Biology subjects

King, R. A.

Publications and source records attributed to King, R. A..

8 recordsLinked to original sources

bioRxiv2026

Smolt migration in relation to latitude, season and migratory distance

Downstream migration and sea entry are periods of high mortality for sea trout smolts and migration timing is a critical aspect of survival. We aimed to investigate migration timing of PIT-tagged sea trout smolts across a latitudinal gradient in five freshwater systems across Europe: Norway, Sweden, Denmark, France and Portugal. In two systems, smolt migration was further examined to assess a) differences in sex, body size and condition between autumn and spring migrants; b) the influence of spatial origin within the stream; and c) relationships between individual body size and migration date. Tagged smolts were not detected migrating in the Portuguese watershed. Spring migration timing differed significantly between watersheds in Norway, Sweden, Denmark and France. Generally, there was a trend of earlier migration at lower latitudes. Autumn vs spring migration was examined in Gudso-Denmark. Autumn migrants were larger in both length and mass, with no differences were found in sex ratios or body condition. In terms of spatial origin, fish originating from an upstream site were more likely to migrate in the autumn compared to the spring and vice versa. Size dependent migration was found in the Swedish system, Haga [a]-Sweden, with larger individuals migrating earlier in the spring than smaller individuals. Outward-migrating smolts were also more likely to originate from a downstream site than an upstream site. Overall, these results show both large-scale geographic and fine-scale individual influences on migration timing. Given that climate change may have large impacts on migration patterns in sea trout, understanding variability in migratory patterns across a latitudinal gradient is an important tool for predicting responses to environmental changes.

ecology↗

bioRxiv2025

Distinct patterns of de novo coding variants contribute to Tourette Syndrome etiology

Tourette syndrome (TS) is a highly heritable childhood-onset neuropsychiatric disorder characterized by persistent motor and vocal tics. While both common and rare variants contribute to TS susceptibility, the role of rare de novo mutations (DNMs) remains incompletely characterized. Here, we report findings from the largest TS whole-exome sequencing study to date, analyzing 1,466 TS trios alongside 6,714 autism spectrum disorder (ASD) trios and 5,880 unaffected sibling controls from the Simons Simplex Collection (SSC) and SPARK cohorts. Leveraging a trio-based design across these cohorts enabled calibrated assessment of DNM burden while controlling for background mutation rates. We observed a significant exome-wide enrichment of protein-truncating DNMs in TS probands, particularly within genes intolerant to loss-of-function variation (pLI [≥] 0.9), with little contribution from damaging missense variants. Notably, TS probands did not exhibit enrichment in previously implicated ASD or developmental delay (DD) genes, but elsewhere in the genome, suggesting a distinct rare variant architecture. Using a Bayesian statistical framework that integrates both de novo and rare inherited coding variants, we identified three candidate TS risk genes with FDR [≤] 0.05: PPP5C, EXOC1, and GXYLT1. Literature shows that they have prior links to neurodevelopmental and psychiatric disorders. These findings reveal a rare variant burden in TS that is genetically distinguishable from ASD, underscore the importance of loss-of-function mutations in TS risk, and nominate novel candidate genes for future functional investigation.

neuroscience↗

bioRxiv2025

The chalk streams of southern England and northern France harbour substantial unique components of the overall genetic diversity of Atlantic salmon (Salmo salar L.)

Populations of Atlantic salmon continue to suffer marked declines in abundance due to stressors acting in both their freshwater and marine habitats. It is therefore an imperative to identify populations in need of increased conservation intervention, with the aim of preserving as much as possible the genetic diversity present within the species. Previous microsatellite-based analyses have shown the chalk rivers of southern England and northern France to hold genetically distinct populations of salmon. However, these salmon populations have never been investigated in the same study. Using a suite of 93 single nucleotide polymorphism loci and samples from 42 British Isles and French rivers, we demonstrate the French and English chalk salmon to be closely related and distinct from salmon inhabiting non-chalk rivers. The identification of a small number of significant FST outliers suggests that this distinction is driven by local adaptation. We propose that the chalk and non-chalk salmon be designated as two distinct Evolutionarily Significant Units that each contain multiple Management Units. The chalk river salmon, especially those from southern England, are identified as making a significant contribution to the overall diversity of the species within the English Channel region. As a consequence, we propose that the salmon populations of the chalk streams may meet the criteria for recognition as a distinct subspecies of salmon, Salmo salar calcariensis. Taken together, the results presented here highlight the urgent need for enhanced conservation and protection for the Atlantic salmon populations inhabiting the chalk rivers of southern England and northern France.

evolutionary biology↗

bioRxiv2024

What are the best practices for curating eDNA custom barcode reference libraries? A case study using Australian subterranean fauna.

Identification of species for environmental assessment and monitoring is essential for understanding anthropogenic impacts on biodiversity, but for subterranean fauna this task is frequently difficult and time consuming. The implementation of environmental DNA (eDNA) metabarcoding for biodiversity discovery and assessment offers considerable promise for improving the rate, accuracy and efficiency of species detection in ecosystems both above and below the ground. Importantly, for a better understanding of the biodiversity and ecology of organisms detected using eDNA, a custom library of known reference sequences with associated correct taxonomic metadata--i.e., a barcode reference library (BRL)--is required. Yet, minimal guidance is currently available on how an effective (i.e. shareable, multi-sequence, that permits metadata and has a unified nomenclature) and accurate (i.e. verified) custom BRL can be achieved. Here, we present a detailed roadmap for curation of a BRL for subterranean fauna. To do this, we (1) curated a custom sequence database of subterranean fauna at an environmentally sensitive location, Bungaroo Creek in the Pilbara region of Western Australia, for four gene loci useful for eDNA metabarcoding (COI, 18S rRNA, 12S rRNA and 16S rRNA); (2) addressed major gaps in taxonomy and disparate nomenclature of subterranean fauna by estimating 17-29 putative new species with standard delimitation methods, including 34 Barcode Index Numbers (BINs) in BOLD, and (3) summarised a best practice workflow for curation of a custom BRL that has broad applicability and can be applied to any taxa. Scientific Significance StatementIn threatened ecosystems, environmental DNA (eDNA) metabarcoding for biodiversity discovery and assessment offers considerable promise for improvement in the rate, efficiency and accuracy of species detection. For a better understanding of the biodiversity and ecology of organisms detected using eDNA, a custom library of known reference sequences with associated correct taxonomic metadata is required. Minimal guidance is currently available on how an effective (i.e. shareable, multi-sequence, permits metadata and provides a unified nomenclature) custom barcode reference library (BRL) can be achieved for subterranean fauna. Here, we present a road map for sound and reliable curation of a BRL using subterranean fauna from Australia as a case study.

evolutionary biology↗

bioRxiv2024

Combining population genomics and transcriptomics to identify signatures of metal tolerance in brown trout inhabiting metal-polluted rivers

Industrial pollution is a major driver of ecosystem degradation, but it can also act as a driver of contemporary evolution. As a result of intense mining activity during the Industrial Revolution, several rivers across the southwest of England are polluted with high concentrations of metals. Despite the documented negative impacts of ongoing metal pollution, brown trout (Salmo trutta L.) survive and thrive in many of these metal-impacted rivers. We used population genomics, transcriptomics, and metal burdens to investigate the genomic and transcriptomic signatures of potential metal tolerance. RADseq analysis of six populations (originating from three metal-impacted and three control rivers) revealed strong genetic substructuring between impacted and control populations. We identified selection signatures at 122 loci, including genes related to metal homeostasis and oxidative stress. Trout sampled from metal-impacted rivers exhibited significantly higher tissue concentrations of cadmium, copper, nickel, and zinc, which remained elevated after 11 days in metal-free water. After depuration, we used RNAseq to quantify gene expression differences between metal-impacted and control trout, identifying 2,042 differentially expressed genes (DEGs) in the gill, and 311 DEGs in the liver. Transcriptomic signatures in the gill were enriched for genes involved in ion transport processes, metal homeostasis, oxidative stress, hypoxia and response to xenobiotics. Our findings reveal shared genomic and transcriptomic pathways involved in detoxification, oxidative stress responses, and ion regulation. Overall, our results demonstrate the diverse effects of metal pollution in shaping both neutral and adaptive genetic variation, whilst also highlighting the potential role of constitutive gene expression in promoting metal tolerance.

evolutionary biology↗

bioRxiv2023

Drivers of population dynamics of at-risk populations change with pathogen arrival

Successful wildlife conservation in an era of rapid global change requires understanding determinants of species population abundance and growth. However, when populations are faced with novel stressors, factors associated with healthy and growing populations can change, necessitating a shift in conservation strategies. For example, emerging infectious diseases can cause conditions previously beneficial or neutral to host populations to increase disease impacts. Here, we paired a population dataset of 265 colonies of the federally endangered Indiana bat (Myotis sodalis) with 50.7 logger-years of environmental data to explore factors that affected colony response to white-nose syndrome (WNS), an emerging fungal disease. We found wide variation in colony responses to WNS, ranging from extirpation to stabilization and persistence. Simulating future population dynamics suggests that most extirpations have already occurred, as the pathogen has been present for several years in most colonies, and that small colonies were more susceptible to extirpation than large ones. Further, while temperature and humidity conditions of hibernacula appeared unassociated with Indiana bat colony growth prior to WNS, extirpation risk following pathogen arrival was elevated in colonies that used colder and wetter hibernacula. Additionally, rates of decline were greater in colder hibernacula, opposite the association for a sympatric bat species. Overall, this study illustrates that emerging infectious diseases can change the factors associated with host population abundance and optimal growth, including through novel environmental associations, which can vary across host species. Consideration of these shifting associations and intrinsic differences between impacted host species will be essential to successful species conservation.

ecology↗

bioRxiv2021

A subset of nucleus accumbens neurons receiving dense and functional prelimbic cortical input are required for cocaine seeking

BackgroundPrelimbic cortical projections to the nucleus accumbens core are critical for cue-induced cocaine seeking, but the identity of the accumbens neuron(s) targeted by this projection, and the transient neuroadaptations contributing to relapse within these cells, remain unknown. MethodsMale Sprague-Dawley rats underwent cocaine or sucrose self-administration, extinction, and cue-induced reinstatement. Pathway-specific chemogenetics, patch-clamp electrophysiology, in vivo electrochemistry, and high-resolution confocal microscopy were used to identify and characterize a small population of nucleus accumbens core neurons that receive dense prelimbic cortical input to determine their role in regulating cue-induced cocaine and natural reward seeking. ResultsChemogenetic inhibition of prelimbic cortical projections to the nucleus accumbens core suppressed cue-induced cocaine relapse and normalized real-time cue-evoked increases in accumbens glutamate release to that of sucrose seeking animals. Furthermore, chemogenetic inhibition of the population of nucleus accumbens core neurons receiving the densest prelimbic cortical input suppressed cocaine, but not sucrose seeking. These neurons also underwent morphological plasticity during the peak of cocaine seeking in the form of dendritic spine expansion and increased ensheathment by astroglial processes at large spines. ConclusionsWe identified and characterized a unique subpopulation of nucleus accumbens neurons that receive dense prelimbic cortical input. The functional specificity of this subpopulation is underscored by their ability to mediate cue-induced cocaine relapse, but not sucrose seeking. This subset of cells represents a novel target for addiction therapeutics revealed by anterograde targeting to interrogate functional circuits imbedded within a known network.

neuroscience↗

bioRxiv2017

Genomic Locus Modulating IOP in the BXD RI Mouse Strains

PurposeIntraocular pressure (IOP) is the primary risk factor for developing glaucoma. The present study examines genomic contribution to the normal regulation of IOP in the mouse.\n\nMethodsThe BXD recombinant inbred (RI) strain set was used to identify genomic loci modulating IOP. We measured the IOP from 532 eyes from 33 different strains. The IOP data will be subjected to conventional quantitative trait analysis using simple and composite interval mapping along with epistatic interactions to define genomic loci modulating normal IOP.\n\nResultsThe analysis defined one significant quantitative trait locus (QTL) on Chr.8 (100 to 106 Mb). The significant locus was further examined to define candidate genes that modulate normal IOP. There are only two good candidate genes within the 6 Mb over the peak, Cdh8 (Cadherin 8) and Cdh11 (Cadherin 11). Expression analysis on gene expression and immunohistochemistry indicate that Cdh11 is the best candidate for modulating the normal levels of IOP.\n\nConclusionsWe have examined the genomic regulation of IOP in the BXD RI strain set and found one significant QTL on Chr. 8. Within this QTL that are two potential candidates for modulating IOP with the most likely gene being Cdh11.

genetics↗