Biology subjects

Hulcr, J.

Publications and source records attributed to Hulcr, J..

6 recordsLinked to original sources

bioRxiv2024

Genome diversification of symbiotic fungi in beetle-fungus mutualistic symbiosis

Ambrosia beetles and their fungal symbionts represent a widespread and diverse insect-fungus mutualism. This study investigates the genomic adaptations associated with the evolution of the ambrosia lifestyle across multiple fungal lineages. We performed comparative genomic analyses on 70 fungal genomes from four families (Irpicaceae, Ceratocystidaceae, Nectriaceae, and Ophiostomataceae), including 24 ambrosia and 34 non-ambrosia lineages. Our phylogenomic analyses reveal multiple independent colonization of insect vectors by the fungi, spanning from the mid-Cretaceous (114.6 Ma) to the early Quaternary (1.9 Ma). Contrary to expectations for obligate symbionts, ambrosia fungi showed no significant genome-wide reductions in size, gene count, or secreted protein repertoire compared to their non-symbiotic relatives. Instead, we observed conservation of most assessed genomic features; where genome traits differ between free-living relatives and ambrosia fungi, the changes are lineage-specific, not convergent. Key findings include lineage-specific expansions in carbohydrate-active enzyme families (AA4 in Nectriaceae, CE4 in Ophiostomataceae, and GH3 in Ophiostomataceae and Ceratocystidaceae), suggesting potential enhancement or loss of lignin modification, hemicellulose deacetylation, and cellulose degradation in different ambrosia lineages. Repeat-Induced Point mutation analysis revealed family-specific patterns rather than lifestyle-associated differences. These results highlight the diverse genomic strategies employed by ambrosia fungi, demonstrating that symbiont evolution can proceed through refined, lineage-specific changes rather than genome-wide, or convergent alterations. Unlike other insect-associated fungi, ambrosia fungi do not seem to be domesticated crops, but rather free-living fungi which co-opted wood boring beetles as vectors via subtle, lineage-specific adaptations.

evolutionary biology↗

bioRxiv2024

Progress in Developing a Bark Beetle Identification Tool

This study presents an initial model for bark beetle identification, serving as a foundational step toward developing a fully functional and practical identification tool. Bark beetles are known for extensive damage to forests globally, as well as for uniform and homoplastic morphology which poses identification challenges. Utilizing a MaxViT-based deep learning backbone which utilizes blocked local and dilated global attention to classify bark beetles down to the genus level from images containing multiple beetles. The methodology involves a comprehensive process of image collection, preparation, and model training, leveraging pre-classified beetle species to ensure accuracy and reliability. The models F1 score estimates of 0.99 and 1.0 indicates a strong ability to accurately classify genera in the collected data, including those previously unknown to the model. This makes it a valuable first step towards building a tool for applications in forest management and ecological research. While the current model distinguishes among 12 genera, further refinement and additional data will be necessary to achieve reliable species-level identification, which is particularly important for detecting new invasive species. Despite the controlled conditions of image collection and potential challenges in real-world application, this study provides the first model capable of identifying the bark beetle genera, and by far the largest training set of images for any comparable insect group. We also designed a function that reports if a species appears to be unknown. Further research is suggested to enhance the models generalization capabilities and scalability, emphasizing the integration of advanced machine learning techniques for improved species classification and the detection of invasive or undescribed species.

ecology↗

bioRxiv2024

Secondary metabolites and their impact on symbiotic interactions in the ambrosia fungus Geosmithia eupagioceri

Ambrosia fungi colonize freshly dead trees, sequester nutrients, and serve as nutritional source for ambrosia beetles in exchange for dispersal. A key aspect of this symbiosis is the ability of fungi to colonize and dominate the wood around the beetle tunnels, forming a monospecific nutritional mycelium in the beetle gallery. Hypotheses for these dynamics include active beetle management, fungal inoculation priority, and the funguss chemical ecology facilitating resource capture and competition. The ecological role of allelochemicals produced by ambrosia fungi is unknown, although they may suppress microbes while being harmless to beetles, which has potential medical or food technology applications. This study presents a comprehensive analysis of secondary metabolites from the ambrosia fungus Geosmithia eupagioceri (Ascomycota: Hypocreales). Eight extracellular compounds were identified in vitro: 5-hydroxymethyl-2-furancarboxylic acid, 4-hydroxybenzoic acid, 2,3-dihydroxybenzoic acid, 3,4-dihydroxybenzoic acid, 4-hydroxyphenylacetic acid (4-HPA), 4-HPA methyl ester, tyrosol, and thymine. Most compounds show cross-taxon activity, suppressing the growth of bacteria, fungi, a nematode, and a mite. We have shown that often overlooked chemically simple compounds may have activities leading to increased fitness of beetle hosts, including previously unconsidered activity against mites and nematodes. For the first time, we point out that these compounds also have the previously unconsidered potential to modulate the physiology of their producer (by inducing symbiotic morphology by quorum sensing mechanisms), the beetle host and associated microbes through synergism. Furthermore, we have shown that the ambrosia fungi have biotechnological potential in the search for growth suppressors of microorganisms and invertebrates, not toxic to humans. IMPORTANCEBark and ambrosia beetles and their microbial symbionts play crucial roles in forest ecosystems by aiding in the decomposition of dead trees, nutrient cycling, and habitat creation. However, they can cause extensive damage to both natural and planted forests by killing trees. Our study has led to a fundamental shift in the understanding of interactions between beetle symbiotic fungi and the environment, mediated by secondary metabolites. Newly, we show that these substances can not only be antimicrobial but also suppress the growth of mites, nematodes, but also can modulate the physiology of the producer fungus and potentially the host beetle and associated microbes. Our study, although conducted on a relatively artificial system with the need for validation on other lineages of ambrosia fungi, suggests entirely new research directions in the understanding of bark beetle holobiont and ambrosia beetles.

microbiology↗

bioRxiv2023

The worldwide invasion history of a pest ambrosia beetle inferred using population genomics

Xylosandrus crassiusculus, a fungus-farming wood borer native to Southeastern Asia, is the most rapidly spreading invasive ambrosia species worldwide. Previous studies focusing on its genetic structure suggested the existence of cryptic genetic variation in this species. Yet, these studies used different genetic markers, focused on different geographical areas, and did not include Europe. Our first goal was to determine the worldwide genetic structure of this species based on both mitochondrial and genomic markers. Our second goal was to study X. crassiusculus invasion history on a global level and identify the origins of the invasion in Europe. We used a COI and RAD sequencing design to characterize 188 and 206 specimens worldwide, building the most comprehensive genetic dataset for any ambrosia beetle to date. The results were largely consistent between markers. Two differentiated genetic clusters were invasive, albeit in different regions of the world. The two markers were inconsistent only for a few specimens found exclusively in Japan. Mainland USA could have acted as a source for further expansion to Canada and Argentina through stepping-stone expansion and bridgehead events. We showed that Europe was only colonized by Cluster 2 through a complex invasion history including several arrivals from multiple origins in the native area, and possibly including bridgehead from the USA. Our results also suggested that Spain was colonized directly from Italy through intracontinental dispersion. It is unclear whether the mutually exclusive allopatric distribution of the two Clusters is due to neutral effects or due to different ecological requirements.

zoology↗

bioRxiv2022

Cosmopolitan Scolytinae: strong common drivers but too many singularities for accurate prediction

AimMany scolytine beetle species have been expanding their range in new territories across geographic barriers, traveling with wood, wood products and plants for planting, sometimes with a high impact on plant health. Here we attempt to quantify the mobility of these cosmopolitan species and to identify the biological drivers of mobility and impact. LocationWorld Major taxa studiedColeoptera; Curculionidae; Scolytinae MethodsMobility was estimated by counting the numbers of landmasses (contiguous pieces of land, surrounded by ocean or sea) colonized by each species. A series of potential drivers (taxonomic tribes; feeding habits; polyphagy; reproductive strategy; host taxa; pheromones and primary attractants) as well as impact on host health were recorded. Results163 species were identified, out of 5546 counted in the whole subfamily. Four tribes (Xyleborini; Ipini; Crypturgini; Hylastini) were significantly over-represented, and two others (Corthylini; Hexacolini) were under-represented. 53% of the 163 species are inbreeding, a very significant excess as compared to the whole subfamily (29%). The inbreeders colonized more landmasses than the outbreeders. There is a significant relationship between the number of host families attacked by a species and the number of colonized landmasses. Species restricted to conifers colonized fewer landmasses than hardwood generalists. Species attacking both types of hosts are the most mobile. Most of the invasive species respond to host primary attractants, only one quarter respond to pheromones. All very mobile species respond to primary attractants, and none responds to pheromones. Very mobile species are all associated with a high or moderate impact. Main conclusionsThe most mobile species belong for a large part to a limited number of subtribes. They are often inbreeding, polyphagous and respond to primary attractants but do not produce pheromones. However, many species that do not, or only partly, belong to these categories, have established in several landmasses, sometimes with a high impact. For example, the outbreeding Scolytus multistriatus, that attacks only 3 host families and produces aggregation pheromones, has established in thirteen landmasses, with a high impact. Therefore, risk prediction needs to assess diversity of species-specific biological traits beyond the few routinely analyzed in literature.

ecology↗

bioRxiv2021

Public science data suggest that fish is the most important factor in reducing small pond biodiversity in Czechia

AO_SCPLOWBSTRACTC_SCPLOWThis project tested a public-science approach to the assessment of freshwater habitat quality via simple invertebrate sampling. We combined a mobile phone application and simple instruction to children to sample 50 ponds in Central Czechia, and we analyzed the data using a standard ecological statistics approach. Despite the limitation in scope and taxonomic precision, our data revealed the same patterns as academic studies of the same topic. Specifically, we conclude that the main cause of invertebrate community decline is fish overstocking, while diverse invertebrate communities require aquatic macrophytes. Pollution detectable by children has an effect on invertebrate community structure, but a different effect than fish has, and not as statistically robust. Importantly, almost all large ponds were found overstocked with fish; therefore, they support not more diversity than small ponds, but less, and serve as ecological traps. Our findings suggest that pond conservation should focus primarily on the restoration of aquatic vegetation, and that the most effective approach will be the removal of excessive fish.

ecology↗