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bioRxiv2021

Spatial pattern analysis of line-segment data in ecology

O_LIThe spatial analysis of linear features (lines and curves) is a challenging and rarely attempted problem in ecology. Existing methods are typically expressed in abstract mathematical formalism, making it difficult to assess their relevance and transferability into an ecological setting. A set of concrete and accessible tools is needed. C_LIO_LIWe develop a new method to analyse the spatial patterning of line-segment data. It is based on a generalisation of Ripleys K-function and includes an analogue of the transformed L-function, together with estimators and theoretical expectation values. We introduce a class of line-segment processes, related to the Boolean model, which we use in conjunction with Monte-Carlo methods and information criteria to generate and compare candidate models. We demonstrate the utility of our method using fallen tree (dead log) data collected from two one-hectare Australian tall eucalypt forest plots. C_LIO_LIComparing six line-segment models, we find for both plots that the distribution of fallen logs is best explained by plot-level spatial heterogeneity. The use of non-uniform distributions to model dead-log orientation on the forest floor improves model performance in one of the two sites. Our case study highlights the challenges of model comparison in spatial-pattern analysis, where Monte-Carlo approaches based on the discrepancy of simulated summary functions can generate a different ranking of models than that of information criteria. C_LIO_LIThese methods are of a general nature and are applicable to any line-segment data. In the context of forest ecology, the integration of fallen logs as linear structural features in a landscape with the point locations of living trees, and a quantification of their interactions, will yield new insights into the functional and structural role of tree fall in forest communities and their enduring post-mortem ecological legacy as spatially distributed decomposing logs. C_LI

ecology↗

bioRxiv2021

Ecological consequences of urbanization on a legume-rhizobia mutualism

Mutualisms are key determinants of community assembly and composition, but urbanization can alter the dynamics of these interactions and associated effects on ecosystem functions. Legume-rhizobia mutualisms are a model interaction to evaluate the ecological and ecosystem-level effects of urbanization, particularly urban-driven eutrophication and nitrogen (N) deposition. Here, we evaluated how urbanization affected the ecology of the mutualism between white clover (Trifolium repens) and its rhizobial symbiont (Rhizobium leguminosarum symbiovar trifolii) along an urbanization gradient. We found that the abundance of rhizobium nodules on white clover decreased with urbanization. White clover acquired N from mixed sources of N fixation and uptake from the soil for the majority of the urbanization gradient, but white clover primarily acquired N from the soil rather than N fixation by rhizobia at the urban and rural limits of the gradient. Importantly, we identified soil N as a critical nexus for urban-driven changes in the white clover-rhizobium mutualism. Taken together, our results demonstrate that urbanization alters the ecological consequences of a legume-rhizobium mutualism, with direct and indirect effects of the urban landscape on an ecologically-important mutualistic interaction.

ecology↗

bioRxiv2021

An objective-based prioritization approach to improve trophic complexity through ecological restoration

O_LIReassembling ecological communities and rebuilding habitats through active restoration treatments requires curating the selection of plant species to use in seeding and planting mixes. Ideally, these mixes should be assembled based on attributes that support ecosystem function and services, promote plant and animal species interactions and ecological networks in restoration while balancing project constraints. Despite these critical considerations, it is common for species mixes to be selected opportunistically. Reframing the selection of seed mixes for restoration around ecological objectives is essential for success but accessible methods and tools are needed to support this effort. C_LIO_LIWe developed a framework to optimize species seed mixes based on prioritizing plant species attributes to best support different objectives for ecosystem functions, services, and trophic relationships such as pollination, seed dispersal, and herbivory. We compared results to approaches where plant species are selected to represent plant taxonomic richness, dominant species, and at random. We tested our framework for 176 plant species found in European alpine grasslands and identified 163 associated attributes affiliated to trophic relationships, ecosystem functions, and services. C_LIO_LIIn all cases, trophic relationships, ecosystem functions, and services can be captured more efficiently through objective-based prioritization using the functional identity of plant species. Solutions (plant species lists) can be compared quantitatively, in terms of costs, species, or objectives. We confirm that a random draw of plant species from the regional plant species pool cannot be assumed to support other trophic groups and ecosystem functions and services. C_LIO_LISynthesis and Applications. Our framework is presented as a proof of concept to help restoration practitioners better apply quantitative decision-support to plant species selection in order to meet ecological restoration outcomes. Our approach may be tailored to any restoration initiative and habitat where seeding or planting mixes will be applied in active treatments. As global priority and resources are increasingly placed into restoration, this approach could be advanced to help make efficient decisions for many stages of the restoration process. C_LI

ecology↗

bioRxiv2021

Large positive ecological changes of small urban greening actions

The detrimental effects of human-induced environmental change on people and other species are acutely manifested in urban environments. While urban greenspaces are known to mitigate these effects and support functionally diverse ecological communities, evidence of the ecological outcomes of urban greening remains scarce. We use a longitudinal observational design to provide empirical evidence of the putative ecological benefits of greening actions. We show how a small greening action quickly led to large positive changes in the richness, demographic dynamics, and network structure of a depauperate insect community. An increase in the diversity and complexity of the plant community led to, after only three years, a large increase in insect species richness, a greater probability of occurrence of insects within the greenspace, and a higher number and diversity of interactions between insects and plant species. We demonstrate how large ecological benefits may be derived from investing in small greening actions and how these contribute to bring indigenous species back to greenspaces where they have become rare or locally extinct. Our findings provide crucial evidence that support best practice in greenspace design and contribute to re-invigorate policies aimed at mitigating the negative impacts of urbanisation on people and other species.

ecology↗

bioRxiv2021

Cascading effects of elephant-human interactions in a savanna ecosystem and the implications for ecology and conservation

Our study monitored the changes in elephant numbers, distribution and ecological impact over a fifty-year period as the free-ranging intermingled movements of wildlife and traditional subsistence pastoralists across the Amboseli ecosystem were disrupted by a national park, livestock ranches, farms, settlements and changing lifestyles and economies. Elephants compressed into the national park by poaching and settlement turned woodlands to grassland and shrublands and swamps into short grazing lawns, causing a reduction of plant and herbivore diversity and resilience to extreme events. The results echo the ecological findings of high-density elephant populations in protected areas across eastern and southern Africa. The impact has led to the view of elephants in parks being incompatible with biodiversity and to population control measures. In contrast to Amboseli National Park, we found woody vegetation grew and plant diversity fell in areas abandoned by elephants. We therefore used naturalist and exclosure experiments to determine the density-dependent response of vegetation to elephants. We found plant richness to peak at the park boundary where elephants and livestock jostled spatially, setting up a creative browsing-grazing tension and a patchwork of habitats explaining the plant richness. A review of prehistorical and historical literature lends support to the Amboseli findings that elephants and people, the two dominant keystone species in the savannas, have been intimately entangled prior to the global ivory trade and colonialism. The findings point to the inadequacy of parks for conserving mega herbivores and as ecological baselines. The Amboseli study underlines the significance of space and mobility in expressing the keystone role of elephants, and to community-based conservation as a way to win space and mobility for elephants, alleviate the ecological disruption of compressed populations and minimize population management.

ecology↗

bioRxiv2021

Global and regional ecological boundaries drive abrupt changes in avian frugivory interactions

Species interactions can propagate disturbances across space, though ecological and biogeographic boundaries may limit this spread. We tested whether large-scale ecological boundaries (ecoregions and biomes) and human disturbance gradients increase dissimilarity among ecological networks, while accounting for background spatial and elevational effects and differences in network sampling. We assessed network dissimilarity patterns over a broad spatial scale, using 196 quantitative avian frugivory networks (encompassing 1,496 plant and 1,003 bird species) distributed across 67 ecoregions and 11 biomes. Dissimilarity in species and interactions, but not in network structure, increased significantly across ecoregion and biome boundaries and along human disturbance gradients. Our findings suggest that ecological boundaries contribute to maintaining the worlds biodiversity of interactions and mitigating the propagation of disturbances at large spatial scales. One-Sentence SummaryEcoregions and biomes delineate the large-scale distribution of plant-frugivore interactions.

ecology↗

bioRxiv2021

Plant-insect chemical communication in ecological communities: an information theory perspective

Cross-species communication, where signals are sent by one species and perceived by others, is one of the most intriguing types of communication that functionally links different species to form complex ecological networks. Yet, global changes and human activities can affect communication by increasing the fluctuations of species composition and phenology, altering signal profiles and intensity, and introducing noises. So far, most studies on cross-species communication have focused on a few specific species isolated from ecological communities. Scaling up investigations of cross-species communication to the community level is currently hampered by a lack of conceptual and practical methodologies. Here, we propose an interdisciplinary framework based on information theory to investigate mechanisms shaping cross-species communication at the community level. We use plants and insects, the cornerstones of most ecosystems, as a showcase; and focus on chemical communication as the key communication channel. We first introduce some basic concepts of information theory, then we illustrate information patterns in plant-insect chemical communication, followed by a further exploration of how to integrate information theory into ecological and evolutionary processes to form testable mechanistic hypotheses. We conclude by highlighting the importance of community-level information as a vehicle to better understand the maintenance of ecological systems, especially when facing rapid global changes.

ecology↗

bioRxiv2021

The structure and Robustness of tripartite ecological networks

Until recently, most ecological network analyses have focused on a single interaction type. In nature, however, diverse interactions co-occur, each of them forming a layer of a multilayer network. Data including information on multiple interactions has recently started to emerge, giving us the opportunity to have a first glance at possible commonalities in the structure of these networks. We studied the structural features of 44 tripartite ecological networks from the literature, each composed of two layers of interactions (e.g. herbivory, parasitism, pollination), and investigated their fragility to species losses. We found that the way in which the different layers of interactions are connected to each other affect how perturbations spread in ecological communities. Our results highlight the importance of considering multiple interactions simultaneously to better gauge the robustness of ecological communities to species loss and to more reliably identify the species that are important for robustness.

ecology↗

bioRxiv2022

Sex and size matter: foraging ecology of offshore harbour porpoises in waters around Greenland

Individuals of different sex or age can vary in their resource use due to differences in behaviour, life history, energetic need, or size. Harbour porpoises are small cetaceans that rely on a constant prey supply to survive. Here, we use bone collagen carbon ({delta}13C) and nitrogen ({delta}15N) isotope compositions to elucidate sex and size differences in the foraging ecology of harbour porpoises from West Greenland. In this region, populations have a unique offshore, deep-water ecology. Female harbour porpoises are larger than males and we find that females have a higher trophic level than males, and {delta}15N positively correlates with size for females only. This indicates that size may matter in the ability of females to handle larger prey and/or dive deeper to catch higher trophic level prey. These results suggest that females, which also feed their calves, may be under different ecological constraints than males. We also analysed the harbour porpoise data with comparable stable isotope data from Greenland populations of belugas and narwhals. Consistent with their small body size, and a diet consisting primarily of capelin, we find that harbour porpoises have a lower trophic level than belugas and narwhals. Furthermore, harbour porpoises have the largest ecological niche of the three species, which is in accordance with tagging studies indicating they have a wide range in shelf and deep offshore waters of the sub-arctic and North Atlantic.

ecology↗

bioRxiv2022

Ecological Drivers of Community Cohesion

From protocellular to societal, networks of living systems are complex and multi-scale. The assembly of these intricate interdependencies, under ecological pressures, can be nearly impossible to understand using pairwise methods. We develop a mathematical and computational model based on a four-strain Saccharomyces cerevisiae synthetic inter-dependent system. Our system leverages transiently structured ecologies for achieving community cohesion. We show how ecological interventions could reverse or slow the extinction rate of a cohesive community. An interconnected system first needs to persist long enough to be a subject of natural selection. Our emulation of Darwins warm little ponds with an ecology governed by transient compartmentalisation provides the necessary persistence. Our results find utility across scales of organisation, stressing the importance of cyclic processes in major evolutionary transitions engineering of synthetic microbial consortia and conservation biology.

ecology↗

bioRxiv2022

Rapid monitoring for ecological persistence

Effective conservation of ecological communities requires accurate and up-to-date information about whether species are persisting or declining to extinction. The persistence of ecological communities is largely supported by its structured architecture of species interactions, known as an ecological network. While the persistence of the network supporting the whole community is the most relevant scale for conservation, in practice, we can only monitor small subsets of these networks due to logistical sampling constraints. There is therefore an urgent need to establish links between the small snapshots of data conservationists are able to collect, and the big picture conclusions about ecosystem health demanded by policy makers, scientists and societies. Here we show that the persistence of small subnetworks in isolation -- that is, their persistence when considered separately from the larger network of which they are a part -- is a reliable probabilistic indicator of the persistence of the network as a whole. Our results are general across both antagonistic and mutualistic interaction networks. Empirically, we show that our theoretical predictions are supported by data on invaded networks in restored and unrestored areas, even in the presence of environmental variability. Our work suggests that coordinated action to aggregate information from incomplete sampling can provide a means to rapidly assess the persistence of entire ecological networks and the expected success of restoration strategies. This could significantly improve our ability to monitor progress towards achieving policy targets, such as those enshrined in the UN Convention on Biological Diversity.

ecology↗

bioRxiv2022

Profile likelihood-based parameter and predictive interval analysis guides model choice for ecological population dynamics

Calibrating mathematical models to describe ecological data provides important insight via parameter estimation that is not possible from analysing data alone. When we undertake a mathematical modelling study of ecological or biological data, we must deal with the trade-off between data availability and model complexity. Dealing with the nexus between data availability and model complexity is an ongoing challenge in mathematical modelling, particularly in mathematical biology and mathematical ecology where data collection is often not standardised, and more broad questions about model selection remain relatively open. Therefore, choosing an appropriate model almost always requires case-by-case consideration. In this work we present a straightforward approach to quantitatively explore this trade-off using a case study exploring mathematical models of coral reef regrowth after some ecological disturbance, such as damage caused by a tropical cyclone. In particular, we compare a simple single species ordinary differential equation (ODE) model approach with a more complicated two-species coupled ODE model. Univariate profile likelihood analysis suggests that the both models are practically identifiable. To provide additional insight we construct and compare approximate prediction intervals using a new parameter-wise prediction approximation, confirming both the simple and complex models perform similarly with regard to making predictions. Our approximate parameter-wise prediction interval analysis provides explicit information about how each parameter affects the predictions of each model. Comparing our approximate prediction intervals with a more rigorous and computationally expensive evaluation of the full likelihood shows that the new approximations are reasonable in this case. All algorithms and software to support this work are freely available as jupyter notebooks on GitHub so that they can be adapted to deal with any other ODE-based models.

ecology↗

bioRxiv2022

Urban ecological connectivity as a planning tool for different animal species.

The application of ecological theory to urban planning is becoming more important as land managers focus on increasing urban biodiversity as a way to improve human welfare. City authorities must decide not only what types of biodiversity-focused infrastructure should be prioritized, but also where new resources should be positioned and existing resources protected or enhanced. Careful spatial planning can contribute to the successful return and conservation of urban nature by maximizing the contribution of green infrastructure to landscape connectivity. By using ecological connectivity theory as a planning tool, governments can quantify the effect of different interventions on the ease with which wildlife can move across the landscape. Here we outline an approach to a) quantify ecological connectivity for different urban wildlife species and b) use this to test different urban planning scenarios using QGIS. We demonstrate four extensions to the work by Deslaurier et al. (2018) and Spanowicz & Jaeger (2019) which improve the application of this method as a planning tool for local government: O_LIA step-by-step method for calculating effective mesh size using the open-source software QGIS. C_LIO_LIConversion of the effective mesh size value (meff) to a "probability of connectedness" (Pc, for easier interpretation by local government and comparisons between planning scenarios). C_LIO_LIGuidance for measuring species-specific connectivity, including how to decide what spatial information should be included and which types of species might be most responsive to connectivity planning. C_LIO_LIAdvice for using the method to measure the outcome of different urban planning scenarios on ecological connectivity. C_LI

ecology↗

bioRxiv2022

Ecological boundaries and constraints on viable eco-evolutionary pathways

Evolutionary dynamics are subject to constraints ranging from limitations on what is physically possible to limitations on the pathways that evolution can take. One set of evolutionary constraints, known as demographic constraints, constrain what can occur evolutionarily due to the population demographic or population dynamical consequences of evolution leading to conditions that make populations susceptible to extinction. These demographic constraints can limit the strength of selection or rates of environmental change populations can experience while remaining extant and the trait values a population can express. Here we further hypothesize that the population demographic and population dynamical consequences of evolution also can constrain the eco-evolutionary pathways that populations can traverse by defining ecological boundaries represented by areas of likely extinction. We illustrate this process using a model of predator evolution. Our results show that the populations that persist over time tend to be those whose eco-evolutionary dynamics have avoided ecological boundaries representing areas of likely extinction due to stochastic deviations from a deterministic eco-evolutionary expectation. We term this subset of persisting pathways viable eco-evolutionary pathways. The potential existence of ecological boundaries constraining evolutionary pathways has important implications for predicting evolutionary dynamics, interpreting past evolution, and understanding the role of stochasticity and ecological constraints on eco-evolutionary dynamics.

ecology↗

bioRxiv2022

Identifying the most probable mammal reservoir hosts for Monkeypox virus based on ecological niche comparisons

BackgroundPrevious human cases or epidemics have suggested that Monkeypox virus (MPXV) can be transmitted through contacts with animals of African rainforests. Although MPXV has been identified in many mammal species, most are likely secondary hosts and the reservoir host has yet to be discovered. Methodology/Principal FindingsIn this study, we provide the full list of African mammal genera (and species) in which MPXV was previously detected and predict the geographic distributions of all species of these genera based on museum specimens and an ecological niche modelling (ENM) method. Then, we reconstruct the ecological niche of MPXV using georeferenced data on animal MPXV sequences and human index cases, and conduct overlap analyses with the ecological niches inferred for 99 mammal species in order to identify the most probable animal reservoir. Conclusions/SignificanceOur results show that the MPXV niche covers three African rainforests, the Congo Basin and Upper and Lower Guinean forests. The four mammal species showing the best niche overlap with MPXV are all arboreal rodents, including three squirrels, Funisciurus anerythrus, Funisciurus pyrropus, and Heliosciurus rufobrachium, and Graphiurus lorraineus. We conclude that the most probable MPXV reservoir is F. anerythrus based on two niche overlap metrics, the areas of higher probabilities of occurrence, and available data on MPXV detection. SummaryMonkeypox (MPX) is an emerging zoonotic disease, endemic to rainforests of West and Central Africa, which manifests as a fever, swollen lymph nodes, and fatigue, followed by a rash with macular lesions progressing from papules to vesicles, pustules and scabs, usually on the face, hands, and feet for two to four weeks. The case fatality rate ranges from 1-3% in West Africa to 5-10% in Central Africa. The disease has been reported in 10 African countries between 1970 and today, with an increasing number of cases over the last decades and several exportations outside the continent, the last one in 2022 resulting in an epidemic involving mostly men who have sex with men, with more than 80,000 cases detected worldwide. Although MPX virus has been identified in many mammal species, most are likely secondary hosts and the reservoir host has yet to be discovered. In this study, we compare the predicted geographic distribution (ecological niche) of the MPX virus with that of 99 mammal species, and conclude that the most probable MPX reservoir is Thomass rope squirrel (Funisciurus anerythrus), followed by three other arboreal rodents, including two squirrels (Funisciurus pyrropus and Heliosciurus rufobrachium) and the Lorrain dormouse (Graphiurus lorraineus).

ecology↗

bioRxiv2023

You shall know a species by the company it keeps: leveraging co-occurrence data to improve ecological prediction

O_LIMaking predictions about species, including how they respond to environmental change, is a central challenge for ecologists. Due to the huge number of species, ecologists seek generalizations based on species traits and phylogenetic relationships, but the predictive power of trait-based and phylogenetic models is often low. Species co-occurrence patterns may contain additional information about species ecological attributes not captured by traits or phylogenies. C_LIO_LIWe propose using ordination to encode the information contained in species co-occurrence data in low-dimensional vectors that can be used to represent species in ecological prediction. We present an efficient method to derive species vectors from co-occurrence data using GloVe, an unsupervised learning algorithm originally designed for language modeling. To demonstrate the method, we used GloVe to generate vectors for nearly 40,000 plant species using co-occurrence statistics derived from a global vegetation dataset and tested their ability to predict elevational range shifts in European montane plant species. C_LIO_LICo-occurrence-based species vectors were weakly correlated with traits or phylogeny, indicating that they encode unique information about species. Models including co-occurrence-based vectors explained twice as much variation in species range shifts as models including only traits or phylogenetic information. C_LIO_LIGiven the widespread availability of species occurrence data, species vectors learned from co-occurrence patterns are a widely applicable and powerful tool for encoding ecological information about species, with many potential applications for describing and predicting the ecology of species, communities, and ecosystems. C_LI

ecology↗

bioRxiv2023

Modeling Tick Populations: An Ecological Test Case forGradient Boosted Trees

General linear models have been the foundational statistical framework used to discover the ecological processes that explain the distribution and abundance of natural populations. Analyses of the rapidly expanding cache of environmental and ecological data, however, require advanced statistical methods to contend with complexities inherent to extremely large natural data sets. Modern machine learning frameworks such as gradient boosted trees efficiently identify complex ecological relationships in massive data sets, which are expected to result in accurate predictions of the distribution and abundance of organisms in nature. However, rigorous assessments of the theoretical advantages of these methodologies on natural data sets are rare. Here we compare the abilities of gradient boosted and linear models to identify environmental features that explain observed variations in the distribution and abundance of blacklegged tick (Ixodes scapularis) populations in a data set collected across New York State over a ten-year period. The gradient boosted and linear models use similar environmental features to explain tick demography, although the gradient boosted models found non-linear relationships and interactions that are difficult to anticipate and often impractical to identify with a linear modeling framework. Further, the gradient boosted models predicted the distribution and abundance of ticks in years and areas beyond the training data with much greater accuracy than their linear model counterparts. The flexible gradient boosting framework also permitted additional model types that provide practical advantages for tick surveillance and public health. The results highlight the potential of gradient boosted models to discover novel ecological phenomena affecting pathogen demography and as a powerful public health tool to mitigate disease risks.

ecology↗

bioRxiv2023

Seed functional ecology in Brazilian rock outcrop vegetation: an integrative synthesis

Background and AimsRock outcrop vegetation is distributed worldwide and hosts a diverse and unique flora that evolved under harsh environmental conditions. Unfortunately, seed ecology in such ecosystems has received little attention, especially regarding seed traits, germination responses to abiotic factors and the potential role of phylogenetic relatedness on such features Here, we provide the first quantitative and phylogenetically-informed synthesis of the seed functional ecology of Brazilian rock outcrop vegetation, with a particular focus on quartzitic and ironstone campo rupestre. MethodsUsing a database of functional trait data, we calculated the phylogenetic signal of seven seed traits for 371 taxa and tested whether they varied among growth forms, geographic distribution, and microhabitats. We also conducted meta-analyses that included 4,252 germination records for 102 taxa to assess the effects of light, temperature, and fire-related cues on the germination of campo rupestre species and explored how the aforementioned ecological groups and seed traits modulate germination responses. Key ResultsAll traits and germination responses showed a moderate-to-strong phylogenetic signal. Campo rupestre species responded positively to light and had maximum germination between 20-25 {degrees}C. The effect of temperatures beyond this range was moderated by growth form, species geographic distribution, and microhabitat. Seeds exposed to heat shocks above 80 {degrees}C lost viability, but smoke accelerated germination. We found a moderating effect of seed mass for in responses to light and heat shocks, with larger, dormant seeds tolerating heat better but less sensitive to light. Species from xeric habitats evolved phenological strategies to synchronise germination during periods of increased soil water availability. ConclusionsPhylogenetic relatedness plays a major role in shaping seed ecology of Brazilian rock outcrop vegetation. Nevertheless, seed traits and germination responses varied significantly between growth forms, species geographic distribution and microhabitats, providing support to the regeneration niche hypothesis and the role of functional traits in shaping germination in these ecosystems.

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