Biology subjects

Paquette, A.

Publications and source records attributed to Paquette, A..

13 recordsLinked to original sources

bioRxiv2026

Urbanization drives dietary specialization in insectivorous bird communities: insights from a multi-prey cafeteria experiment monitored by innovative cameras

1. Urbanization is widely associated with functional homogenization of ecological communities, including declines in insectivorous bird species and concomitant restructuring of arthropod assemblages. While these changes are often assumed to alter ecosystem functioning through trophic interactions, it remains unclear whether bird insectivory in cities can be inferred from community composition alone, or whether it also depends on which species actively forage, on natural prey availability and on the arthropod guilds exploited. 2. We hypothesized that urbanization (i) restructures both insectivorous bird communities and arthropod prey assemblages, thereby (ii) increasing divergence between trait-based potential and realized insectivory, while (iii) prey use is shaped by natural prey availability and active prey selection. 3. We used 25 plots distributed along a controlled urbanization gradient in Montreal, Canada. We combined acoustic monitoring of insectivorous bird communities, arthropod surveys, and camera-monitored cafeteria-like experiments deployed on 73 trees to quantify trait-based potential insectivory, realized insectivory through direct foraging interactions, natural prey availability and prey selection among three arthropod guilds (lepidopteran larvae, spiders and ants). 4. Urbanization reduced bird functional diversity while also decreasing the availability of high-quality prey, particularly lepidopteran larvae and spiders. Realized insectivory was consistently decoupled from community-based expectations, with actively foraging assemblages systematically less insect-specialized than predicted by broader community compositions (potential insectivory). This mismatch was non-random and only weakly related to urban and vegetation gradients. Prey use was largely independent of natural prey availability and instead reflected consistent preferences for larval prey over other guilds, with some indication that the functional composition of bird foraging assemblages further shaped which prey were exploited. 5. Our results show that realized trophic interactions emerge through successive ecological filters rather than directly from community composition: environmental conditions restructure bird communities and prey availability, subsequent foraging filters determine which species actively participate, and prey selection governs which guilds are consumed. Predicting ecosystem functioning in cities therefore requires considering not only biodiversity patterns but also the ecological processes linking community composition to realized trophic interactions.

ecology↗

bioRxiv2026

Montreal Urban Observatory: research platform to monitor urban forest ecosystems for global change adaptation and health

As urban populations grow, cities are increasingly seen not only as drivers of climate change but also as critical arenas for implementing mitigation and adaptation strategies. Urban forests and green infrastructure play a vital role in shaping environmental quality and human health, yet access to these benefits remains inequitable. The Montreal Urban Observatory was designed to investigate the complex relationships among biodiversity, ecosystem functioning, and human health. Twenty-five permanent plots were established across the Island of Montreal, strategically located along gradients in vegetation cover, population density, and mean household income. Interdisciplinary research within the Observatory focuses on themes including urban forest structure and function, abiotic conditions, biodiversity, ecological interactions, natures contributions to people, related human health outcomes, and developing novel methodological approaches. The Observatory supports long-term, cross-scale monitoring and fosters collaborative research on urban social-ecological systems, thus contributing to global initiatives to enhance urban sustainability and equity through nature-based solutions. Early results confirm the relevance of the main gradients for several organisms and response variables, from microbes to trees and abiotic factors. For example, sampling all trees, public and private, within a radius of 200m centered on each plot revealed significant differences in the diversity and structure of private and public trees, including an overwhelming dominance of Thuya occidentalis not captured in commonly used public tree inventories.

ecology↗

bioRxiv2025

Season and city shape urban bioaerosol composition beyond vegetation and socioeconomic gradients

Urban vegetation varies with socio-economic gradients, as lower-income neighborhoods often host sparser and less diverse green spaces. This disparity may affect respiratory health by influencing exposure to bioaerosols. Understanding the characteristics of this aerobiome could help anticipate risks related to allergies and other respiratory conditions. Here, we hypothesized that urban vegetation cover and socio-economic status shape urban bioaerosols. We sampled bioaerosols at 65 sites across three Canadian cities of varying population size and density using an active air sampler over four months, and characterized their bacterial, fungal, and pollen composition using amplicon sequencing. Seasonal alpha diversity varied significantly for fungi and pollen. Based on beta diversity, sampling period alone explained up to 40% of pollen, 29% of fungal, and 11% of bacterial community composition variation. In contrast, vegetation cover explained only a minor portion of the variance in bioaerosol composition, and median household income, almost none. These findings provide a critical baseline for understanding the urban aerobiome and highlight the need to study how vegetation identity and diversity, rather than cover alone, may shape bioaerosol dynamics in cities. As cities grow and urban greening initiatives expand, demystifying the aerobiome dynamics becomes an urgent public health priority.

microbiology↗

bioRxiv2025

Native species of the Atlantic Forest for urban environments based on functional groups: an approach to make cities in southern Brazil more resilient

Planting the proper trees can mitigate and adapt cities to the adverse impacts of climate change, in particular through increasing diversity. Despite being located in one of the most biodiverse countries in the world, low diversity and overabundance of exotic species in Brazilian urban forests are common. Our objective with this study is to group species based on their functional traits to provide a tool to help planners create more resistant urban forests in cities in the domain of the Dense Ombrophilous Forest (DOF), Atlantic Forest, in southern Brazil, as well as incentivize the use of DOF species based on their functional traits. We classified 77 native trees of the DOF in Santa Catarina state, southern Brazil, with potential use in urban environments into functional groups according to the following traits: seed mass, wood density, average height, and leaf persistence, using a hierarchical cluster analysis. The different groups formed represent species with different ecological strategies. Combining species from different groups will help create more resistant urban forests in cities of the DOF domain. We hope the method will also help to increase the use of native species from DOF. Furthermore, the method can be adapted to urban forests of different domains in Brazil and other countries.

ecology↗

bioRxiv2024

Urban tree diversity fosters bird insectivory despite a loss in bird diversity with urbanization

Urbanization is one of the main drivers of biotic homogenization in bird communities worldwide. Yet, only a few studies have addressed its functional consequences on the top-down control birds exert on insect herbivores. We hypothesized that their inconsistent results reflect the overlooked heterogeneity of the urban habitat for birds, and in particular the distribution and diversity of urban trees. We monitored tree diversity, bird diversity, avian predation attempts on artificial prey, and the effect of bird exclusion on insect herbivory in 97 trees distributed among 24 urban experimental plots in the city of Montreal, Canada. We characterized urbanization levels through a combination of variables related to tree density, impervious surfaces, anthropic noise, and human population density. Bird diversity decreased with increasing urbanization, whereas the frequency of generalist synurbic species increased. We found no significant relationship between predation and urbanization or between predation and bird diversity. However, tree diversity was positively correlated with predation attempts on artificial prey, irrespective of bird diversity. We revealed a mismatch between the effects of urbanization on bird diversity and on the regulation service and unraveled the functional importance of tree diversity in shaping the avian predation function in urban ecosystems. Our study advocates for the consideration of intra-urban heterogeneity in the investigation of trophic cascades within cities.

ecology↗

bioRxiv2024

Self-pruning in tree crowns is influenced by functional strategies and neighborhood interactions

As canopy closure causes forest stands to face increasing light limitation, trees lower branches begin to die back. This process, called self-pruning, defines a crowns base and depth and shapes the structure of entire stands. Self-pruning is often thought to occur after shading causes individual branches to transition from net carbon sources to sinks. Under this explanation, we would expect resource-conservative and shade-tolerant species to initiate self-pruning under deeper shade because their branches need less light to maintain a positive carbon balance. However, the notion that branches are fully autonomous may be complicated by correlative inhibition, in which plants preferentially allocate resources towards sunlit branches. Consistent with this idea, we predicted that within species, trees with sunlit tops would initiate self-pruning at a higher light threshold. Lastly, we predicted that plot-level diversity in self-pruning strategies would correlate with productivity and total crown volume. We tested these predictions in an experiment where 12 temperate tree species were planted in plots of varying diversity and composition. We measured characteristics of crown size and position as well as the light level at the crown base (denoted Lbase), which we took as an estimate of the light threshold of self-pruning. As we predicted, more shade-tolerant and resource-conservative species self-pruned at a deeper level of shade (lower Lbase). In addition, most species had higher Lbase when they had more light at the crown top, suggestive of correlative inhibition. With respect to their neighbors traits, though, conservative and acquisitive species showed contrary patterns of plasticity: conservative species had lower Lbase around conservative neighbors, while acquisitive species had lower Lbase around acquisitive neighbors. However, all species declined in crown depth when they grew alongside larger, more acquisitive neighbors. As predicted, plots with a greater interspecific diversity of Lbase had greater basal area and crown volume. Using simulations, we showed that plasticity in crown depth between monocultures and mixtures strengthened the relationship with crown volume, primarily due to competitive release experienced by acquisitive species. By placing shade-induced self-pruning in a comparative context, we clarify how forest function emerges from competition for light between individual trees.

ecology↗

bioRxiv2023

Latitudinal gradients in predation persist in urban environments

Urbanization can profoundly disrupt local ecology. But while urban areas now stretch across latitudes, little is known about urbanizations effects on macroecological patterns. We used standardized experiments to test whether urbanization disrupts latitudinal gradients in seed predation, a macroecological pattern that shapes community assembly and diversity. Using >56,000 seeds, we compared predation in urbanized and natural areas across 14,000 km of latitude, spanning the Americas. Predation increased 5-fold from high latitudes to the tropics, and latitudinal gradients in predation persisted in urban areas despite significant habitat modification. Urbanization reduced predation by vertebrates, but not invertebrates, and seemed to increase ant predation specifically. Our results show that macroecological patterns in predation intensity can persist in urbanized environments, even as urbanization alters the relative importance of predators. One-Sentence SummaryAcross 56,000 seeds and 112{degrees} of latitude, latitudinal gradients in seed predation are equally strong in natural vs. urban areas

ecology↗

bioRxiv2022

Higher aboveground carbon stocks in mixed-species planted forests than monocultures - a meta-analysis

Natural forest is declining globally as the area of planted forest increases. Planted forests are often monocultures, despite results suggesting that higher species richness improves ecosystem functioning and stability. To test if this is generally the case, we performed a meta-analysis of available results. We assessed aboveground carbon stocks in mixed-species planted forests vs (a) the average of constituent species monocultures, (b) the best constituent species monoculture, and (c) commercial species monocultures. We investigated whether any advantage of mixtures over monocultures was positively related to species richness, as well as potential mechanisms driving differences in carbon stocks between mixtures and monocultures. The meta-analysis dataset included 79 comparisons from 21 sites. Carbon stocks in mixed planted forests were higher than the average of stocks in monocultures of their constituent species, containing on average 70% more carbon. Mixed planted forests also out-performed commercial monocultures, containing on average 77% more carbon. There was c.25% more carbon in mixed planted forests relative to the best performing monocultures, although this difference was not statistically significant. Overyielding was highest in four-species mixtures (richness range 2-6 species). More data providing better coverage of richness and age gradients (study sites aged 3.5-28 years) is needed to increase confidence in these results. None of the potential mechanisms we examined (nitrogen-fixer present vs absent; native vs non-native/mixed origin; tree diversity experiment vs forestry plantation) consistently explained variation in the diversity effects. This suggests that our findings are driven by a combination of small (statistically insignificant) effects from these sources or further unidentified mechanisms or some combination of the two. We conclude that increasing tree species richness in planted forests can increase carbon stocks while bringing other potential benefits associated with diversification. However, implementation will depend on the balance of these benefits relative to the operational challenges and costs of diversification.

ecology↗

bioRxiv2021

Biotic interactions are more important at species' warm vs. cool range-edges: a synthesis

Predicting which ecological factors constrain species distributions is a fundamental question in ecology and critical to forecasting geographic responses to global change. Darwin hypothesized that abiotic factors generally impose species high-latitude and high-elevation (typically cool) range limits, whereas biotic interactions more often impose species low-latitude/low-elevation (typically warm) limits, but empirical support has been mixed. Here, we clarify three predictions arising from Darwins hypothesis, and show that previously mixed support is partially due to researchers testing different predictions. Using a comprehensive literature review (886 range limits), we find that biotic interactions, including competition, predation, and parasitism, influenced species warm limits more often than species cool limits. At cool limits, abiotic factors were consistently more important than biotic interactions, but temperature contributed strongly to cool and warm limits. Our results suggest that most range limits will be sensitive to climate warming, but warm limit responses will depend strongly on biotic interactions. O_QD"When we travel southward and see a species decreasing in numbers, we may feel sure that the cause lies quite as much in other species being favored, as in this one being hurt. (Whereas)... the number of species, and therefore of competitors, deceases northwards; hence in going northward or in ascending a mountain, we far oftener meet with stunted forms, due to the directly injurious action of climate" -Darwin 1859 C_QD

ecology↗

bioRxiv2020

Mutually inclusive mechanisms of drought-induced tree mortality

An extreme summer drought caused unprecedented tree dieback across Central Europe in 2018, highlighting the need for a better mechanistic understanding of drought-induced tree mortality. While numerous physiological risk factors have been identified, the principal mechanisms, hydraulic failure and carbon starvation, are still debated. We studied 9,435 trees from 12 temperate species planted in a diversity experiment in 2013 to assess how hydraulic traits, carbon dynamics, pest infestation, tree height and neighbourhood competition influence individual mortality risk. We observed a reduced mortality risk for trees with wider hydraulic safety margins, while a rising sugar fraction of the non-structural carbohydrate pool and bark beetle infestation were associated with higher risk. Taller trees had a lower mortality risk. The sign and magnitude of neighbourhood effects on mortality risk depended on the species-identity of the involved trees, with most species having beneficial and some having deleterious effects on their neighbours. While severe tissue dehydration causing hydraulic failure precedes drought-induced tree mortality, we show that the probability of this event depends on a series of mutually inclusive processes including pest infestation and starch depletion for osmotic adjustment, and is modulated by the size and species identity of a tree and its neighbours.

ecology↗

bioRxiv2020

Insect herbivory on urban trees: Complementary effects of tree neighbours and predation

O_LIInsect herbivory is an important component of forest ecosystems functioning and can affect tree growth and survival. Tree diversity is known to influence insect herbivory in natural forest, with most studies reporting a decrease in herbivory with increasing tree diversity. Urban ecosystems, on the other hand, differ in many ways from the forest ecosystem and the drivers of insect herbivory in cities are still debated. C_LIO_LIWe monitored 48 urban trees from five species - three native and two exotic - in three parks of Montreal (Canada) for leaf insect herbivory and predator activity on artificial larvae, and linked herbivory with both predation and tree diversity in the vicinity of focal trees. C_LIO_LILeaf insect herbivory decreased with increasing tree diversity and with increasing predator attack rate. C_LIO_LIOur findings indicate that tree diversity is a key determinant of multitrophic interactions between trees, herbivores and predators in urban environments and that managing tree diversity could contribute to pest control in cities. C_LI This article has been peer-reviewed and recommended by Peer Community in Ecology https://doi.org/10.24072/pci.ecology.100061

ecology↗

bioRxiv2020

Biotic and abiotic drivers of soil microbial functions across tree diversity experiments

AimSoil microorganisms are essential for the functioning of terrestrial ecosystems. Although soil microbial communities and functions may be linked to the tree species composition and diversity of forests, there has been no comprehensive study of how general potential relationships are and if these are context-dependent. A global network of tree diversity experiments (TreeDivNet) allows for a first examination of tree diversity-soil microbial function relationships across environmental gradients. LocationGlobal Major Taxa StudiedSoil microorganisms MethodsSoil samples collected from eleven tree diversity experiments in four biomes across four continents were used to measure soil basal respiration, microbial biomass, and carbon use efficiency using the substrate-induced respiration method. All samples were measured using the same analytical device in the same laboratory to prevent measurement bias. We used linear mixed-effects models to examine the effects of tree species diversity, environmental conditions, and their interactions on soil microbial functions. ResultsAcross biodiversity experiments, abiotic drivers, mainly soil water content, significantly increased soil microbial functions. Potential evapotranspiration (PET) increased, whereas soil C-to-N ratio (CN) decreased soil microbial functions under dry soil conditions, but high soil water content reduced the importance of other abiotic drivers. Tree species richness and phylogenetic diversity had overall similar, but weak and context-dependent (climate, soil abiotic variables) effects on soil microbial respiration. Positive tree diversity effects on soil microbial respiration were most pronounced at low PET, low soil CN, and high tree density. Soil microbial functions increased with the age of the experiment. Main conclusionsOur results point at the importance of soil water content for maintaining high levels of soil microbial functions and modulating effects of other environmental drivers. Moreover, overall tree diversity effects on soil microbial functions seem to be negligible in the short term (experiments were 1-18 years old). However, context-dependent tree diversity effects (climate, soil abiotic variables) have greater importance at high tree density, and significant effects of experimental age call for longer-term studies. Such systematic insights are key to better integrate soil carbon dynamics into the management of afforestation projects across environmental contexts, as todays reforestation efforts remain focused largely on aboveground carbon storage and are still dominated by less diverse forests stands of commercial species.

ecology↗

bioRxiv2016

Resolving the Functional Significance of BRCA1 RING Domain Missense Substitutions

Part 1Development and calibration of suitably accurate functional assays for BRCA1 RING domain and BRCT domain missense substitutions could dramatically accelerate clinical classification of rare missense substitutions observed in that gene. Leveraging data from 68,000 full sequence tests of BRCA1 and BRCA2, plus data from the limited number of already classified BRCA1 RING domain missense substitutions, we used logistic regression and related techniques to evaluate three BRCA1 RING domain assays. These were recently described high throughput yeast 2-hybrid and E3 ubiquitin ligase assays, plus a newly developed mammalian 2-hybrid assay. While there were concerns about the accuracy of the yeast 2-hybrid assay and the indirect nature of the ubiquitin ligase assay, the mammalian 2-hybrid assay had excellent correlation with existing missense substitution classifications. After calibration, this assay contributed to classification of one newly reported BRCA1 missense substitution. In principal, the mammalian 2-hybrid assay could be converted to a high-throughput format that would likely retain suitable accuracy. Part 2How does one achieve clinically applicable classification of the vast majority of all possible sequence variants in disease susceptibility genes? BRCA1 is a high-risk susceptibility gene for breast and ovarian cancer. Pathogenic protein truncating variants are scattered across the open reading frame, but all known missense substitutions that are pathogenic because of missense dysfunction are located in either the amino-terminal RING domain or the carboxy-terminal BRCT domain. Heterodimerization of the BRCA1 and BARD1 RING domains is a molecularly defined obligate activity. Hence, we tested every BRCA1 RING domain missense substitution that can be created by a single nucleotide change for heterodimerization with BARD1 in a Mammalian 2-hybrid (M2H) assay. Downstream of the M2H laboratory assay, we addressed three additional challenges: assay calibration, validation thereof, and integration of the calibrated results with other available data such as computational evidence and patient/population observational data to achieve clinically applicable classification. Overall, we found that about 20% of BRCA1 RING domain missense substitutions are pathogenic. Using a Bayesian point system for data integration and variant classification, we achieved clinical classification of about 89% of observed missense substitutions. Moreover, among missense substitutions not present in the human observational data used here, we find an additional 47 with concordant computational and functional assay evidence in favor of pathogenicity; these are particularly likely to be classified as Likely Pathogenic once human observational data become available.

genetics↗