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bioRxiv2017

How ecosystems recover from pulse perturbations: A theory of short- to long-term responses

Quantifying stability properties of ecosystems is an important problem in ecology. A common approach is based on the recovery from pulse perturbations, and posits that the faster ecosystems return to their pre-perturbation state, the more stable they are. In theoretical studies the recovery dynamics are often collapsed into a single quantity: the long-term rate of return, called asymptotic resilience. However, empirical studies typically measure the recovery dynamics at much shorter time scales. In this paper we explain why asymptotic resilience is rarely representative of the short-term recovery. First, we show that, in contrast to asymptotic resilience, short-term return rates depend on features of the perturbation, in particular on the way its intensity is distributed over species. We argue that empirically relevant predictions can be obtained by considering the median response over a set of perturbations, for which we provide explicit formulas. Next, we show that the recovery dynamics are controlled through time by different species: abundant species tend to govern the short-term recovery, while rare species often dominate the long-term recovery. This shift from abundant to rare species typically causes short-term return rates to be unrelated to asymptotic resilience. Finally, we discuss how these findings might help to better connect empirical observations and theoretical predictions.

ecology↗

bioRxiv2017

Demographic variability in spruce-fir-beech forest stands in Europe

1Many studies have predicted large changes in forest dynamics during the next century because of global warming. Although empirical approaches and studies based on species distribution models provide valuable information about future changes, they do not take into account biotic interactions and stand-level demographic variations. The objective of this study was to quantify the local and regional variability of the growth and regeneration of three important forest species growing often in mixed stands in Europe (Picea abies (L.) Karst., Abies alba Mill., Fagus sylvatica), and to assess the climatic drivers of this variability. For that purpose, we collected a large forestry data set compiling the long-term (up to 100 years) evolution of species and size distributions for 163 stands across Europe, in the mesic distribution area of these forests. We used an inverse modeling approach, Approximate Bayesian Computation, to calibrate an individual-based model of forest dynamics on these data. Our study revealed that the variability of the demographic processes was of the same order of magnitude between stands of a same forest as between different forests. Out of the three species and two demographic processes studied, only the fir growth strongly varied with temperature. Water availability did not explain any demographic variation over stands. For these forests experiencing mesic conditions, local unmeasured factors seem therefore to have an influence at least as important as macro-environmental factors on demographic variations. Efforts to include these important factors in projection scenarios should therefore be prioritized. Besides, our study demonstrates that inverse modelling methods make possible the analysis of long-term forestry data. Such data should therefore be more widely compiled and used for ecological and global change research.

ecology↗

bioRxiv2017

Does circadian regulation lead to optimal gas exchange regulation?

Optimal stomatal theory is an evolutionary model proposing that leaves trade-off Carbon (C) for water to maximise C assimilation (A) and minimise transpiration (E), thereby generating a marginal water cost of carbon gain ({lambda}) that remains constant over short temporal scales. The circadian clock is a molecular timer of metabolism that controls A and stomatal conductance (gs), amongst other processes, in a broad array of plant species. Here, we test whether circadian regulation contributes towards achieving optimal stomatal behaviour. We subjected bean (Phaseolus vulgaris) and cotton (Gossypium hirsutum) canopies to fixed, continuous environmental conditions of photosynthetically active radiation, temperature and vapour pressure deficit over 48 hours. We observed a significant and self-sustained circadian oscillation in A and in stomatal conductance (gs) which also led to a circadian oscillation in{lambda} . The lack of constant marginal water cost indicates that circadian regulation does not directly lead to optimal stomatal behaviour. However, the temporal pattern in gas exchange, indicative of either maximizing A or of minimizing E, depending upon time of day, indicates that circadian regulation could contribute towards optimizing stomatal responses. More broadly, our results add to the emerging field of plant circadian ecology and show that molecular controls may partially explain leaf-level patterns observed in the field.

ecology↗

bioRxiv2017

The Structure Of Plant Spatial Association Networks Increases Plant Diversity In Global Drylands

AimDespite their widespread use and value to unveil the complex structure of the interactions within ecological communities and their value to assess the resilience of communities, network analyses have seldom been applied in plant communities. We aim to evaluate how plant-plant interaction networks vary in global drylands, and to assess whether network structure is related to plant diversity in these ecosystems.\n\nLocation185 dryland ecosystems from all continents except Antarctica.\n\nMethodsWe built networks using the local spatial association between all the perennial plant species present in the communities studied, and used structural equation models to evaluate the effect of abiotic factors (including geography, topography, climate and soil conditions) and network structure on plant diversity.\n\nResultsThe structure of plant networks found at most study sites (72%) was not random and presented properties representative of robust systems, such as high link density and structural balance. Moreover, network indices linked to system robustness had a positive and significant effect on plant diversity, sometimes higher that the effect of abiotic factors.\n\nMain conclusionsOur results constitute the first empirical evidence showing the existence of a common network architecture structuring terrestrial plant communities at the global scale, and provide novel evidence of the importance of the network of interactions for the maintenance of biodiversity. Furthermore, they highlight the importance of system-level approaches to explain the diversity and structure of interactions in plant communities, two major drivers of terrestrial ecosystem functioning and resilience against the likely impacts derived from global change.

ecology↗

bioRxiv2017

Spatially-induced nestedness in a neutral model of phage-bacteria networks

Ecological networks, both displaying mutualistic or antagonistic interactions, seem to share common structural traits: the presence of nestedness and modularity. A variety of model approaches and hypothesis have been formulated concerning the significance and implications of these properties. In phage-bacteria bipartite infection networks, nestedness seems to be the rule in many different contexts. Modeling the coevolution of a diverse virus-host ensemble is a difficult task, given the dimensionality and multi parametric nature of a standard continuous approximation. Here we show that this can actually be overcome by using a simple model of coevolving digital genomes on a spatial lattice and having exactly the same properties, i.e. a genome-independent fitness associated to fixed growth and death parameters. A matching allele model of phage-virus recognition rule is enough to generate a complex, diverse ecosystem with heterogeneous patterns of interaction and nestedness, provided that interactions take place under a spatially-constrained setting. It is found that nestedness seems to be an emergent property of the coevolutionary dynamics. Our results indicate that the enhanced diversity resulting from localized interactions strongly promotes the presence of nested infection matrices.

ecology↗

bioRxiv2017

An experimental approach to understanding elevation limits in a montane terrestrial salamander, Plethodon montanus

Understanding the abiotic and biotic factors that determine the limits to species range is an essential goal in ecology, biogeography, evolutionary biology, and conservation biology. Moreover, predictions of shifts in species distributions under future changes in climate can be improved through understanding the spatial variation in survival, growth, and reproduction. A long-standing hypothesis postulates that, for Northern Hemisphere species, abiotic factors like temperature limit northern and/or higher elevation extents, while biotic factors like competition limit the southern and/or lower elevation range edges; though amphibians may not follow this general trend. Therefore, we combined environmental suitability models and a reciprocal transplant experiment across an elevational gradient to explore the role of the abiotic environment on the range limits of a montane salamander (Plethodon montanus). We first determined suitability of the abiotic environment for P. montanus, under current (1960 - 2000) and future (2050) climate scenarios. Second, we collected juveniles from each of three elevations and transplanted them within mesocosms such that each origin population was represented within each transplant location and vice-versa. We found that environmental suitability in 2050 decreased throughout the range compared to current predictions, especially at lower elevations. Additionally, we found that individuals starting body condition and transplant location were important predictors of survival, growth, and reproduction condition; importantly, individuals transplanted to low elevation had lower survival and growth rates compared to those moved to mid or high elevations. Our study provides experimental support that the abiotic environment limits the lower elevation distribution of P. montanus and, unfortunately, our results also paint a possible bleak future for this species and likely other montane terrestrial plethodontids. The abiotic environment, which will become increasingly limited under future changes in climate, was found to have more influence on survival and growth than population identity.

ecology↗

bioRxiv2017

Niche filtering, not interspecific resource competition, explains the co-occurrence of butterfly species across the Japanese archipelago

The relevance of interspecific resource competition in the context of community assembly by herbivorous insects is a well-known topic in ecology. Most previous studies focused on local species assemblies, that shared host plants. Few studies evaluated species pairs within a single taxon when investigating the effects of host plant sharing at the regional scale. Herein, we explore the effect of plant sharing on the geographical co-occurrence patterns of 232 butterflies distributed across the Japanese archipelago; we use two spatial scales (10 x 10 km and 1 x 1 km grids) to this end. We considered that we might encounter one of two predictable patterns in terms of the relationship between co-occurrence and host sharing among butterflies. On the one hand, host sharing might promote distributional exclusivity attributable to interspecific resource competition. On the other hand, sharing of host plants may promote co-occurrence attributable to filtering by resource niche. At both grid scales, we found significant negative correlations between host use similarity and distributional exclusivity. Our results support the hypothesis that the butterfly co-occurrence pattern across the Japanese archipelago is better explained by filtering via resource niche rather than interspecific resource competition.

ecology↗

bioRxiv2017

Sex-Specific Changes In Gene Expression And Delayed Sex Differentiation In Response To Estrogen Pollution In Grayling (Salmonidae)

The synthetic 17-ethinylestradiol (EE2) is an estrogenic compound of oral contraceptives and therefore a common pollutant that has been suspected to affect the demography of river-dwelling salmonids. We study a population of European grayling (Thymallus thymallus) that suffers from sex ratio distortions. Here we test how ecologically relevant concentrations of EE2 affect sex-specific gene expression around early stages of sex differentiation. We collected gametes from F1s of wild spawners, used them for in vitro fertilizations, and raised the resulting embryos singly under experimentally controlled conditions. Embryos were either exposed to 1ng/L EE2 or sham-exposed. RNA was collected from samples taken 10 days before hatching, at the day of hatching, and towards the end of the yolk-sac stage, to study gene expression and relate it to genetic sex (sdY genotype). We found that EE2 affects gene expression of a very large number of genes especially at the day of hatching. The effects of EE2 on gene expression is strongly sex-specific. At the day of hatching, EE2 affected about twice as many genes in females than in males, and towards the end of the yolk-sac larval stage, EE2 effects were nearly exclusively observed in females. Among the many effects was, for example, a surprising EE2-induced molecular masculinization in the females heads. Histological examination of gonadal development of EE2-treated or sham-exposed juveniles during the first 4.5 months after hatching revealed a delaying effect of EE2 on sex differentiation. Because grayling sex determination goes through an all-male stage (a rare case of undifferentiated gonochorism), the rate of EE2-induced sex reversal could not be unequivocally determined during the observational period. However, two EE2-treated genetic males had ovarian tissues at the end of the study. We conclude that common levels of EE2 pollution affect grayling from very early stages on by interfering with male and female gene expression around the onset of sex differentiation, by delaying sex differentiation, and by feminizing some males.\n\nAuthor contributionMRR and CW initiated the project. OS, DM, LW, LMC, and CW sampled the adult fish, did the experimental in vitro fertilizations, and prepared the embryos for experimental rearing in the laboratory. All further manipulations on the embryos and the larvae were done by OS, DM, LW, and LMC. The RNA-seq data were analyzed by OS, JR, and MRR, the histological analyses were done by DM, supervised by SK, the molecular genetic sexing was performed by OS and DM, and EV supervised the EE2 analytics. OS and CW performed the remaining statistical analyses and wrote the first version of the manuscript that was then critically revised by all other authors.

ecology↗

bioRxiv2017

The Kobresia pygmaea ecosystem of the Tibetan highlands – origin, functioning and degradation of the world’s largest pastoral alpine ecosystem

Kobresia pastures in the eastern Tibetan highlands occupy 450000 km2 and form the worlds largest pastoral alpine ecosystem. The main constituent is an endemic dwarf sedge, Kobresia pygmaea, which forms a lawn with a durable turf cover anchored by a felty root mat, and occurs from 3000 m to nearly 6000 m a.s.l. The existence and functioning of this unique ecosystem and its turf cover have not yet been explained against a backdrop of natural and anthropogenic factors, and thus its origin, drivers, vulnerability or resilience remain largely unknown. Here we present a review on ecosystem diversity, reproduction and ecology of the key species, pasture health, cycles of carbon (C), water and nutrients, and on the paleo-environment. The methods employed include molecular analysis, grazing exclusion, measurements with micro-lysimeters and gas exchange chambers, 13C and 15N labelling, eddy-covariance flux measurements, remote sensing and atmospheric modelling.\n\nThe following combination of traits makes Kobresia pygmaea resilient and highly competitive: dwarf habit, predominantly below-ground allocation of photo assimilates, mixed reproduction strategy with both seed production and clonal growth, and high genetic diversity. Growth of Kobresia pastures is co-limited by low rainfall during the short growing season and livestock-mediated nutrient withdrawal. Overstocking has caused pasture degradation and soil deterioration, yet the extent remains debated. In addition, we newly describe natural autocyclic processes of turf erosion initiated through polygonal cracking of the turf cover, and accelerated by soil-dwelling endemic small mammals. The major consequences of the deterioration of the vegetation cover and its turf include: (1) the release of large amounts of C and nutrients and (2) earlier diurnal formation of clouds resulting in (3) decreased surface temperatures with (4) likely consequences for atmospheric circulation on large regional and, possibly global, scales.\n\nPaleo-environmental reconstruction, in conjunction with grazing experiments, suggests that the present grazing lawns of Kobresia pygmaea are synanthropic and may have existed since the onset of pastoralism. The traditional migratory rangeland management was sustainable over millennia and possibly still offers the best strategy to conserve, and possibly increase, the C stocks in the Kobresia turf, as well as its importance for climate regulation.

ecology↗

bioRxiv2017

The Paradox Of Constant Oceanic Plastic Debris: Evidence For Evolved Microbial Biodegradation?

Although the presence of vast amounts of plastic in the open ocean has generated great concern due to its potential ecological consequences, recent studies reveal that its measured abundance is much smaller than expected. Regional and global studies indicate that the difference between expected and actual estimates is enormous, suggesting that a large part of the plastic has been degraded by either physical and biotic processes. A paradoxical observation is the lack of a trend in plastic accumulation found in the North Atlantic Subtropical Gyre, despite the rapid increase in plastic production and disposal. In this paper we show, using mathematical and computer models, that this observation could be explained by the nonlinear coupling between plastic (as a resource) and an evolved set of organisms (the consumers) capable of degrading it. The result is derived using two different resource-consumer mathematical approaches as well as a spatially-dependent plastic-microbial model incorporating a minimal hydrodynamical coupling with a two-dimensional fluid. The potential consequences of the evolution of marine plastic garbage and its removal are outlined.

ecology↗

bioRxiv2017

Conserving Phylogenetic Diversity Can Be A Poor Strategy For Conserving Functional Diversity

For decades, academic biologists have advocated for making conservation decisions in light of evolutionary history. Specifically, they suggest that policymakers should prioritize conserving phylogenetically diverse assemblages. The most prominent argument is that conserving phylogenetic diversity (PD) will also conserve diversity in traits and features (functional diversity; FD), which may be valuable for a number of reasons. The claim that PD-maximized ( maxPD) sets of taxa will also have high FD is often taken at face value and in cases where researchers have actually tested it, they have done so by measuring the phylogenetic signal in ecologically important functional traits. The rationale is that if traits closely mirror phylogeny, then saving the maxPD set of taxa will tend to maximize FD and if traits do not have phylogenetic structure, then saving the maxPD set of taxa will be no better at capturing FD than criteria that ignore PD. Here, we suggest that measuring the phylogenetic signal in traits is uninformative for evaluating the effectiveness of using PD in conservation. We evolve traits under several different models and, for the first time, directly compare the FD of a set of taxa that maximize PD to the FD of a random set of the same size. Under many common models of trait evolution and tree shapes, conserving the maxPD set of taxa will conserve more FD than conserving a random set of the same size. However, this result cannot be generalized to other classes of models. We find that under biologically plausible scenarios, using PD to select species can actually lead to less FD compared to a random set. Critically, this can occur even when there is phylogenetic signal in the traits. Predicting exactly when we expect using PD to be a good strategy for conserving FD is challenging, as it depends on complex interactions between tree shape and the assumptions of the evolutionary model. Nonetheless, if our goal is to maintain trait diversity, the fact that conserving taxa based on PD will not reliably conserve at least as much FD as choosing randomly raises serious concerns about the general utility of PD in conservation.

ecology↗

bioRxiv2017

Defining Marine Microbial Biomes From Environmental And Dispersal Filtered Metapopulations

Energy and matter fluxes essential for all life1 are modulated by spatial and temporal shifts in microbial community structure resulting from environmental and dispersal filtering2,3, emphasizing the continued need to characterize microbial biogeography4,5. Yet, application of metapopulation theory, traditionally used in general ecology for understanding shifts in biogeographical patterns among macroorganisms, has not been tested extensively for defining marine microbial populations filtered by environmental conditions and dispersal limitation at global ocean scales. Here we show, from applying metapopulation theory on two major global ocean datasets6,7, that microbial populations exhibit core- and satellite distributions with cosmopolitan compared to geographically restricted distributions of populations. We found significant bimodal occupancy-frequency patterns (the different number of species occupying different number of patches) at varying spatial scales, where shifts from bimodal to unimodal patterns indicated environmental and dispersal filtering. Such bimodal occupancy-frequency patterns were validated in Longhursts classical biogeographical framework and in silico where observed bimodal patterns often aligned with specific biomes and provinces described by Longhurst and where found to be non-random in randomized datasets and mock communities. Taken together, our results show that application of metapopulation theory provides a framework for determining distinct microbial biomes maintained by environmental and dispersal filtering.

ecology↗

bioRxiv2017

Coordinated Shifts In Allocation Among Reproductive Tissues Across 14 Coexisting Plant Species

Plant species differ in the amounts of energy allocated to different reproductive tissues, driving differences in their ecology and energy flows within ecosystems. While it is widely agreed that energy allocation is key to reproductive outcomes, few studies have estimated how reproductive effort (RE) is partitioned among different pools, for multiple species in a community. In plants, RE can be partitioned in several meaningful ways: seed versus non-seed tissues; into flowers that form seeds and those that fail to develop; into pre-versus post-pollination tissues, and into successful versus aborted ovules. Evolutionary theory suggests several hypotheses about how these tissues should be coordinated across species. To quantify variation in allocation to different reproductive tissues, we collected detailed RE measurements for a year from 14 perennial species in a recurrent-fire coastal heath community in eastern Australia. Overall we found that total accessory costs - the proportion of RE not directly invested in provisioning the seed - were very large, varying from 95.8% to 99.8% across the study species. These results suggest that studies using seed or fruit production as measures of RE may underestimate it by 10-to 500-fold. We propose a suitable alternative that well-approximates true RE. When comparing species, we found strong support for three evolutionary trade-offs that are predicted to arise when a given energy pool is divided into different tissue masses and counts across species: 1) between successful pollen-attraction costs and mature ovule count, 2) between total reproductive costs and seed count, and 3) between seedset and relative investment in pollen-attraction costs. As a result of these trade-offs, species were also predicted to show coordinated shifts in the amounts invested in floral construction, in seedset and seed size. These shifts in investment were indeed observed, with the amount allocated to discarded tissues increasing with seed size and the amount allocated to pollen-attraction decreasing with seed size. It is already well-established that the seed size axis aligns with the colonization-competition life history spectrum; here we show that relative construction costs of pollen-attraction versus provisioning tissues and seedset are also part of this trajectory, expanding our understanding of the relatives sizes of floral and fruiting structures observed across angiosperms.

ecology↗

bioRxiv2017

Pre-dispersal conditions and presence of opposite sex modulate density dependence and sex bias of dispersal

Density-dependent dispersal (DDD) has been demonstrated in many species and has several ecological and evolutionary consequences. Yet we know little about how robust DDD is to the various conditions experienced by individuals. In this study, we use three independent experiments on laboratory populations of Drosophila melanogaster to examine the effects of pre-dispersal adult density, sex of the dispersers and presence of mates on the robustness of DDD patterns. We show that DDD can be greatly affected by both pre-dispersal density and interaction between the sexes. Moreover, the direction of sex-biased dispersal can reverse completely due to an interaction between the pre-dispersal and dispersal densities. We also show that interaction between the sexes can lead to negative DDD at the population level, even if, by themselves, neither sex exhibits DDD. Finally, we discuss potential implications of our results for processes like evolutionary rescue from extinctions and genetic divergence of populations.

ecology↗

bioRxiv2017

Species-specific adaptations determine how aridity and biotic interactions drive the assembly of dryland plant communities

O_LIDespite being a core ecological question, disentangling individual and interacting effects of plant-plant interactions, abiotic factors and species-specific adaptations as drivers of community assembly is challenging. Studies addressing this issue are growing rapidly, but they generally lack empirical data regarding species interactions and local abundances, or cover a narrow range of environmental conditions.\nC_LIO_LIWe analysed species distribution models and local spatial patterns to isolate the relative importance of key abiotic (aridity) and biotic (facilitation and competition) drivers of plant community assembly in drylands worldwide. We examined the relative importance of these drivers along aridity gradients and used information derived from the niches of species to understand the role that species-specific adaptations to aridity play in modulating the importance of community assembly drivers.\nC_LIO_LIFacilitation, together with aridity, was the major driver of plant community assembly in global drylands. Due to community specialization, the importance of facilitation as an assembly driver decreased with aridity, and became non significant at the border between arid and semiarid climates. Under the most arid conditions, competition affected species abundances in communities dominated by specialist species. Due to community specialization, the importance of aridity in shaping dryland plant communities peaked at moderate aridity levels.\nC_LIO_LISynthesis: We showed that competition is an important driver of community assembly even under harsh environments, and that the effect of facilitation collapses as driver of species relative abundances under high aridity because of the specialization of the species pool to extremely dry conditions. Our findings pave the way to develop more robust species distribution models aiming to predict the consequences of ongoing climate change on community assembly in drylands, the largest biome on Earth.\nC_LI

ecology↗

bioRxiv2017

Phytoplankton functional types: A trait perspective

Phytoplankton functional types are groupings of many species into a smaller number of types according to their ecological or biogeochemical role. Models describe phytoplankton functional types by a set of traits that determine their growth rates or fitness. Traits for functional types are often determined from observations on a small number of species under laboratory conditions. Functional types can be composed of a large number of species with very different trait values, so the representation of a type by an average trait value may not be appropriate. A potential solution is to estimate trait values from observations of the aggregate biomass of phytoplankton functional types in natural populations. We report on some recent efforts to extract trait values from time-series data using Bayesian statistical models and discuss some challenges of this approach.

ecology↗

bioRxiv2017

Faster carbon accumulation in global forest soils

Comparing soil organic carbon (SOC) stocks across space and time is a fundamental issue in global ecology. However, the conventional approach fails to determine SOC stock in an equivalent volume of mineral-soil, and therefore, SOC stock changes can be under- or overestimates if soils swell or shrink during forest development or degradation. Here, we propose to estimate SOC stock as the product of mineral-soil mass in an equivalent mineral-soil volume and SOC concentration expressed as g C Kg-1 mineral-soil. This method enables researchers to compare SOC stocks across space and time. Our results show an unaccounted SOC accumulation of 2.4 - 10.1 g C m-2 year-1 in the 1m surface mineral-soils in global forests. This unaccounted SOC amounts to an additional C sink of 0.12 - 0.25 Pg C year-1, which equals 30 - 62% of the previously estimated annual SOC accumulation in global forests. This finding suggests that forest soils are stronger C sinks than previously recognized.

ecology↗

bioRxiv2017

Soil community assembly varies across body sizes in a tropical forest

The relative influence of deterministic niche-based (i.e. abiotic conditions, biotic interactions) and stochastic-distance dependent neutral processes (i.e. demography, dispersal) in shaping communities has been extensively studied for various organisms, but is far less explored jointly across the tree of life, in particular in soil environments. Here, using a thorough DNA-based census of the whole soil biota in a large tropical forest plot, we show that soil aluminium, topography, and plant species identity are all important drivers of soil richness and community composition. Body size emerges as an important feature of the comparative ecology of the different taxa at the studied spatial scale, with microorganisms being more importantly controlled by environmental factors, while soil mesofauna rather display random spatial distribution. We infer that niche-based processes contribute differently to community assembly across trophic levels due to spatial scaling. Body size could hence help better quantifying important properties of multitrophic assemblages.

ecology↗