Biology subjects

Beger, M.

Publications and source records attributed to Beger, M..

18 recordsLinked to original sources

bioRxiv2025

Causal modelling reveals lower coral genetic diversity in more heterogenous reef environments

Conserving genetic diversity is crucial for maintaining species evolutionary potential and resilience to environmental change. Yet, directly measuring genetic diversity across large spatial scales remains resource-intensive and impractical for conservation planning. Identifying reliable, accessible, and cost-effective spatial predictors of genetic diversity would significantly enhance our ability to incorporate genetic diversity into conservation efforts. Caribbean coral reefs represent a compelling system for investigating such predictors, as these ecosystems face unprecedented threats from disease outbreaks and climate change. Here, we investigate the utility of several environmental proxies as surrogates for genetic diversity, which may be useful for conservation planning in resource- or data-poor regions. To achieve this goal, we used reduced-representation genomic sequencing to estimate intraspecific genetic diversity, and in doing so, identified two genetically distinct and sympatric cryptic coral species in the Agaricia tenuifolia species complex. We employed a causal inference approach to assess the relationships between genetic alpha diversity and habitat area and connectivity, habitat heterogeneity, and temperature. Statistical investigations revealed that increased habitat heterogeneity, derived from remotely sensed habitat maps, was associated with lower genetic diversity within coral populations, suggesting that habitat characteristics promoting species diversity may not maintain high genetic diversity within a single species. Habitat area and connectivity, and temperature have predominantly negative effects on genetic diversity with coral habitat area and connectivity showing markedly contrasting responses in two cryptic taxa. Thus, our findings reveal that context matters greatly, as results differ between cryptic species, across variables, and among spatial scales.

evolutionary biology↗

bioRxiv2025

Potential yield and food provisioning gains from rebuilding the worlds coral reef fish stocks

Many coral reefs have fish stocks that are depleted below the level at which sustainable production is maximized. Lower production means that millions of people are losing out on potential food, income and livelihoods. Rebuilding these stocks to maximize sustainable production can contribute towards ending hunger and malnutrition but requires active and effective fisheries management. Yet, for fish stock recovery plans to be implemented, recovery benefits, targets and timeframes need to be quantified. Here, using 1211 individual reef sites and 23 jurisdictions identified globally as being below maximum sustainable production levels, we show that reefs have the potential to increase sustainable yields by nearly 50% if allowed to recover towards their maximum production levels. For individual jurisdictions this recovery represents from 20,000 up to 162 million additional sustainable servings of reef fish per year in comparison to current sustainable production, meeting recommended seafood intake for up to 1. 4 million additional people a year. However, such growth and food provisioning will require fish stocks to double their standing biomass (increase by a median of 32 t/km2). Recovery timeframes range from 6.4 years under the most stringent scenario (a seascape moratorium) to 49.7 years under the maximum harvest scenario that results in recovery. We find that locations with the greatest potential for sustainable gains in yield are among those with the greatest food and micronutrient deficiencies, underscoring both the challenges and opportunities in recovering fish assemblages to achieve their maximum sustainable potential. Significance StatementCoral reef fisheries are a critical food source for people throughout the tropics. However, most reefs around the globe have fish biomass values below those enabling maximal sustainable production, risking food availability, income, and livelihoods. Rebuilding fish assemblages can increase sustainable food supplies, and, if these are well distributed, directly contribute towards enhanced food security. We show that recovering fish stocks on coral reefs can significantly increase the number of sustainable fish servings produced per year and the number of people meeting fish intake recommendations, particularly for countries with high malnutrition. Our study highlights the sustainable food provisioning potential of recovering reef fisheries and quantifies how much recovery would be needed and the time such recovery would take.

ecology↗

bioRxiv2024

Inferring species interactions from co-occurrence networks with environmental DNA metabarcoding data in a coastal marine food-web

Improved understanding of biotic interactions is necessary to accurately predict the vulnerability of ecosystems to climate change. Recently, co-occurrence networks built from environmental DNA (eDNA) metabarcoding data have been advocated as a means to explore interspecific interactions in ecological communities exposed to different human and environmental pressures. Co-occurrence networks have been widely used to characterise microbial communities, but it is unclear if they are effective for characterising eukaryotic ecosystems, or whether biotic interactions drive inferred co-occurrences. Here, we assess spatiotemporal variability in the structure and complexity of a North Sea coastal ecosystem inferred from co-occurrence networks and food webs using 60 eDNA samples covering vertebrates and other eukaryotes. We compare topological characteristics and identify potential keystone species, i.e., highly connected species, across spatial and temporal subsets, to evaluate variance in community composition and structure. We find consistent trends in topological characteristics across co-occurrence networks and food webs, despite trophic interactions forming a minority of significant co-occurrences. Known keystone species in food webs were not highly connected in co-occurrence networks. The lack of significant trophic interactions detected in co-occurrence networks may result from ecological complexities such as generalist predators having flexible interactions or behavioural partitioning, as well as methodological limitations such as the inability to distinguish age class with eDNA, or co-occurrences being driven by other interaction types or shared environmental requirements. Deriving biotic interactions with co-occurrence networks constructed from eDNA requires further validation in well-understood ecosystems, and improved reporting of methodological limitations, such as species detection uncertainties, which could influence inferred ecosystem complexity.

ecology↗

bioRxiv2023

Environmental DNA reveals fine scale spatial and temporal variation of prey species for marine mammals in a Scottish marine protected area

Marine mammal foraging grounds are popular focal points for marine protected area (MPA) implementation, but may be temporally dynamic, requiring continuous monitoring to infer prey availability and abundance. Marine mammal distributions are assumed to be driven by their prey in foraging areas, but limited understanding of prey distributions often prevents us from exploring how shifting prey availability impacts both seasonal and long-term marine mammal distributions. Environmental DNA (eDNA) metabarcoding could enhance understanding of marine mammal habitat use in relation to their prey through simultaneous monitoring of both. However, eDNA applications focused on marine mammals or predator-prey dynamics have been limited to date. In this study, we assess spatiotemporal changes in the availability and abundance of minke whale (Balaenoptera acutorostrata) prey species in a newly established MPA, employing eDNA metabarcoding. We recovered 105 molecular operational taxonomic units (OTUs) from marine vertebrates using two primer sets targeting 12S and 16S genes, along with 112 OTUs from a broader eukaryotic primer set targeting 18S rRNA. Overall, key forage fish prey species, sandeels and clupeids, were the most abundant teleost fishes detected, although their availability varied temporally and with distance from shore. We also found clear spatial partitioning between coastal bottlenose dolphins and the more pelagic minke whales and harbour porpoises, paralleling availability of their main prey species. Other species of conservation interest were also detected including the critically endangered European eel (Anguilla anguilla), blue fin tuna (Thunnus thynnus), and the invasive pink salmon (Oncorhynchus gorbuscha). This study demonstrates the application of eDNA to detect spatiotemporal trends in the occurrence and abundance of cetacean predators and their prey, furthering our understanding of fine-scale habitat use within MPAs. Future, long-term monitoring of predator-prey dynamics with eDNA could improve our ability to predict climate-induced shifts in foraging grounds and enhance rapid responses with appropriate management actions.

ecology↗

bioRxiv2023

Marine predator spatial conservation priorities are taxon-specific

Marine predators are globally threatened by anthropogenic stressors, but are key for ecosystem functioning. Their worsening conservation statuses indicate that current management is failing, requiring us to urgently reimagine their conservation needs to ensure their survival. Their life histories, threats, and resource needs are diverse. Consequently, spatial conservation areas targeting all species will overlook such heterogeneity, contributing to the problem. Here, we demonstrate that marine mammals, elasmobranchs and teleost fishes return drastically different spatial conservation priority areas, based on Marxan scenarios for 42 marine predator species in the Mediterranean Sea. None of the marine predators are sufficiently covered by the current marine protected area (MPA) system, with marine mammals being the least protected despite having the greatest designated MPA extent, highlighting disconnects between conservation goals and current management outcomes. To save marine predators, taxon specific ecological requirements and resulting spatial heterogeneity need to be accounted for in marine spatial planning.

ecology↗

bioRxiv2022

High-latitude marginal reefs support fewer but bigger corals than their tropical counterparts

AimDespite the awareness that climate change impacts are typically detrimental to tropical coral reefs, the effect of increasing environmental stress and variability on the population size structure of coral species remains poorly understood. This gap in knowledge limits our ability to effectively conserve coral reef ecosystems because size specific dynamics are rarely incorporated. Our aim is to quantify variation in the size structure of coral populations along a tropical-to-subtropical environmental gradient. Location20 coral populations along a latitudinal gradient on the east coast of Australia ([~]23{degrees}S to 30{degrees}S). Time PeriodBetween 2010 and 2018. Major taxa studiedScleractinian corals. MethodsWe apply two methods to quantify the relationship between environmental covariates and coral population size structure along a latitudinal environmental gradient. First, we use linear regression with summary statistics, such as median size as response variables; a method frequently favoured by ecologists. The second method is compositional functional regression, a novel method using entire size-frequency distributions as response variables. We then predict coral population size structure with increasing environmental stress and variability. ResultsCompared to tropical reefs, we find fewer but larger coral colonies in marginal reefs, where environmental conditions are more variable and stressful for corals in the former. Our model predicts that coral populations may become gradually dominated by larger colonies (> 148 cm2) with increasing environmental stress. Main conclusionsWith increasing environmental stress and variability, we can expect shifts in coral population size structure towards more larger colonies. Fewer but bigger corals suggest low survival, slow growth, and poor recruitment. This finding is concerning for the future of coral reefs as it implies populations may have low recovery potential from disturbances. We highlight the importance and usefulness of continuously monitoring changes to population structure over large spatial scales. Data availabilityData is supplied in the supplementary information, or upon request. Once accepted for publication it will be made openly available on Dryad.

ecology↗

bioRxiv2022

Sustainable reference points for multispecies coral reef fisheries

Sustainably managing fisheries requires regular and reliable evaluation of stock status. However, most multispecies reef fisheries around the globe tend to be data-poor and lack research and monitoring capacity (e.g., long-term fishery data), preventing the estimation of sustainable reference points against which stocks can be assessed. Here, combining fish biomass data for more than 2000 coral reefs with catch estimates from 99 jurisdictions, we estimate site-specific sustainable reference points for coral reef fisheries and use these to assess the status of coral reef fish stocks. We reveal that more than half of jurisdictions with available information have stocks of conservation concern, having failed at least one fisheries sustainability benchmark. We quantify the trade-offs between biodiversity, mean fish length, and ecosystem functions relative to key benchmarks and highlight the ecological benefits of increasing sustainability. Our approach yields multispecies sustainable reference points for coral reef fisheries using environmental conditions, a promising means for enhancing the sustainability of the worlds coral reef fisheries. TeaserA global assessment of the sustainability of multispecies reef fisheries indicates that more than half of jurisdictions have failed at least one of two key sustainability benchmarks.

ecology↗

bioRxiv2022

Sampling from commercial vessel routes can capture marine biodiversity distributions effectively

Collecting fine-scale occurrence data for marine species across large spatial scales is logistically challenging, but is important to determine species distributions and for conservation planning. Inaccurate descriptions of species ranges could result in designating protected areas with inappropriate locations or boundaries. Optimising sampling strategies therefore is a priority for scaling up survey approaches using tools such as environmental DNA (eDNA) to capture species distributions. eDNA can detect diverse taxa simultaneously, but to date has rarely been applied across large spatial scales relevant for conservation planning. In a marine context, commercial vessels, such as ferries, could provide sampling platforms allowing access to under-sampled areas and repeatable sampling over time to track community changes. However, sample collection from commercial vessels could be biased and may not represent biological and environmental variability. Here, we evaluate whether sampling along Mediterranean ferry routes can yield unbiased biodiversity survey outcomes, based on perfect knowledge from a stacked species distribution model (SSDM) of marine megafauna. Simulations were carried out representing different sampling strategies (random vs systematic), frames (ferry routes vs unconstrained) and number of sampling points. SSDMs were remade from different sampling simulations and compared to the perfect knowledge SSDM to quantify the bias associated with different sampling strategies. Ferry routes detected more species and were able to recover known patterns in species richness at smaller sample sizes better than unconstrained sampling points. However, to minimise potential bias, ferry routes should be chosen to cover the variability in species composition and its environmental predictors in the SSDMs. The workflow presented here can be used to design effective eDNA sampling strategies using commercial vessel routes globally. This approach has potential to provide a cost-effective method to access remote oceanic areas on a regular basis, and can recover meaningful data on spatiotemporal biodiversity patterns.

ecology↗

bioRxiv2022

Evolutionary processes, not environmental drivers, determine the resilience of natural populations

Escalating climatic and anthropogenic pressures expose ecosystems worldwide to increasingly frequent disturbances. Yet, our ability to forecast the responses of natural populations to these disturbances is impeded by a limited understanding for how exposure to stochastic environments shapes population resilience. Instead, the resilience, and vulnerability, of natural populations to ongoing global change is often presumed based on their contemporary exposure to environmental stochasticity. To test the validity of this assumption, we investigated the association between the resilience attributes (e.g., resistance and recovery) of natural animal and plant populations, and measures of local environmental stochasticity (e.g., spectral frequency and abiotic range); collating data from 2,242 populations across 369 animal, plant, and algal species. Unexpectedly, recent abiotic stochasticity regimes from the past 50 years do not predict the inherent ability of populations to resist or recover from disturbances. Instead, population resilience is strongly affected by phylogenetic relationships among species, with survival and developmental investments shaping their responses to stochastic regimes. Contrary to the classical assumption that exposure to recent environmental shifts confers a greater ability to cope with current and future global change, our findings suggest that population resilience is a consequence of evolutionary processes and/or deep-time environmental regimes. Significance statementPopulations that currently endure more variable abiotic conditions are often expected to be less vulnerable to future increases in climatic variability. However, without defining the link between abiotic variability and the capacity for populations to resist and recover following disturbances (i.e., their resilience), we cannot predict the consequences of ongoing community reassembly. Evaluating the association between measures of abiotic variability and the resilience attributes of 2,242 animal, plant, and algae populations, we discredit the assumption that contemporary exposure to more frequent environmental shifts confers a greater ability to cope with future global change. Instead, the resilience attributes of natural populations appear to have been moulded over longer-term evolutionary timeframes and are thus not a response to more recent experiences.

ecology↗

bioRxiv2021

Coral assemblages at higher latitudes favour short-term potential over long-term performance

The persistent exposure of coral communities to more variable abiotic regimes is assumed to augment their resilience to future climatic variability. Yet, while the determinants of coral population resilience across species remain unknown, we are unable to predict the winners and losers across reef ecosystems exposed to increasingly variable conditions. Using annual surveys of 3171 coral individuals across Australia and Japan (2017-2019), we explore spatial variation across the short- and long-term dynamics of competitive, stress-tolerant, and weedy assemblages to evaluate how thermal variability mediates the structural composition of coral communities. We illustrate how, by promoting short-term potential over long-term performance, coral assemblages can reduce their vulnerability to stochastic environments. However, compared to stress-tolerant, and weedy assemblages, competitive coral taxa display a reduced capacity for elevating their short-term potential. Accordingly, future climatic shifts threaten the structural complexity of coral assemblages in variable environments, emulating the degradation expected across global tropical reefs.

ecology↗

bioRxiv2021

Life history mediates the trade-offs among different components of demographic resilience

Summary paragraphAccelerating rates of biodiversity loss underscore the need to understand how species achieve resilience -their ability to resist and recover from a/biotic disturbances. Yet, the factors determining the resilience of species remain poorly understood, due to disagreements on its definition and the lack of large-scale analyses. Here, we investigate how the life history of 785 natural populations of animals and plants predict their intrinsic ability to be resilient. We show that demographic resilience can be achieved through different combinations of compensation, resistance, and recovery after a disturbance. We demonstrate that these resilience components are highly correlated with life history traits related to the species pace of life and reproductive strategy. Species with longer generation times require longer recovery times post-disturbance, while those with greater reproductive capacity have greater resistance and compensation. Our findings highlight the key role of life history traits to understand species resilience, improving our ability to predict how natural populations cope with disturbance regimes.

ecology↗

bioRxiv2021

Transient amplification enhances the persistence of tropicalising coral populations in marginal high latitude environments.

Predicting the viability of species exposed to increasing climatic stress requires an appreciation for the mechanisms underpinning the success or failure of marginal populations. Rather than traditional metrics of long-term population performance, here we illustrate that short-term (i.e. transient) demographic characteristics, including measures of resistance, recovery, and compensation, are fundamental in the poleward range expansion of hard corals, facilitating the establishment of coral populations at higher-latitudes. Through the annual census of tropical and subtropical Acropora spp. colonies in Japan, between 2017-2019, we show how the transient amplification potential of a subtropical coral population supports its enhanced growth within unstable environmental conditions. The transient dynamics of both the tropical and subtropical populations were strongly influenced by their corresponding recruitment patterns. However, we demonstrate that variation in colony survival and fragmentation patterns between the two populations determines their relative capacities for transient amplification. This latitudinal variation in the transient dynamics of Acropora spp. populations emphasizes that coral populations can possess the demographic plasticity necessary for exploiting more variable, marginal conditions.

ecology↗

bioRxiv2021

Transient demographic approaches can drastically expand the toolbox of coral reef science

Coral communities are threatened by an increasing plethora of abiotic and biotic disturbances. Preventing the ensuing loss of coral coverage and diversity calls for a mechanistic understanding of resilience across coral species and populations that is currently lacking in coral reef science. Assessments into the dynamics of coral populations typically focus on their long-term (i.e. asymptotic) characteristics, tacitly assuming stable environments in which populations can attain their long-term characteristics. Instead, we argue that greater focus is needed on investigating the transient (i.e. short-term) dynamics of coral populations to describe and predict their characteristics and trajectories within unstable environments. Applying transient demographic approaches to the evaluation and forecasting of the responses of coral populations to disturbance holds promise for expediting our capacity to predict and manage the resilience of coral populations, species, and communities.

ecology↗

bioRxiv2020

Towards a comparative framework of demographic resilience

In times of global biodiversity crisis, developing tools to define, quantify, compare and predict ecological resilience is essential for understanding species responses to global change. Disparate interpretations of ecological resilience have, however, hampered the development of a common currency to quantify and compare resilience across natural systems. Most frameworks of study have focused on upper levels of biological organisation, especially ecosystems or communities, which adds layers of complication to measuring resilience with empirical data. To overcome such limitations, we suggest quantifying resilience using demographic data. Surprisingly, a quantifiable definition of resilience does not exist at the demographic level. Here, we present a framework of demographic resilience with a set of metrics that are comparable across species, and facilitate cost-effective management decisions.

ecology↗

bioRxiv2019

Aquatic and terrestrial organisms display contrasting life history strategies as a result of environmental adaptations

AimsAquatic and terrestrial realms display stark differences in key environmental factors and phylogenetic composition. Despite such differences, their consequences for the evolution of species life history strategies remain poorly understood. Here, we examine whether and how life history strategies vary between terrestrial and aquatic species.\n\nLocationGlobal.\n\nTime periodVariable, the earliest year being in 1906 and the most recent in 2015.\n\nMajor taxa studiesMacroscopic animals and plants species.\n\nMethodsWe use demographic information for 638 terrestrial and 117 aquatic animal and plant species, to derive key life history traits capturing their population turnover, and investments in survival, development, and reproduction. We use phylogenetically corrected least squares regression to explore the differences in the trade-offs between life history traits in both realms. We then quantify the life history strategies of aquatic and terrestrial species using a phylogenetically corrected principal component analysis.\n\nResultsWe find that the same trade-offs structure terrestrial and aquatic life histories, resulting in two dominant axes of variation describing species pace- of-life and reproductive spread through time. Life history strategies differ between aquatic and terrestrial environments, with phylogenetic relationships playing a minor role. We show that adaptations of plants and animals to terrestrial environments have resulted in different life history strategies, particularly with their reproductive mode and longevity. Terrestrial plants display a great diversity of life history strategies, including the species with the longest lifespans. Aquatic animals, on the contrary, exhibit higher reproductive frequency than terrestrial animals, likely due to reproductive adaptations (i.e. internal fecundation) of the later to land.\n\nMain conclusionsOur findings show that aquatic and terrestrial species are ruled by the same life history principles, but have evolved different strategies due to distinct selection pressures. Such contrasting life history strategies have important consequences for the conservation and management of aquatic and terrestrial species.

ecology↗

bioRxiv2018

Operationalizing ecological connectivity in spatial conservation planning with Marxan Connect

O_LIGlobally, protected areas are being established to protect biodiversity and to promote ecosystem resilience. The typical spatial conservation planning process leading to the creation of these protected areas focuses on representation and replication of ecological features, often using decision support systems such as Marxan. Unfortunately, Marxan currently requires manual input or specialised scripts to explicitly consider ecological connectivity, a property critical to metapopulation persistence and resilience.\nC_LIO_LI\"Marxan Connect\" is a new open source, open access Graphical User Interface (GUI) designed to assist conservation planners in the systematic operationalization of ecological connectivity in protected area network planning.\nC_LIO_LIMarxan Connect is able to incorporate estimates of demographic connectivity (e.g. derived from tracking data, dispersal models, or genetics) or structural landscape connectivity (e.g. isolation by resistance). This is accomplished by calculating metapopulation-relevant connectivity metrics (e.g. eigenvector centrality) and treating those as conservation features, or using the connectivity data as a spatial dependency amongst sites to be included in the prioritization process.\nC_LIO_LIMarxan Connect allows a wide group of users to incorporate directional ecological connectivity into conservation plans. The least-cost conservation solutions provided by Marxan Connect, combined with ecologically relevant post-hoc testing, are more likely to support persistent and resilient metapopulations (e.g. fish stocks) and provide better protection for biodiversity than if connectivity is ignored.\nC_LI

ecology↗

bioRxiv2017

A Theory For Ecological Survey Methods To Map Individual Distributions

Spatially-explicit approaches are widely recommended for ecosystem management. The quality of the data, such as presence/absence or habitat maps, affects the management actions recommended, and is, therefore, key to management success. However, available data are often biased and incomplete. Previous studies have advanced ways to resolve data bias and missing data, but questions remain about how we design ecological surveys to develop a dataset through field surveys. Ecological surveys may have multiple spatial scales, including the spatial extent of the target ecosystem (observation window), the resolution for mapping individual distributions (mapping unit), and the survey area within each mapping unit (sampling unit). We developed an ecological survey method for mapping individual distributions by applying spatially-explicit stochastic models. We used spatial point processes to describe individual spatial placements using either random or clustering processes. We then designed ecological surveys with different spatial scales and individual detectability. We found that the choice of mapping unit affected the presence mapped fraction, and the fraction of the total individuals covered by the presence mapped patches. Tradeoffs were found between these quantities and the map resolution, associated with equivalent asymptotic behaviors for both metrics at sufficiently small and large mapping unit scales. Our approach enabled consideration of the effect of multiple spatial scales in surveys, and estimation of the survey outcomes such as the presence mapped fraction and the number of individuals situated in the presence detected units. The developed theory may facilitate management decision-making and inform the design of monitoring and data gathering.

ecology↗

bioRxiv2017

Spatially Explicit Approach To Population Abundance Estimation In Field Surveys

The abundance of species is a fundamental consideration in ecology and conservation biology. Although broad models have been proposed to estimate the population abundance using existing data, available data is often limited. With no information available, a population estimation will rely on time consuming field surveys. Typically, time is a critical constraint in conservation and often management decisions must be made quickly under the data limited situation. Depending on time and budgetary constraints, the required accuracy of field survey changes significantly. Hence, it is desirable to set up an effective survey design to minimize time and effort of sampling given required accuracy. We examine a spatially-explicit approach to population estimation using spatial point processes, enabling us to explicitly and consistently discuss various sampling designs. We find that the accuracy of abundance estimation varies with both ecological factors and survey design. Although the spatial scale of sampling does not affect estimation accuracy when the underlying individual distribution is random, it decreases with the sampled unit size if individuals tend to form clusters. These results are derived analytically and checked numerically. Obtained insights provide a benchmark to predict the quality of population estimation, and improve survey designs for ecological studies and conservation.

ecology↗