Biology subjects

Cottrell, J.

Publications and source records attributed to Cottrell, J..

9 recordsLinked to original sources

bioRxiv2026

Developments in the European parasitoid community of Dryocosmus kuriphilus

The invasive gallwasp Dryocosmus kuriphilus was first detected in Italy in 2002, although likely to have initially arrived in the late 90s. Its ability to utilise sweet chestnut species non-native to its original Chinese range has allowed it to spread rapidly, and throughout Europe via European sweet chestnut Castanea sativa. Given the severity of its impact on C. sativa crop production, particularly in Mediterranean countries, previous studies have aimed to assess damage levels caused by D. kuriphilus, the efficacy of and potential non-target effects of the introduced biocontrol agent Torymus sinensis, and the possibility of regulation by native parasitoids. As yet a broad overview and analytical synthesis of these native parasitoid communities are absent. This review focuses on important aspects of the D. kuriphilus invasion. In particular, the invasion history and currently known distribution of D. kuriphilus, and several aspects of its associated parasitoid community. For native species to plausibly suppress D. kuriphilus, we might expect rates of parasitoid attack to increase with establishment time as native populations adapt to exploit the new resource, and this is a key focus of the review. We answer the following questions: 1) What is the distribution of D. kuriphilus in Europe, and has D. kuriphilus fully utilised the available niche space within its 20+ years in Europe? 2) Which species of native parasitoids attack D. kuriphilus in Europe and what are their ecological characteristics? 3) How consistent is the parasitoid community of D. kuriphilus across its range, and are there signs of convergence over time? 4) What effect does establishment time have on the species richness and abundance of parasitoid communities? We report the following: 1) D. kuriphilus has expanded its range throughout Europe and is present in nearly every major region where sweet chestnut is present. Native and non-native naturalised chestnut forests may be less susceptible to invasion than areas of industry due to differing socioeconomic and ecological factors, though areas with large chestnut industries also tend to be in the most heavily forested areas in the non-native range of sweet chestnut. D. kuriphilus has reportedly been eradicated from some countries, and effectively eradicated in a number of countries implementing biocontrol with T. sinensis, although successive invasions from neighbouring regions are still possible, and eradication may be transient. 2) 72 parasitoid species are identified attacking D. kuriphilus in Europe (far more species than any other gallwasp in the Western Palearctic). Its members are predominantly oak gallwasp parasitoids (82% of species), followed by gall-specialists of different host plants, leaf miner parasitoids and a minority of others with differing host life stages and ecologies. Parasitoids attacking D. kuriphilus are dominated by idiobiont ectoparasitoids of the superfamily Chalcidoidea (>96%). 3) The parasitoid community is highly variable, both temporally and spatially, although the vast proportion (>95%) of parasitoids at any one time are composed of locally common generalist oak gall parasitoids. The most common members include Bootanomyia dorsalis, Eupelmus urozonus, Eurytoma brunniventris, Mesopolobus sericeus and Torymus flavipes. 4) The length of establishment time has minimal effect on the species richness, abundance, and composition of the community, suggesting that regulation by natives, if it occurs, may take longer than the 20+ years that D. kuriphilus has persisted. While little evidence of increasing parasitoid attack of D. kuriphilus is apparent, we exercise caution by stating that the heterogeneity in available data are large, and that common biocontrol interventions using T. sinensis interrupt the natural process of community development dramatically. D. kuriphilus has been present in Europe for nearly three decades and few localities have repeated years of data collection. Even fewer studies have communities with establishment times exceeding ten years. Proper biocontrol by natives may not occur within short timeframes, although studies of other gallwasp invaders find similar results over periods exceeding 40 years. Given that many countries have chosen to implement T. sinensis for biocontrol, the focus may be better spent monitoring native gall communities for potential non-target effects.

ecology↗

bioRxiv2026

Phytochemical profiling, antioxidant capacity, and in vivo safety assessment of Warrigal spinach (Tetragonia tetragonioides) and Kensington Pride mango (Mangifera indica) extracts using Zebrafish larvae

Plant-derived bioactive compounds are recognised for their antioxidant potential and benefit for human diseases, including age-related diseases caused by oxidative stress. However, their antioxidant composition and safety profiles remain insufficiently understood. This study integrates phytochemical profiling, antioxidant evaluation, and in vivo toxicological assessment of Warrigal spinach (Tetragonia tetragonioides) and Kensington Pride mango (Mangifera indica). Spinach exhibited greater antioxidant capacity, and higher total phenolic and flavonoid content than mango: TPC (14.2 {+/-} 0.6 mg GAE/g vs 1.30 {+/-} 0.07 mg GAE/g) and TFC (9.61 {+/-} 0.39 mg QE/g vs 0.08 {+/-} 0.0 mg QE/g). LC-ESI-QTOF-MS/MS identified 187 metabolites dominated by flavonoids (53.5%) and phenolic acids (16%), with spinach showing greater chemical diversity. Quantitative analysis revealed higher levels of hydroxycinnamic acids and flavonoid glycosides in spinach, whereas mango contained distinct metabolites, including mangiferin and pyrogallol. Zebrafish embryo / larval assays demonstrated high safety margins, with LC50 values of 478.8 mg/L (spinach) and >480 mg/L (mango). At 480 mg/L spinach displayed developmental abnormalities and malformations. These findings demonstrate that antioxidant capacity is linked to phenolic composition, but does not predict toxicity. Thus, integrated phytochemical and safety evaluation for extracts with complex compound mixtures are critical to identify botanicals suitable for future drug development. HighlightsO_LIWarrigal spinach exhibited >10-fold higher phenolic content and antioxidant capacity than Kensington Pride mango. C_LIO_LILC-ESI-QTOF-MS/MS identified 187 metabolites, with flavonoids as the dominant phytochemical class. C_LIO_LIZebrafish assays confirmed high safety margins, demonstrating no direct correlation between antioxidant capacity and toxicity. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/720960v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@f82bbeorg.highwire.dtl.DTLVardef@ffd6d4org.highwire.dtl.DTLVardef@711481org.highwire.dtl.DTLVardef@1f94d7d_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

pharmacology and toxicology↗

bioRxiv2025

Genetic basis of traits and local adaptation in UK silver birch

Knowledge of the genomic basis of phenotypes in forest trees lags that of other economically important organisms. We sequenced the genomes of 2054 silver birch trees from 20-year-old field trials at three locations in Britain. Each trial site contains trees from the same 29 source populations, and one trial site (Drummond) is outside the climate envelope of the source sites. We discovered many single nucleotide polymorphisms (SNP), and a structural polymorphism, associated with several growth traits. Using models trained with genome-wide SNPs we estimate the genomic breeding values of 148 plus trees. We discover 117 SNPs significantly associated with source-site environmental variables, but genetic offset estimates using these SNPs provide poor predictions of tree growth rates (Drummond excluded). They are outperformed in this task by offset estimates using thousands of non-significant SNPs. Such estimates for Drummond in current climates are higher than for source sites under a future worst case climate scenario.

genomics↗

bioRxiv2024

Evidence of genetic isolation and differentiation among historically fragmented British populations of common juniper, Juniperus communis L.

Habitat fragmentation and populations isolation pose a threat to the genetic diversity and adaptability of many species. The common juniper, Juniperus communis L., a keystone species for juniper scrub habitat and one of only three conifers that are native to the UK, has been in decline for more than a century in the UK and across its European range. Remnant UK juniper populations are now highly fragmented and often small, which has raised concerns for their resilience, especially in the face of climate change and the introduction of novel pathogens, such as Phytophthora austrocedri. This work presents a baseline genetic survey of native UK juniper populations and compares patterns of diversity between populations and among three population centres in southern England, the Lake District, and Scotland using both Single Nucleotide Polymorphism (SNP) and Simple Sequence Repeat (SSR) genetic markers. The aim was to evaluate the standing genetic diversity of native juniper stands, the impacts of habitat fragmentation, and to determine whether juniper populations are genetically isolated from one another. We found that juniper populations, while not completely isolated from one another, face substantial barriers to gene flow, especially between the three population centres. These centres also show different patterns of genetic diversity, indicating varying levels of internal gene flow and inbreeding. Our findings can form a baseline from which to monitor the effectiveness of conservation activities, prioritize populations of concern, and guide genetic rescue efforts.

genetics↗

bioRxiv2024

Not like other conifers: evaluation of phenotypic diversity in British common juniper, Juniperus communis, indicates genetic isolation and local adaptations among remnant populations

Habitat fragmentation and genetic isolation pose threats to the genetic diversity and resilience of natural populations. Protecting the genetic diversity of populations, and the processes that sustain it, optimises their ability to adapt to changing conditions and new threats: conservation efforts with this specific goal are known as "dynamic conservation." The common juniper, Juniperus communis, is a keystone species that provides habitat and resources for many plants and animals. It is a highly polymorphic species, and across its natural range it grows in a variety of habitats and growth forms. Juniper populations have been shrinking and becoming increasingly fragmented for over a century in the UK and elsewhere in Europe, raising concerns about the genetic diversity present in juniper populations and their ability to adapt to changing conditions, or their adaptive potential. This paper presents an analysis of the partitioning of phenotypic diversity among regions, populations and families from 16 UK populations assessed in a common garden trial. Our findings suggest high phenotypic variation among populations compared to the variation among families within populations, indicating barriers to gene flow between juniper populations, relatively homogenous populations and, consequently, potentially reduced adaptive potential. This information is a useful baseline for conservation managers and can also help to infer the genetic diversity and adaptive potential of populations.

genetics↗

bioRxiv2023

Conifers concentrate large numbers of NLR immune receptor genes on one chromosome

Nucleotide-binding domain and Leucine-rich Repeat (NLR) immune receptor genes form a major line of defence in plants, acting in both pathogen recognition and resistance machinery activation. NLRs are reported to form large gene clusters in limber pine (Pinus flexilis) but it is unknown how widespread this genomic architecture may be among the extant species of conifers (Pinophyta). We used comparative genomic analyses to assess patterns in the abundance, diversity and genomic distribution of NLR genes. Chromosome-level whole genome assemblies and high-density linkage maps in the Pinaceae, Cupressaceae, Taxaceae and other gymnosperms were scanned for NLR genes using existing and customised pipelines. Discovered genes were mapped across chromosomes and linkage groups, and analysed phylogenetically for evolutionary history. Conifer genomes are characterised by dense clusters of NLR genes, highly localised on one chromosome. These clusters are rich in TNL-encoding genes, which seem to have formed through multiple tandem duplication events. In contrast to angiosperms and non-coniferous gymnosperms, genomic clustering of NLR genes is ubiquitous in conifers. NLR-dense genomic regions are likely to influence a large part of the plants resistance, informing our understanding of adaptation to biotic stress and the development of genetic resources through breeding. Plain language summaryNLR immune receptor genes are important in pest, disease and drought resistance of plants. In the giga-genomes of conifers, they concentrate on very small chromosomal regions. These regions act as important reservoirs for NLR diversity and can be used in breeding to improve the resilience of conifer trees.

genomics↗

bioRxiv2021

Adaptive introgression and standing genetic variation, two facilitators of adaptation to high latitudes in European aspen (Populus tremula L.)

Understanding local adaptation in plants from a genomic perspective has become a key research area given the ongoing climate challenge and the concomitant requirement to conserve genetic resources. Perennial plants, such as forest trees, are good models to study local adaptation given their wide geographic distribution, largely outcrossing mating systems and demographic histories. We evaluated signatures of local adaptation in European aspen (Populus tremula) across Europe by means of whole genome re-sequencing of a collection of 411 individual trees. We dissected admixture patterns between aspen lineages and observed a strong genomic mosaicism in Scandinavian trees, evidencing different colonization trajectories into the peninsula from Russia, Central and Western Europe. As a consequence of the secondary contacts between populations after the last glacial maximum (LGM), we detected an adaptive introgression event in a genome region of [~]500kb in chromosome 10, harboring a large-effect locus that has previously been shown to contribute to adaptation to the short growing seasons characteristic of northern Scandinavia. Demographic simulations and ancestry inference suggest an Eastern origin - probably Russian - of the adaptive Nordic allele which nowadays is present in a homozygous state at the north of Scandinavia. The strength of introgression and positive selection signatures in this region is a unique feature in the genome. Furthermore, we detected signals of balancing selection, shared across regional populations, that highlight the importance of standing variation as a primary source of alleles that facilitate local adaptation. Our results therefore emphasize the importance of migration-selection balance underlying the genetic architecture of key adaptive quantitative traits.

evolutionary biology↗

bioRxiv2020

Identifying and testing marker-trait associations for growth and phenology in three pine species

In tree species, genomic prediction offers the potential to forecast mature trait values in early growth stages, if robust marker-trait associations can be identified. Here we apply a novel multispecies approach using genotypes from a new genotyping array, based on 20,795 SNPs from three closely related pine species (Pinus sylvestris, Pinus uncinata and Pinus mugo), to test for associations with growth and phenology data from a common garden study. Predictive models constructed using significantly associated SNPs were then tested and applied to an independent multisite field trial of P. sylvestris and the capability to predict trait values was evaluated. One hundred and eighteen SNPs showed significant associations with the traits in the pine species. Common SNPs (MAF > 0.05) associated with bud set were only found in genes putatively involved in growth and development, whereas those associated with growth and budburst were also located in genes putatively involved in response to environment and, to a lesser extent, reproduction. At one of the two independent sites, the model we developed produced highly significant correlations between predicted values and observed height data (YA, height 2020: r = 0.376, p < 0.001). Predicted values estimated with our budburst model were weakly but positively correlated with duration of budburst at one of the sites (GS, 2015: r = 0.204, p = 0.034; 2018: r = 0.205, p = 0.034-0.037) and negatively associated with budburst timing at the other (YA: r = -0.202, p = 0.046). Genomic prediction resulted in the selection of sets of trees whose mean height was taller than the average for each site. Our results provide tentative support for the capability of prediction models to forecast trait values in trees, while highlighting the need for caution in applying them to trees grown in different environments.

plant biology↗

bioRxiv2019

Insights into protein structural, physicochemical, and functional consequences of missense variants in 1,330 disease-associated human genes

Interpretation of the colossal number of genetic variants identified from sequencing applications is one of the major bottlenecks in clinical genetics, with the inference of the effect of amino acid-substituting missense variants on protein structure and function being especially challenging. Here we evaluated the burden of amino acids affected in pathogenic variants (n=32,923) compared to the variants (n=164,915) from the general population in 1,330 disease-associated genes on forty protein features using over 14,000 experimentally-solved 3D structures. By analyzing the whole gene/variant set jointly, we identified 18 features associated with 3D mutational hotspots that are generally important for protein fitness and stability. Individual analyses performed for twenty-four protein functional classes further revealed 240 characteristics of mutational hotspots in total, including new associations recapitulating the sheer diversity across proteins essential structural regions. We demonstrated that the function-specific features of variants correspond to the readouts of mutagenesis experiments and positively correlate with clinically-interpreted pathogenic and benign missense variants. Finally, we made our results available through a web server to foster accessibility and downstream research. Our findings represent a crucial step towards translational genetics, from highlighting the impact of mutations on protein structure to rationalizing the pathogenicity of variants in terms of the perturbed molecular mechanisms.

genetics↗