Evolution, Adaptation and Biodiversity

published in  : 2020 - 2019 - 2018 - 2017 - 2016

2021

Homologous chromosomes and recombination in asexual rotifer

Simion P, Narayan J, Houtain A, Derzelle A, Baudry L, Nicolas E, Arora R, Cariou M, Cruaud C, Gaudray FR, Gilbert C, Guiglielmoni N, Hespeels B, Kozlowski DKL, Labadie K, Limasset A, Llirós M, Marbouty M, Terwagne M, Virgo J, Cordaux R, Danchin EGJ, Hallet B, Koszul R, Lenormand T, Flot J-F, Van Doninck K. Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga. Science Advances 7:eabg4216. DOI: 10.1126/sciadv.abg4216.

Bdelloid rotifers are notorious as a speciose ancient clade comprising only asexual lineages. Thanks to their ability to repair highly fragmented DNA, most bdelloid species also withstand complete desiccation and ionizing radiation. Producing a well-assembled reference genome is a critical step to developing an understanding of the effects of long-term asexuality and DNA breakage on genome evolution. Here, the first high-quality chromosome-level genome assemblies for the bdelloid Adineta vaga are presented. The observed large-scale losses of heterozygosity are signatures of recombination between homologous chromosomes, either during mitotic DNA double-strand break repair or when resolving programmed DNA breaks during a modified meiosis. The presented results trigger the reappraisal of potential meiotic processes in bdelloid rotifers and help unravel the factors underlying their long-term asexual evolutionary success.

cyanoFilter: An R package

Olusoji OD, Spaak JW, Holmes M, Neyens T, Aerts M, De Laender F. 2021. cyanoFilter: An R package to identify phytoplankton populations from flow cytometry data using cell pigmentation and granularity. Ecological Modelling 460:109743. DOI: 10.1016/j.ecolmodel.2021.109743.

Flow cytometry is often employed in ecology to measure traits and population size of bacteria and phytoplankton. This technique allows measuring millions of particles in a relatively small amount of time. However, distinguishing between different populations is not a straightforward task. Gating is a process in the identification of particles measured in flow cytometry. Gates can either be created manually using known characteristics of these particles, or by using automated clustering techniques. Available automated techniques implemented in statistical packages for flow cytometry are primarily developed for medicinal applications, while only two exist for phytoplankton. cyanoFilter is an R package built to identify phytoplankton populations from flow cytometry data. This study demonstrates how its performance depends on strain similarity, using a model system of six cyanobacteria strains. Using the same system, the performance of the central gating function in the package to similar functions in other packages is compared.

Stressors / productivity / biodiversity

Holmes M, Spaak JW, De Laender F. Stressor richness intensifies productivity loss but mitigates biodiversity loss. Ecology and Evolution n/a. DOI: 10.1002/ece3.8182.

Ecosystems are subject to a multitude of anthropogenic environmental changes. Experimental research in the field of multiple stressors has typically involved varying the number of stressors, here termed stressor richness, but without controlling for total stressor intensity. Mistaking stressor intensity effects for stressor richness effects can misinform management decisions when there is a trade-off between mitigating these two factors. We incorporate multiple stressors into three community models and show that, at a fixed total stressor intensity, increasing stressor richness aggravates joint stressor effects on ecosystem functioning, but reduces effects on species persistence and composition. In addition, stressor richness weakens the positive selection and negative complementarity effects on ecosystem function. We identify the among-species variation of stressor effects on traits as a key determinant of the resulting community-level stressor effects. Taken together, our results unravel the mechanisms linking multiple environmental changes to biodiversity and ecosystem function.

Species richness increases fitness differences

Spaak JW, Carpentier C, Laender FD. Species richness increases fitness differences, but does not affect niche differences. Ecology Letters n/a. DOI: 10.1111/ele.13877.

A key question in ecology is what limits species richness. Modern coexistence theory presents the persistence of species as a balance between niche differences and fitness differences that favour and hamper coexistence, respectively. With most applications focusing on species pairs, however, little is known about if and how this balance changes with species richness. Here, recently developed definitions of niche and fitness differences, based on invasion analysis are applied to multispecies communities. The first mathematical proof is presented that, for invariant average interaction strengths, the average fitness difference among species increases with richness, while the average niche difference stays constant. Extensive simulations with more complex models and analyses of empirical data confirmed these mathematical results. Combined, this work suggests that, as species accumulate in ecosystems, ever-increasing fitness differences will at some point exceed constant niche differences, limiting species richness. These results contribute to a better understanding of coexistence multispecies communities.

Mapping species niche and fitness differences

Spaak JW, Godoy O, Laender FD. Mapping species niche and fitness differences for communities with multiple interaction types. Oikos n/a. DOI: 10.1111/oik.08362.

Modern coexistence theory (MCT) holds the potential to study the ability of species to avoid extinction (i.e. to persist) across community types but is rarely applied beyond pairs of competing species. Here, we show that this limitation can be overcome by mapping species according to their niche (urn:x-wiley:00301299:media:oik13253:oik13253-math-0001) and fitness differences (urn:x-wiley:00301299:media:oik13253:oik13253-math-0002). This application provides three main benefits to study processes of multispecies persistence across trophic levels. First, urn:x-wiley:00301299:media:oik13253:oik13253-math-0003 mapping introduces a novel categorization of species and communities according to the high-level processes at play: frequency dependence (negative or positive), the occurrence of positive species interactions (facilitation and mutualism) and whether persistence is possible without the presence of other species because of trophic interactions, such as herbivory or predation. Therefore, this mapping can be seen as a toolbox to describe how species persistence depends on species interactions. Second, urn:x-wiley:00301299:media:oik13253:oik13253-math-0004 mapping facilitates studying how species persistence responds to environmental changes that shift intrinsic growth rates and the strength and sign of species interactions. Third, urn:x-wiley:00301299:media:oik13253:oik13253-math-0005 mapping has the potential to foster synthesis across community types because it can accommodate co-occurrence of positive, negative and neutral interactions between species. We, therefore, argue that urn:x-wiley:00301299:media:oik13253:oik13253-math-0006 mapping can promote collaboration across sub-fields, as it provides a common concept to link disparate ecological communities.

Biometric conversion factors for invasive freshwater bivalves

Coughlan NE, Cunningham EM, Cuthbert RN, Joyce PWS, Anastácio P, Banha F, Bonel N, Bradbeer SJ, Briski E, Butitta VL, Čadková Z, Dick JTA, Douda K, Eagling LE, Ferreira-Rodríguez N, Hünicken LA, Johansson ML, Kregting L, Labecka AM, Li D, Liquin F, Marescaux J, Morris TJ, Nowakowska P, Ożgo M, Paolucci EM, Peribáñez MA, Riccardi N, Smith ERC, Spear MJ, Steffen GT, Tiemann JS, Urbańska M, Doninck KV, Vastrade M, Vong GYW, Wawrzyniak-Wydrowska B, Xia Z, Zeng C, Zhan A, Sylvester F. Biometric conversion factors as a unifying platform for comparative assessment of invasive freshwater bivalves. Journal of Applied Ecology n/a. DOI: 10.1111/1365-2664.13941.

Invasive bivalves continue to spread and negatively impact freshwater ecosystems worldwide. Different metrics for body size and biomass are frequently used to standardise bivalve-related ecological impacts (e.g. respiration and filtration rates) which are, however, not broadly applicable. This hinders reliable comparisons across bivalve populations. This study reports body size and biomass conversion equations for six invasive freshwater bivalves worldwide and tested their reliability. They rapidly estimate the biologically active biomass of the assessed species, which allows for the calculation of approximate average indicators that, when combined with density data, can be used to estimate biomass per geographical unit-area and contribute to quantification of population-level effects. These general equations will support meta-analyses, and allow for comparative assessment of historic and contemporary data. Overall, these equations will enable conservation managers to better understand and predict ecological impacts of these bivalves.

Stability of ecological networks

Carpentier C, Barabás G, Spaak JW, De Laender F. 2021. Reinterpreting the relationship between number of species and number of links connects community structure and stability. Nature Ecology & Evolution:1–8. DOI: 10.1038/s41559-021-01468-2.

For more than 50 years, scientists try to understand how the number of interspecific interactions changes with the number of species and thus, contribute to ecosystem stability. The traditional approach is to take an inventory of the number of species and the number of interactions in several ecosystems and to determine the most appropriate mathematical equation to describe the relationship between these two variables. This approach suggests that a single equation characterises all ecosystems. However, there is no consensus as to the exact form of this equation. Camille et al. propose now an alternative approach: the equation that unites the number of species and the number of interactions would be specific to each ecosystem and not common to all observable ecosystems on Earth. Based on this assumption, they achieved to mathematically link the number of species in an ecosystem, the number of interactions between these species and the stability of this ecosystem. Their equations can thus predict the response of a given ecosystem. They confirmed their results by analysing 435 empirical networks. Not enough, their method further applies to other interaction networks such as cellular, communication or transport networks.

Overcoming uncollapsed haplotypes in long-read assemblies

Guiglielmoni N, Houtain A, Derzelle A, Van Doninck K, Flot J-F. 2021. Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms. BMC Bioinformatics 22:303. DOI: 10.1186/s12859-021-04118-3.

Long-read sequencing is revolutionizing genome assembly: as PacBio and Nanopore technologies become more accessible in technicity and in cost, long-read assemblers flourish and are starting to deliver chromosome-level assemblies. However, these long reads are usually error-prone, making the generation of a haploid reference out of a diploid genome a difficult enterprise. This study tested different assembly strategies on the genome of the rotifer Adineta vaga, a non-model organism. The most popular assemblers are evaluated. This study highlights several strategies using pre- and post-processing approaches to generate haploid assemblies with high continuity and completeness. This benchmark will help users to improve haploid assemblies of non-model organisms, and evaluate the quality of their own assemblies.

Moving apart together

Parmentier T, Claus R, De Laender F, Bonte D. 2021. Moving apart together: co-movement of a symbiont community and their ant host, and its importance for community assembly. Movement Ecology 9:25. DOI: 10.1186/s40462-021-00259-5.

Species interactions may affect spatial dynamics when the movement of one species is determined by the presence of another one. The most direct species-dependence of dispersal is the vectored, usually cross-kingdom, movement of immobile parasites, diseases or seeds by mobile animals, for example the diverse community of arthropods (myrmecophiles) associated with red wood ants studied here. An astonishingly high number of obligate myrmecophiles was recorded outside red wood ant nests. They preferentially co-moved with the host ants. These observations suggest that myrmecophiles resort to the host to move away from the nest, and this to a much higher extent than hitherto anticipated. Predatory myrmecophiles were moving more frequently and further from the nest than detritivorous myrmecophiles. This shows that movement in social insect symbiont communities may be heterogeneous and functional group-dependent, but clearly affected by host movement. Ultimately, this co-movement leads to directional movement and allows a fast colonisation of new patches, but not in a predictable way. This study highlights the importance of spatial dynamics of local and regional networks in symbiont metacommunities, of which those of symbionts of social insects are prime examples.

Revised phylogeny of mint

Heylen OCG, Debortoli N, Marescaux J, Olofsson JK. 2021. A Revised Phylogeny of the Mentha spicata Clade Reveals Cryptic Species. Plants 10:819. DOI: 10.3390/plants10040819.

Cryptic and hyperdiverse species complexes with large distribution ranges are excellent model systems for studying the evolutionary processes shaping biodiversity. However, the genotype–phenotype links are not always clear in such taxa, making it difficult to describe their taxonomic structure. The genus Mentha is taxonomically and phylogenetically challenging due to complex genomes, polyploidization and an extensive historical nomenclature, potentially hiding cryptic taxa. This study introduces a fundamentally different viewpoint on the evolutionary relationships among Spicate mints. An innovative phylogeny is presented implying refreshing insights on previous hybridization concepts and cryptic taxa. By combining genetic and morphological data, authors were able to discern cryptic mint species and uncover new taxonomic units.

Coexistence, richness and ecosystem function

Spaak JW, Laender FD. 2021. Effects of pigment richness and size variation on coexistence, richness and function in light limited phytoplankton. Journal of Ecology n/a. DOI: https://doi.org/10.1111/1365-2745.13645.

Trait diversity is traditionally seen as promoting species richness and ecosystem function. This study first uses theory and simulations for light‐limited phytoplankton and confirms that combing photosynthetic pigments is indeed a necessary condition for coexistence and stimulates ecosystem function. However, pigment richness does mostly not permit the coexistence of more than two species, and increases productivity at most 40% compared to single‐pigment communities. That is because blending in more pigments leads to coexistence of species with many pigments and therefore flat absorption spectra, which equalizes their fitness but decreases their niche differences. Similarly, seeding species with more variable size leads to an excess of large‐celled species, which does not only decrease fitness differences, but also niche differences. Empirical data and additional simulations suggest that pigment richness effects can be stronger during transient dynamics but inevitably weaken with time, i.e. pigment richness effects on species richness and function are likely short‐lived. These results highlight the need to apply coexistence theory to understand the long‐term effects of trait diversity on biodiversity and ecosystem function.

2020

Consumer-resource models predict species dominance

De Rijcke M, Baert JM, Brion N, Vandegehuchte MB, De Laender F, Janssen CR. 2020. Monoculture-based consumer-resource models predict species dominance in mixed batch cultures of dinoflagellates. Harmful Algae 99:101921. DOI: 10.1016/j.hal.2020.101921.

Global change will disturb the frequency, scale and distribution of harmful algal blooms (HABs), but we are unable to predict future HABs due to our limited understanding of how physicochemical changes in the environment affect interspecific competition between dinoflagellates. Trait-based mechanistic modelling is an important tool to unravel and quantify various direct and indirect interactions between species. The present study explores whether MacArthur's consumer-resource model can be used as a viable base model to predict dinoflagellate growth in closed multispecies systems. The results suggest that consumer-resource models provide a promising basis for trait-based modelling of interspecific competition between (harmful) algae.

Iron Ladies - rotifer resistance to radiation

Hespeels B, Penninckx S, Cornet V, Bruneau L, Bopp C, Baumlé V, Redivo B, Heuskin A-C, Moeller R, Fujimori A, Lucas S, Van Doninck K. 2020. Iron Ladies – How Desiccated Asexual Rotifer Adineta vaga Deal With X-Rays and Heavy Ions? Frontiers in Microbiology 11. DOI: 10.3389/fmicb.2020.01792.

 This study prepared the mission of bdelloid rotifers to space. Here, resistance of desiccated (for some radiation also hydrated) Adineta vaga individuals exposed to increasing doses of X-ray, protons and Fe ions was tested. Survival and the capacity of irradiated animals to produce viable offspring were evaluated, as well as the capacity to repair DNA breaks. Lethal doses could be determined (5,000 to 7,500 Gy using low and high LET radiation for X-ray and Proton, respectively). Results achieved through this study consolidate our knowledge about the radioresistance of A. vaga and improve our capacity to compare extreme resistance against radiation among living organisms including metazoan.

 

Decomposers and ecosystem health

Beaumelle L, De Laender F, Eisenhauer N. 2020. Biodiversity mediates the effects of stressors but not nutrients on litter decomposition. eLife 9:e55659. DOI: 10.7554/eLife.55659.

This study brings new insights into the real-world patterns relating ecosystem function to non-random changes in biodiversity induced by environmental change. The authors gathered the results from 69 independent studies on animal and microbial decomposer diversity and litter decomposition conducted across the globe. Meta-analysis and structural equation modelling showed that chemical stressors caused the diversity and abundance of decomposers to decline, which reduced the breakdown of leaf litter, as expected. However, the outcomes of excess nutrients were more varied. Low levels of excess nutrients increased the breakdown of leaf litter, but at high levels slowed down the rate leaves decomposed. Furthermore, the effect excess nutrients had on biodiversity in decomposer communities changed according to the types of organisms in the ecosystem. This suggests that variations in biodiversity can impact ecosystems differently depending on the type of environmental change.

Stochasticity and epigenetics

Biwer C, Kawam B, Chapelle V, Silvestre F. The role of stochasticity in the origin of epigenetic variation in animal populations. Integrative and Comparative Biology. DOI: 10.1093/icb/icaa047.

Epigenetic mechanisms such as DNA methylation modulate gene expression and thus contribute to phenotypic variation in natural populations of organisms. Interactions between genetics and epigenetics are multifaceted and epigenetic variation stands at the crossroad between genetic and environmental variance, which make these mechanisms prominent in the processes of adaptive evolution. Epigenetic variance can be attributed to genetic, environmental or stochastic factors, then referred to spontaneous epimutations. This review explores potential sources of such stochastic epigenetic variability in animals, with a focus on DNA methylation. Quantifying the importance of stochasticity in epigenetic variability remains a challenge. However, comparisons between the mutation and the epimutation rates showed a high level of the latter, suggesting a significant role of spontaneous epimutations in adaptation.

Niche and fitness differences

Spaak JW, De Laender F. 2020. Intuitive and broadly applicable definitions of niche and fitness differences. Ecology Letters n/a. DOI: 10.1111/ele.13511

Resource partitioning, vulnerability to predators, occupation of distinct microhabitats, etc. have been defined to increase ’niche differences’ (N) and permit species to coexist. Available definitions of N in modern coexistence theory are, however, difficult to interpret, differ in the way N links to species’ interactions and often apply to specific community types only. This article presents a new definition of N that is intuitive and applicable to a broader set of (modelled and empirical) communities, filling a main gap in the literature. Given N, the authors also redefine fitness differences (F) and illustrate how N and F determine coexistence. Application to theoretical models and experimental data are provided as well as ideas comparison in community ecology.

Salmon don't like it hot

Bernard B, Leguen I, Mandiki SNM, Cornet V, Redivo B, Kestemont P. 2020. Impact of temperature shift on gill physiology during smoltification of Atlantic salmon smolts (Salmo salar L.). Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology 244:110685. DOI: 10.1016/j.cbpa.2020.110685.

In spring, Atlantic salmon juveniles transform to seawater-tolerant smolts and travel downstream. This transformation is caused by external cues and an internal rhythm. Temperature strongly influences the onset of salmon migration and the development of the hypo-osmoregulatory capacity. Rapid temperature increases, as can be found between the Meuse river and its tributaries (here: Ourthe) due to the presence of a nuclear power plant, impact on smoltification processes and even lead to desmoltification. This study shows changes of gill transcriptional patterns and other physiological parameters in salmon juveniles due to temperature increase. As a consequence, survival chances at sea-entry are impaired.

Consequences of infections in early life of Zebrafish

Cornet V, Douxfils J, Mandiki SNM, Kestemont P. 2020. Early-life infection with a bacterial pathogen increases expression levels of innate immunity related genes during adulthood in zebrafish. Developmental & Comparative Immunology 108:103672. DOI: 10.1016/j.dci.2020.103672.

Infections during early life can have various consequences on fish health development later in life. This study investigated the expression of genes involved in immune responses against bacterial challenges during adulthood in zebrafish, that had been infected at 18 days after fertilization. The fish showed a fast and strong stimulation of mpx gene probably contributing to the destruction of the pathogen. At the same time, genes involved in inflammatory reactions, ptsg2 and tfa, decreased. A single primary infection of a 1-month-old zebrafish was enough to train the innate immune system to deal with a secondary infection. On the other hand, chronic infections lowered the beneficial effects provided by the primary infection on innate immune responses.

Melatonin release and immune markers of pike perch

Baekelandt S, Milla S, Cornet V, Flamion E, Ledoré Y, Redivo B, Antipine S, Mandiki SNM, Houndji A, Kertaoui NE, Kestemont P. 2020. Seasonal simulated photoperiods influence melatonin release and immune markers of pike perch Sander lucioperca. Scientific Reports 10:1–10. DOI: 10.1038/s41598-020-59568-1.

Melatonin is the time-keeping hormone acting on important physiological functions of teleost fish. Its influence on reproduction and development is well described, contrary to its potential role on immune functions. This study simulates fall and spring with two photoperiod regimes to see whether subsequent changes in melatonin release act on the immune status of pikeperch. For the first time it could be shown that immune markers vary according to the season-simulated photoperiod. Lysozyme, complement and peroxidase activities, were stimulated by the fall-simulated photoperiod and a significant correlation was made with plasma melatonin. In contrast, only lysozyme showed a decrease under the spring-simulated photoperiod. As the time-keeping hormone, melatonin is one of the main mediators acting on fish immune system.

Resilience trinity to safeguard ecosystems

Weise H, Auge H, Baessler C, Bärlund I, Bennett EM, Berger U, Bohn F, Bonn A, Borchardt D, Brand F, Chatzinotas A, Corstanje R, De Laender F, Dietrich P, Dunker S, Durka W, Fazey I, Groeneveld J, Guilbaud CSE, Harms H, Harpole S, Harris J, Jax K, Jeltsch F, Johst K, Joshi J, Klotz S, Kühn I, Kuhlicke C, Müller B, Radchuk V, Reuter H, Rinke K, Schmitt–Jansen M, Seppelt R, Singer A, Standish RJ, Thulke HH, Tietjen B, Weitere M, Wirth C, Wolf C, Grimm V. 2020. Resilience trinity: safeguarding ecosystem functioning and services across three different time horizons and decision contexts. Oikos n/a. DOI: 10.1111/oik.07213.

Ensuring ecosystem resilience is fundamental to safeguard the functioning of ecosystem services (ES).  However, resilience is a multi‐faceted concept that is difficult utilise in practice. While it makes intuitive sense to manage for resilience it is unclear which actions should follow from this goal. This paper suggests a conceptual framework, resilience trinity, to facilitate management based on resilience mechanisms in three distinctive decision contexts and time‐horizons: 1) reactive, when there is an imminent threat to ES resilience and a high pressure to act, 2) adjustive, when the threat is known in general but there is still time to adapt management, and 3) provident, when time horizons are very long and the nature of the threats is uncertain, leading to a low willingness to act. This proposed trinity could help ensuring that longer‐term management actions are not missed while urgent threats to ES are given priority.

2019

Urbanisation & cross‐taxon declines

Piano E, Souffreau C, Merckx T, Baardsen LF, Backeljau T, Bonte D, Brans KI, Cours M, Dahirel M, Debortoli N, Decaestecker E, Wolf KD, Engelen JMT, Fontaneto D, Gianuca AT, Govaert L, Hanashiro FTT, Higuti J, Lens L, Martens K, Matheve H, Matthysen E, Pinseel E, Sablon R, Schön I, Stoks R, Doninck KV, Dyck HV, Vanormelingen P, Wichelen JV, Vyverman W, Meester LD, Hendrickx F. 2019. Urbanization drives cross-taxon declines in abundance and diversity at multiple spatial scales. Global Change Biology n/a. DOI: 10.1111/gcb.14934.

Urbanisation is supposed to alter (semi-) natural environments and lead to a major decline in species abundance and diversity. However, comprehensive studies that analyse this effect across multiple animal groups and at multiple spatial scales are rare. This study includes aquatic (cladocerans), limnoterrestrial (bdelloid rotifers) and terrestrial (butterflies, ground beetles, ground- and web spiders, macro-moths, orthopterans and snails) invertebrate groups. It uses a hierarchical spatial design wherein three local-scale (200 m × 200 m) urbanization levels were repeatedly sampled across three landscape-scale (3 km × 3 km) urbanization levels. Abundances of the terrestrial active dispersers declined in response to local urbanization, with reductions up to 85% for butterflies, while passive dispersers did not show any clear trend. Species richness also declined with increasing levels of urbanization, but responses were highly heterogeneous among the different groups. These results provide strong support to the general negative impact of urbanization on abundance and species richness within habitat patches and highlight the importance of considering multiple spatial scales and taxa to assess the impacts of urbanisation.

Carbon cycles & climate change

Reyns W, Rineau F, Spaak JW, Franken O, Berg MP, Van Der Plas F, Bardgett RD, Beenaerts N, De Laender F. 2019. Food Web Uncertainties Influence Predictions of Climate Change Effects on Soil Carbon Sequestration in Heathlands. Microbial Ecology. DOI: 10.1007/s00248-019-01444-1.

Carbon cycling models consider soil carbon sequestration a key process for climate change mitigation. However, these models mostly focus on abiotic soil processes and do not explicitly include interacting soil organisms. This literature study shows that even a relatively simple soil community (heathland soils) contains large uncertainties in temporal and spatial food web structure. A Lotka–Volterra-based food web model further demonstrates that, due to these uncertainties, climate change can either increase or decrease soil carbon sequestration. Hence, even for a soil community with a few dominant functional groups and a simulation model with a few parameters, filling these knowledge gaps is a critical first step towards the explicit integration of soil food web dynamics into carbon cycling models in order to better assess the role soils play in climate change mitigation.

Ecosystems & climate change

Rineau F, Malina R, Beenaerts N, Arnauts N, Bardgett RD, Berg MP, Boerema A, Bruckers L, Clerinx J, Davin EL, Boeck HJD, Dobbelaer TD, Dondini M, Laender FD, Ellers J, Franken O, Gilbert L, Gudmundsson L, Janssens IA, Johnson D, Lizin S, Longdoz B, Meire P, Meremans D, Milbau A, Moretti M, Nijs I, Nobel A, Pop IS, Puetz T, Reyns W, Roy J, Schuetz J, Seneviratne SI, Smith P, Solmi F, Staes J, Thiery W, Thijs S, Vanderkelen I, Landuyt WV, Verbruggen E, Witters N, Zscheischler J, Vangronsveld J. 2019. Towards more predictive and interdisciplinary climate change ecosystem experiments. Nature Climate Change 9:809–816. DOI: 10.1038/s41558-019-0609-3.

Despite great advances, experiments concerning the response of ecosystems to climate change still face considerable challenges, including the high complexity of climate change in terms of environmental variables, constraints in the number and amplitude of climate treatment levels, and the limited scope of responses and interactions covered. Drawing on the expertise of researchers from a variety of disciplines, this Perspective outlines how computational and technological advances can help in designing experiments that can contribute to overcoming these challenges, and also outlines a first application of such an experimental design.

Niche or fitness?

Spaak JW, Carpentier C, Laender FD. 2019. Fitness differences, not niche differences, limit species richness. bioRxiv:823070. DOI: 10.1101/823070.

A key question in ecology is what limits species richness. Coexistence theory presents the persistence of species amidst heterospecifics as a balance between niche differences and fitness differences that favour and hamper coexistence, respectively. With most applications focusing on species pairs, we know little about how niche and fitness differences respond to species richness, i.e. what constraints richness most. This paper presents analytical proof that, in absence of higher-order interactions, the average fitness difference increases with richness, while the average niche difference stays constant. Analysis of a simple model with higher-order interactions, extensive simulations that relaxed all assumptions, and analyses of empirical data, confirmed these results. This work thus shows that fitness differences, not niche difference, limit species richness. The results contribute to the expansion of coexistence theory towards multi-species communities.

Invasive Corbicula Clams in Ireland

Sheehan R, Etoundi E, Minchin D, Doninck KV, Lucy F. 2019. Identification of the Invasive Form of Corbicula Clams in Ireland. Water 11:1652. https://doi.org/10.3390/w11081652.

The invasive Corbicula clam is prevalent in Ireland's rivers since 2010. Morphological identification is problematic due to a large variability of the shells. Here, the effectiveness of combined morphological and genetic approaches (both mitochondrial and nuclear markers) are demonstrated to resolve the identification of these bivalves. Only one lineage of Corbicula has invaded Ireland, a form also found across Europe and America. The method developed is thus a useful tool to identify invasive Corbicula populations properly to adapt management plans and limit impacts to ecosystem services. Most probably, the approach can be extended to identify and distinguish other invasive species.

Salmon migration and temperature

Bernard B, Mandiki SNM, Duchatel V, Rollin X, Kestemont P. 2019. A temperature shift on the migratory route similarly impairs hypo-osmoregulatory capacities in two strains of Atlantic salmon (Salmo salar L.) smolts. Fish Physiology and Biochemistry. DOI: 10.1007/s10695-019-00666-x.

Migrating salmons need to travers a smolting process involving morphological, physiological and behavioural changes to survive the transition from fresh to seawater. Smoltification is influenced by photoperiod and temperature and affects the development of hypo-osmoregulatory capacity of smolts. Anthropogenic use of water systems may cause temperature fluctuations between tributaries and large rivers. In case of the River Ourthe and the Meuse, these regularly exceed 4°C. The study demonstrates that such a temperature shift during downstream migration reduces hypo-osmoregulatory capacities of smolts, which dramatically impairs their survival chances at sea-entry. However, the fish remained resilient to this temperature impact for at least 1 week. Thus, favouring & accelerating the downstream migration of salmons may mitigate the physiological consequences of such a rapid temperature increase.

Light, melatonin and pikeperch

Baekelandt S, Mandiki SNM, Kestemont P. Are cortisol and melatonin involved in the immune modulation by the light environment in pikeperch Sander lucioperca? Journal of Pineal Research 0:e12573. DOI: 10.1111/jpi.12573.

The effects of red and white light spectra and two light intensities on pike perch physiological and immune responses were studied. High light intensities imposed on pikeperch induced 1) a state of stress and 2) a decrease of melatonin production. Melatonin is a crucial hormone produced by the pineal gland, regulating numerous physiological processes. This lead to negative growth rates and immune depression. Light spectrum had only little influences.

Horizontal and vertical diversity & food web stability

Zhao Q, Brink PJV den, Carpentier C, Wang YXG, Rodríguez‐Sánchez P, Xu C, Vollbrecht S, Gillissen F, Vollebregt M, Wang S, De Laender F. 2019. Horizontal and vertical diversity jointly shape food web stability against small and large perturbations. Ecology Letters 0. DOI: 10.1111/ele.13282.

Food webs are composed of horizontal (i.e. within trophic levels) and vertical diversity (i.e. the number of trophic levels). Their effects on stability are, however, mostly considered individually. This study examines their joint effects on the stability of hypothetical (modelled) and empirical food webs. In modelled food webs, producer diversity had a stronger positive effect on stability at higher consumer diversity. These predictions were confirmed in experiments with an empirical plankton food web. The findings highlight the need to conserve horizontal biodiversity at different trophic levels to ensure stability.

Stability, disturbance, dimensions

Radchuk V, Laender FD, Cabral JS, Boulangeat I, Crawford M, Bohn F, De Raedt J, Scherer C, Svenning J-C, Thonicke K, Schurr FM, Grimm V, Kramer‐Schadt S. 2019. The dimensionality of stability depends on disturbance type. Ecology Letters 22:674–684. DOI: 10.1111/ele.13226.

Ecosystems respond in various ways to disturbances. To quantify ecological stability, one has to determine several aspects such as resistance, recovery, persistence and invariability. These can be correlated with each other, reducing the number of dimensions of stability, which simplifies the study system. How does then disturbance affect such correlations? This study used process‐based models reflecting natural systems to test the effect of disturbance on the dimensionality of stability of populations and communities. In most cases, monitoring of stability at these levels required multiple stability properties, and the use of a single proxy was not justified.

2 x Killifish & genes

Fellous A, Earley RL, Silvestre F. 2019a. The Kdm/Kmt gene families in the self-fertilizing mangrove rivulus fish, Kryptolebias marmoratus, suggest involvement of histone methylation machinery in development and reproduction. Gene 687:173–187. DOI: 10.1016/j.gene.2018.11.046.

Fellous A, Earley RL, Silvestre F. 2019b. Identification and expression of mangrove rivulus (Kryptolebias marmoratus) histone deacetylase (HDAC) and lysine acetyltransferase (KAT) genes. Gene 691:56–69. DOI: 10.1016/j.gene.2018.12.057.

Two articles that investigate histone modifications during embryogenesis of a fish model, the mangrove rivulus, and what this means for epigenetic mechanisms in adaptation to the environment. These studies provide a basis about the epigenetic actors that probably regulate histone acetylation in a self-fertilizing fish.

Weise H, Auge H, Baessler C, Baerlund I, Bennett EM, Berger U, Bohn F, Bonn A, Borchardt D, Brand F, Chatzinotas A, Corstanje R, De Laender F, ... Grimm V. 2019. Resilience trinity: safeguarding ecosystem services across three different time horizons and decision contexts. bioRxiv:549873. DOI: 10.1101/549873.

2018

Prudent parasitic beetles

Parmentier T, De Laender F, Wenseleers T, Bonte D. 2018. Prudent behavior rather than chemical deception enables a parasite to exploit its ant host. Behavioral Ecology 29:1225–1233. DOI: 10.1093/beheco/ary134.

Parasites of social insects often mimic chemical characteristics (e.g. odour) of their host to avoid detection. This is, however, not the case for the unspecialized rove beetle (Thiasophila angulata) that parasitizes the red wood ant (Formica rufa). The beetle rather adapted its behaviour to avoid aggression by the ants. In the presence of ants, the beetle was hiding more frequently and avoided risky runs. Thus, for relatively unspecialized parasites, general strategies such as prudent behaviour can be equally effective as more specialized deception strategies to evade host detection.

Ants, spiders & springtails

Parmentier T, De Laender F, Wenseleers T, Bonte D. 2018. Contrasting indirect effects of an ant host on prey–predator interactions of symbiotic arthropods. Oecologia 188:1145–1153. DOI: 10.1007/s00442-018-4280-6.

Community dynamics follow a complex set of antagonistic, neutral and mutualistic interactions. Direct interactions such as symbiosis and predation have been largely been studied. But also indirect interactions are abundant and strongly shape community dynamics as well. This study shows that having many ants in a nest, increases their agressive interactions with spiders, which in turn capture less springtails, which in turn survive in higher numbers.

Bottom-up & Top-down

Fronhofer EA, Legrand D, Altermatt F, Ansart A, Blanchet S, Bonte D, Chaine A, Dahirel M, De Laender F, De Raedt J, ... 2018. Bottom-up and top-down control of dispersal across major organismal groups. Nature Ecology & Evolution 2:1859. DOI: 10.1038/s41559-018-0686-0.

Dispersal is a central life-history trait, but the identification of its general drivers remains challenging. The authors investigate how dispersal is influenced by the food web context, specifically, bottom-up and top-down forces. Their work sheds a new light on the importance of behavioural decisions for dispersal ecology. Most importantly, it calls for a rethinking of (evolutionary) metacommunity ecology, where dispersal is often seen as neutral and random. Their coordinated effort, that involved species from protists to vertrebrates and labs across Europe (Project dispNet), demonstrates the contrary and calls for an extension of theory.

A new theoretical framework for community‐ and ecosystem‐level effects

De Laender F. 2018, Community‐ and ecosystem‐level effects of multiple environmental change drivers: Beyond null model testing. Global Change Biology, no 00:1–10. https://doi.org/10.1111/gcb.14382

The effects of multiple drivers of environmental changes on communities and ecosystems are currently tested with various types of null-models. Drivers are said to combine synergistically (antagonistically) when their observed joint effect is larger (smaller) than that predicted. However, these models lack a mechanistic basis and deviations from, or correspondence to, observations can therefore not advance insight. Based on ecological theory, a new framework making a clear distinction between two different kinds of drivers (resource ratio shifts and multiple stressors) is proposed. Its assumptions are clear, so that different kinds of deviations between predictions and observed effects can guide new experiments and theory improvement.

Living in cities impacts on body size

Merckx T, Souffreau C, Kaiser A, …. Debortoli N, … Van Doninck K, De Meester L, Van Dyck H. 2018, Body-size shifts in aquatic and terrestrial urban communities. Nature 558, no 7708: 113‑16. https://doi.org/10.1038/s41586-018-0140-0.

Cities are urban heat islands characterized by increased temperatures that result in increased metabolic costs and are expected to drive shifts to smaller body sizes. The authors investigated ten animal taxonomic groups and show that the majority of urban communities consist of smaller species. At the same time, urban habitats are extremely fragmented and poorly connected, which favours mobile, i.e. often large species. Thus, three taxa display a shift to larger species along the urbanization gradients. This means that the general trend towards smaller-sized species is overruled by filtering for larger species when better mobility is more important. The two effects (urban-heat-island and habitat fragmentation) are thus associated with contrasting community-level shifts in body size. Since body size determines the structure and dynamics of ecological networks, such shifts may affect urban ecosystem function.

DNA methylation in adults and during development of the self-fertilizing mangrove rivulus

Fellous A, Labed‐Veydert T, Locrel M, Voisin A‐S, Earley RL, Silvestre F. 2018. DNA methylation in adults and during development of the self‐fertilizing mangrove rivulus, Kryptolebias marmoratus. Ecology and Evolution. 8:6016–6033. https://doi.org/10.1002/ece3.4141

This article depicts the DNA methylation profile of the mangrove rivulus (Kryptolebias marmoratus), in adult fish and during embryogenesis. It also characterizes the main enzymes involved in this process. The results presented open the door to a new hypothesis on how a fish with low genetic diversity could use epigenetic mechanisms to adapt to its environment. A long and deep DNA methylation reprogramming is detected during development, which could be involved in such adaptation mechanisms. More generally, the study gives clues about the role of epigenetic variability in evolution.

Soil decomposition of heathlands is slow due to melanin content of fungi

Lenaers, M, Reyns, W, Czech, J, Carleer, R, Basak, I, Deferme, W, Krupinska, P, Yildiz, T, Saro, S, Remans, T, Vangronsveld, J, Laender, FD, & Rineau, F 2018, ‘Links Between Heathland Fungal Biomass Mineralization, Melanization, and Hydrophobicity’, Microbial Ecology, pp. 1–9, doi: 10.1007/s00248-018-1167-3

Besides the burning of fossil fuels, the decomposition of the dead biomass may add to the atmospheric CO2 pool. Some ecosystems have slower decomposition rates, e.g heathlands, where fungal biomass is high. Comprehending this process is crucial to properly model carbon cycles. Studies on plant biomass demonstrate that extrinsic properties—defining interactions with the environment—control to a much higher extent decomposition rate than intrinsic properties, such as chemical composition. This study showed the opposite: that intrinsic properties (here: melanin content) significantly slowed down the decomposition process.

Stimulate Atlantic salmon to migrate seawards

Bernard, B, Sobandi, KC, Darras, V, Rollin, X, Mandiki, SNM & Kestemont, P 2018, ‘Influence of strain origin on osmoregulatory and endocrine parameters of two non-native strains of Atlantic salmon (Salmo salar L.)’, General and Comparative Endocrinology, vol. 258, pp. 205–212. DOI: 10.1016/j.ygcen.2018.01.004

Atlantic salmon (Salmo salar) are threatened by overfishing and habitat destruction. For re-establishment efforts where populations are extinct, non-native strains are used. However, environmental cues like photoperiod and temperature influence the smolting process (seaward migration). This study used Na+/K+ATPase activity as an indicator to proof that strains from very different origins (one from a cold and short river in Ireland (Cong) and another from a long and warm river in France (Loire-Allier)) could smolt successfully and simultaneously when reared under Belgian conditions. Thus, environmental cues can prevail over genetic factors for smoltification.

Corticosteroids impact on physiological processes in Eurasian perch

Milla, S, Massart, S, Mathieu, C, Wang, N, Douny, C, Douxfils, J, Scippo, M-L, De Pauw, E, Dieu, M, Silvestre, F & Kestemont, P 2018, ‘Physiological and proteomic responses to corticosteroid treatments in Eurasian perch, Perca fluviatilis: Investigation of immune-related parameters’, Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, vol. 25, pp. 86–98. DOI: 0.1016/j.cbd.2017.11.005

Corticosteroids are a class of steroid hormones that play an important role in various physiologic processes. In teleost fish, corticosteroids are involved in stress regulation, immune and inflammatory responses, energetic metabolism and osmoregulation. This study shows that chronic exposure to corticosteroids may affect the glucose metabolism and immunity of Eurasian perch (Perca fluviatilis).

Debortoli N, Laender FD, Doninck KV. 2018. Immigration from the metacommunity affects bdelloid rotifer community dynamics most. bioRxiv:450627. DOI: 10.1101/450627.

Flot J-F, Debortoli N, Hallet B, Narayan J, Doninck KV. 2018. Reply to Cross-Contamination Explains “Inter and Intraspecific Horizontal Genetic Transfers” between Asexual Bdelloid Rotifers (Wilson, Nowell & Barraclough 2018). bioRxiv:368209. DOI: 10.1101/368209.

2017

Baert, JM, Jaspers, S, Janssen, CR, Aerts, M & De Laender, F 2017, 'Non-linear partitioning of biodiversity effect on ecosystem functioning'  Methods in Ecology and Evolution, vol 8, no. 10. DOI: 10.1111/2041-210X.12804

Kulkarni, D & De Laender, F 2017, 'The combined effects of biotic and abiotic stress on species richness and connectance' PLoS ONE, vol 12, no. 3, e0172828. DOI: 10.1371/journal.pone.0172828

Spaak, JW, Baert, JM, Baird, DJ, Eisenhauer, N, Maltby, L, Pomati, F, Radchuk, V, Rohr, JR, Van den Brink, PJ & De Laender, F 2017, 'Shifts of community composition and population density substantially affect ecosystem function despite invariant richness' Ecology Letters, vol 20, no. 10, pp. 1315-1324. DOI: 10.1111/ele.12828

2016

Baert, JM, Janssen, CR, Sabbe, K & De Laender, F 2016, 'Per capita interactions and stress tolerance drive stress-induced changes in biodiversity effects on ecosystem functions' Nature Communications, no. 7, 12486. DOI: 10.1038/ncomms12486

Baert, JM, De Laender, F, Sabbe, K & Janssen, CR 2016, 'Biodiversity increases functional and compositional resistance, but decreases resilience in phytoplankton communities' Ecology, vol 97, no. 12, pp. 3433-3440. DOI: 10.1002/ecy.16011

Barral, A, Gomez, B, Zorrilla, JM, Serrano, JM, Yans, J, Cazedebat, M, Daviero-Gomez, V, Ewin, TAM & Lécuyer, C 2016, 'Local-scale analysis of plant community from the Early Cretaceous riparian ecosystem of Hautrage, Belgium' Palaeogeography, Palaeoclimatology, Palaeoecology, vol 443, pp. 107-122. DOI: 10.1016/j.palaeo.2015.11.026

Debortoli N, Li X, Eyres I, Fontaneto D, Hespeels B, Tang CQ, Flot J-F, Van Doninck K. 2016. Genetic Exchange among Bdelloid Rotifers Is More Likely Due to Horizontal Gene Transfer Than to Meiotic Sex. Current Biology 26:723–732. DOI: 10.1016/j.cub.2016.01.031.

De Laender, F, Rohr, JR, Ashauer, R, Baird, DJ, Berger, U, Eisenhauer, N, Grimm, V, Hommen, U, Maltby, L, Meliàn, CJ, Pomati, F, Roessink, I, Radchuk, V & Van den Brink, PJ 2016, 'Reintroducing Environmental Change Drivers in Biodiversity–Ecosystem Functioning Research' Trends in Ecology and Evolution, vol 31, no. 12, pp. 905-915. DOI: 10.1016/j.tree.2016.09.007

Marescaux, J, Falisse, É, Lorquet, J, Van Doninck, K, Beisel, J-N & Descy, J-P 2016, 'Assessing filtration rates of exotic bivalves: dependence on algae concentration and seasonal factors' Hydrobiologia. DOI: 10.1007/s10750-016-2764-0

Marescaux, J, Latli, A, Lorquet, J, Virgo, J, Van Doninck, K & Beisel, JN 2016, 'Benthic macro-invertebrate fauna associated with Dreissena mussels in the Meuse River: from incapacitating relationships to facilitation' Aquatic Ecology, vol 50, no. 1, pp. 15-28. DOI: 10.1007/s10452-015-9540-5

Marescaux, J, von Oheimb, KCM, Etoundi, E, von Oheimb, PV, Albrecht, C, Wilke, T & Van Doninck, K 2016, 'Unravelling the invasion pathways of the quagga mussel (Dreissena rostriformis) into Western Europe' Biological Invasions, vol 18, no. 1, pp. 245-264. DOI: 10.1007/s10530-015-1005-1

Radchuk, V, De Laender, F, Van den Brink, PJ & Grimm, V 2016, 'Biodiversity and ecosystem functioning decoupled: Invariant ecosystem functioning despite non-random reductions in consumer diversity' OIKOS, vol 125, no. 3, pp. 424-433. DOI: 10.1111/oik.02220

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