Early-life conditions shape baseline immune gene expression, but not pathogen-induced immune activation, in brown trout

Early-life environment and parental background can shape immune phenotypes, but whether such differences persist during infection and influence the immune response remains unclear. We used single-cell RNA sequencing to characterize kidney immune responses in brown trout (Salmo trutta) from three origins differing in parental history and early rearing: wild parents with offspring reared in the wild; wild parents with offspring reared in a hatchery; and hatchery parents with offspring reared in a hatchery. All fish originated from the same river and showed no detectable genetic population structure. Fish were exposed to Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease, and analyzed 25 days later alongside unexposed controls. Across 18 scRNA-seq datasets, we identified 30 cell clusters and found a clear transcriptional imprint of developmental and parental history in the resting immune system. In unexposed fish, origin was associated with pronounced differences in gene expression, particularly in B cells. When fish were subsequently exposed to the pathogen and developed subclinical infections, both immune-cell composition and transcriptional state experienced pronounced changes: T cells increased in relative abundance, while B cells, neutrophils and proliferating progenitors showed the strongest transcriptional responses, consistent with an active but controlled subclinical response. Strikingly, the strong origin-dependent differences present before exposure largely disappeared after infection. Fish from all three backgrounds converged on a shared transcriptional response, and genes associated with origin showed little overlap with those responding to infection. Thus, at single-cell resolution in vivo, we identify infection-induced transcriptional convergence across distinct environmental and parental backgrounds. Our findings show that substantial baseline immune variation can persist under resting conditions yet be overridden by pathogen exposure, constraining distinct immune states towards a common response.

immunology↗

bioRxiv2025

Single-cell RNA sequencing reveals influences of rearing environment on cellular immunity in brown trout (Salmo trutta)

Vertebrate immune systems exhibit striking evolutionary diversity, yet our understanding remains biased toward mammalian models. Here, we generate a single-cell atlas of immune cells from the ecologically and economically important salmonid Salmo trutta (brown trout), a lineage characterized by an ancestral whole-genome duplication (WGD). Profiling over 83,000 kidney-derived immune cells, we resolved 34 transcriptionally distinct populations, identified core immune lineages, and uncovered novel markers in neutrophils, macrophages, T- and B-cells. We detected pervasive transcriptional divergence between WGD-derived ohnologue pairs, indicating putative sub- and neofunctionalization in immune gene regulation. We further show that the transcriptional identity of immune cells is shaped by rearing history: fish raised in hatcheries--whether for one or multiple generations--showed shifts in immune gene expression across cell types. These included genes involved in G protein-coupled receptor signalling, a process which has previously been implicated in domestication. Our findings provide insight into the evolution of vertebrate immunity and raise concerns about the immunological fitness of hatchery-reared fish released into the wild.

immunology↗

bioRxiv2025

Single-cell and spatial transcriptomics uncover the role of B chromosomes in driving plant invasiveness

Invasive plants pose a major threat to global biodiversity, yet the molecular and genomic mechanisms underlying their success remain poorly understood. Here, we investigate the common reed (Phragmites australis), a grass species that became invasive in North America after introduction from Europe, to unravel the molecular mechanisms of its invasiveness. By integrating single-cell RNA sequencing, spatial transcriptomics, and comparative genomics, we constructed a single-cell atlas of P. australis and identified 19 transcriptionally distinct cell types, including shoot apical meristem, epidermal, and vascular tissues. Comparative analysis of common garden-grown native (European) and invasive (North American) populations revealed a significant proportion of differentially expressed genes (DEGs) located on B chromosomes, which underwent copy number expansion in invasive genomes. The proportion of B chromosome genes in DEGs varies across cell types, with the highest proportions observed in the epidermis and mesophyll, and lower proportions in the vascular tissues. Gene IMPA-3, a B chromosome gene likely derived from transposable element activity, exhibited an elevated mutation rate compared to its ancestral counterparts, potentially enhancing adaptive evolution in invasive populations. Invasive individuals also displayed molecular regulatory networks related to photosynthetic efficiency, stress tolerance, and growth-defense trade-offs. Together, our findings provide a cell-type-resolved molecular atlas of a non-model invasive plant and offer key insights into the cellular and genomic architecture of plant invasiveness, with implications for ecological management.

evolutionary biology↗

bioRxiv2022

High nucleotide diversity accompanies differential DNA methylation in naturally diverging populations

Epigenetic mechanisms such as DNA methylation (DNAme) are thought to comprise an invaluable adaptive toolkit in the early stages of local adaptation, especially when genetic diversity is constrained. However, the link between genetic diversity and DNAme has been scarcely examined in natural populations, despite its potential to shed light on the evolutionary forces acting on methylation state. Here, we analysed reduced-representation bisulfite sequencing and whole genome pool-seq data from marine and freshwater stickleback populations to examine the relationship between DNAme variation (between- and within-population), and nucleotide diversity in the context of freshwater adaptation. We find that sites that are differentially methylated between populations have higher underlying standing genetic variation, with diversity higher among sites that gained methylation in freshwater than those that lost it. Strikingly, while nucleotide diversity is generally lower in the freshwater population as expected from a population bottleneck, this is not the case for sites which lost methylation which instead have elevated nucleotide diversity in freshwater compared to marine. Subsequently, we show that nucleotide diversity is higher among sites with ancestrally variable methylation and also positively correlates with the sensitivity to environmentally induced methylation change. Both suggest that as selection on the control of methylation state becomes relaxed, so too does selection against mutations at the sites themselves. Increased epigenetic variance in a population is therefore likely to precede genetic diversification.

evolutionary biology↗

bioRxiv2018

Effects of Orientation Change during Environmental Learning on Age-Related Difference in Spatial Memory

It has been suggested that older adults suffer a greater degree of decline in environmental learning when navigating in an environment than when reading a map of the environment. However, the two types of spatial learning differ not only in perspectives (i.e., navigation is done with a ground-level perspective; a map is read from an aerial perspective) but also in orientations (i.e., orientations vary during navigation; spatial information is drawn from a single orientation in a map), making it unclear which factor critically affects older adults spatial learning. The present study addressed this issue by having younger and older participants learn the layout of a large-scale environment through an aerial movie that contained changes in orientations from which the environment was depicted. Results showed that older participants memories for the environmental layout were as distorted as those created through a ground-level movie (which involved the same orientation changes), whereas they formed more accurate memories through another aerial movie in which an orientation was fixed. By contrast, younger participants learned the environment equally well from the three movies. Taken together, these findings suggest that there is age-related alteration specifically in the ability to process multiple orientations of an environment while encoding its layout in memory. It is inferred that this alteration stems from functional deterioration of the medial temporal lobe, and possibly that of posterior cingulate areas as well (e.g., the retrosplenial cortex), in late adulthood.

neuroscience↗