Biology subjects

Gilbert, B.

Publications and source records attributed to Gilbert, B..

9 recordsLinked to original sources

bioRxiv2025

The Impact of Habitat Impermanence on Metapopulation Viability and Size

Habitat is often impermanent causing the amount and spatial distribution of habitat patches available to species to vary through time. Theory calls for metrics that fully account for the impact of habitat impermanence on metapopulations, yet all use averages that homogenize spatiotemporal impacts of habitat impermanence in some manner. We develop a novel modelling approach using a deterministic variation of the widely used spatially realistic Levins model paired with a continuous time Markov chain to capture the stochastic impacts of habitat impermanence on finite metapopulations. From this model we derive analytic expectations of metapopulation viability and size by weighting landscape capacities and equilibrium occupancies by the quasi-equilibrium distribution of habitat configurations exhibited by landscapes characterized by a simplest form of habitat impermanence (i.e. random and independent habitat patch loss and gain at constant rates). These provide expectations of metapopulation viability and size in absence of transient metapopulation dynamics. We then show how dispersal and colonization/extinction rates, relative to rates of habitat change, separately impact metapopulation viability and size. Using simulations of our model, we show the measures we propose invariably improve estimation of metapopulation viability and size from earlier estimates, but ultimately overestimate both when species less able to keep pace with rates of change from habitat impermanence in the landscapes they occupy. Our research identifies the importance of fully accounting for spatial habitat configurations through time, and highlights the importance of transient dynamics as rates of habitat impermanence increase.

ecology↗

bioRxiv2022

Reconceptualizing beta diversity: a hypervolume geometric approach

Beta diversity--the variation among community compositions in a region--is a fundamental measure of biodiversity. Despite a diverse set of measures to quantify beta diversity, most measures have posited that beta diversity is maximized when each community has a single distinct species. However, this assumption overlooks the ecological significance of species interactions and non-additivity in ecological systems, where the function and behaviour of species depend on other species in a community. Here, we introduce a geometric approach to measure beta diversity as the hypervolume of the geometric embedding of a metacommunity. This approach explicitly accounts for non-additivity and captures the idea that introducing a unique, species-rich community composition to a metacommunity increases beta diversity. We show that our hypervolume measure is closely linked to and naturally extends previous information- and variation-based measures while providing a unifying geometric framework for widely adopted extensions of beta diversity. Applying our geometric measures to empirical data, we address two long-standing questions in beta diversity research--the latitudinal pattern of beta diversity and the effect of sampling effort--and present novel ecological insights that were previously obscured by the limitations of traditional approaches. In sum, our geometric approach reconceptualizes beta diversity, offering an alternative and complementary perspective to previous measures, with immediate applicability to existing data.

ecology↗

bioRxiv2022

Vector diversity and malaria prevalence: global trends and local determinants

Identifying determinants of global infectious disease burden is a central goal of disease ecology. While it is widely accepted that host diversity structures parasite diversity and prevalence across large spatial scales, the influence of vector diversity on disease risk has rarely been examined despite the role of vectors as obligatory intermediate hosts for many parasites. Malaria, for instance, can be transmitted by over 70 species of mosquitoes, but the impact of this diversity on malaria risk remains unclear. Further, such relationships are likely dependent on the context in which disease transmission occurs, as arthropod life history and behavior are highly sensitive to environmental factors such as temperature. We studied the relationship between vector diversity, malaria prevalence, and environmental attributes using a unique dataset we curated by integrating several open-access sources. Globally, the association between vector species richness and malaria prevalence differed by latitude, indicating that this relationship is strongly dependent on underlying environmental conditions. Structural equation models further revealed different processes by which the environment impacts vector community assemblage and function, and subsequently disease prevalence, in different regions. In Africa, the environment exerted a top-down influence on disease through its role in shaping vector communities, whereas in Southeast Asia, disease prevalence is influenced by more complex interactions between the physical and socioeconomic environment (i.e., rainfall and GDP) and vector diversity across sites. This work highlights the key role of vector diversity in structuring disease distribution at large spatial scales and offers crucial insights to vector management and disease control. Significance statementThe global health threat from persistent and emerging vector-borne diseases continues to increase and is exacerbated by rapid environmental and societal change. Predicting how disease burden will shift in response to these changes necessitates a clear understanding of existing determinants of disease risk. We focused on an underappreciated potential source of variation in disease burden - vector diversity - and its role in structuring global malaria distribution. Our work revealed that vector diversity influences malaria prevalence and that the strength and nature of this association strongly depend on local environmental context. Extending disease transmission theory, surveillance, and control to embrace heterogeneity in vector community structure and function across space and time is an asset in the fight against vector-borne diseases.

ecology↗

bioRxiv2020

Climate influences the response of community functional traits to local conditions

Functional traits determine an organisms performance in a given environment and as such determine which organisms will be found where. Species respond to local conditions, but also to larger scale gradients, such as climate. Trait ecology links these responses of species to community composition and species distributions. Yet, we often do not know which environmental gradients are most important in determining community trait composition at either local or biogeographical scales, or their interaction. Here we quantify the relative contribution of local and climatic conditions to the structure and composition of functional traits found within bromeliad invertebrate communities. We conclude that climate explains more variation in invertebrate trait composition within bromeliads than does local conditions. Importantly, climate mediated the response of traits to local conditions; for example, invertebrates with benthic life-history traits increased with bromeliad water volume only under certain precipitation regimes. Our ability to detect this and other patterns hinged on the compilation of multiple fine-grained datasets, allowing us to contrast the effect of climate vs. local conditions. We suggest that, in addition to sampling communities at local scales, we need to aggregate studies that span large ranges in climate variation in order to fully understand trait filtering at local, regional and global scales.

ecology↗

bioRxiv2020

Sensing of endogenous nucleic acids by ZBP1 induces keratinocyte necroptosis and skin inflammation

Aberrant detection of endogenous nucleic acids by the immune system can cause inflammatory disease. The scaffold function of the signalling kinase RIPK1 limits spontaneous activation of the nucleic acid sensor ZBP1. Consequently, loss of RIPK1 in keratinocytes induces ZBP1-dependent necroptosis and skin inflammation. Whether nucleic acid sensing is required to activate ZBP1 in RIPK1 deficient conditions and which immune pathways are associated with skin disease remained open questions. Using knock-in mice with disrupted ZBP1 nucleic acid binding activity, we report that sensing of endogenous nucleic acids by ZBP1 is critical in driving skin pathology characterised by antiviral and IL-17 immune responses. Inducing ZBP1 expression by interferons triggers necroptosis in RIPK1-deficient keratinocytes and epidermis-specific deletion of MLKL prevents disease, demonstrating that cell-intrinsic events cause inflammation. These findings indicate that dysregulated sensing of endogenous nucleic acid by ZBP1 can drive inflammation and may contribute to the pathogenesis of IL-17-driven inflammatory skin conditions such as psoriasis. SummaryDevos, Tanghe et al. find that the recognition of endogenous nucleic acids by the nucleic acid sensor ZBP1 causes necroptosis of RIPK1-deficient keratinocytes. This process drives the development of an inflammatory skin disease characterised by an IL-17 immune response.

immunology↗

bioRxiv2019

An experimental manipulation of species’ phenologies overturns competitive hierarchies

Ecological theory produces opposing predictions about whether differences in the timing of life history transitions, or phenology, promote or limit coexistence. Phenological separation is predicted to create temporal niche differences, increasing coexistence, yet phenological separation may competitively favour one species, increasing fitness differences and hindering coexistence. We experimentally manipulated relative germination timing, a critical phenological event, of two annual grass species, Vulpia microstachys and V. octoflora, to test these contrasting predictions. We parameterized a competition model to estimate within-season niche differences, fitness differences, and coexistence, and to estimate coexistence when among-year fluctuations of germination timing occur. Increasing germination separation caused parallel changes in niche and fitness differences, with the net effect of weakening within-year coexistence. Both species experienced a competitive advantage by germinating earlier, strongly enough to allow the generally inferior competitor to exclude the other with at least a four day head start. The overall consequence of germination separation was to limit coexistence within a given year, although among-year variation in relative timing of germination was sufficient to support long-term coexistence. Our results clarify how phenological differences structure competitive interactions, and highlight the need to quantify among-year variation in these differences to better understand species coexistence.

ecology↗

bioRxiv2018

The filtering metaphor revisited: competition and environment jointly structure invasibility and coexistence

Filtering, or the reduction in species diversity that occurs because not all species can persist in all locations, is thought to unfold hierarchically, at large scales due to the environment and at small scales due to competition. However, the ecological effects of competition and the environment are not independent, and observational approaches preclude investigation into their interplay. We use a demographic approach with 30 plant species to experimentally test (i) the effect of competition on species persistence in two soil moisture environments, and (ii) the effect of environmental conditions on the mechanisms underlying competitive coexistence. We find that competitors cause differential persistence of species across environments even when these effects are lacking in the absence of competition, and that the traits that determine persistence depend on the competitive environment. Changing environmental conditions generated idiosyncratic effects on coexistence outcomes, increasing competitive exclusion of some species while promoting coexistence of others. Our results highlight the importance of considering environmental filtering in light of, rather than in isolation from, competition, and challenge community assembly models and approaches to projecting future species distributions.

ecology↗

bioRxiv2017

IMPROVEMENTS TO BAYESIAN GENE ACTIVITY STATE ESTIMATION FROM GENOME-WIDE TRANSCRIPTOMICS DATA

An important question in many biological applications, is to estimate or classify gene activity states (active or inactive) based on genome-wide transcriptomics data. Recently, we proposed a Bayesian method, titled MultiMM, which showed superior results compared to existing methods. In short, MultiMM performed better than existing methods on both simulated and real gene expression data, confirming well-known biological results and yielding better agreement with fluxomics data. Despite these promising results, MultiMM has numerous limitations. First, MultiMM leverages co-regulatory models to improve activity state estimates, but information about co-regulation is incorporated in a manner that assumes that networks are known with certainty. Second, MultiMM assumes that genes that change states in the dataset can be distinguished with certainty from those that remain in one state. Third, the model can be sensitive to extreme measures (outliers) of gene expression. In this manuscript, we propose a modified Bayesian approach, which addresses these three limitations by improving outlier handling and by explicitly modeling network and other uncertainty yielding improved gene activity state estimates when compared to MultiMM.

genomics↗

bioRxiv2017

Frequency-dependent Maternal Effects across Species and Environments

O_LIMaternal provisioning of offspring in response to environmental conditions (\"maternal environmental effects\") has been argued as the missing link in plant life histories. Although empirical evidence suggests that maternal responses to abiotic conditions are common, there is little understanding of the prevalence of maternal provisioning in competitive environments.\nC_LIO_LIWe tested how competition in two soil moisture environments affects maternal provisioning of offspring seed mass. Specifically, we varied conspecific frequency from 90% (intraspecific competition) to 10% (interspecific competition) for 15 pairs of annual plant species that occur in California.\nC_LIO_LIWe found that conspecific frequency affected maternal provisioning (seed mass) in 48% of species, and that these responses included both increased (20%) and decreased (24%) seed mass. In contrast, 68% of species responded to competition through changes in per capita fecundity (seed number), which generally decreased as conspecific frequency increased. The direction and magnitude of frequency-dependent seed mass depended on the identity of the competitor, even among species in which fecundity was not affected by competitor identity.\nC_LIO_LISynthesis. Our research demonstrates how species responses to different competitive environments manifest through maternal provisioning, and that these responses alter previous estimates of environmental maternal effects and reproductive output; future study is needed to understand their combined effects on population and community dynamics.\nC_LI

ecology↗