Institute of Life, Earth and Environment
Biodiversity & Evolutionary Adaptation
published in: 2023 - 2022 - 2021 - 2020 - 2019 - 2018 - 2017 - 2016
2024
The European Reference Genome Atlas
Mc Cartney AM, et al. Dennis AB, 2024. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics. npj Biodiversity 3:1–17. DOI: 10.1038/s44185-024-00054-6.
recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.Attention to origin of the zebrafish lineages
Chevalier C, Denis C, Nedjar S-A, Ledoré Y, Silvestre F, Schaerlinger B, Milla S. 2024. Comparative study of the growth, stress status and reproductive capabilities of four wild-type zebrafish (Danio rerio) lines. Biological Research 57:67. DOI: 10.1186/s40659-024-00549-3.
available, each with a unique domestication background, potentially resulting in intraspecies differences in specific biological functions. Few studies have compared multiple zebrafish lines under identical conditions to investigate both inter- and intra-line variability related to different functions. However, such variability could pose a challenge for the reproducibility of results in studies utilising zebrafish, particularly when the line used is not clearly specified. This studyassessed growth, stress status (cortisol, serotonin) and reproductive capabilities (maturity, fecundity, fertilisation rate, sperm quality) of four commonly used wild-type zebrafish lines (AB, SJD, TU, WIK) using standardized protocols...Domestication and behavior in zebrafish
Diakos E, Chevalier C, Shahjahan M, Hardy A, Lambert S, Kestemont P, Fontaine P, Pasquet A, Lecocq T. 2024. Early impact of domestication on aggressiveness, activity, and stress behaviors in zebrafish (Danio rerio) using mirror test and automated videotracking. Scientific Reports 14:21036. DOI: 10.1038/s41598-024-71451-x.
leads to phenotypic changes over generations, sometimes from the very first generation. Behavioral traits are among the first to change. However, in fish, potential behavioral changes during early domestication have been little studied. Therefore,we studied potential behavioral changes among early and advanced levels of domestication in a model species, the zebrafish (Danio rerio), using a mirror test experiment, commonly used to assess traits involved in activity, aggressiveness, and stress in this species. We compared these traits between wild zebrafish in captivity (F0; Level 1), the first generation of their captive-born offspring (F1; Level 4), and three laboratory strains (AB, TU, and WIK; Level 5)...Sperm cryotolerance
Erraud A, Cornet V, D’Halluin F, Lambert J, Neus Y, Kestemont P. 2024. Sperm cryotolerance in mature male parr of Atlantic salmon (Salmo salar L. 1758): Effects of dietary lipid content and n-3 essential fatty acids composition. Aquaculture 593:741326. DOI: 10.1016/j.aquaculture.2024.741326.
The nutrition of broodstock fish affects the quality of gametes. This study aimed to assess the impact of four diets on the quality of fresh and cryopreserved sperm of sexually mature salmon parr during spermatogenesis. Highlights: A high level of plant lipids positively affects the sperm motility of precocious parr. Feeding salmon males parrduring spermatogenesis alters the cryotolerance of sperm. Higher sperm cryotolerance on a high-fat diet, regardless of fatty acid composition...Dispersal in biodiverse spatially structured systems
Fronhofer EA, Bonte D, Bestion E, Cote J, Deshpande JN, Duncan AB, Hovestadt T, Kaltz O, Keith SA, Kokko H, Legrand D, Malusare SP, Parmentier T, Saade C, Schtickzelle N, Zilio G, Massol F. 2024. Evolutionary ecology of dispersal in biodiverse spatially structured systems: what is old and what is new? Philosophical Transactions of the Royal Society B: Biological Sciences 379:20230142. DOI: 10.1098/rstb.2023.0142.
traditionally been studied in single-species metapopulations so that it remains unclear how dispersal evolves in metacommunities and metafoodwebs, which are characterized by a multitude of species interactions. Since most natural systems are both species-rich and spatially structured, this knowledge gap should be bridged. Here, we discuss whether knowledge from dispersal evolutionary ecology established in single-species systems holds in metacommunities and metafoodwebs and we highlightgenerally valid and fundamental principles...Oligocene primate communities
Marivaux L, Benammi M, Baidder L, Saddiqi O, Adnet S, Charruault A-L, Tabuce R, Yans J, Benammi M. 2024. A new primate community from the earliest Oligocene of the Atlantic margin of Northwest Africa: Systematic, paleobiogeographic, and paleoenvironmental implications. Journal of Human Evolution 193:103548. DOI: 10.1016/j.jhevol.2024.103548.
A new Paleogene primate community is discovered in the uppermost part of the Samlat Formation in the south of Morocco (DAK C2, Dakhla). Fossils consist of isolated teeth, which were extracted by wet screening of estuarine sediments dating from the earliest Oligocene (ca. 33.5 Ma). These dental remains testify to the presence of at least eight primate species, from distinct families. 
This is the first Oligocene primate community from NW Africa, especially from the Atlantic margin of that landmass. The taxonomic proximity at the generic (even specific) level with famousEgyptian fossil-bearing localities suggests the existence of an east–west ‘trans-North African’ environmental continuum during the latest Eocene–earliest Oligocene time interval. The particularly diverse mammal fauna from DAK C2recorded suggests that this tropical region was seemingly less affected, if at all, by the cooling and associated paleoenvironmental and biotic changes documented at that time or at least that the effects were delayed.Stability in ant symbiont communities
Parmentier T, Bonte D, De Laender F. 2024. A successional shift enhances stability in ant symbiont communities. Communications Biology 7:1–9. DOI: 10.1038/s42003-024-06305-3.
Throughout succession, communities undergo structural shifts, which can alter the relative abundances of species and how they interact. It is frequently asserted that these alterations beget stability, i.e. that succession selects for communities better able to resist perturbations. Yet, whether and how alterations of network structure affect stability during succession in complex communities is rarely studied in natural 
ecosystems. Here, we explore how network attributes influence stability of different successional stages of a natural network: symbiotic arthropod communities forming food webs inside red wood ant nests...Intraspecific demographic and trait responses
de Bruin T, De Laender F, Jadoul J, Schtickzelle N. 2024. Intraspecific demographic and trait responses to environmental change drivers are linked in two species of ciliate. BMC Ecology and Evolution 24:47. DOI: 10.1186/s12862-024-02241-2.
Over the past decade, theory and observations have suggested intraspecific variation, trait-based differences within species, as a buffer against biodiversity loss from multiple environmental changes. This buffering effect can only occur when different populations of the same species respond differently to environmental change. More specifically, variation of demographic responses fosters buffering of demography, while variation of trait responses fosters buffering of
functioning. Understanding how both responses are related is important for predicting biodiversity loss and its consequences. In this study, we aimed to empirically assess whether population-level trait responses to multiple environmental change drivers are related to the demographic response to these drivers...Gene & allele-specific expression in electric fish
Cheng F, Dennis AB, Baumann O, Kirschbaum F, Abdelilah-Seyfried S, Tiedemann R. 2024. Gene and Allele-Specific Expression Underlying the Electric Signal Divergence in African Weakly Electric Fish. Molecular Biology and Evolution 41:msae021. DOI: 10.1093/molbev/msae021.
In the African weakly electric fish genus Campylomormyrus, electric organ discharge signals are strikingly different in shape and duration among closely related species, contribute to prezygotic isolation, and may have triggered an adaptive radiation. We performed mRNA sequencing on electric organs and skeletal muscles (from which the electric organs derive) from 3 species with short (0.4 ms), medium (5 ms), and long (40 ms) electric organ discharges and 2 different cross-species hybrids. We identified 1,444 upr
egulated genes in electric organ shared by all 5 species/hybrid cohorts, rendering them candidate genes for electric organ–specific properties in Campylomormyrus. We further identified several candidate genes, including KCNJ2 and KLF5, and their upregulation may contribute to increased electric organ discharge duration...Genome Annotation for the Tree of Life
Brown T, Collier KA, Cruz F, Gkanogiannis A, Joye-Dind S, Nevers Y, Saenko S, Alioto T, Bretaudeau A, Charleston M, Doan PD, Hahn C, Harrop TW, Herron KE, Kebaso F, Libouban R, Mansueto L, Manu S, Oba A, Swarbreck D, Syme A, Zanarello F, Aury J-M, Gómez-Garrido J, Dennis AB. 2024. Genome Annotation and Other Post-Assembly Workflows for the Tree of Life. DOI: 10.37044/osf.io/fy49g.
Rapid advances in genome sequencing technologies have resulted in an explosion of referencequality genome assemblies across the tree of life. While these resources will be invaluable towards goals of species and biodiversity conservation, their application is limited when they lack accurate annotations of their functional elements. The European Reference Genome Atlas (ERGA) is the European node of the Earth Biogenome Project (EBP) and aims to share resources and knowledge to create fully-annotated reference genomes. ERGA strives to do this in a distributed manner, bringing together researchers from across the world, with common goals and understandings. In the BioHackathon Europe 2023, we came together to construct and test tools, pipelines and workflows for annotating protein-coding regions in assembled genomes...Ionizing radiation & desiccation responses
Moris VC, Bruneau L, Berthe J, Heuskin A-C, Penninckx S, Ritter S, Weber U, Durante M, Danchin EGJ, Hespeels B & Doninck KV. 2024. Ionizing radiation responses appear incidental to desiccation responses in the bdelloid rotifer Adineta vaga. BMC Biology 22:11. DOI: 10.1186/s12915-023-01807-8.
The remarkable resistance to ionizing radiation found in anhydrobiotic organisms, such as some bacteria, tardigrades, and bdelloid rotifers has been hypothesized to be incidental to their desiccation resistance. Both stresses produce reactive oxygen species and cause damage to DNA and other macromolecules. However, this hypothesis has only been investigated
in a few species. - In this study, we analyzed the transcriptomic response of the bdelloid rotifer Adineta vaga to desiccation and to low- (X-rays) and high- (Fe) LET radiation to highlight the molecular and genetic mechanisms triggered by both stresses. We identified numerous genes encoding antioxidants, but also chaperones, that are constitutively highly expressed, which may contribute to the protection of proteins against oxidative stress during desiccation and ionizing radiation...2023
Long-term vegetation dynamics in the Succulent Karoo
Schmiedel U, Hanke W, Mayer C, Oldeland J, Hoffman MT. 2023. Vegetation dynamics over 18 years in response to seasonal climatic conditions and land use in the Kamiesberg mountains of the succulent Karoo, South Africa. Journal of Arid Environments 219:105085. DOI: 10.1016/j.jaridenv.2023.105085.
Projections of vegetation change in response to future global change conditions are challenged by the lack of long-term, empirical data on how vegetation responds to the variability in climatic conditions. This is particularly true for biodiverse systems that are threatened by climate change such as the winter-rainfall Succulent Karoo biome of southern Africa. In this study we analyse long-term data (2002–2019) of two biodiversity observatories from the Kamiesberg Mountains in the Succulent Karoo. We employed the R package GLMMtmb to 
analyse counts of abundance and estimated cover values of vegetation as response variables and seasonal Standardised Precipitation-Evapotranspiration Index (SPEI), annual livestock density, topography and soil surface structure as predictors for the interannual change of life forms under low and high land use intensity. We compared the life form composition at the two contrasting land use types and found the cover and abundance of leaf succulents to be higher under low grazing intensity and that of stem succulents to be higher under high grazing intensity...Long-distance avian migration
Lathouwers M, Dendoncker N, Artois T, Beenaerts N, Conway G, Henderson I, Shewring M, Cross T, Ulenaers E, Evens R. 2023. Multi-scale habitat selection throughout the annual cycle of a long-distance avian migrant. Ecological Indicators 156:111099. DOI: 10.1016/j.ecolind.2023.111099.
Long-distance migrants are constrained by widely separated hospitable habitats in geographically isolated locations, making them vulnerable to environmental change, both through natural and anthropogenic causes. Knowledge about their resource selection decisions is imperative to understand the drivers of their declines. The distinct periods within an annual cycle, when individuals experience different environmental circumstances, are inextricably linked through carry-over effects which can have important consequences for the individual, and consequently the population. In this study, we employ precise archival GPS-tracking data of European Nightjars (Caprimulgus 
europaeus) and high-resolution global land cover data to examine habitat selection during the sedentary wintering and breeding periods, as well as during autumn and spring migration, using a correlational approach. We demonstrate how nightjars use general habitat characteristics, such as landscape diversity, for high-order habitat selection, while resource selection at a finer spatial scale is reliant on fine-scale variables related to a habitat’s suitability, such as surface area of grassland and shrubland...The pitfalls of plural valuation
Jacobs S, Kelemen E, O’Farrell P, Martin A, Schaafsma M, Dendoncker N, Pandit R, Mwampamba TH, Palomo I, Castro AJ, Huambachano MA, Filyushkina A, Gunimeda H. 2023. The pitfalls of plural valuation. Current Opinion in Environmental Sustainability 64:101345. DOI: 10.1016/j.cosust.2023.101345.
This paper critically examines the current political context in which valuation studies of nature are undertaken. It challenges the belief that somehow, more and technically better valuation will drive the societal change toward more just and sustainable futures. Instead, we argue that current and proposed valuation practices risk to continue to overrepresent the values of those who hold power and dominate the valuation space, and to perpetuate the discrimination of the views and values of nondominant 
stakeholders. In tackling this politically sensitive issue, we define a political typology of valuations, making explicit the roles of power and discrimination. This is done to provide valuation professionals and other actors with a simple framework to determine if valuation actions and activities are constructive, inclusive, resolve injustices and enable systemic change, or rather entrench the status quo or aggravate existing injustices. The objective is to buttress actors in their decisions to support, accept, improve, oppose, or reject such valuations.Five steps towards transformative valuation of nature
Termansen M, Jacobs S, Pandit R, Mwampamba TH, Dendoncker N, Schaafsma M, Contreras V, González-Jiménez D, Gundimeda H, Lee H, Filyushkina A, Huambachano M, Palomo I, Castro AJ. 2023. Five steps towards transformative valuation of nature. Current Opinion in Environmental Sustainability 64:101344. DOI: 10.1016/j.cosust.2023.101344.
values in decisions. Furthermore, improving valuation practice requires guidelines that utilise quality criteria for valuation of nature and ensure a balance between them. This paper proposes three such quality criteria: relevance, robustness and resource efficiency. The paper argues that the five steps and three Rs can generate a practical checklist to support commissioning, evaluation and performance of more plural valuations. Such guidelines can provide the next steps needed to improve uptake of nature valuation in decision-making.Aphids and ants
Parmentier T. 2023. Differential transport of a guild of mutualistic root aphids by the ant Lasius flavus. Current Zoology 69:409–417. DOI: 10.1093/cz/zoac060.
Mutually beneficial associations are widespread in ecological networks. They are typically assembled as multispecies guilds of symbionts that compete for 
one or more host species. The ant Lasius flavus engages in an intriguing and obligate mutualistic association with a community of aphids that are cultivated on plant roots in its nests. The ant displays a repertoire of amicable behaviors toward the aphids, including their transport. I examined whether L. flavus preferentially carried some of the root aphids. Using a no-choice and a choice experiment, I comparatively analyzed the transport rate of 5 obligate and one loosely associated species back to the ant nest and used the transport rate of the ant larvae as a reference....Environmental Epigenomes
Perera BPU, Silvestre F. 2023. Environmental Epigenomes. Epigenomes 7:21. DOI: 10.3390/epigenomes7030021.
Research in epigenetics has dramatically risen during the last decade to include aspects of environmental biology. However, many questions remain regarding the effects of environmental stressors on the epigenome, incorporating the particular role of epigenetic mechanisms in the adaptation and evolution of organisms in changing environments. Epigenetics is commonly defined as mitotically and/or meiotically heritable changes in gene function that occur without altering the underlying DNA sequence. It encompasses DNA (hydroxy)methylation, histone modifications, chromatin structure, and non-coding RNAs that may be inherited across generations under certain circumstances. Epigenetic mechanisms are perfect candidates to extend our understanding of the impact of environmental stressors on organisms and to explain the rapid phenomenon of adaptive evolution...Diverse values of nature for sustainability
Pascual U, Balvanera P, Anderson CB, Chaplin-Kramer R, Christie M, González-Jiménez D, Martin A, Raymond CM, Termansen M, Vatn A, Athayde S, Baptiste B, Barton DN, Jacobs S, Kelemen E, Kumar R, Lazos E, Mwampamba TH, Nakangu B, O’Farrell P, Subramanian SM, van Noordwijk M, Ahn S, Amaruzaman S, Amin AM, Arias-Arévalo P, Arroyo-Robles G, Cantú-Fernández M, Castro AJ, Contreras V, De Vos A, Dendoncker N, Engel S, Eser U, Faith DP, Filyushkina A, Ghazi H, Gómez-Baggethun E, Gould RK, Guibrunet L, Gundimeda H, Hahn T, Harmáčková ZV, Hernández-Blanco M, Horcea-Milcu A-I, Huambachano M, Wicher NLH, Aydın Cİ, Islar M, Koessler A-K, Kenter JO, Kosmus M, Lee H, Leimona B, Lele S, Lenzi D, Lliso B, Mannetti LM, Merçon J, Monroy-Sais AS, Mukherjee N, Muraca B, Muradian R, Murali R, Nelson SH, Nemogá-Soto GR, Ngouhouo-Poufoun J, Niamir A, Nuesiri E, Nyumba TO, Özkaynak B, Palomo I, Pandit R, Pawłowska-Mainville A, Porter-Bolland L, Quaas M, Rode J, Rozzi R, Sachdeva S, Samakov A, Schaafsma M, Sitas N, Ungar P, Yiu E, Yoshida Y, Zent E. 2023. Diverse values of nature for sustainability. Nature 620:813–823. DOI: 10.1038/s41586-023-06406-9.
Twenty-five years since foundational publications on valuing ecosystem services for human well-being, addressing the
global biodiversity crisis still implies confronting barriers to incorporating nature’s diverse values into decision-making. These barriers include powerful interests supported by current norms and legal rules such as property rights, which determine whose values and which values of nature are acted on. A better understanding of how and why nature is (under)valued is more urgent than ever.....Skyglow & crepuscular birds
Evens R, Lathouwers M, Pradervand J-N, Jechow A, Kyba CCM, Shatwell T, Jacot A, Ulenaers E, Kempenaers B, Eens M. 2023. Skyglow relieves a crepuscular bird from visual constraints on being active. Science of The Total Environment 900:165760. DOI: 10.1016/j.scitotenv.2023.165760.
Artificial light at night significantly alters the predictability of the natural light cycles that most animals use as an
essential Zeitgeber for daily activity. Direct light has well-documented local impacts on activity patterns of diurnal and nocturnal organisms. However, artificial light at night also contributes to an indirect illumination of the night sky, called skyglow, which is rapidly increasing. The consequences of this wide-spread form of artificial night light on the behaviour of animals remain poorly understood, with only a few studies performed under controlled (laboratory) conditions. ...Participatory research on ecosystem services
Barnaud C, De Longueville F, Gonella G, Antona M, Dendoncker N, Waylen KA. 2023. Participatory research on ecosystem services in the face of disputed values and other uncertainties: A review. Ecosystem Services 63:101551. DOI: 10.1016/j.ecoser.2023.101551.
Participatory approaches are widely used in ecosystem services (ES) research. They are particularly advocated for 
situations characterized by complexity, uncertainties and multiple values. This paper is based on a systematic literature review to examine how participatory ES research is implemented in practice. It explores how – and how far – various practices elicit and consider different types of uncertainties related to ES, namely ethical uncertainties (plurality of worldviews, values and interests), epistemic uncertainties (multiple representations) and radical uncertainties (unpredictability)... You are what your host eats
Parmentier T, Boeckx P, Bonte D, De Laender F. You are what your host eats: The trophic structure and food chain length of a symbiont community are coupled with the plastic diet of the host ant. Journal of Animal Ecology n/a. DOI: 10.1111/1365-2656.13994.
The trophic structure and food chain length of a symbiont community are coupled with the plastic diet of the 
host ant: Food chain length provides key information on the flow of nutrients and energy in ecosystems. Variation in food chain length has primarily been explained by environmental drivers (e.g. ecosystem size, productivity). Here, red wood ant nests differing in size served as natural experiments to quantify the drivers of trophic structure and food chain length of their symbiont arthropod communities...Rotifers under fire
Perrot A, Hespeels B, Van Doninck K, Heuskin A-C. 2023. Adineta vaga under fire: simulating the impact of radiation. Hydrobiologia. DOI: 10.1007/s10750-023-05324-1.
Previous studies have demonstrated the remarkable resistance of bdelloid rotifers to ionizing radiation, 
making them an interesting model system for studying radiation effects on living organisms. In this study, simulations examined whether all bdelloids are affected equally by radiation exposure and explored the relationship between biological data and energy deposition patterns induced by low and high linear energy transfer (LET) radiation. To this end, tool for particle simulation (TOPAS), a simulation tool, widely used in the field of medical physics and radiation therapy, was utilized...Cryptic species...remains cryptic
Inäbnit T, Tiedemann R, Dennis A. 2023. Molecular Species Delimitation and Morphometry in the Melampus bidentatus (Panpulmonata, Ellobiidae) Cryptic Species Complex. Bulletin of the Society of Systematic Biologists 2. DOI: 10.18061/bssb.v2i2.9165.
The coffee bean snail Melampus bidentatus occurs in coastal salt marshes along the North American Atlantic and Gulf 
coasts, and the Caribbean. It was recently found that this large geographical span is actually occupied by a complex of three apparently cryptic species (preliminary called “North”, “South” and “Gulf”) with partially overlapping distributions. Until now it was not clear whether there are any morphological differences between the three species or which of the available names can be applied to which of the cryptic species. We used the already known distribution patterns of the cryptic species, as well as new barcode sequences to assign available names to the three cryptic species...Air-filled porosity of soil
Smet S, Plougonven E, Léonard A, Degré A. 2023. Characterization by X-ray μCT of the air-filled porosity of an agricultural soil at different matric potentials. European Journal of Soil Science 74:e13387. DOI: 10.1111/ejss.13387.
To describe various important soil processes like the release of greenhouse gases or the proliferation of microorganisms, it is necessary to assess quantitatively how the geometry and in particular the connectivity of the air-filled pore space of a soil evolves as it is progressively dried. The availability of X-ray computed microtomography (µCT) images of soil samples now allows this information to be obtained directly, without having to rely on the interpretation of macroscopic 
measurements using capillary theory, as used to be the case. In this general context, we present different methods to describe quantitatively the configuration of the pore space in 3D µCT images of 20 separate samples of a loamy soil equilibrated at different matric potentials. Even though measures using µCT on such multi-scale materials strongly depends on image resolution, our results show that in general, soil samples most often behave as expected, e.g., connectivity increases with higher negative matric potential, while tortuosity decreases. However, simple correlations could not be found between the evolution of quantitative descriptors of the pore space at the different matric potentials and routinely measured macroscopic soil parameters. A statistical analysis of all soil samples concurrently confirmed this lack of correspondence.Non-linear competitive interactions
Spaak JW, Millet R, Ke P-J, Letten AD, De Laender F. 2023. The effect of non-linear competitive interactions on quantifying niche and fitness differences. Theoretical Ecology 16:161–170. DOI: 10.1007/s12080-023-00560-6.
The niche and fitness differences of modern coexistence theory separate mechanisms into stabilizing and equalizing components. Although this decomposition can help us predict and understand species coexistence, the extent to which mechanistic inference is sensitive to the method used to partition niche and fitness differences remains unclear. We apply two alternative methods to assess niche and fitness differences to four well-known community models. We show that because standard methods based on linear approximations do not capture the full community dynamics, they can sometimes lead to incorrect predictions of coexistence and misleading interpretations of stabilizing and equalizing mechanisms. Specifically, they fail when both species occupy the same niche or in the presence of positive 
frequency dependence. Conversely, a more recently developed method to decompose niche and fitness differences, which accounts for the full non-linear dynamics of competition, consistently identifies the correct contribution of stabilizing and equalizing components. This approach further reveals that when the true complexity of the system is taken into account, essentially all mechanisms comprise both stabilizing and equalizing components and that local maxima and minima of stabilizing and equalizing mechanisms exist.Stability of natural aquatic food webs
Zhao Q, Van den Brink PJ, Xu C, Wang S, Clark AT, Karakoç C, Sugihara G, Widdicombe CE, Atkinson A, Matsuzaki SS, Shinohara R, He S, Wang YXG, De Laender F. 2023. Relationships of temperature and biodiversity with stability of natural aquatic food webs. Nature Communications 14:3507. DOI: 10.1038/s41467-023-38977-6.
Temperature and biodiversity changes occur in concert, but their joint effects on ecological stability of natural food webs are unknown. Here, we assess these relationships in 19 planktonic food webs. We estimate stability as structural stability (using the volume contraction rate) and temporal stability (using the temporal variation of species abundances). Warmer temperatures were associated with lower structural and temporal stability, while biodiversity had no consistent effects on either stability property. While species richness was associated with lower structural stability and higher temporal stability, Simpson diversity was associated with higher temporal stability. The responses of structural stability were linked to disproportionate contributions from two trophic groups (predators and 
consumers), while the responses of temporal stability were linked both to synchrony of all species within the food web and distinctive contributions from three trophic groups (predators, consumers, and producers). Our results suggest that, in natural ecosystems, warmer temperatures can erode ecosystem stability, while biodiversity changes may not have consistent effects.Change through transdisciplinary learning
Atienza Casas S, Calicis C, Candiago S, Dendoncker N, Desair J, Fickel T, Finne EA, Frison C, Haensel M, Hinsch M, Kulfan T, Kumagai JA, Mialyk O, Nawrath M, Nevzati F, Washbourne C, Wübbelmann T. 2023. Head in the clouds, feet on the ground: how transdisciplinary learning can foster transformative change—insights from a summer school. Biodiversity and Conservation. DOI: 10.1007/s10531-023-02603-0.
There is a pressing need for transformative change, with a vision of long-term human well-being within planetary boundaries. The lack of progress—despite increasing awareness and action—illustrates how challenging it is to foster change in our complex global society. Education and learning are needed to enable change. Transdisciplinary learning, which meaningfully integrates diverse knowledge and perspectives, contributes to developing an integrative understanding—a necessity for tackling complex challenges. We explore how transdisciplinary learning for early-career researchers can foster transformative change and lead to 
increased biodiversity conservation. This paper focuses on a case study of the authors’ shared experiences during the 2021 Alternet Summer School, which focused on transformative change for biodiversity conservation and human well-being. In this introspective research, we gained insights through an online survey for participants and organizers of the summer school (n = 27). The gained insights point to the benefit of transdisciplinary learning opportunities that empower young researchers to take up their part in fostering transformative change.Effects of environmental change on coexistence
De Laender F, Carpentier C, Carletti T, Song C, Rumschlag SL, Mahon MB, Simonin M, Meszéna G, Barabás G. Mean species responses predict effects of environmental change on coexistence. Ecology Letters n/a. DOI: 10.1111/ele.14278.
Environmental change research is plagued by the curse of dimensionality: the number of communities at risk and the number of environmental drivers are both large. This raises the pressing question if a general understanding of ecological effects is achievable. Here, we show evidence that this is indeed possible. Using theoretical and simulation-based evidence for bi- and tritrophic communities, we show that environmental change effects on coexistence are proportional to 
mean species responses and depend on how trophic levels on average interact prior to environmental change. We then benchmark our findings using relevant cases of environmental change, showing that means of temperature optima and of species sensitivities to pollution predict concomitant effects on coexistence. Finally, we demonstrate how to apply our theory to the analysis of field data, finding support for effects of land use change on coexistence in natural invertebrate communities.Trends of stream macroinvertebrate biodiversity
Rumschlag SL, Mahon MB, Jones DK, Battaglin W, Behrens J, Bernhardt ES, Bradley P, Brown E, De Laender F, Hill R, Kunz S, Lee S, Rosi E, Schäfer R, Schmidt TS, Simonin M, Smalling K, Voss K, Rohr JR. 2023. Density declines, richness increases, and composition shifts in stream macroinvertebrates. Science Advances 9:eadf4896. DOI: 10.1126/sciadv.adf4896.
scopes. We analyzed biodiversity and composition of assemblages of >500 genera, spanning 27 years, and 6131 stream sites across forested, grassland, urban, and agricultural land uses throughout the United States. In this dataset, macroinvertebrate density declined by 11% and richness increased by 12.2%, and insect density and richness declined by 23.3 and 6.8%, respectively, over 27 years. In addition, differences in richness and composition between urban and agricultural versus forested and grassland streams have increased over time. Urban and agricultural streams lost the few disturbance-sensitive taxa they once had and gained disturbance-tolerant taxa. These results suggest that current efforts to protect and restore streams are not sufficient to mitigate anthropogenic effects.Genomics and biodiversity conservation
Theissinger K, et al. (Alice Dennis) 2023. How genomics can help biodiversity conservation. Trends in Genetics 0. DOI: 10.1016/j.tig.2023.01.005.
The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such 
as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.Genome assembly of an African electric fish
Cheng F, Dennis AB, Osuoha JI, Canitz J, Kirschbaum F, Tiedemann R. 2023. A new genome assembly of an African weakly electric fish (Campylomormyrus compressirostris, Mormyridae) indicates rapid gene family evolution in Osteoglossomorpha. BMC Genomics 24:129. DOI: 10.1186/s12864-023-09196-6.
Within teleost fish, the African weakly electric fish (Mormyroidei, Osteoglossomorpha), which have radiated into numerous species. Within the mormyrids, the genus Campylomormyrus is mostly endemic to the Congo Basin. The genus serves as a model to understand mechanisms of adaptive radiation and ecological speciation, especially with regard to its highly diverse species-specific electric organ discharges (EOD). We report a new high-quality genome of C. compressirostris, 
representing an important contribution to understand the evolution of electric fish and Osteoglossomorpha fish genomes. Our gene family analysis relative to representatives of many teleost fish genomes reveals a more rapid turnover rate and a higher expanded/contracted gene family number ratio in Osteoglossomorpha. The functional importance of these gene families requires further investigation but provides many avenues for understanding the unique adaptations in these fishes. Our exhaustive efforts to localize these genes (including detection of a novel tandem duplication) underline the potential our new genome may hold towards an improved understanding of electric fish and Osteoglossomorpha evolution.Back to the roots
Hespeels B, Fontaneto D, Cornet V, Penninckx S, Berthe J, Bruneau L, Larrick JW, Rapport E, Bailly J, Debortoli N, Iakovenko N, Janko K, Heuskin A-C, Lucas S, Hallet B, Van Doninck K. 2023. Back to the roots, desiccation and radiation resistances are ancestral characters in bdelloid rotifers. BMC Biology 21:72. DOI: 10.1186/s12915-023-01554-w.
Bdelloid rotifers tolerate desiccation and other types of stress such as high doses of ionizing radiation (IR). It was hypothesized that this resistance may be attributed to their potential ability to repair DNA double-strand breaks (DSBs). Here, these properties are investigated and compared among nine bdelloid species collected from both mild and harsh habitats. Results show that DNA repair prevails in somatic cells of both desiccation-tolerant and desiccation-sensitive bdelloid species after exposure to X-ray radiation. Species belonging to both categories can withstand high doses of ionizing radiation, without negative effects on their survival. However, the fertility of two desiccation-sensitive species was more severely impacted by low doses of radiation, which was, surprisingly, not related to their original habitat. Indeed, bdelloids isolated from Atacama Desert or Antarctica were not characterized by a higher radioresistance than species found in more temperate environments. Tolerance to desiccation and radiation are supported as ancestral features of bdelloid rotifers, with a group of species of the genus Rotaria having lost this trait after colonizing permanent water habitats.Science meets art
Vermeulen A, Maranan DS, Steyaert P, Versbraegen N, Peeters A, Verschuren J, Pereira F, Faber N, Mirzada F, Hespeels B, Doninck K. 2022. Ēngines of Ēternity: An Artistic Inquiry into Space Settlement Ideology Using Rotifer Experiments on Board the ISS. In: Conference papers; 73rd International Astronautical Congress (IAC); Paris, France. Link
Ēngines of Ēternity is a transdisciplinary project that takes the biological phenomena of cloning and DNA repair as metaphorical departure points for an 
art installation about humanity’s enthrallment with cultural immortality. In a series of space biology experiments, rotifers were sent to the ISS in 2019 and 2020. Artists (SEADS) sent a series of thumb-printed glyphs along with the rotifers. This code formed the algorithmic seed for an evolving artwork. After each space mission, genetic data of the rotifers was used to parametrically evolve the art. As such, Ēngines of Ēternity engenders new forms of co-creation between humans, biological organisms, algorithms, and outer space. In this paper, the core concepts of the Ēngines of Ēternity project are presented, together with reflections on transdisciplinary research and the need for a more holistic perspective on our future in outer space.Predicting effects of multiple interacting global change drivers
van Moorsel SJ, Thébault E, Radchuk V, Narwani A, Montoya JM, Dakos V, Holmes M, De Laender F, Pennekamp F. 2022. Predicting effects of multiple interacting global change drivers across trophic levels. Global Change Biology n/a. DOI: 10.1111/gcb.16548.
Global change encompasses many co-occurring anthropogenic drivers, which can act synergistically or antagonistically on ecological systems. Predicting how different global change drivers simultaneously contribute to observed biodiversity change is a key challenge for ecology and conservation. However, we lack the mechanistic understanding of how multiple global change drivers influence the vital rates of multiple interacting species. We propose that reaction norms, the relationships between a driver and vital rates like growth, mortality, and consumption, provide insights to the underlying mechanisms of community responses to multiple drivers. 
Understanding how multiple drivers interact to affect demographic rates using a reaction-norm perspective can improve our ability to make predictions of interactions at higher levels of organization – i.e., community and food web. Building on the framework of consumer-resource interactions and widely studied thermal performance curves, we illustrate how joint driver impacts can be scaled up from the population- to the community-level. A simple proof-of-concept model demonstrates how reaction norms of vital rates predict the prevalence of driver interactions at the community level. A literature search suggests that our proposed approach is not yet used in multiple driver research. We outline how realistic response surfaces can be inferred by parametric and nonparametric approaches. Response surfaces have the potential to strengthen our understanding of how multiple drivers affect communities as well as improve our ability to predict when interactive effects emerge, two of the major challenges of ecology today.2022
Data challenges in human decision-making
Robinson DT, van Vliet J, Brown C, Dendoncker N, Holzhauer S, Moseley D, Vulturius G, Rounsevell MDA. 2022. Chapter 5 - Identifying data challenges to representing human decision-making in large-scale land-use models. In: Pereira P, Gomes E, Rocha J eds. Mapping and Forecasting Land Use. Elsevier, 115–126. DOI: 10.1016/B978-0-323-90947-1.00013-2.
Land-use models are by now an accepted method in scientific research, both to increase our understanding of land-use change processes and to project future land-use trajectories. Many of these models simulate changes as a function of spatial data layers, such as elevation, accessibility and soil type. However, land-use changes are ultimately the result of human decisions. Therefore representing human decision-making processes in models is essential to advance our understanding of land-use change processes as well as our capacity to support policy making. Agent-based models allow human decision-making to be represented explicitly. However, their application is constrained by the availability of data about actors and their decision-making processes. Empirical data can be obtained from case studies, but the geographic extent of these case studies is constrained by time and resources. Therefore we argue that we need new sources of data to support model representation of these processes. In this chapter, we further specify this data demand and discuss potential methods of data acquisition. Data acquisition methods include metastudies, aligning with various ongoing large-scale data collection efforts, dedicated projects and crowdsourcing.Agroecological practices & ecosystem services
Palomo-Campesino S, García-Llorente M, Hevia V, Boeraeve F, Dendoncker N, González JA. 2022. Do agroecological practices enhance the supply of ecosystem services? A comparison between agroecological and conventional horticultural farms. Ecosystem Services 57:101474. DOI: 10.1016/j.ecoser.2022.101474.
Agricultural intensification has strongly impacted ecosystems and accelerated the process of global change. Agroecological practices are biodiversity-based solutions that aim to generate sustainable and resilient agroecosystems, enhancing the supply of ecosystem services. They are being increasingly adopted. This study compared agroecological and conventional horticultural farms in terms of agroecological practices and ecosystem services supply via biophysical samplings and interviews on 24 farms in Spain. Agroecological farmers applied more agroecological practices compared to conventional farmers. Agroecological farms had a higher potential to supply regulating, provisioning, and cultural services. Some agroecological practices, such as crop diversification, light tillage, and the use of organic pesticides, were associated with enhancing soil fertility, pest control, and pollination services. This is empirical evidence that agroecological practices enhance ecosystem services at horticultural farms, which is extremely relevant to upscaling agroecology in the current context of ongoing European policy reforms.Green space and foetal development
Dockx Y, Bijnens E, Saenen N, Aerts R, Aerts J-M, Casas L, Delcloo A, Dendoncker N, Linard C, Plusquin M, Stas M, Van Nieuwenhuyse an, Van Orshoven J, Somers B, Nawrot T. 2022. Residential green space in association with the methylation status in a CpG site within the promoter region of the placental serotonin receptor HTR2A. Epigenetics 0:1–12. DOI: 10.1080/15592294.2022.2088464.
Green space could influence adult cognition and childhood neurodevelopment, and is hypothesized to be partly driven by epigenetic modifications. However, it remains unknown whether some of these associations are already evident during foetal development. Similar biological signals shape the developmental processes in the foetal brain and placenta. This study hypothesized that green space can modify epigenetic processes of cognition-related pathways in placental tissue, such 
as DNA-methylation of the serotonin receptor HTR2A. Overall, a significant positive association was found between the amount of green space surrounding the residential address of the participating women and the methylation of the placental serotonin receptor, coded by the HTR2A gene. Future research is needed to understand better how these epigenetic changes are related to functional modifications in the placenta and the consequent implications for foetal development. Nevertheless, these results are a first step to establish a potential association between green space exposure and epigenetic changes within placental tissue, that might give further support to the importance of green space, in particular, in early developmental processes.Signalling functions for early feathers
Cincotta A, Nicolaï M, Campos HBN, McNamara M, D’Alba L, Shawkey MD, Kischlat E-E, Yans J, Carleer R, Escuillié F, Godefroit P. 2022. Pterosaur melanosomes support signalling functions for early feathers. Nature:1–5. DOI: 10.1038/s41586-022-04622-3.
Remarkably well-preserved soft tissues in Mesozoic fossils have yielded substantial insights into the evolution of feathers. New evidence of branched feathers in pterosaurs suggests that feathers originated in the avemetatarsalian ancestor of pterosaurs and dinosaurs in the Early Triassic, but the homology of these pterosaur structures with feathers is controversial. Reports of pterosaur feathers with homogeneous ovoid melanosome geometries suggest that they exhibited limited variation in colour, supporting hypotheses that early feathers functioned primarily in thermoregulation. This study reports the presence of diverse melanosome geometries in 
the skin and simple and branched feathers of a tapejarid pterosaur from the Early Cretaceous found in Brazil. The melanosomes form distinct populations in different feather types and the skin, a feature previously known only in theropod dinosaurs, including birds. These tissue-specific melanosome geometries in pterosaurs indicate that manipulation of feather colour—and thus functions of feathers in visual communication—has deep evolutionary origins. These features show that genetic regulation of melanosome chemistry and shape was active early in feather evolution.
Measuring individual-level trait diversity
Olusoji OD, Barabás G, Spaak JW, Fontana S, Neyens T, De Laender F, Aerts M. 2022. Measuring individual-level trait diversity: a critical assessment of methods. Oikos n/a:e09178. DOI: 10.1111/oik.09178.
One form of biodiversity is trait diversity (TD) that connects structure to functioning and co-determines ecosystem responses to environmental change. It has been found that individual-level trait diversity is an essential component TD, influencing community assembly and structure. Traditionally, one employs TD indices to measure facets of individual-level TD (divergence, richness and evenness). However, the application of species-level TD indices to individual-level traits data
and their implications have not been adequately studied. Here, the authors examine trait diversity metrics using simulations and experimental data from a growth experiment with cyanobacteria. Comparing the observed trends from the indices with the expected trends, the main lesson learned was that most of the available indices do not perform as expected. Only the trait divergence indices (FDis and Rao) produced the expected trends in the simulation scenarios and experimental data. In summary, applying these individual-level TD indices to quantify anything except trait divergence may lead to misinterpretation of the original situation of trait distribution in the trait space if their specific properties are not adequately considered.Salinity & spatial COI diversity of Corbicula lineages
Zeng C, Tang Y, Vastrade M, Coughlan NE, Zhang T, Cai Y, Van Doninck K, Li D. 2022. Salinity appears to be the main factor shaping spatial COI diversity of Corbicula lineages within the Chinese Yangtze River Basin. Diversity and Distributions n/a. DOI: 10.1111/ddi.13666.
To date, few studies have examined the phylogenetics of Corbicula clams in their native range and the environmental parameters influencing their distribution, although this could provide great insights into the biological adaptation and invasion dynamics of Corbicula clams. We sought to identify the genetic lineages of native Corbicula clams and elucidate the environmental factors shaping the distributions of identified lineages in China, mainly the Yangtze River Basin. The alignment comprised 558 COI sequences including samples from China and 222 COI sequences from published studies. This dataset was used to generate phylogenetic trees and compare 
population diversity. We used dbRDA method to assess the relationship between these COI data and environmental factors measured to identify the important factors affecting Corbicula's distribution. The Corbicula COI haplotypes found within the Yangtze River Basin had distinct distribution preferences, with the invasive androgenetic lineages being the most abundant and widely distributed. Genetic diversity was higher in this native region than in invaded areas in Europe and America, while it decreased with increasing distance from the river mouth. Salinity appeared to be the main environmental factor shaping the COI haplotype distribution of Corbicula lineages within their native range.Genetic mixing within the clam genus Corbicula
Vastrade M, Etoundi E, Bournonville T, Colinet M, Debortoli N, Hedtke SM, Nicolas E, Pigneur L-M, Virgo J, Flot J-F, Marescaux J, Van Doninck K. 2022. Substantial genetic mixing among sexual and androgenetic lineages within the clam genus Corbicula. Peer Community Journal 2. DOI: 10.24072/pcjournal.180.
“Occasional” sexuality occurs when a species combines clonal reproduction and genetic mixing. This strategy is predicted to combine the advantages of both asexuality and sexuality, but its actual consequences on the genetic diversity and species longevity are poorly understood. Androgenesis, a reproductive mode in which the offspring inherits its entire nuclear genome from the father, is often reported as a strictly clonal reproductive mode. Androgenesis is the predominant reproductive mode within the hermaphroditic, invasive lineages of the mollusk genus Corbicula. Their ability to reproduce clonally through androgenesis has been determinant in their invasive success, having colonized during the 20th century American and European freshwater systems, where they became notorious invaders with a widespread, global distribution. However, in androgenetic Corbicula clams, occasional genetic mixing between distinct lineages has also been observed when the sperm of one lineage fertilizes the oocyte of another one. Because of these occasional introgressions, the genetic relationships between Corbicula species remained unclear, and the biogeographic origins of the invasive androgenetic lineages have been challenging to identify. To address these issues, we analyzed the patterns of allele sharing for several nuclear and mitochondrial molecular markers 
among Corbicula individuals collected across both the native and invasive range. Our results show the occurrence of an allelic pool encompassing all Corbicula freshwater species worldwide, including sexual and androgenetic ones, which highlights the substantial genetic mixing within this genus. However, the differences in allele sharing patterns between invasive lineages, and the low diversity within each lineage, suggest recent, distinct biogeographic origins of invasive Corbicula androgenetic lineages. Finally, the polyploidy, high heterozygosity, and hybrid phenotypes and genotypes found in our study probably originated from hybridization events following egg parasitism between distinct Corbicula lineages. This extensive cross-lineage mixing found in Corbicula may generate nuclear diversity in an otherwise asexually reproducing species.DNA repair of bdelloid rotifers
Terwagne M, Nicolas E, Hespeels B, Herter L, Virgo J, Demazy C, Heuskin A-C, Hallet B, Van Doninck K. 2022. DNA repair during nonreductional meiosis in the asexual rotifer Adineta vaga. Science Advances 8:eadc8829. DOI: 10.1126/sciadv.adc8829.
Rotifers of the class Bdelloidea are microscopic animals notorious for their long-term persistence in the apparent absence of sexual 
reproduction and meiotic recombination. This evolutionary paradox is often counterbalanced by invoking their ability to repair environmentally induced genome breakage. By studying the dynamics of DNA damage response in the bdelloid species Adineta vaga, we found that it occurs rapidly in the soma, producing a partially reassembled genome. By contrast, germline DNA repair is delayed to a specific time window of oogenesis during which homologous chromosomes adopt a meiotic-like juxtaposed configuration, resulting in accurate reconstitution of the genome in the offspring. Our finding that a noncanonical meiosis is the mechanism of germline DNA repair in bdelloid rotifers gives previously unidentified insights on their enigmatic long-term evolution.Different measures tell different tales
Spaak JW, Ke P-J, Letten AD, De Laender F. 2022. Different measures of niche and fitness differences tell different tales. Oikos n/a:e09573. DOI: 10.1111/oik.09573.
In modern coexistence theory, species coexistence can either arise via strong niche differences or weak fitness differences. Having a common currency for interpreting these mechanisms is essential for synthesizing knowledge across different studies and systems. However, several methods for quantifying niche and fitness differences exist, with little guidance on how and why these methods differ. Here, we first organize the available methods into three groups and review their differences from a conceptual point of view. Next, we apply four methods to quantify niche and fitness differences to one simulated and one empirical data set. We show that these methods do not only differ quantitatively, but affect how we interpret coexistence. Specifically, the different methods disagree on how resource supply rates (simulated data) or plant traits (empirical data) affect niche and fitness differences. We argue for a better theoretical understanding of what connects and sets apart different methods and more precise empirical measurements to foster appropriate method selection in coexistence theory.Population Epigenetics
Chapelle V, Silvestre F. 2022. Population Epigenetics: The Extent of DNA Methylation Variation in Wild Animal Populations. Epigenomes 6:31. DOI: 10.3390/epigenomes6040031.
Population epigenetics explores the extent of epigenetic variation and its dynamics in natural populations encountering changing environmental conditions. In contrast to population genetics, the basic concepts of this field are still in their early stages, especially in animal populations. Epigenetic variation may play a crucial role in phenotypic plasticity and local adaptation as it can be affected by the environment, it is likely to have higher spontaneous mutation rate than nucleotide sequences do, and it may be inherited via non-mendelian processes. This review brings together natural animal 
population epigenetic studies to generate new insights into ecological epigenetics and its evolutionary implications. The authors first provide an overview of the extent of DNA methylation variation and its autonomy from genetic variation in wild animal population. DNA methylation dynamics are discussed which create observed epigenetic population structures by including basic population genetics processes. The relevance of DNA methylation variation as an evolutionary mechanism is highlighted in the extended evolutionary synthesis and new research directions in the population epigenetics field are designated.Dispersal syndromes in challenging environments
Cote J, Dahirel M, Schtickzelle N, Altermatt F, Ansart A, Blanchet S, Chaine AS, De Laender F, De Raedt J, Haegeman B, Jacob S, Kaltz O, Laurent E, Little CJ, Madec L, Manzi F, Masier S, Pellerin F, Pennekamp F, Therry L, Vong A, Winandy L, Bonte D, Fronhofer EA, Legrand D. Dispersal syndromes in challenging environments: A cross-species experiment. Ecology Letters n/a. DOI: 10.1111/ele.14124.
Dispersal is a central biological process tightly integrated into life-histories, morphology, physiology and behaviour. Such associations, or syndromes, are anticipated to impact the eco-evolutionary dynamics of spatially structured populations, and cascade into ecosystem processes. As for dispersal on its own, these syndromes are likely neither fixed nor random, but conditional on the experienced environment. We experimentally studied how dispersal propensity varies with individuals' phenotype and local environmental harshness using 15 species ranging from protists to vertebrates. We reveal a general phenotypic dispersal syndrome across studied species, with dispersers being larger, more active and having a marked locomotion-oriented morphology and a strengthening of the link between dispersal and some phenotypic traits with environmental harshness. Our proof-of-concept metacommunity model further reveals cascading effects of context-dependent syndromes on the local and regional organisation of functional diversity. Our study opens new avenues to advance our understanding of the functioning of spatially structured populations, communities and ecosystems.Skin immunity & antimicrobial capacity in goldfish
Roosta Z, Falahatkar B, Sajjadi M, Paknejad H, Akbarzadeh A, Kestemont P. 2023. Sex and reproductive development impact skin mucosal epithelium immunity, antimicrobial capacity, and up-regulation of immune-related gene of goldfish (Carassius auratus). Developmental & Comparative Immunology 138:104494. DOI: 10.1016/j.dci.2022.104494.
The non-specific, innate immune system of fish comprises physical barrier, epidermis, mucosal membranes and their secretions, besides cellular effectors and humoral factors. The skin mucosal layer, a gel coating surface aligned with epidermis cells, is the first and most important line of defense. This study evaluated the epidermis mucosal capacity of goldfish (Carassius auratus) during different stages of reproductive development in both females and males. The activity of mucolytic immune enzymes, i.e., lysozyme, complement and peroxidase, as well as the activity of alkaline phosphatase (ALP) were studied. 
Results show that during vitellogenesis, innate immune enzymes from epithelium surface are distinctively active. Further, the lysozyme of mucosa, a direct antibacterial agent against Gram-positive bacteria, strengthens the immunity of the female epidermis. The antimicrobial activity of the skin mucus is increased as a result of yolk protein accumulation binding bacteria. During maturation, the secretion of mucosa lysozyme from the skin upregulates the gene expression of c-lys. Overall, the findings revealed that vtg process improves mucosal innate immunity that leads to activate antimicrobial components at spawning season.Niche differences and coexistence
Buche L, Spaak JW, Jarillo J, De Laender F. 2022. Niche differences, not fitness differences, explain predicted coexistence across ecological groups. Journal of Ecology n/a. DOI: 10.1111/1365-2745.13992.
Niche and fitness differences (i.e, how species limit themselves compared to others and species’ differences in competitive ability, respectively) permit studying the consequences of species interactions. Yet, the multitude of methods to compute niche and fitness differences hampers cross-community comparisons. Here, we standardised niche and fitness differences across 953 species pairs to investigate species coexistence across ecological groups and methodological settings using data gathered from 29 empirical papers. Species pairs predicted to coexist have larger niche differences but not smaller fitness differences than species pairs predicted not to coexist. Also, species pairs group into two clear clusters along the niche difference axis: those predicted to coexist and those that are not. Surprisingly, ecological or methodological settings do not drive these clusters. Overall, our results show that species
coexistence is mainly influenced by mechanisms acting on niche differences, highlighting the importance of sustaining mechanisms that promote niche differences to maintain species coexistence. In addition, our results provide evidence that communities predicted to coexist differ from those that are not in ways that transcend their ecological grouping.Migration routes and timing of European Nightjars
Lathouwers M, Nussbaumer R, Liechti F, Davaasuren B, Artois T, Beenaerts N, Dendoncker N, Ulenaers E, Evens R. 2022. Migration routes and timing of European Nightjars (Caprimulgus europaeus) breeding in eastern Mongolia. Journal of Ornithology. DOI: 10.1007/s10336-022-02000-4.
The phenology and routes of long-distance migrations of European Nightjars are well described for Western European individuals migrating within the East Atlantic and Mediterranean flyways, while little is known about populations from other parts of the Eurasian breeding range. We describe the route choice and timing of European Nightjars breeding in eastern Mongolia, migrating within the Asia–East Africa flyway to reach wintering destinations in South-East Africa. After covering about 15,000 km during autumn migration, Mongolian nightjars arrived 1 month later in their wintering grounds compared to nightjars breeding in Western Europe. 
A similar difference was also observed in the timing of their arrival back at their respective breeding grounds illustrating the differences in timing of migration events between the two populations. We identify the steppes of Central Asia and the savannah of the Horn of Africa and Eastern Africa as key stopover zones for nightjars associated with the crossing of an ecological barrier formed by the deserts and mountains of the Iranian Plateau and the Arabian Peninsula.Spatial and Ecological Scaling of Stability in Spatial Community Networks
Jarillo J, Cao-García FJ, De Laender F. 2022. Spatial and Ecological Scaling of Stability in Spatial Community Networks. Frontiers in Ecology and Evolution 10. https://doi.org/10.3389/fevo.2022.861537
Ecological stability is a property that can be broadly defined as the ability of an ecosystem to remain unaltered when challenged by perturbations. There are many scales at which to quantify stability in spatial and ecological networks. Local-scale analyses focus on specific nodes of the spatial network, while regional-scale analyses consider the whole network. Similarly, species- and community-level analyses either account for single species or for the whole community. Furthermore, stability itself can
be defined in multiple ways, including resistance (the inverse of the relative displacement caused by a perturbation), initial resilience (the rate of return after a perturbation), and invariability (the inverse of the relative amplitude of the population fluctuations). Here, we analyze the scale-dependence of these stability properties. More specifically, we ask how spatial scale (local vs. regional) and ecological scale (species vs. community) influence these stability properties. We find that scaling of stability depends on the metric considered, and we present a reliable framework to estimate these metrics.Editor's choice: The evolution of trait variance
Barabás G, Parent C, Kraemer A, Van de Perre F, De Laender F. 2022. The evolution of trait variance creates a tension between species diversity and functional diversity. Nature Communications 13:2521. DOI: 10.1038/s41467-022-30090-4.
Here we show that even without such effects, the evolution of functional trait variance can erase or even reverse the expected positive relationship between species- and functional diversity. We present theory showing that trait-based eco-evolutionary processes force species to evolve narrower trait breadths in more tightly packed, species-rich communities, in their effort to avoid competition with neighboring species. This effect is so strong that it leads to an overall reduction in trait space coverage whenever a new species establishes. Empirical data from land snail communities on the Galápagos Islands are consistent with this claim. The finding that the relationship between species- and functional diversity can be negative implies that trait data from species-poor communities may misjudge functional diversity in species-rich ones, and vice versa.Interactive effects of multiple stressors
Turschwell MP, Connolly SR, Schäfer RB, De Laender F, Campbell MD, Mantyka-Pringle C, Jackson MC, Kattwinkel M, Sievers M, Ashauer R, Côté IM, Connolly RM, van den Brink PJ, Brown CJ. Interactive effects of multiple stressors vary with consumer interactions, stressor dynamics and magnitude. Ecology Letters 25:1483–1496. DOI: 10.1111/ele.14013.
synergistically, additively or antagonistically. Here, we use process-based models to study how interactions generalise across three levels of biological organisation (physiological, population and consumer-resource) for a two-stressor experiment on a seagrass model system. We found that the same underlying processes could result in synergistic, additive or antagonistic interactions, with interaction type depending on initial conditions, experiment duration, stressor dynamics and consumer presence. Our results help explain why meta-analyses of multiple stressor experimental results have struggled to identify predictors of consistently non-additive interactions in the natural environment. Experiments run over extended temporal scales, with treatments across gradients of stressor magnitude, are needed to identify the processes that underpin how stressors interact and provide useful predictions to management.Intergenerational Effects of Early-Life Starvation
Paul SC, Singh P, Dennis AB, Müller C. 2022. Intergenerational Effects of Early-Life Starvation on Life History, Consumption, and Transcriptome of a Holometabolous Insect. The American Naturalist: E000–E000. DOI: 10.1086/719397.
Intergenerational effects, also known as parental effects in which the offspring phenotype is influenced by the parental phenotype, can occur in response to factors that occur not only in early but also in late parental life. However, little is known about how these parental life stage–specific environments interact with each other and with the offspring environment to influence offspring phenotypes, particularly in organisms that realize distinct niches across ontogeny. This study examines the effects of parental larval starvation and adult reproductive environment on offspring traits under matching or mismatching offspring larval starvation conditions using the holometabolous, haplodiploid insect Athalia rosae (turnip sawfly). Parent
al larval starvation had trait-dependent intergenerational effects on both life history and consumption traits of offspring larvae, partly in interaction with offspring conditions, while there was no significant effect of parental adult reproductive environment. In addition, while offspring larval starvation led to numerous gene- and pathway-level expression differences, parental larval starvation impacted far fewer genes and only the ribosomal pathway. These findings reveal that parental starvation evokes complex intergenerational effects on offspring life history traits, consumption patterns, and gene expression, although the effects are less pronounced than those of offspring starvation.Biodiversity promotes ecosystem functioning despite environmental change
Hong P, Schmid B, De Laender F, Eisenhauer N, Zhang X, Chen H, Craven D, De Boeck HJ, Hautier Y, Petchey OL, Reich PB, Steudel B, Striebel M, Thakur MP, Wang S. 2022. Biodiversity promotes ecosystem functioning despite environmental change. Ecology Letters 25:555–569. DOI: 10.1111/ele.13936.
Three decades of research have demonstrated that biodiversity can promote the functioning of ecosystems. Yet, it is unclear whether the positive effects of biodiversity on ecosystem functioning will persist under various types of global environmental change drivers. This meta-analysis of 4
6 factorial experiments manipulating both species richness and the environment tests how global change drivers (i.e. warming, drought, nutrient addition or CO2 enrichment) modulated the effect of biodiversity on multiple ecosystem functions across three taxonomic groups (microbes, phytoplankton and plants). Results show that biodiversity increased ecosystem functioning in both ambient and manipulated environments, but often not to the same degree. In particular, biodiversity effects on ecosystem functioning were larger in stressful environments induced by global change drivers, indicating that high-diversity communities were more resistant to environmental change. A subset of studies demonstrated that the positive effects of biodiversity were mainly driven by interspecific complementarity and that these effects increased over time in both ambient and manipulated environments. These findings support biodiversity conservation as a key strategy for sustainable ecosystem management in the face of global environmental change.Rush or relax: migration tactics of a nocturnal insectivore birds
Lathouwers M, Artois T, Dendoncker N, Beenaerts N, Conway G, Henderson I, Kowalczyk C, Davaasuren B, Bayrgur S, Shewring M, Cross T, Ulenaers E, Liechti F, Evens R. 2022. Rush or relax: migration tactics of a nocturnal insectivore in response to ecological barriers. Scientific Reports 12:4964. DOI: 10.1038/s41598-022-09106-y.
Nightjars (Caprimulgus europaeus) adopt variable migrations tactics during active autumn migration. Ecological barriers, where opportunities for foraging are limited, are crossed at a higher pace. This allows individuals to avoid risks and minimize the time they spend in these inhospitable areas. In contrast, where food resources are available, nightjar seemingly spend less time migrating per day while foraging efforts are increased. The ability to opportunistically exploit available resources in between active migratory flight, in our view, could serve to (partially) negate unforeseen poor foraging opportunities en route. While this study provides a first look into how nightjars balance active migration with potential refuelling outside of stationary stopover periods, in future research we will investigate how these different migration tactics during active migration relate to behaviour during prolonged stopovers, allowing investigations on the impact of global land use change on individual migration patterns and tactics.Conservation, genomics, and reference genomes
Formenti G et al. 2022. The era of reference genomes in conservation genomics. Trends in Ecology & Evolution 37:197–202. DOI: 10.1016/j.tree.2021.11.008. contribution by A. Dennis
Although the primary route to preserving biodiversity comprises protection of species and restoration of habitats and ecosystems, genomics provides a rapidly expanding array of novel tools to characterize biodiversity and assist such conservation efforts. Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. 
These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics. A large and inclusive community of scientists has recently gathered as the European hub of the EBP to promote the generation of a European Reference Genome Atlas (ERGA). This initiative is building a pan-European open access infrastructure to streamline ethical and legally compliant sample and metadata collection, sequencing and assembly, annotation, and release in public archives of high-quality genomic information, thus creating reference genomes for a wide variety of eukaryotic species.2021
Mineralization & mammalian biostratigraphy
Yans J, Verhaert M, Gautheron C, Antoine P-O, Moussi B, Dekoninck A, Decrée S, Chaftar H-R, Hatira N, Dupuis C, Pinna-Jamme R, Jamoussi F. 2021. (U-Th)/He Dating of Supergene Iron (Oxyhydr-)Oxides of the Nefza-Sejnane District (Tunisia): New Insights into Mineralization and Mammalian Biostratigraphy. Minerals 11:260. DOI: 10.3390/min11030260.
For nearly 15 years, the Geologists (team around Johan Yans) have been interested in the mineralization (Pb-Zn, Fe-Mn, U-REE-Au, clays) of the Nefza district in Tunisia. This article is a synthesis of their research, which highlights the iron oxide (goethite) dating of meteoric alteration events ~9 and ~1 million years ago. The originality of the article is that – for the very first time! - these dates make it possible to date certain Rhinoceroidae in the region with greater precision. 
The study was carried out in partnership with various Belgian, French and Tunisian research institutes.Biotic community and landscape changes around the Eocene–Oligocene transition in Peru
Antoine P-O, Yans J, Castillo AA, Stutz N, Abello MA, Adnet S, Custódio MA, Benites-Palomino A, Billet G, Boivin M, Herrera F, Jaramillo C, Mártinez C, Moreno F, Navarrete RE, Negri FR, Parra F, Pujos F, Rage J-C, Ribeiro AM, Robinet C, Roddaz M, Tejada-Lara JV, Varas-Malca R, Ventura Santos R, Salas-Gismondi R, Marivaux L. 2021. Biotic community and landscape changes around the Eocene–Oligocene transition at Shapaja, Peruvian Amazonia: Regional or global drivers? Global and Planetary Change 202:103512. DOI: 10.1016/j.gloplacha.2021.103512.
The Eocene-Oligocene transition (EOT, ca. 33.9 million years ago) was one of the most dramatic episodes of climatic, environmental, and biotic change recorded throughout the Cenozoic era with oceanic reorganization, global cooling (ca. 4 °C), and the onset of semi-permanent ice sheets on Antarctica. Basically, the EOT marks the rapid shift from the Paleocene–Eocene “greenhouse” Earth to the “icehouse” Earth during the earliest Oligocene. In this study, the late Eocene–early Oligocene Shapaja section was extensively sampled for chemostratigraphy (δ13C on dispersed organic matter and pedogenic carbonate nodules), to allow for refining the location of the 
EOT. The section yielded nine fossil localities with plant remains (leaves, wood, charophytes, and palynomorphs), mollusks, decapods, and/or vertebrates (selachians, actinopterygians, lungfishes, amphibians, sauropsids, and mammals), documenting ~130 distinct taxa. Two biotic turnovers are retrieved (metatherians, rodents, and fish): one during the late Eocene (ca. 35‐–36 Ma) and another one several thousand years after the EOT (ca. 33 Ma). The paleocommunities from Shapaja exemplify a local response of terrestrial and aquatic organisms to drastic regionally- then globally-driven changes over the late Eocene–early Oligocene interval, at low latitudes in South America.Eocene rodents from Peru
Boivin M, Marivaux L, Aguirre-Diaz W, Andriolli Custódio M, Benites-Palomino A, Pujos F, Roddaz M, Salas-Gismondi R, Stutz N, Tejada-Lara JV, Yans J, Antoine P-O. 2021. Eocene caviomorph rodents from Balsayacu (Peruvian Amazonia). PalZ. DOI: 10.1007/s12542-021-00551-0.
The Paleogene record of caviomorph rodents has substantially increased over the last decades, and their evolutionary history is better 
understood since the discovery of their earliest representatives, so far recorded in several pre-Deseadan localities in Peruvian Amazonia. This study discovered new caviomorph fossils from the Balsayacu area in Peru. Their close investigation revises and refines the taxonomic assignments of previously described specimens. These low-latitude stem caviomorph faunas provide new insights into the early evolutionary history and paleodiversity of that group immediately before the rise of modern superfamilies.New fossil records in France
Vautrin Q, Tabuce R, Lihoreau F, Bronnert C, Gheerbrant E, Godinot M, Metais G, Yans J, Dutour Y, Vialle N, Philip J, Billet G. 2021. New remains of Lophiaspis maurettei (Mammalia, Perissodactyla) from the Early Eocene of France and the implications for the origin of the Lophiodontidae. Journal of Vertebrate Paleontology 0:e1878200. DOI: 10.1080/02724634.2020.1878200
The Lophiodontidae, tapir-like animals, are endemic to Europe and flourished during the Eocene. Despite their preponderance in the European fossil record, their exact origin and relationships within the perissodactyls remain unknown due to the rare and fragmentary material in the early Ypresian, the time of their earliest radiation. Lophiaspis maurettei is the oldest and earliest diverging lophiodontid known to date but is unfortunately poorly known. 
This paper describes the results of new excavations of the type locality of Palette. Important new material including complete skulls, mandibles, post-cranial elements and juvenile specimens lead to a revision of L. maurettei from Palette and other localities and to the description of a novel morphology for this species. The resulting topology does not support the previously proposed inclusion of the lophiodontids within the Ceratomorpha (tapirs & rhinos) and supports a position within the suborder Ancylopoda, close to some Eomoropidae representatives.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 (
) and fitness differences (
). This application provides three main benefits to study processes of multispecies persistence across trophic levels. First, 
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, 
mapping facilitates studying how species persistence responds to environmental changes that shift intrinsic growth rates 
and the strength and sign of species interactions. Third, 
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 
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
Land use change models refine biodiversity scenarios
Marshall L, Beckers V, Vray S, Rasmont P, Vereecken NJ, Dendoncker N. 2020. High thematic resolution land use change models refine biodiversity scenarios: A case study with Belgian bumblebees. Journal of Biogeography . DOI: https://doi.org/10.1111/jbi.14000.
Projections of biodiversity scenarios often rely solely on climate change to inform species distribution shifts in the future. Land use projections are rarely used due to their unavailability and, when available, are often at coarse spatial and thematic resolutions, making them unsuitable to capture fine scale habitat suitability. This study aims at (a) showing how coupled land use change (LUC) models of high thematic resolution (HTR) can be used in species distribution m
odels (SDM), (b) comparing the impacts of HTR and low thematic resolution (LTR) explanatory predictors on biodiversity scenarios and (c) assessing the impact of species' present area of occupancy on the effect of thematic resolution in SDMs. Belgian bumblebees were used as case study. The results illustrate the importance of using ecologically relevant explanatory variables in SDMs, particularly for rare and localized species with specific habitat requirements. The results also indicate the need for large‐scale LUC projections to improve future biodiversity scenarios under climate change and to improve the ability of conservationists and policymakers to use SDM projections.Bumblebees moving up
Marshall L, Perdijk F, Dendoncker N, Kunin W, Roberts S, Biesmeijer JC. 2020. Bumblebees moving up: shifts in elevation ranges in the Pyrenees over 115 years. Proceedings of the Royal Society B: Biological Sciences 287:20202201. DOI: 10.1098/rspb.2020.2201.
warming climate, species are expected to shift their geographical ranges to higher elevations and latitudes, and if interacting species shift at different rate
s, networks may be disrupted. To quantify the effects of ongoing climate change, repeating historical biodiversity surveys are necessary. This study compares the distribution of a plant–pollinator community with 115 years between the surveys in the Pyrenees (France). The composition of the bumblebee community remained quite stable, but clear shifts to higher elevations for bumblebees (averaging 129 m) and plants (229 m) can be observed. These provide preliminary evidence that some bumblebee species shift with the plants they visit. Some species were able to occupy the same climate range in both periods by shifting elevation range. The results suggest the need for long-term monitoring to determine the role and impact of the different drivers of global change, especially in montane habitats where the impacts of climate changes are anticipated to be more extreme.Science-policy interface on ecosystems and people
Balvanera P, Jacobs S, Nagendra H, O’Farrell P, Bridgewater P, Crouzat E, Dendoncker N, Goodwin S, Gustafsson KM, Kadykalo AN, Krug CB, Matuk FA, Pandit R, Sala JE, Schröter M, Washbourne C-L. 2020. The science-policy interface on ecosystems and people: challenges and opportunities. Ecosystems and People 16:345–353. DOI: 10.
1080/26395916.2020.1819426.
Urbanization and agricultural dynamics in Belgium
Beckers V, Poelmans L, Rompaey AV, Dendoncker N. 2020. The impact of urbanization on agricultural dynamics: a case study in Belgium. Journal of Land Use Science 0:1–18. DOI: 10.1080/1747423X.2020.1769211.
Urbanization leads to a continuous loss of agricultural land through direct land take, but also indirectly through the use of agricultural l
and for non-productive rural activities (recreation, horse keeping, hobby farming). This makes farming activities harder through reduced agricultural land, negative externalities and the competition for land. The aim of this paper was to present a modelling approach that combines the different fields of agricultural and urban modelling to analyse the impact of direct and indirect urbanization on farming in the urban fringe under different scenarios. An agricultural agent-based model was combined with spatially explicit urbanization scenarios and with different agricultural subsidizing policies for the case study of Belgium. Due to an aging farming population and low succession rates, simulations until 2035 showed a continuous decline of farmers in all scenarios; a trend that will continue for as long as not every farmer that quits his activities is replaced. Even the most farmer-friendly scenario is expected to result in a further loss of farmland and farms. The continued strong decrease in the number of farmers also leads, in spite of the decrease in farmland area, to a continued increasing average farm size. These declines are expected to be higher in the rural-urban fringe.Collaboration between ecosystem service communities and the IPBES
Washbourne C-L, Dendoncker N, Jacobs S, Mascarenhas A, De Longueville F, Oudenhoven APE van, Schröter M, Willemen L, Campagne S, Jones SK, Garcia-Llorente M, Iniesta-Arandia I, Baró F, Fisher J, Förster J, Jericó-Daminelo C, Lecina-Diaz J, Lavorel S, Lliso B, Talero CM, Morán-Ordóñez A, Roces-Díaz JV, Schlaepfer MA, Dijk JV. 2020. Improving collaboration between ecosystem service communities and the IPBES science-policy platform. Ecosystems and People 16:165–174. DOI: 10.1080/26395916.2020.1766573.
The creation of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) in 2012 constitutes a milestone towards multi- and transdisciplinarity and multiculturality in nature-society research and practice. Lessons to be learned from the experiences with the first work program are to close persisting regional and expertise gaps, increase transparency and encourage collaboration. This perspective paper summarises reflections from a workshop and emerging discussions from a range of ecosystem services (ES) researchers and practitioners. Recommendations to IPBES include increasing supportive conditions (e.g. funding), engaging in ES research spaces such 
as conferences, increasing transparency on contribution and selection processes, and improving communication. Recommendations to the ES community include working towards being more collaborative and policy-relevant by integrating more social scientists, researchers from developing countries, ECRs and policy-makers to increase policy and societal relevance.Drastic shifts in Belgian bumble bees
Rollin O, Vray S, Dendoncker N, Michez D, Dufrêne M, Rasmont P. 2020. Drastic shifts in the Belgian bumblebee community over the last century. Biodiversity and Conservation. DOI: 10.1007/s10531-020-01988-6.
Bumblebees, important pollinators of crops and wild flowers, are threatened by habitat loss and fragmentation, agricultural intensification, and climate change. Long-term records are necessary to estimate population trends precisely and to propose appropriate mitigation strategies. This study compares records (museum collections, scientific monitoring, and opportunistic citizen data) of Belgian bumble bee populations through three time-periods covering the past 100 years. Overall, species richness decreased, but some regions retained relatively species-rich communities. A strong shift in community composition occurred. Several species that were once widespread declined drastically, especially those preferring open habitats. 
Only a few species, preferring wooded habitats, increased in distribution. This study also demonstrates that historical data from various sampling protocols can be combined to study long-term community patterns, when appropriate statistical methods are applied.Perception of Agroecology
Boeraeve F, Dufrêne M, Dendoncker N, Dupire A, Mahy G. 2020. How Are Landscapes under Agroecological Transition Perceived and Appreciated? A Belgian Case Study. Sustainability 12:2480. DOI: 10.3390/su12062480.
Transition initiatives in agricultural systems are increasing, definitely adding value to Ecosystem Services (ES) as proven by many studies. This also reshapes the landscape. This study assesses the extent to which locals (local inhabitants and farmers) appreciate and view landscapes undergoing agricultural transitions and compared it to the opinion of ‘ES experts’. The agroecological scenario was the most appreciated, while the conventional one was the least appreciated by both groups and seen as the one delivering the least ES. The authors discuss how these results call for the assessment of the multi-performance of agricultural systems in terms of ES rather than focusing on yield only, and
how future research addressing agroecological transition should rely on integrated valuations and mixed methods to better embrace the complexity of such transitioning systems.Models to estimate tree diversity
Stas M, Aerts R, Hendrickx M, Dendoncker N, Dujardin S, Linard C, Nawrot T, Van Nieuwenhuyse A, Aerts J-M, Van Orshoven J, Somers B. 2020. An evaluation of species distribution models to estimate tree diversity at genus level in a heterogeneous urban-rural landscape. Landscape and Urban Planning 198:103770. DOI: 10.1016/j.landurbplan.2020.103770.
Trees in cities provide important ecosystem services that improve the environment and human health (limit urban heat peaks, filter particles, etc.). Such effects may be related to the diversity of trees within green spaces. However, spatial data to evaluate this association is often missing. This study evaluates two methods to model tree diversity at genus level based on environmental covariates and presence point data. The aim is to identify the drivers and suitable methods for urban and rural tree diversity models in the heterogeneous region of Flanders, Belgium. 
Generic tree diversity estimates were better when presences derived from distribution models were simply added up (binary stacking vs. probability stacking), which thus seems a suitable approach to estimate regional diversity.Agroecological farming & ecosystem services
Boeraeve F, Dendoncker N, Cornélis J-T, Degrune F, Dufrêne M. 2020. Contribution of agroecological farming systems to the delivery of ecosystem services. Journal of Environmental Management 260:109576. DOI: 10.1016/j.jenvman.2019.109576.
Today's challenge in agriculture is to maintain high productivity while sustaining the environment and its functions. Agroecology seems a promising concept by optimizing ecological processes that deliver ecosystem services (ES) to replace external inputs. This study provides the novelty of assessing simultaneously multiple stakeholder-relevant ES and their interactions in real-life AFS. The findings suggest that the studied agroecological farming systems (AFS) succeed in providing a wider array of regulating services than their neighbouring conventional farming systems (CFS). However, CFS achieve a higher grain production and a better performance in some aspects of fodder quality. While this ‘productivity gap’ may be due to the still-evolving state of the studied AFS, 
the need is arising to shift from a volume-focused production system to a system that also values the ecological processes underpinning crop production and other benefits to society.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 struct
ural 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
Geological analysis of fossil-bearing Dakhla
Benammi M, Adnet S, Marivaux L, Yans J, Noiret C, Tabuce R, Surault J, Kati IE, Enault S, Baidder L, Saddiqi O, Benammi M. 2019. Geology, biostratigraphy and carbon isotope chemostratigraphy of the Palaeogene fossil-bearing Dakhla sections, southwestern Moroccan Sahara. Geological Magazine 156:117–132. DOI: 10.1017/S0016756817000851.
Nature and age of the sedimentological deposits exposed in the Dakhla region (Sahara, Morocco) were described and refined based on lithological, palaeomagnetic, carbon isotope chemostratigraphy and biochronological data to date its Palaeogene faunas.
Analyses show that the rodent assemblage (a high diversity of micromammals) found in the region represents the first Oligocene record of rodents from north-western Saharan Africa.Land use interacts with climate change
Berckmans J, Hamdi R, Dendoncker N. 2019. Bridging the gap between policy-driven land use changes and regional climate projections. Journal of Geophysical Research: Atmospheres 0. DOI: 10.1029/2018JD029207.
The impact of land surface changes on the local and regional climate can be as large as the impact of increasing greenhouse gas emissions. This study models the near future climate state for Western Europe, based on a policy-driven land use change scenario at high resolution. 
Relatively uniform temperature increases (0.3-0.6°C) contrast with highly heterogeneous changes of land surface. Deforestation and conversion to arable land can diminish climate change effects, while urbanisation enhances the effect of climate change, especially temperature increase.Power, equity & ecosystem services
Vallet A, Locatelli B, Levrel H, Dendoncker N, Barnaud C, Quispe Conde Y. 2019. Linking equity, power, and stakeholders’ roles in relation to ecosystem services. Ecology and Society 24. DOI: 10.5751/ES-10904-240214.
Stakeholders who benefit from ESs are not necessarily able or authorized to participate in the management of ESs. Their governance is profoundly linked to issues of power and equity. Using an example from the Mariño watershed, one of the poorest regions in Peru, this article proposes an analytical framework to identify and qualify stakeholders’ roles based on the ES benefits received and their participation in ES management. 
Clear differences in the identity of stakeholders who managed or benefited from ESs showed up, creating structural interdependencies and power relationships among stakeholders. Participatory management could be a way to empower less influential stakeholders.Stakeholder's ideas of nature
De Vreese R, Van Herzele A, Dendoncker N, Fontaine CM, Leys M. 2019. Are stakeholders’ social representations of nature and landscape compatible with the ecosystem service concept? Ecosystem Services 37:100911. DOI: 10.1016/j.ecoser.2019.100911.
Implementing planning and management processes that are based on ecosystem services (ES) in practice remains limited, as well as mainstreaming the results in decision-making. This may be caused by a limited overlap between the ES concept and stakeholders’ representations of nature. Both have an anthropocentric view in common, 
but stakeholders also stress the role and responsibility of humans in sustaining ecosystems and regulating nature, which is a relational value. The presented social representations technique provides solutions for more effective ES-based planning and management processes and improved understanding among stakeholders as well as between stakeholders and process managers.Ecosystem disservices matter
Blanco J, Dendoncker N, Barnaud C, Sirami C. 2019. Ecosystem disservices matter: Towards their systematic integration within ecosystem service research and policy. Ecosystem Services 36:100913. DOI: 10.1016/j.ecoser.2019.100913.
Ecosystem disservices (EDS) are defined as “the ecosystem generated functions, processes and attributes that result in negative impacts on human wellbeing”. While the ES (Ecosystem services) concept is frequently applied (e.g. analytical research framework, operational tool for decision and policy making), EDS remain poorly investigated. The authors consider them complementary to ES and propose to consider EDS to improve the understanding of people’s views and actions with regard to ecosystems. An integrated ES/EDS framework could provide a more holistic understanding of SES, and contribute to a better integration of the perspectives of different stakeholders and practitioners.Bumble bees & landscape changes
Vray S, Rollin O, Rasmont P, Dufrêne M, Michez D, Dendoncker N. 2019. A century of local changes in bumblebee communities and landscape composition in Belgium. Journal of Insect Conservation. DOI: 10.1007/s10841-019-00139-9.
Bumblebees are declining in most parts of Western Europe, as often shown, due to agricultural intensification and urbanisation. However, ver
y few studies have explored bumblebee communities prior to the onset of these major land use changes, mostly based on low-resolution spatial data. Here, landscape composition and bumblebee occurrence records between the early twentieth century (1910–1930) and the contemporary period (2013–2015) were compared in four localities representative of Belgium. Bumblebee assemblages changed drastically over this period, and that the decline in richness was strongest in areas with the greatest increase in urbanization and agricultural intensification.Old, feathered dinosaurs
Cincotta A, Pestchevitskaya EB, Sinitsa SM, Markevich VS, Debaille V, Reshetova SA, Mashchuk IM, Frolov AO, Gerdes A, Yans J, Godefroit P. 2019. The rise of feathered dinosaurs: Kulindadromeus zabaikalicus, the oldest dinosaur with ‘feather-like’ structures. PeerJ 7:e6239. DOI: 10.7717/peerj.6239.
A first dating of the Kulinda locality (south-eastern Siberia) is presented, the locality of the primitive ornithischian dinosaur Kulindadromeus zabaikalicus. The method combines U-Pb analyses (LA-ICP-MS) on detrital zircons and monazites from sedimentary rocks of volcanoclastic origin with palynological observations. 
Evidence of a Bathonian age—between 168.3 ± 1.3 Ma and 166.1 ± 1.2 Ma—for Kulindadromeus is provided. This is older than the previous Late Jurassic to Early Cretaceous ages tentatively based on local stratigraphic correlations. Thus, Kulindadromeus is the oldest known dinosaur with “feather-like” structures discovered so far.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.
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.
he 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
Sow wheat!
Baltazar S, Visser M, Dendoncker N. 2018. Au-delà des idées reçues. L’exemple de Li Mestère, réseau de semences wallon. Études rurales:18–35. DOI: 10.4000/etudesrurales.14553.
Innovation platforms that support interaction among various stakeholders can improve agricultural innovation systems. For example, seed networks such as Li Mestère, that brings together a diverse range of stakeholders to manage the crop diversity of cereals. It facilitates the circulation of seeds, knowledge and know-how that are otherwise inaccessible in the formal seed system. 
Due to its quick growth, the network struggles with organisational challenges and misrepresentation issues, and finds itself between “idealisation” and “realisation”. By delving beyond preconceived ideas about seed networks, the article highlights these challenges and the efforts to foster an agro-ecological transition.ADAM - Agricultural Dynamics through Agent-based Modelling
Beckers V, Beckers J, Vanmaercke M, Van Hecke E, Van Rompaey A, Dendoncker N. 2018. Modelling Farm Growth and Its Impact on Agricultural Land Use: A Country Scale Application of an Agent-Based Model. Land 7:109. DOI: 10.3390/land7030109.
Farmers are under ongoing economic pressure today and small, uncompetitive farms have to be given up. The land is then often taken over by neighbouring farmers which leads to a decrease in numbers of farmers but an increase of farm size. Such an agricultural transition has socioeconomic and environmental consequences. An agent-based (autonomous decision-making objects) model is presented to obtain insights in the farmer population and its impact on agricultural land at a national scale level using the example of Belgium.Participatory identification and selection of ecosystem services
Boeraeve, F, Dufrene, M, De Vreese, R, Jacobs, S, Pipart, N, Turkelboom, F, Verheyden, W, & Dendoncker, N 2018, ‘Participatory identification and selection of ecosystem services: building on field experiences’, Ecology and Society, vol. 23, no. 2, doi: 10.5751/ES-10087-230227
The concept of ecosystem services (ESs) clarifies how ecosystems contribute to human well-being. It is often used to support decision making for sustainable management of natural resources. Valuations should start with a participatory identification of the most relevant ESs to be included. Nevertheless, experiences of researchers with real-life applications are seldom reported. The authors aim at advancing the organization and implementation of participatory ES identification and selection by providing a self-reflective evaluation of experiences and discussion of five case studies.Reality check of Ecosystem Services valuation
Dendoncker, N, Turkelboom, F, Boeraeve, F, Boerema, A, Broekx, S, Fontaine, C, Demeyer, R, De Vreese, R, Devillet, G, Keune, H, Janssens, L, Liekens, I, Lord-Tarte, E, Popa, F, Simoens, I, Smeets, N, Ulenaers, P, Van Herzele, A, Van Tichelen, K, & Jacobs, S 2018, ‘Integrating Ecosystem Services values for sustainability? Evidence from the Belgium Ecosystem Services community of practice’, Ecosystem Services, vol. 31, pp. 68–76, doi: 10.1016/j.ecoser.2018.03.006
Communities of Practice (CoP) are effective to stimulate learning and foster innovation among practitioners in various sectors, including ecological restoration. The BElgium Ecosystem Services (BEES) CoP is an open and flexible network that interfaces between different societal actors (e.g., scientists, policy-makers, businesses, NGOs). One of its main aims is to bridge the gap between science and practice and improve the societal relevance of scientific work on ecosystem services. This study evaluates how Ecosystem Services valuation is performed within BEES. Transdisciplinary studies are fostered apprpriately by facilitating the inclusion of a broad range of values and actors. Nevertheless, impacts on decision-making need to be reinforced, real transdisciplinary studies, co-constructed by scientists and stakeholders are yet to be undertaken, and sustainability issues (thresholds & fairness) should be included.Ecosystem services, social interdependencies, and collective action
Barnaud, C, Corbera, E, Muradian, R, Salliou, N, Sirami, C, Vialatte, A, Choisis, J-P, Dendoncker, N, Mathevet, R, Moreau, C, Reyes-García, V, Boada, M, Deconchat, M, Cibien, C, Garnier, S, Maneja, R, & Antona, M 2018, ‘Ecosystem services, social interdependencies, and collective action: a conceptual framework’, Ecology and Society, vol. 23, no.1, DOI: 10.5751/ES-09848-230115
Collective action mechanisms are rarely considered to manage ecosystem services (ES). To illustrate existing or potential collective actions, a conceptual framework is recommended that highlights social interdependencies among people. This framework can contribute in particular to agroecological transitions that require innovations at a landscape level and mechanisms to coordinate land users and managerForest cover improves water quality
Brogna, D, Dufrêne, M, Michez, A, Latli, A, Jacobs, S, Vincke, C, & Dendoncker, N 2018, ‘Forest cover correlates with good biological water quality. Insights from a regional study (Wallonia, Belgium)’, Journal of Environmental Management, vol. 211, pp. 9–21, DOI: 0.1016/j.jenvman.2018.01.017
Water quality management policies (e.g. the European Water Framework Directive) are highly important since water and freshwater systems particularly threatened by human activities. This paper quantifies the forest cover effect on biological water quality in Belgium. This was measured using biological indices based on diatoms and macro-invertebrates. The the entire Walloon region and five natural ecoregions were analysed. Forest cover was systematically positively correlated with higher biological water quality. Considered alone, it explained around 30% of the biological water quality at the regional scale and 15 - 70% across ecoregions.Integrated valuation of ecosystem services supports agroecological transitions
Dendoncker, N, Boeraeve, F, Crouzat, E, Dufrêne, M, König, A, & Barnaud, C 2018, ‘How can integrated valuation of ecosystem services help understanding and steering agroecological transitions?’, Ecology and Society, vol. 23, no.1, DOI: 0.5751/ES-09843-230112
Ecosystem services (ES) are the numerous benefits that humans freely gain from healthy ecosystems. Agroecology has been proposed as a promising concept to optimize ecosystem services. Agroecological transition stands for the transformation of conventional, intensive farm systems to agroecological ones (e.g., diversified cropping systems, mosaic landscapes, low anthropogenic inputs further including the ecological and social environment). This article proposes a four-step integrated ES assessment framework that is specifically targeted at understanding and steering agricultural transitions and that is generic enough to be applied in different contexts.Baltazar S, Visser M, Dendoncker N. 2018. Au-delà des idées reçues. L’exemple de Li Mestère, réseau de semences wallon. Études rurales:18–35. DOI: 10.4000/etudesrurales.14553.
Marshall, L, Biesmeijer, JC, Rasmont, P, Vereecken, NJ, Dvorak, L, Fitzpatrick, U, Francis, F, Neumayer, J, Ødegaard, F, Paukkunen, JPT, Pawlikowski, T, Reemer, M, Roberts, SPM, Straka, J, Vray, S & Dendoncker, N 2018, 'The interplay of climate and land use change affects the distribution of EU bumblebees' Global Change Biology, vol 24, no. 1, pp. 101-116 DOI: 10.1111/gcb.13867
Understanding fossil fauna
Solé F, Noiret C, Desmares D, Adnet S, Taverne L, De Putter T, Mees F, Yans J, Steeman T, Louwye S, Folie A, Stevens NJ, Gunnell GF, Baudet D, Yaya NK, Smith T. 2018. Reassessment of historical sections from the Paleogene marine margin of the Congo Basin reveals an almost complete absence of Danian deposits. Geoscience Frontiers. https://doi.org/10.1016/j.gsf.2018.06.002.
The early Paleogene is critical for understanding global biodiversity patterns in modern ecosystems. During this interval, Southern Hemisphere continents were largely characterized by isolation and faunal endemism following the breakup of Gondwana. Africa has been proposed as an important source area for the origin of several marine vertebrate groups but its Paleogene record is poorly sampled, especially from sub-Saharan Africa. To document the early Paleogene marine ecosystems of Central Africa, we revised the stratigraphic context of sedimentary deposits from three fossil-rich vertebrate localities: the Landana section in the Cabinda exclave (Angola), and the Manzadi and Bololo localities in western Democratic Republic of Congo.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
Alexander, P, Prestele, R, Verburg, PH, Arneth, A, Baranzelli, C, Batista e Silva, F, Brown, C, Butler, A, Calvin, K, Dendoncker, N, Doelman, JC, Dunford, R, Engström, K, Eitelberg, D, Fujimori, S, Harrison, PA, Hasegawa, T, Havlik, P, Holzhauer, S, Humpenöder, F, Jacobs-Crisioni, C, Jain, AK, Krisztin, T, Kyle, P, Lavalle, C, Lenton, T, Liu, J, Meiyappan, P, Popp, A, Powell, T, Sands, RD, Schaldach, R, Stehfest, E, Steinbuks, J, Tabeau, A, van Meijl, H, Wise, MA & Rounsevell, MDA 2017, 'Assessing uncertainties in land cover projections' Global Change Biology, vol 23, no. 2, pp. 767-781. DOI: 10.1111/gcb.13447
Brogna, D, Michez, A, Jacobs, S, Dufrêne, M, Vincke, C & Dendoncker, N 2017, 'Linking forest cover to water quality: A multivariate analysis of large monitoring datasets' Water, vol 9, no. 3, 176. DOI: 10.3390/w9030176
Brogna, D, Vincke, C, Brostaux, Y, Soyeurt, H, Dufrêne, M & Dendoncker, N 2017, 'How does forest cover impact water flows and ecosystem services? Insights from “real-life” catchments in Wallonia (Belgium)' Ecological Indicators, vol 72, pp. 675-685. DOI: 10.1016/j.ecolind.2016.08.011
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
Marivaux L, Adnet S, Benammi M, Tabuce R, Yans J, Benammi M. 2017. Earliest Oligocene hystricognathous rodents from the Atlantic margin of northwestern Saharan Africa (Dakhla, Morocco): systematic, paleobiogeographical, and paleoenvironmental implications. Journal of Vertebrate Paleontology 37:dem. DOI: 10.1080/02724634.2017.1357567.
Barral, A, Gomez, B, Zorrilla, JM, Serrano, JM, Yans, J, Daviero-Gomez, V, Ewin, TAM & Lécuyer, C 2017, 'Analysing the representativeness of local-scale palaeodiversity measurements: a case from the Lower Cretaceous plant assemblage of Hautrage (Mons Basin, Belgium)' Lethaia, vol 50, no. 2, pp. 244-257. DOI: 10.1111/let.12194
2016
De Vreese R, Leys M, Dendoncker N, Van Herzele A, Fontaine CM. 2016. Images of nature as a boundary object in social and integrated ecosystem services assessments. Reflections from a Belgian case study. Ecosystem Services 22:269–279. DOI: 10.1016/j.ecoser.2016.06.008.
De Vreese, R, Leys, M, Fontaine, C & Dendoncker, N 2016, 'Social mapping of perceived ecosystem services supply-The role of social landscape metrics and social hotspots for integrated ecosystem services assessment, landscape planning and management' Ecological Indicators, vol 66, pp. 517-533. DOI: 10.1016/j.ecolind.2016.01.048
Iserbyt, S, Vray, S, Dendoncker, N, Viart, S & Rasmont, P 2016, 'High-resolution distribution of bumblebees (Bombus spp.) in a mountain area marked by agricultural decline' Annales de la Societe Entomologique de France, pp. 1-17. DOI: 10.1080/00379271.2016.1141664
Jacobs, S, Dendoncker, N, Martín-López, B, Barton, DN, Gomez-Baggethun, E, Boeraeve, F, McGrath, FL, Vierikko, K, Geneletti, D, Sevecke, KJ, Pipart, N, Primmer, E, Mederly, P, Schmidt, S, Aragão, A, Baral, H, Bark, RH, Briceno, T, Brogna, D, Cabral, P, De Vreese, R, Liquete, C, Mueller, H, Peh, KSH, Phelan, A, Rincón, AR, Rogers, SH, Turkelboom, F, Van Reeth, W, van Zanten, BT, Wam, HK & Washbourn, CL 2016, 'A new valuation school: Integrating diverse values of nature in resource and land use decisions' Ecosystem Services, vol 22, pp. 213-220. DOI: 10.1016/j.ecoser.2016.11.007
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
Noiret, C, Steurbaut, E, Tabuce, R, Marandat, B, Schnyder, J, Storme, JY & Yans, J 2016, 'New bio-chemostratigraphic dating of a unique early eocene sequence from southern europe results in precise mammalian biochronological tie-points' Newsletters on Stratigraphy, vol 49, no. 3, pp. 469-480. DOI: 10.1127/nos/2016/0336
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
2015
Fossil Feathers
Lindgren J, Sjövall P, Carney RM, Cincotta A, Uvdal P, Hutcheson SW, Gustafsson O, Lefèvre U, Escuillié F, Heimdal J, Engdahl A, Gren JA, Kear BP, Wakamatsu K, Yans J, Godefroit P. 2015. Molecular composition and ultrastructure of Jurassic paravian feathers. Scientific Reports 5:13520. DOI: 10.1038/srep13520.
Feathers are extremely complex epidermal structures. Their evolutionary trajectory across dinosaurs and basal birds is well documented. Melanosome-like microbodies preserved in association with fossil plumage have been used to reconstruct original colour, behaviour and physiology. However, these putative ancient melanosomes might alternatively represent microorganismal residues, a conflicting interpretation compounded by a lack of unambiguous chemical data. The authors used sensitive molecular imaging to provide novel insights into the early evolution of feathers at the sub-cellular level, and unequivocally determine that melanosomes can be preserved in fossil feathers.