Jiri Hulcr
· Forest EntomologyVerifiedUniversity of Florida · Forest Resources and Conservation
Active 2004–2026
About
PitchTube is the website of the University of Florida Forest Entomology (UFFE) lab, a destination for those who love, fear, or are curious about this amazing biological system of beetles, fungi, and trees. And for those who don’t know yet, the real pitch tube is a defensive blob of resin exuded by a pine attacked by a bark beetle.
Research topics
- Biology
- Ecology
- Botany
- Evolutionary biology
- Agroforestry
- Zoology
Selected publications
Figshare · 2026-04-24
datasetOpen accessSenior authorPublic DNA archives support large-scale biodiversity assessment, yet are constrained by taxonomic misidentifications and unrecognized cryptic structure. The challenge is especially acute in hyperdiverse, economically important groups like bark and ambrosia beetles, where morphological conservatism can conceal deep genetic divergence. We applied an investigative data-mining framework to full publicly available GenBank COI sequences for this clade at the time of download, initially retrieving 8,899 sequences from more than 1,000 species. After quality filtering and replication criteria, 3,650 sequences representing 75 species were retained for analysis. Under assemble species by automatic partitioning (ASAP), all 75 species - 100% - contained multiple barcode partitions. However, divergence depth and pattern varied widely. Under a conservative criterion of p-distance, 26 species were flagged as candidate species complexes, and all the remaining ones exhibited continuous structure or fine-scale partitioning of shallow divergences between populations. Concordance delimitation indicated that these patterns are not method artefacts. While cryptic divergence is ubiquitous among scolytines, it has arisen via at least four evolutionary mechanisms, which we demonstrate using case studies. Deeply divergent geographical COI lineages suggesting cryptic complexes are demonstrated with <i>Xyleborus ferrugineus</i> (Fabricius). By contrast, shallow population structure rather than distinct lineages are shown with<i> Tomicus piniperda</i> (Linnaeus) which exhibited high haplotype diversity but minimal inter-MOTU divergence. A taxonomic name–sequence mismatch is exemplified with<i> Ambrosiodmus rubricollis </i>(Eichhoff) which comprised several deeply divergent Asian COI lineages, one of which has spread across Europe and North America. Lastly, a sharp split between European and North American lineages whose taxonomy remains unresolved is shown with<i> Dryocoetes autographus </i>(Ratzeburg). Our findings show that critically analyzed public barcodes can flag cryptic complexes (not formal species delimitation) from shallow structure and clarify the identities of globally significant invasive species. This approach - starting with all available sequences rather than hand-picked groups - provides a scalable framework to use large, uncurated genetic repositories and highlights the need for integrative taxonomy.
Figshare · 2026-04-24
datasetOpen accessSenior authorPublic DNA archives support large-scale biodiversity assessment, yet are constrained by taxonomic misidentifications and unrecognized cryptic structure. The challenge is especially acute in hyperdiverse, economically important groups like bark and ambrosia beetles, where morphological conservatism can conceal deep genetic divergence. We applied an investigative data-mining framework to full publicly available GenBank COI sequences for this clade at the time of download, initially retrieving 8,899 sequences from more than 1,000 species. After quality filtering and replication criteria, 3,650 sequences representing 75 species were retained for analysis. Under assemble species by automatic partitioning (ASAP), all 75 species - 100% - contained multiple barcode partitions. However, divergence depth and pattern varied widely. Under a conservative criterion of p-distance, 26 species were flagged as candidate species complexes, and all the remaining ones exhibited continuous structure or fine-scale partitioning of shallow divergences between populations. Concordance delimitation indicated that these patterns are not method artefacts. While cryptic divergence is ubiquitous among scolytines, it has arisen via at least four evolutionary mechanisms, which we demonstrate using case studies. Deeply divergent geographical COI lineages suggesting cryptic complexes are demonstrated with <i>Xyleborus ferrugineus</i> (Fabricius). By contrast, shallow population structure rather than distinct lineages are shown with<i> Tomicus piniperda</i> (Linnaeus) which exhibited high haplotype diversity but minimal inter-MOTU divergence. A taxonomic name–sequence mismatch is exemplified with<i> Ambrosiodmus rubricollis </i>(Eichhoff) which comprised several deeply divergent Asian COI lineages, one of which has spread across Europe and North America. Lastly, a sharp split between European and North American lineages whose taxonomy remains unresolved is shown with<i> Dryocoetes autographus </i>(Ratzeburg). Our findings show that critically analyzed public barcodes can flag cryptic complexes (not formal species delimitation) from shallow structure and clarify the identities of globally significant invasive species. This approach - starting with all available sequences rather than hand-picked groups - provides a scalable framework to use large, uncurated genetic repositories and highlights the need for integrative taxonomy.
Objective risk assessment of bark and ambrosia beetles non‐indigenous to North America
Ecological Applications · 2025-07-01 · 2 citations
articleOpen accessSenior authorPest risk assessment informs regulatory decisions to facilitate safe trade while also protecting a country's agricultural and environmental resources. The first step in pest risk assessment is pest categorization which can help determine whether an in-depth examination is needed. We created a model to predict the potential impact of non-indigenous bark and ambrosia beetles (Curculionidae: Scolytinae). This model uses biological variables derived from extensive assessment of alien species and produces a five-point scale of impact prediction. We accommodate uncertainty and missing data using random decision tree forests with Monte Carlo simulations. Non-indigenous bark beetles include both invasive species with significant ecological impacts, such as widespread tree death, and others that pose little risk. We assembled a comprehensive list of 60 introduced non-native bark beetle species in the continental United States as the training set. Forty-two potentially predictive variables were chosen from reports on behaviors, pestilence, recorded damage/interpretations in literature, biological traits, and interactions with fungi including plant pathogens. The model builds upon strategies used by USDA-APHIS in existing risk assessments, specifically the Objective Prioritization of Exotic Pests (OPEP) model, with changes in the following: (1) a transparent dataset for building and training the model enabling future updates and use in other systems, (2) uncertainty simulations using values derived from an extensive natural history matrix rather than an assumed equal distribution, and (3) predictions made on the probability of multiple impact levels, allowing users to decide based on acceptable risk. The model is designed for pest risk analysis for Scolytinae in the continental United States but can be adapted to other pests or regions. We tested the model's performance by iteratively removing each species from the training set and retraining the model. The retrained models accurately predicted the removed species. To demonstrate the model's application, we predicted the impact of scolytine beetles not yet present in the continental United States, Xylosandrus morigerus and Hypoborus ficus, plus an additional hypothetical species with no known data. Our model predicts that these species are likely to have moderate impacts and unlikely to have high impacts if they were introduced.
Fungal ecology · 2025-02-10 · 4 citations
articleOpen accessAmbrosia fungi colonize dead trees, providing nutrition for ambrosia beetles. A key aspect of this symbiosis is the ability of fungi to colonize and dominate the wood around the beetle tunnels. Hypotheses for these dynamics include active beetle management, fungal inoculation priority, and the chemical ecology of the fungus. The ecological role of allelochemicals produced by ambrosia fungi is unknown. This study presents an analysis of secondary metabolites from Geosmithia eupagioceri (Ascomycota: Hypocreales). Eight extracellular compounds were identified: 5-hydroxymethyl-2-furancarboxylic acid, several hydroxybenzoic acid derivatives, 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 also point out that these compounds also have potential to modulate the physiology of their producer, the beetle host and associated microbes through synergism.
Scolytine beetle diversity along an altitudinal gradient in Papua New Guinea
Insect Conservation and Diversity · 2025-04-03 · 4 citations
articleOpen accessSenior authorCorrespondingAbstract Tropical elevation gradients support highly diverse assemblages, but competing hypotheses suggest either peak species richness in lowland rainforests or at mid‐elevations. We investigated scolytine beetles—phloem, ambrosia and seed‐feeding beetles—along a tropical elevational gradient in Papua New Guinea. Highly standardised sampling from 200 to 3700 m above sea level (asl) identified areas of highest and lowest species richness, abundance and other biodiversity variables. Using passive flight intercept traps at eight elevations from 200 to 3500 m asl, we collected over 9600 specimens representing 215 species. Despite extensive sampling, species accumulation curves suggest that diversity was not fully exhausted. Scolytine species richness followed a unimodal distribution, peaking between 700 and 1200 m asl, supporting prior findings of highest diversity at low‐to‐mid elevations. Alternative models, such as a monotonous decrease from lowlands to higher elevations and a mid‐elevation maximum, showed lesser fit to our data. Abundance is greatest at the lowest sites, driven by a few extremely abundant species. The turnover rate—beta diversity between elevation steps—is greatest between the highest elevations. Among dominant tribes—Dryocoetini, Xyleborini and Cryphalini—species richness peaked between 700 and 2200 m asl. Taxon‐specific analyses revealed distinct patterns: Euwallacea spp. abundance uniformly declined with elevation, while other genera were driven by dominant species at different elevations. Coccotrypes and phloem‐feeding Cryphalus have undergone evolutionary radiations in New Guinea, with many species still undescribed. Species not yet known to science are most likely to be found at lower and middle elevations, where overall diversity is highest.
Florida Entomologist · 2025-01-01
articleOpen accessSenior authorAbstract Sentinel gardens are a proactive and effective tool for detecting potential pest and pathogen threats before they establish in new regions. By observing interactions between native insects and non-native plants, sentinel gardens provide direct assessments of biological risks posed by these novel interactions. As part of a global sentinel garden network, six ecologically and economically significant Asian tree species were planted in a sentinel garden established by the Forest Entomology Lab at the University of Florida in 2022. The primary goal was to detect local insect species capable of colonizing Asian tree species, which could become serious invasive pests if they are introduced to Asia. This effort complements reciprocal sentinel gardens of American trees planted in Asia. To date, five tree species have successfully established under the conditions in Florida, allowing for herbivory observations. Monitoring revealed frequent, non-lethal herbivory by various Lepidoptera across most tree species, and by sawflies on Chinese pines. Only secondary woodborers were observed colonizing dead twigs and stems, with no evidence of wood borer attacks on living trees or tree mortality.
Progress in developing a bark beetle identification tool
PLoS ONE · 2025-06-05 · 3 citations
articleOpen accessSenior authorCorrespondingThis 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 local and global attention to classify bark beetles down to the genus level from images containing multiple beetles. The methodology involves a process of image collection, preparation, and model training, leveraging pre-classified beetle species to ensure accuracy and reliability. The model's 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 model's generalization capabilities and scalability, emphasizing the integration of advanced machine learning techniques for improved species classification and the detection of invasive or undescribed species.
Figshare · 2025-01-01
datasetOpen accessSenior authorTable S2 To maximize transparency and utility of the data, here we include the full record of wood borers and the colonized plant hosts. Vitality corresponds to tree scores evaluated by standards in Table S1. The 28S and COI represent the partial sequences of large subunit ribosomal RNA gene and the partial sequences of mitochondrial cytochrome c oxidase subunit I gene. Tissues correspond to the specific tissue colonized by the sampled wood borers. The IncidenceID corresponds to the supplementary folder names of the insect's images and sequences.Data for the manuscript titled "Pre-invasion assessment of potential invasive wood borers on North American tree species in Chinese sentinel gardens"<br>
Florida Entomologist · 2025-01-02 · 2 citations
articleOpen accessSenior authorAbstract Recent surveys of bark and ambrosia beetles (Coleoptera: Curculionidae: Scolytinae) in Florida, both in natural environments and in collections, allowed us to record species new to the state or the continent, clarify the taxonomic status of rarely studied species, and propose taxonomic changes. Five new synonymys are proposed: Dryocoetoides vexans (Schedl, 1972) (= Dryocoetoides reticulatus Atkinson, 2009 syn. nov. ); Hypothenemus atomus Hopkins, 1915 (= Stephanoderes buscki Hopkins, 1915 syn. nov. ); Hypothenemus californicus Hopkins, 1915 (= Stephanoderes gossypii Hopkins, 1915, syn. nov. , Hypothenemus beameri Wood, 1954, syn. nov. ); Xyleborinus gracilis (Eichhoff, 1868) (= Xyleborus quercus Hopkins, 1915: p. 63 syn. nov. ). Hypothenemus brunneus (Hopkins, 1915) stat. res. and Monarthrum praeustum (Eggers, 1941) stat. res. are removed from synonymy and reinstated as valid species. Ambrosiophilus osumiensis (Murayama, 1934) is reported for the first time in Florida. New records to the continental United States are reported for four species: Chramesus annectens (Wood, 1956) (native to Mexico), Hypothenemus suspectus Wood, 1974 (native to Central and South America), Hypothenemus villosus Bright, 2019, Monarthrum praeustum (Eggers, 1941), and Xyleborinus subgranulatus (Eggers, 1930).
EPPO Bulletin · 2025-01-17 · 3 citations
articleOpen accessAbstract The invasive polyphagous shot hole borer Euwallacea fornicatus (Eichhoff, 1868) was recorded in a public garden in Granada province, Andalusia, Southern Spain in April, 2022. This is the first record of a self‐sustaining population of this pest in an outdoor environment in Europe. This paper describes the morphological and molecular identification of the haplotype found in Spain. A recommended regulatory response is described, including a delimiting survey and an eradication program. The Spanish government is taking action to eradicate the pest.
Recent grants
Ambrosia beetles and fungi: a comprehensive global survey of an increasingly important symbiosis
NSF · $720k · 2016–2022
NSF · $490k · 2013–2017
IRCN: Coordinating research on bark beetle - fungal interactions in South Africa and the U.S.
NSF · $497k · 2018–2024
Frequent coauthors
- 63 shared
You Li
China Agricultural University
- 36 shared
Craig Bateman
Florida Museum of Natural History
- 35 shared
James Skelton
- 32 shared
Demian F. Gómez
US Forest Service
- 29 shared
Andrew J. Johnson
- 25 shared
Jeff Eickwort
Maryland Sea Grant
- 25 shared
Miroslav Kolařík
- 25 shared
David R. Coyle
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