Biology subjects

Knight, T.

Publications and source records attributed to Knight, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Optimizing plant species selection for automated monitoring of plant-pollinator interactions

Automated monitoring camera systems offer an efficient approach for quantifying pollinator biodiversity and plant-pollinator interactions, but financial and logistical constraints limit the number of flowering plant species that can be monitored. Using a large European database of plant-pollinator networks, we evaluated whether plant subsampling can capture key metrics of interest (i.e. pollinator richness and network structure). We compared abundance-based, flower-shape-informed, phylogenetically informed and random plant sampling. Abundance-based sampling consistently outperformed random sampling, while adding flower shape provided little additional benefit and phylogenetic selection performed similarly to random sampling. Overall, monitoring 12-15 flowering species was sufficient to characterize key network properties across varying community sizes. Performance of abundance-based plant sampling declined in species-rich communities and when rare but highly attractive plants were present in the community, while a specific subset of pollinator species was consistently missed even by the best sampling strategy. Based on their relative contribution to interactions within each network, only 12.6% of pollinator species accounted for 95% of interactions, suggesting that AI classifiers could prioritize a relatively small subset of species. Our results provide practical guidance for designing efficient camera-based pollinator monitoring schemes at large spatial scales.

ecology↗

bioRxiv2026

Water-related leaf traits associated with epiphytism in the Neotropical megadiverse genus Anthurium (Araceae)

Background and Aims Epiphytes comprise approximately 10% of global vascular plant diversity and play key roles in many tropical ecosystems. They possess traits allowing survival under limited water availability (i.e. the epiphytic trait syndrome), but knowledge of these trait combinations is taxonomically biased and their generality remains unclear. The megadiverse genus Anthurium (Araceae), with ~600 epiphytic species, offers an opportunity to address this gap by examining patterns of leaf trait covariation, their phylogenetic context, and differences among life forms. Methods A common garden experiment was conducted using 40 species from 13 sections spanning a gradient of epiphytic incidence. Twenty-one anatomical, morphological, and physiological leaf traits were quantified. Patterns of trait variation were assessed, and associations between leaf traits and epiphytism were evaluated both with and without accounting for phylogenetic relationships. Key Results Leaf trait variation was captured by two principal components. The first axis was negatively associated with stomatal density and size, leaf thickness, and leaf water content, while the second axis described a trade-off between leaf mass per area (LMA) and water loss rate. Epiphytic species generally exhibited smaller, more numerous stomata and higher LMA, consistent with adaptations for water retention. Epiphytism showed a phylogenetic signal; however, trait covariation patterns were not influenced by phylogenetic relatedness. Conclusions We found consistent associations between epiphytism and several water-related leaf traits in Anthurium, but some of these associations departed from general expectations of an epiphytic trait syndrome. Water-related traits showed variable phylogenetic signal and reflected multiple functional strategies for coping with intermittent water supply. These findings highlight the diversity of functional strategies underlying epiphytism and expand current understanding beyond well-studied taxa.

plant biology↗

bioRxiv2026

Seasonal variation mediates the importance of species attributes in plant-pollinator interactions

Predicting species interactions remains a major challenge, as multiple species attributes operate simultaneously and their relative importance may vary seasonally and with temporal resolution. Here, we assess how the relative contributions of abundance, trait matching, and phenology to plant-pollinator interactions vary through a flowering season and across temporal resolutions using interaction data from three European botanical gardens. We show that predictive models explain a substantial proportion of variation in visitation patterns, with floral and pollinator abundances consistently explaining most variation across the flowering season. Trait matching between pollinator body size and floral size also contributes to visitation patterns, playing a secondary but persistent role in shaping interactions, while phenology plays a relatively minor role at broader temporal resolutions but becomes more important at finer temporal scales. Additionally, null models accounting for spatio-temporal variation in floral and pollinator abundance reveal consistent patterns of pollinator preference and avoidance, indicating that abundance alone cannot explain the observed interaction patterns. Our results show that seasonal variation and temporal resolution differentially shape the importance of species attributes, highlighting the need for multi-variable approaches that account for temporal dynamics to accurately explain and predict ecological interactions.

ecology↗

bioRxiv2026

Herbivores and pathogens can modulate plant population responses to future climate conditions

Climate change is expected to alter plant populations not only through direct environmental shifts but also via changes in biotic interactions, such as with herbivores and pathogens. As plant species are also expected to differ in their responses to both climate and antagonists, plant responses to both factors are expected to be variable and species-specific. To assess whether interactive effects of climate and antagonists on plant population dynamics are common and whether the strength and direction of plant responses vary across species, we conducted a multi-year field experiment that manipulated realistic climate change and experimentally reduced insect herbivores and fungal pathogens. We measured responses of plant vital rates, such as survivorship, growth, and reproduction across six grassland species. Using Integral Projection Models (IPMs) and Life Table Response Experiments (LTREs), we quantified changes in population growth rate across experimental treatments and the contribution of each vital rate to that observed change. Two of the study species declined so drastically over the course of the experiment that demographic quantification of population growth rates was not possible. From the remaining species, Bromus erectus and Plantago lanceolata show significant interactive responses of climate and antagonist reduction on population growth rates. In contrast, Dianthus carthusianorum and Tragopogon orientalis showed limited responses to experimental treatments. Notably, our results indicate that in some species biotic interactions may amplify the effects of climate change: the presence of plant antagonists exacerbates the negative effects of the future climate treatment on plant population dynamics. Our findings highlight the complexity in predicting plant population responses to climate change and provide insights for grassland management under future environmental conditions.

ecology↗

bioRxiv2026

Organoid-like Functional Adrenal Gland Cortex Derived From Human Pluripotent Stem Cells

The adrenal cortex is a critical for life endocrine system. It manages metabolic homeostasis, electrolyte balance, stress response, and sex development. This is accomplished through the release of various steroids from a dynamically changing landscape of concentric cellular zones/layers. Adrenocortical dysfunction is implicated in pathologies ranging from adrenal insufficiency to hypertension. The in-depth investigation of adrenal gland biology, pathology and drug discovery has been hampered by a lack of human, experimentally tractable models. Particularly missing are models that recapitulate the cellular diversity of the adrenal cortex with representation of all fetal and adult cell layers and the capsule. Here, we employ human pluripotent stem cells (hPSCs) to generate cells of all three cortex zones alongside capsular cells in a single 2D platform. This platform mimics the cellular diversity expected from an organoid, yet it provides the simplicity of monolayer cultures, that are better suited for drug discovery and high-throughput settings. These cultures secrete zone-specific steroids (cortisol, aldosterone, and DHEA-S) and exhibit robust, physiologically relevant ACTH stimulation responses. Transcriptomic analysis revealed sequential acquisition of profiles consistent with adrenocortical development, zonation, and signaling programs consistent with zone maintenance. Our platform is validated by a literature meta-analysis that defines transcriptomic signatures for each human cortical cell type, spanning fetal and adult stages. Together, this novel adrenocortical platform enables investigation of adrenal development, disease mechanisms, and therapeutic strategies. Significance StatementWe describe a hPSC-based 2D differentiation strategy with the cell type complexity of an organoid and the technical simplicity necessary for high-throughput assays. The platform contains all cortical subtypes that mediate electrolyte regulation, stress response, sex development and self-maintenance of the tissue. This co-differentiation offers a unique opportunity to study human adrenal development, biology, pathology and enables drug discovery.

developmental biology↗

bioRxiv2026

Molecular Basis of Histone H3 Reading and Writing by Legionella pneumophila SET Domain Lysine Methyltransferases

RomA and its highly conserved strain ortholog LegAS4 are SET and ankyrin domain-containing effector proteins of the intracellular bacterial pathogen Legionella pneumophila. These enzymes are secreted into host cells, where they translocate to the nucleus and methylate Lys14 in histone H3 (H3K14), a novel post-translation modification (PTM) that reprograms gene expression and promotes bacterial replication. To elucidate their H3K14 substrate specificity, we determined the crystal structures of LegAS4 and RomA bound to histone H3 peptides and characterized nucleosome binding and methylation by the enzymes. The results reveal a distinctive bipartite engagement of the histone H3 N-terminal tail by the enzymes SET and ankyrin domains. Further, the ankyrin domain distinguishes different PTMs at H3R2 and H3K4, which is crucial for nucleosome engagement and H3K14 methylation. Together, these studies yield new insights into histone H3 reading and writing by the L. pneumophila histone lysine methyltransferases during host cell infection.

biochemistry↗

bioRxiv2026

Duplicating At-Risk Breadfruit (Artocarpus spp.) Accessions Using Air-Layer Propagation

Breadfruit (Artocarpus altilis (Parkinson) Fosberg) is a culturally and nutritionally significant perennial crop of the Pacific Islands. National Tropical Botanical Gardens Kahanu Garden (Maui, Hawai i) maintains a breadfruit collection representing more than 150 traditional varieties, some unique or irreplaceable and requiring safety duplication to safeguard genetic diversity. However, aging trees exhibit variable vigor, potentially limiting clonal propagation outcomes. We assessed air layering as a strategy for conservation duplication, conducting 163 air-layer attempts across 26 priority accessions. We evaluated the influence of tree vigor, age, and branch characteristics on rooting success and survival to out-planting. Overall, 17% successfully rooted and 75% of those survived to out-planting, resulting in successful duplication of 16 of 26 at-risk accessions. Rooting success differed among vigor classes (33% for high-vigor trees; 11-16% for normal and feeble trees) and increased modestly with source tree age, while survival to out-planting declined with increasing age. Branch length and fruiting season were not associated with outcomes. These findings indicate that air layering can support conservation propagation in living collections, but success is strongly influenced by source tree age and condition. Initiating safety duplication while trees are physiologically robust is likely to improve long-term conservation outcomes.

plant biology↗

bioRxiv2025

Two hundred years of changes in orchid pollination revealed using herbarium specimens

Orchids are one of the most diverse plant families and are renowned for their highly specialised interactions with pollinators. Despite growing evidence of orchid population decline, pollinator decline and rising concerns for orchid reproductive success, long-term changes remain poorly understood. To address this gap, we analysed changes in pollinarium removal, as a proxy for pollination success, in herbarium specimens of three species-rich orchid genera (Disa, Oncidium and Ophrys) hosted at the Royal Botanic Gardens, Kew, which has a rich and diverse orchid collection spanning the past two centuries. The selected genera occur in different major regions (subtropical and tropical Africa, predominantly temperate Europe, and tropical America, respectively). Our analysis reveals that pollinarium removal declined significantly in Disa and Oncidium, particularly among species with deceptive strategies or specialised pollination mechanisms. In contrast, Ophrys showed a significant increase, driven by Apidae-pollinated species, whereas pollinarium removal for Andrenidae-pollinated species declined over time. These contrasting findings reflect the role of orchid identity, pollinator availability and pollination strategy in shaping reproductive success under anthropogenic change. Overall, this study demonstrates the power of herbarium specimens to reveal long-term ecological changes, providing unique insights into the response of specific plant-pollinator interactions to increasing anthropogenic pressure.

plant biology↗

bioRxiv2025

Conditioned orienting predicts preference for, and affective response to, amphetamine after multiple exposures in male rats.

Conditioned orienting (OR) is a form of cue-directed behavior that is thought to reflect a behavioral phenotype of increased incentive-motivational processing of conditioned stimuli. Previous research has shown that OR also represents a cognitive phenotype that includes impaired attentional function and response inhibition, increased novelty seeking and, in females, resistance to extinction of conditioned place preference (CPP) for the stimulant drug amphetamine (AMP). The following experiments aim to increase our understanding of the OR cognitive phenotype in drug reward processing in male rats. In the first experiment, preference for AMP in males with or without an OR phenotype is assessed using CPP. In the second experiment, our understanding of OR as a predictor of AMP reward response is expanded by measuring potential behavioral mechanisms including affective and motor response to multiple AMP administrations. The results of the two experiments suggest that while the OR phenotype is not a predictor of resistance to extinction of AMP preference in males, OR as a discrete response variable predicts AMP preference after repeated exposures (i.e., AMP challenge). Moreover, we observed that rats with an OR phenotype had a higher positive affective response, measured via ultrasonic vocalizations (USVs) in the 50 kHz range, after multiple AMP administrations. OR scores predicted USVs but did not alter the gross motor response to AMP. Taken together, these results suggest that orienting behavior is a predictor of AMP preference in males, particularly after multiple exposures, and that one behavioral mechanism that could explain this is that male Orienters have a strong positive affective response to AMP.

animal behavior and cognition↗

bioRxiv2025

Climatic niche conservatism in non-native plants depends on introduction history and biogeographic context

Many tools informing preventive invasion management build on the assumption that introduced species will conserve their climatic niches outside their native ranges. Previous research testing the validity of this assumption found contradictory results regarding niche conservatism vs. niche switching for non-native species. An open question is in how far these contradictions reflect context dependency, yet only few studies compared the niche dynamics of species introduced to multiple regions. Here, we used an ordination-based approach to quantify the climatic niche changes (stability, unfilling, expansion) of 316 plant species introduced to eight different regions across the world, including the Pacific region with extreme isolation between island groups. We then performed multiple phylogenetic regressions to assess how the regional context and species characteristics affect niche dynamics. Niche conservatism varied across regions, even within species. While niche expansion into previously unoccupied climates was generally low, niche unfilling varied strongly between regions. Generally, region-specific introduction history and species biogeographic attributes were more important for explaining niche changes than ecological traits. Niche expansion was consistently higher for species with small native range sizes, and niche stability increased. In contrast, niche unfilling decreased with time since introduction which could suggest that the lack of niche conservatism observed in many regions might be transient and potentially related to dispersal limitations. Overall, our results shed light on the context dependency of climatic niche changes when species are introduced to new regions, highlighting that the species and region-specific context should be accounted for when assessing the potential for niche changes. Significance StatementAs non-native species are introduced to new regions by humans, they may occupy the same climatic conditions as in their native ranges, leave parts of their native niche unfilled or expanding into previously unoccupied conditions. Knowing to which extent these niche dynamics generally occur is essential for understanding and managing biological invasions. Here, we evaluate regional differences in the climatic niche dynamics of non-native plants that were introduced to multiple regions across the world. We found marked variation across regions, influenced by factors such as the time that has passed since species were introduced, or biogeographic attributes of both the native and non-native ranges. These findings indicate that a lack of apparent niche changes is likely a temporary phenomenon.

ecology↗

bioRxiv2025

Alterations in Lipid Saturation Trigger Remodeling of the Outer Mitochondrial Membrane

Lipid saturation is a key determinant of membrane function and organelle health, with changes in saturation triggering adaptive quality control mechanisms to maintain membrane integrity. Among cellular membranes, the mitochondrial outer membrane (OMM) is an important interface for many cellular functions, but how lipid saturation impacts OMM function remains unclear. Here, we show that increased intracellular unsaturated fatty acids (UFAs) remodel the OMM by promoting the formation of multilamellar mitochondrial-derived compartments (MDCs), which sequester proteins and lipids from the OMM. These effects depend on the incorporation of UFAs into membrane phospholipids, suggesting that changes in membrane bilayer composition mediate this process. Furthermore, elevated UFAs impair the assembly of the OMM protein translocase (TOM) complex, with unassembled TOM components captured into MDCs. Collectively, these findings suggest that alterations in phospholipid saturation may destabilize OMM protein complexes and trigger an adaptive response to sequester excess membrane proteins through MDC formation. Significance StatementO_LIMitochondrial-derived compartments are multilamellar structures that sequester protein and lipids of the outer mitochondrial membrane in response to metabolic and membrane perturbations, but it is largely unknown how membrane fluidity influences this pathway. C_LIO_LIIncreased levels of unsaturated phospholipids may disrupt the TOM complex, a large multi-subunit complex on the outer mitochondrial membrane, to promote the formation of mitochondrial-derived compartments, while increased levels of saturated phospholipids inhibits formation of mitochondrial-derived compartments. C_LIO_LIThese findings reveal a link between phospholipid composition and protein stress in driving mitochondrial-derived compartment biogenesis, and thus mitochondrial quality control. C_LI

cell biology↗

bioRxiv2024

Uncertainty in blacklisting potential Pacific plant invaders using species distribution models

O_LIInvasive alien species pose a growing threat to global biodiversity, underscoring the need for evidence-based prevention strategies. Species distribution models (SDMs) are a widely used tool to estimate the potential distribution of alien species and to inform blacklists based on establishment risk. Yet, data limitations and modelling decisions can introduce uncertainty in these predictions. Here, we aim to quantify the contribution of four key sources of uncertainty in SDM-based blacklists: species occurrence data, environmental predictors, SDM algorithms, and thresholding methods for binarising predictions. C_LIO_LIFocusing on 82 of the most invasive plant species on the Hawaiian Islands, we built SDMs to quantify their establishment potential in the Pacific region. To assess uncertainty, we systematically varied four modelling components: species occurrence data (native vs. global), environmental predictors (climatic vs. edapho-climatic), four SDM algorithms, and three thresholding methods. From these models, we derived blacklists using three alternative blacklisting definitions and quantified the variance in establishment risk scores and resulting species rankings attributable to each source of uncertainty. C_LIO_LISDMs showed fair predictive performance overall. Among the sources of uncertainty, thresholding method had the strongest and most consistent influence on risk scores across all three blacklist definitions but resulted in only minor changes in blacklist rankings. In contrast, algorithm choice had the most pronounced effect on blacklist rankings, followed by smaller but important effects of species occurrence data and environmental predictors. Notably, models based only on native occurrences often underestimated establishment potential. C_LIO_LISDMs can provide valuable support for planning the preventive management of alien species. However, our findings show that blacklist outcomes are highly sensitive to modelling decisions. While ensemble modelling across multiple algorithms is a recommended best practice, our results reinforce the importance of incorporating global occurrence data when available and carefully evaluating the trade-offs of including additional environmental predictors. Given the strong influence of thresholding on risk scores, we emphasise the need for transparent, context-specific threshold selection. More broadly, explicitly assessing uncertainty in SDM outputs can improve the robustness of blacklists and support scientifically informed, precautionary decision-making, particularly in data-limited situations where pragmatic modelling choices must be taken. C_LI

ecology↗

bioRxiv2023

Effects of climate change and grassland management on plant population dynamics are mediated by changes in reproductive success

Climate change is one of the largest threats to grassland plant species, which can be modified by land management. Although climate change and land management can separately and interactively influence plant demography this has been rarely considered within one experimental set-up. We used a large-scale experiment to quantify the effects of grassland management, climate change and their joint effect on the demography and population growth rate of 11 native plant species. We parameterized integral projection models with four years of demographic data to project the population growth rate. We hypothesized, plants would perform better in ambient than in the future climate treatment that creates hotter and drier summer conditions and that plant performance in grazing vs. mowing would vary across species and depend on their traits. Due to extreme drought events, over half of our study species went quasi extinct, which highlights how extreme climate events can influence long term experimental results. Of the persistent species, only one supported our expectations, and the rest either had higher population growth rates in the future climate treatment or showed no significant difference in population growth between climate treatments. Species with shorter flowering durations performed better in the mowing treatment while those with longer flowering durations performed better in the grazing treatment. The population growth rates of these species were sensitive to changes in vital rates related to reproduction and recruitment. Depending on the species we found effects of land management and climate change on population growth rates but we did not find strong support for interactive effects among both factors. Experiments combined with measuring plant demographic responses provide a way to isolate the effects of different drivers on the long-term persistence of species, and to identify the demographic vital rates that are critical to manage in the future. Our study suggests that it will become increasingly difficult to maintain species with preferences for moister soil conditions, that traits such as flowering duration might predict responses to management, and that vital rates such as reproduction and recruitment are disproportionately important.

ecology↗

bioRxiv2022

Spatial replication should be prioritized to advance our understanding of population responses to climate

Understanding the responses of plant populations dynamics to climatic variability is frustrated by the need for long-term datasets. Here, we advocate for new studies that estimate the effects of climate by sampling replicate populations in locations with similar climate. We first use data analysis on spatial locations in the conterminous USA to assess how far apart spatial replicates should be from each other to minimize temporal correlations in climate. We find that on average spatial locations separated by 316 Km (SD = 149Km) have moderate (0.5) correlations in annual precipitation. Second, we use simulations to demonstrate that spatial replication can lead to substantial gains in the range of climates sampled during a given set of years so long as the climate correlations between the populations are at low to moderate levels. Third, we use simulations to quantify how many spatial replicates would be necessary to achieve the same statistical power of a single-population, long-term data set under different strengths and directions of spatial correlations in climate between spatial replicates. Our results indicate that spatial replication is an untapped opportunity to study the effects of climate on demography and to rapidly fill important knowledge gaps in the field of population ecology.

ecology↗

bioRxiv2022

Interacting abiotic and biotic drivers shape woody invasions across Hawaiian forests

The same features that generate native biodiversity patterns across and within oceanic islands over evolutionary time - climate, soil age, topography, and biotic interactions - also influence their vulnerability to biological invasions. Here, we identify the factors that shape the richness and abundance of alien woody species in forest communities across the Hawaiian archipelago, and assess the relative importance of abiotic, biotic, and anthropogenic factors and their interactions on the establishment and dominance of woody alien species. Using a database of 460 forest plots distributed across the six major Hawaiian islands, we examine variation in i) relative alien species richness and abundance as a function of abiotic and anthropogenic factors (e.g., temperature, aridity, soil age, and the human influence index) and ii) establishment and dominance of alien species as a function of the same abiotic and anthropogenic factors, as well as phylogenetic and trait distinctiveness. We found that relative alien species richness and abundance were higher in areas where temperature was high and aridity low. Gradients in temperature, aridity, soil age, and human influence also modulated the importance of biotic factors in determining establishment of alien species. In contrast, whether these alien species could become locally dominant was not strongly influenced by abiotic or biotic factors, or their interactions. Our results suggest that environmental filtering mediates the strength of biotic filtering in determining where woody aliens are able to colonize and establish on these oceanic islands, but not whether they become dominant. The context dependence of multi-species invasions highlights the complexity of developing management strategies to mitigate the biodiversity and ecosystem impacts of biological invasions.

ecology↗

bioRxiv2022

Rpadrino: an R package to access and use PADRINO, an open access database of Integral Projection Models

O_LIDiscrete time structured population projection models are an important tool for studying population dynamics. Within this field, Integral Projection Models (IPMs) have become a popular method for studying populations structured by continuously distributed traits (e.g. height, weight). Databases of discrete time, discrete state structured population models, for example DATLife (life tables) and COMPADRE & COMADRE (matrix population models), have made quantitative syntheses straightforward to implement. These efforts allow researchers to address questions in both basic and applied ecology and evolutionary biology. There are now over 300 peer-reviewed publications containing IPMs. We describe a novel framework to quickly reconstruct these models for subsequent analyses using Rpadrino R package, which serves as an interface to PADRINO, a new database of structured population models. C_LIO_LIWe introduce an R package, Rpadrino, which enables users to download, subset, reconstruct, and extend published IPMs. Rpadrino makes use of recently created software, ipmr, to provide an engine to reconstruct a wide array of IPMs from their symbolic representations and conduct subsequent analyses. Rpadrino and ipmr are extensively documented to help users learn their usage. C_LIO_LIRpadrino currently enables users to reconstruct 280 IPMs from 40 publications that describe the demography of 14 animal and 26 plant species. All of these IPMs are tested to ensure they reproduce published estimates. Rpadrino provides an interface to augment PADRINO with external data and modify parameter values, creating a platform to extend models beyond their original purpose while retaining full reproducibility. C_LIO_LIPADRINO and Rpadrino provide a toolbox for asking new questions and conducting syntheses with peer-reviewed published IPMs. Rpadrino provides a user-friendly interface so researchers do not need to worry about the database structure or syntax, and can focus on their research questions and analyses. Additionally, Rpadrino is thoroughly documented, and provides numerous examples of how to perform analyses which are not included in the packages functionality. C_LI

ecology↗

bioRxiv2022

Historical records of plant-insect interactions in subarctic Finland

Historical ecological records document the diversity and composition of communities decades or centuries ago and provide a valuable benchmark for modern comparisons. Historical datasets on plant-animal interactions allow for modern comparisons that examine the stability of species and interaction networks over long periods of time and in response to anthropogenic change. Here we present a curated dataset of interactions between plants and insects in subarctic Finland, generated from digitizing a historical document from the late 19th century and updating the taxonomy using currently accepted nomenclature. The resulting dataset contains 654 records of plant-insect interactions observed during the years 1895-1900, and includes 498 unique interactions between 86 plant species and 173 insect taxa. Syrphidae, Apidae and Muscidae were the insect families involved in most interactions, and interactions were most observed with the plant species Angelica archangelica, Salix caprea, and Chaerophyllum prescottii. Interaction data are available as csv-file and provide a valuable resource on plant-insect interactions over 120 years ago in a high latitude ecosystem that is undergoing rapid climate change.

ecology↗

bioRxiv2021

ipmr: Flexibly implement Integral Projection Models in R

O_LIIntegral projection models (IPMs) are an important tool for studying the dynamics of populations structured by one or more continuous traits (e.g. size, height, color). Researchers use IPMs to investigate questions ranging from linking drivers to plant population dynamics, planning conservation and management strategies, and quantifying selective pressures in natural populations. The popularity of stage-structured population models has been supported by R scripts and packages (e.g. IPMpack, popbio, popdemo, lefko3) aimed at ecologists, which have introduced a broad repertoire of functionality and outputs. However, pressing ecological, evolutionary, and conservation biology topics require developing more complex IPMs, and considerably more expertise to implement them. Here, we introduce ipmr, a flexible R package for building, analyzing, and interpreting IPMs. C_LIO_LIThe ipmr framework relies on the mathematical notation of the models to express them in code format. Additionally, this package decouples the model parameterization step from the model implementation step. The latter point substantially increases ipmrs flexibility to model complex life cycles and demographic processes. C_LIO_LIipmr can handle a wide variety of models, including density dependence, discretely and continuously varying stochastic environments, and multiple continuous and/or discrete traits. ipmr can accommodate models with individuals cross-classified by age and size. Furthermore, the package provides methods for demographic analyses (e.g. asymptotic and stochastic growth rates) and visualization (e.g. kernel plotting). C_LIO_LIipmr is a flexible R package for integral projection models. The package substantially reduces the amount of time required to implement general IPMs. We also provide extensive documentation with six vignettes and help files, accessible from an R session and online. C_LI

ecology↗