Biology subjects

Jones, O. R.

Publications and source records attributed to Jones, O. R..

10 recordsLinked to original sources

bioRxiv2025

Individual heterogeneity drives a plant macroparasites life history

The population dynamics and life histories of macroparasites are fundamental to examine their impacts on hosts and ecosystems. Still, macroparasite population models often ignore parasite individual heterogeneity and are rarely applied to parasitic plants, where demographic strategies are less well understood. Using a 10-year dataset on European mistletoe (Viscum album), we examine how this macroparasites traits influence its performance. V. album survival and reproduction depend on its size and, to a lesser extent, height on the host tree, with a strong growth-reproduction trade-off. We parameterise these relationships in an integral projection model to compare the life history strategy of V. album with two other macroparasites and 490 free-living plants. Contrary to our hypothesis, V. album and other macroparasites do not follow an extreme strategy, suggesting that parasitic plants may not escape the life history constraints experienced by non-parasitic plants. Our results highlight how incorporating parasite heterogeneity can improve macroparasite models.

ecology↗

bioRxiv2024

Coupling hydrodynamic drifting simulations and seasonal demographics to forecast the occurrence of jellyfish blooms

O_LIAlthough jellyfish are an important component of coastal marine communities, their public perception is often tainted by their proclivity for aggregating in vast numbers, known as jellyfish blooms. Jellyfish blooms occur worldwide and are associated with major economic ramifications, particularly throughout the fisheries, aquaculture, and tourism sectors. C_LIO_LIForecasting jellyfish blooms is critical in order to manage and mitigate their ecological and economic impacts, but the complex life cycles and cryptic life stages exhibited by most jellyfish species largely precludes accurate predictions of their temporal and spatial occurrence. C_LIO_LIHere we introduce a predictive framework, combining state-of-the-art hydrodynamic simulations and periodic population modelling approaches, to forecast spatial and temporal patterns in the formation of jellyfish blooms. While this framework is sufficiently flexible for accommodating various bloom-forming jellyfish species and impacted coastal regions worldwide, we focus on moon jellyfish (Aurelia aurita) populations within the Baltic Sea as an illustrative example. C_LIO_LIWe emphasise how, through the iterative process of forecasting and model validation, this framework can provide valuable insights for resolving key gaps in our understanding of the drivers of bloom events. Indeed, our framework offers an approach for identifying the, to date, unknown locations of polyp-beds; a crucial parameter in enhancing our capacity to accurately predict the occurrence of jellyfish blooms. Accordingly, our framework, represents a key decision-support tool for mitigating the socioeconomic impacts of bloom formation. C_LI

ecology↗

bioRxiv2023

Uncertainty propagation in matrix population models: gaps, importance, and guidelines

O_LIMatrix population models (MPMs), which describe the demographic behaviour of a population based on age or stage through discrete time, are popular in ecology, evolutionary biology, and conservation biology. MPMs provide a tool for guiding management decisions and can give insight into life history trade-offs, patterns of senescence, transient dynamics, and population trajectories. These models are parameterised with estimates of vital rates (e.g. survival and reproduction) and can have multiple layers of underlying statistical analyses, all of which introduce uncertainty. For accurate and transparent results, this uncertainty should be propagated through to quantities derived from the MPMs. However, full propagation is not always achieved, leading to omitted uncertainty, and negative consequences for the reliability of inferences drawn. C_LIO_LIWe summarised the state-of-the-art regarding vital rate uncertainty reporting and propagation, by reviewing papers using MPMs from 2010-2019. We then used reported uncertainties as the basis for a simulation study to explore the impact of uncertainty omission on inferences drawn from the analysis of MPMs. We simulated four scenarios of vital rate propagation and evaluated their impact on population growth rate estimates. C_LIO_LIAlthough around 78% of MPM papers report some kind of uncertainty in their findings, only half of those report uncertainty in all aspects. Additionally, only 31% of papers fully propagate uncertainty through to derived quantities. Our simulations demonstrate that, even under a median uncertainty level, incomplete propagation introduces bias. Omitting uncertainty may substantially alter conclusions, particularly for results showing small changes in population size. Biased conclusions were most common when uncertainty in the most influential vital rates for population growth were omitted. C_LIO_LIWe suggest comprehensive guidelines for reporting and propagating uncertainty in MPMs. Standardising methods and reporting will increase the reliability of MPMs and enhance the comparability of different models. These guidelines will improve the accuracy, transparency, and reliability of population projections, increasing our confidence in results that can inform conservation efforts, ultimately contributing to biodiversity preservation. C_LI

ecology↗

bioRxiv2023

A standard protocol to report discrete stage-structured demographic information

O_LIStage-based demographic methods, such as matrix population models (MPMs), are powerful tools used to address a broad range of fundamental questions in ecology, evolutionary biology, and conservation science. Accordingly, MPMs now exist for over 3,000 species worldwide. These data are being digitised as an ongoing process and periodically released into two large open-access online repositories: the COMPADRE Plant Matrix Database and the COMADRE Animal Matrix Database. During the last decade, data archiving and curation of COMPADRE and COMADRE, and subsequent comparative research, have revealed pronounced variation in how MPMs are parameterized and reported. C_LIO_LIHere, we summarise current issues related to the parameterisation and reporting of MPMs that arise most frequently and outline how they affect MPM construction, analysis, and interpretation. To quantify variation in how MPMs are reported, we present results from a survey identifying key aspects of MPMs that are frequently unreported in manuscripts. We then screen COMPADRE and COMADRE to quantify how often key pieces of information are omitted from manuscripts using MPMs. C_LIO_LIOver 80% of surveyed researchers (n=60) state a clear benefit to adopting more standardised methodologies for reporting MPMs. Furthermore, over 85% of the 300 MPMs assessed from COMPADRE and COMADRE omitted one or more elements that are key to their accurate interpretation. Based on these insights, we identify fundamental issues that can arise from MPM construction and communication and provide suggestions to improve clarity, reproducibility, and future research utilising MPMs and their required metadata. To fortify reproducibility and empower researchers to take full advantage of their demographic data, we introduce a standardized protocol to present MPMs in publications. This standard is linked to www.compadre-db.org, so that authors wishing to archive their MPMs can do so prior to submission of publications, following examples from other open-access repositories such as DRYAD, Figshare, and Zenodo. C_LIO_LICombining and standardising MPMs parameterized from populations around the globe and across the tree of life opens up powerful research opportunities in evolutionary biology, ecology, and conservation research. However, this potential can only be fully realised by adopting standardised methods to ensure reproducibility. C_LI

ecology↗

bioRxiv2021

Plant demographic knowledge is biased towards short-term studies of temperate-region herbaceous perennials

O_LIPlant population dynamics research has a long history, and data collection rates have increased through time. The inclusion of this information in databases enables researchers to investigate the drivers of demographic patterns globally and study life history evolution. C_LIO_LIStudies aiming to generalise demographic patterns rely on data being derived from a representative sample of populations. However, the data are likely to be biased, both in terms of the species and ecoregions investigated and in how the original studies were conducted. C_LIO_LIMatrix population models (MPMs) are a widely-used tool in plant demography, so an assessment of publications that have used MPMs is a convenient way to assess the distribution of plant demographic knowledge. We assessed bias in this knowledge using data from the COMPADRE Plant Matrix Database, which contains MPMs for almost 800 plant species. C_LIO_LIWe show that tree species and tropical ecoregions are under-represented, while herbaceous perennials and temperate ecoregions are over-represented. In addition, there is a positive association between the number of studies per country and the wealth of the country. Furthermore, we found a strong tendency towards low spatiotemporal replication: More than 50% of the studies were conducted over fewer than 4 years, and only 17% of the studies have replication across >3 sites. This limited spatiotemporal coverage means that the data may not be representative of the environmental conditions experienced by the species. C_LIO_LISynthesis: The biases and knowledge gaps we identify are a challenge for the progress of theory and limit the usefulness of current data for determining patterns that would be useful for conservation decisions, such as determining general responses to climate change. We urge researchers to close these knowledge gaps with novel data collection. C_LI

ecology↗

bioRxiv2021

Rcompadre and Rage - two R packages to facilitate the use of the COMPADRE and COMADRE databases and calculation of life history traits from matrix population models

O_LIMatrix population models (MPMs) are an important tool for biologists seeking to understand the causes and consequences of variation in vital rates (e.g., survival, reproduction) across life cycles. Empirical MPMs describe the age- or stage-structured demography of organisms and usually represent the life history of a population during a particular time frame at a specific geographic location. C_LIO_LIThe COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database are the most extensive resources for MPM data, collectively containing >12,000 individual projection matrices for >1,100 species globally. Although these databases represent an unparalleled resource for researchers, land managers, and educators, the current computational tools available to answer questions with MPMs impose significant barriers to potential COM(P)ADRE database users by requiring advanced knowledge to handle diverse data structures and program custom analysis functions. C_LIO_LITo close this knowledge gap, we present two interrelated R packages designed to (i) facilitate the use of these databases by providing functions to acquire, quality control, and manage both the MPM data contained in COMPADRE and COMADRE, and a users own MPM data (Rcompadre), and (ii) present a range of functions to calculate life history traits from MPMs in support of ecological and evolutionary analyses (Rage). We provide examples to illustrate the use of both. C_LIO_LIRcompadre and Rage will facilitate demographic analyses using MPM data and contribute to the improved replicability of studies using these data. We hope that this new functionality will allow researchers, land managers, and educators to unlock the potential behind the thousands of MPMs and ancillary metadata stored in the COMPADRE and COMADRE matrix databases, and in their own MPM data. C_LI

ecology↗

bioRxiv2021

Life-history predicts global population responses to the weather in the terrestrial mammals

With the looming threat of abrupt ecological disruption due to a changing climate, predicting which species are most vulnerable to environmental change is critical. The life-history of a species is an evolved response to its environmental context, and therefore a promising candidate for explaining differences in climate-change responses. However, we urgently need broad empirical assessments from across the worlds ecosystems to explore these predictions. Here, we use long-term abundance records from 157 species of terrestrial mammal and a two-step Bayesian meta-regression framework to investigate the link between annual weather anomalies, population growth rates, and species-level life-history. Overall, we found no consistent effect of temperature or precipitation anomalies on annual population growth rates. Furthermore, population responses to weather anomalies were not predicted by phylogenetic covariance, and instead there was variability in weather responses for populations within a species. Crucially, however, long-lived mammals with smaller litter sizes had responses with a reduced absolute magnitude compared to their shorter-living counterparts with larger litters. These results highlight the role of species-level life-history in driving responses to the environment.

ecology↗

bioRxiv2020

Short-lived plants have stronger demographic responses to climate

To mitigate and adapt to climate change, there is an urgent need to synthesize the state of our knowledge on plant responses to climate. The availability of open-access data, combined with our understanding of plant physiology and life history theory provide opportunities to examine quantitative generalizations regarding which biomes and species are most responsive to climate drivers. Here, we synthesized time series of structured population models from 165 populations from 62 plants around the globe to link plant population growth rates to precipitation and temperature drivers. We expected: (1) more pronounced demographic responses to precipitation than temperature, especially in arid biomes; (2) a higher climate sensitivity in short-lived rather than long-lived species; and (3) a stronger response to climate by species that reproduce more frequently. We found that precipitation anomalies have a nearly three-fold larger effect on{lambda} than temperature. Precipitation has substantially more pronounced effects in more arid sites, but large noise makes this relationship non-significant. Species with shorter generation time have much stronger absolute responses to climate anomalies, while the degree of iteroparity does not correlate with population responses to climate. We conclude that key species-level traits can predict plant population responses to climate, and discuss the relevance of this generalization for conservation planning and evolutionary theory.

ecology↗

bioRxiv2020

Drivers of large-scale spatial demographic variation in a perennial plant

To understand how the environment drives spatial variation in population dynamics, we need to assess the effects of a large number of potential drivers on the vital rates (survival, growth and reproduction), and explore these relationships over large geographical areas and long environmental gradients. In this study, we examined the effects of a broad variety of abiotic and biotic environmental factors, including intraspecific density, on the demography of the forest understory herb Actaea spicata between 2017 and 2019 at 40 sites across Sweden, including the northern range margin of its distribution. We assessed the effect of potential environmental drivers on vital rates using generalized linear mixed models (GLMMs), and then quantified the impact of each important driver on population growth rate ({lambda}) using integral projection models (IPMs). Population dynamics of A. spicata were mostly driven by environmental factors affecting survival and growth, such as air humidity, soil depth and forest tree species composition, and thus those drivers jointly determined the realized niche of the species. Soil pH had a strong effect on the flowering probability, while the effect on population growth rate was relatively small. In addition to identifying specific drivers for A. spicatas population dynamics, our study illustrates the impact that spatial variation in environmental conditions can have on {lambda}. Assessing the effects of a broad range of potential drivers, as done in this study, is important not only to quantify the relative importance of different drivers for population dynamics but also to understand species distributions and abundance patterns.

plant biology↗

bioRxiv2019

Global analysis reveals complex demographic responses of mammals to climate change

Approximately 25 % of mammals are threatened globally with extinction, a risk that is amplified under climate change1. Persistence under climate change is determined by the combined effects of climatic factors on multiple demographic rates (survival, development, reproduction), and hence, on population dynamics2. Thus, to quantify which species and places on Earth are most vulnerable to climate-driven extinction, a global understanding of how demographic rates respond to climate is needed3. We synthesise information on such responses in terrestrial mammals, where extensive demographic data are available4. Given the importance of assessing the full spectrum of responses, we focus on studies that quantitatively link climate to multiple demographic rates. We identify 106 such studies, corresponding to 86 mammal species. We reveal a strong mismatch between the locations of demographic studies and the regions and taxa currently recognised as most vulnerable to climate change5,6. Moreover, we show that the effects of climate change on mammals will operate via complex demographic mechanisms: a vast majority of mammal populations display projected increases in some demographic rates but declines in others. Assessments of population viability under climate change therefore need to account for multiple demographic responses. We advocate to prioritise coordinated actions to assess mammal demography holistically for effective conservation worldwide.

ecology↗