Biology subjects

Adamson, K.

Publications and source records attributed to Adamson, K..

3 recordsLinked to original sources

bioRxiv2023

Climate, host and geography shape insect and fungal communities of trees

Non-native pests, climate change, and their interactions are likely to alter relationships between trees and tree-associated organisms with consequences for forest health. To understand and predict such changes, factors structuring tree-associated communities need to be determined. Here, we analysed the data consisting of records of insects and fungi collected from dormant twigs from 155 tree species at 51 botanical gardens or arboreta in 32 countries. Generalized dissimilarity models revealed similar relative importance of studied climatic, host-related and geographic factors on differences in tree-associated communities. Mean annual temperature, phylogenetic distance between hosts and geographic distance between locations were the major drivers of dissimilarities. The increasing importance of high temperatures on differences in studied communities indicate that climate change could affect tree-associated organisms directly and indirectly through host range shifts. Insect and fungal communities were more similar between closely related vs. distant hosts suggesting that host range shifts may facilitate the emergence of new pests. Moreover, dissimilarities among tree-associated communities increased with geographic distance suggesting that human-mediated transport may facilitate the introductions of new pests. The results of this study highlight the need to limit the establishment of tree pests and increase the resilience of forest ecosystems to changes in climate.

ecology↗

bioRxiv2019

Relative performance of Oxford Nanopore MinION vs. Pacific Biosciences Sequel third-generation sequencing platforms in identification of agricultural and forest pathogens

Culture-based molecular characterization methods have revolutionized detection of pathogens, yet these methods are either slow or imprecise. The second-generation sequencing tools have much improved precision and sensitivity of detection, but the analysis processes are costly and take several days. Of third-generation techniques, the portable Oxford Nanopore MinION device has received much attention because of its small size and possibility of rapid analysis at reasonable cost. Here, we compare the relative performance of two third-generation sequencing instruments, MinION and Pacific Biosciences Sequel in identification and diagnostics of pathogens from conifer needles and potato leaves and tubers. We demonstrate that Sequel is efficient in metabarcoding of complex samples, whereas MinION is not suited for this purpose due to the high error rate and multiple biases. However, we find that MinION can be utilized for rapid and accurate identification of dominant pathogenic organisms from plant tissues following both amplicon-based and metagenomics-based approaches. Using the PCR-free approach with shortened extraction and incubation times, we performed the entire MinION workflow from sample preparation through DNA extraction, sequencing, bioinformatics and interpretation in two and half hours. We advocate the use of MinION for rapid diagnostics of pathogens, but care needs to be taken to control or account for all potential technical biases.\n\nIMPORTANCEWe develop new and rapid protocols for MinION-based third-generation diagnostics of plant pathogens that greatly improves the speed and precision of diagnostics. Due to high error rate and technical biases in MinION, PacBio Sequel platform is more useful for amplicon-based metabarcoding from complex biological samples.

microbiology↗

bioRxiv2017

Genome-wide population diversity in Hymenoscyphus fraxineus points to an eastern Russian origin of European Ash dieback.

European forests are experiencing extensive invasion from the Ash pathogen Hymenoscyphus fraxineus, an ecological niche competitor to the non-pathogenic native congener H. albidus. We report the genome-wide diversity and population structure in Asia (native) and Europe (the introduced range). We show H. fraxineus underwent a dramatic bottleneck upon introduction to Europe around 30-40 generations ago, leaving a genomic signature, characterized by long segments of fixation, interspersed with \"diversity islands\" that are identical throughout Europe. This means no effective secondary contact with other populations has occurred. Genome-wide variation is consistently high within sampled locations in Japan and the Russian Far East, and lack of differentiation amongst Russian locations suggests extensive gene flow, similar to Europe. A local ancestry analysis supports Russia as a more likely source population than Japan. Negligible latency, rapid host-range expansion and viability of small founding populations specify strong biosecurity forewarnings against new introductions from outside Europe.

genomics↗