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1. Genomic signatures accompanying the dietary shift to phytophagy in polyphagan beetles

Author

Mathieu Seppey, Panagiotis Ioannidis, Brent C. Emerson, Camille Pitteloud, Marc Robinson-Rechavi, Julien Roux, Hermes E. Escalona, Duane D. McKenna, Bernhard Misof, Seunggwan Shin, Xin Zhou, Robert M. Waterhouse, and Nadir Alvarez

Subjects
Gene family evolution, Beetle-plant trophic interactions, Beetle diversification, Detoxification enzymes, Biology (General), QH301-705.5, Genetics, QH426-470
Abstract

Abstract Background The diversity and evolutionary success of beetles (Coleoptera) are proposed to be related to the diversity of plants on which they feed. Indeed, the largest beetle suborder, Polyphaga, mostly includes plant eaters among its approximately 315,000 species. In particular, plants defend themselves with a diversity of specialized toxic chemicals. These may impose selective pressures that drive genomic diversification and speciation in phytophagous beetles. However, evidence of changes in beetle gene repertoires driven by such interactions remains largely anecdotal and without explicit hypothesis testing. Results We explore the genomic consequences of beetle-plant trophic interactions by performing comparative gene family analyses across 18 species representative of the two most species-rich beetle suborders. We contrast the gene contents of species from the mostly plant-eating suborder Polyphaga with those of the mainly predatory Adephaga. We find gene repertoire evolution to be more dynamic, with significantly more adaptive lineage-specific expansions, in the more speciose Polyphaga. Testing the specific hypothesis of adaptation to plant feeding, we identify families of enzymes putatively involved in beetle-plant interactions that underwent adaptive expansions in Polyphaga. There is notable support for the selection hypothesis on large gene families for glutathione S-transferase and carboxylesterase detoxification enzymes. Conclusions Our explicit modeling of the evolution of gene repertoires across 18 species identifies putative adaptive lineage-specific gene family expansions that accompany the dietary shift towards plants in beetles. These genomic signatures support the popular hypothesis of a key role for interactions with plant chemical defenses, and for plant feeding in general, in driving beetle diversification.

Published
2019
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2. Biogeography and Ecological Diversification of a Mayfly Clade in New Guinea

Author

Camille-Sophie Cozzarolo, Michael Balke, Sven Buerki, Nils Arrigo, Camille Pitteloud, Morgan Gueuning, Nicolas Salamin, Michel Sartori, and Nadir Alvarez

Subjects
amplicon-sequencing, altitudinal shifts, freshwater insects, tropical diversity, Thraulus, Evolution, QH359-425, Ecology, QH540-549.5
Abstract

Understanding processes that have driven the extraordinary high level of biodiversity in the tropics is a long-standing question in biology. Here we try to assess whether the large lineage richness found in a New Guinean clade of mayflies (Ephemeroptera), namely the Thraulus group (Leptophlebiidae) could be associated with the recent orogenic processes, by applying a combination of phylogenetic, biogeographic and ecological shift analyses. New Guinean representatives of the Thraulus group appear monophyletic, with the possible exception of a weakly-supported early-diverging clade from the Sunda Islands. Dating analyses suggest an Eocene origin of the Thraulus group, predating by several million years current knowledge on the origin of other New Guinean aquatic organisms. Biogeographic inferences indicate that 27 of the 28 inferred dispersals (96.4%) occurred during the Eocene, Oligocene and Miocene, while only one dispersal (3.6%) took place during the Pliocene-Pleistocene. This result contrasts with the higher number of altitudinal shifts (15 of 22; 68.2%) inferred during the Pliocene-Pleistocene. Our study illustrates the role played by—potentially ecological—diversification along the elevation gradient in a time period concomitant with the establishment of high-altitude ecological niches, i.e., during orogenesis of the central New Guinean mountain range. This process might have taken over the previous main mode of diversification at work, characterized by dispersal and vicariance, by driving lineage divergence of New Guinean Leptophlebiidae across a wide array of habitats along the elevation gradient. Additional studies on organisms spanning the same elevation range as Thraulus mayflies in the tropics are needed to evaluate the potential role of the ecological opportunity or taxon cycles hypotheses in partly explaining the latitudinal diversity gradient.

Published
2019
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3. Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens.

Author

Tomasz Suchan, Camille Pitteloud, Nadezhda S Gerasimova, Anna Kostikova, Sarah Schmid, Nils Arrigo, Mila Pajkovic, Michał Ronikier, and Nadir Alvarez

Subjects
Medicine, Science
Abstract

In the recent years, many protocols aimed at reproducibly sequencing reduced-genome subsets in non-model organisms have been published. Among them, RAD-sequencing is one of the most widely used. It relies on digesting DNA with specific restriction enzymes and performing size selection on the resulting fragments. Despite its acknowledged utility, this method is of limited use with degraded DNA samples, such as those isolated from museum specimens, as these samples are less likely to harbor fragments long enough to comprise two restriction sites making possible ligation of the adapter sequences (in the case of double-digest RAD) or performing size selection of the resulting fragments (in the case of single-digest RAD). Here, we address these limitations by presenting a novel method called hybridization RAD (hyRAD). In this approach, biotinylated RAD fragments, covering a random fraction of the genome, are used as baits for capturing homologous fragments from genomic shotgun sequencing libraries. This simple and cost-effective approach allows sequencing of orthologous loci even from highly degraded DNA samples, opening new avenues of research in the field of museum genomics. Not relying on the restriction site presence, it improves among-sample loci coverage. In a trial study, hyRAD allowed us to obtain a large set of orthologous loci from fresh and museum samples from a non-model butterfly species, with a high proportion of single nucleotide polymorphisms present in all eight analyzed specimens, including 58-year-old museum samples. The utility of the method was further validated using 49 museum and fresh samples of a Palearctic grasshopper species for which the spatial genetic structure was previously assessed using mtDNA amplicons. The application of the method is eventually discussed in a wider context. As it does not rely on the restriction site presence, it is therefore not sensitive to among-sample loci polymorphisms in the restriction sites that usually causes loci dropout. This should enable the application of hyRAD to analyses at broader evolutionary scales.

Published
2016
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5. Soil nematode abundance and functional group composition at a global scale.

Author

Johan van den Hoogen, Stefan Geisen, Devin Routh, Howard Ferris, Walter Traunspurger, David A. Wardle, Ron G. M. de Goede, Byron J. Adams, Wasim Ahmad, Walter S. Andriuzzi, Richard D. Bardgett, Michael Bonkowski, Raquel Campos-Herrera, Juvenil E. Cares, Tancredi Caruso, Larissa de Brito Caixeta, Xiaoyun Chen, Sofia R. Costa, Rachel Creamer, José Mauro da Cunha Castro, Marie Dam, Djibril Djigal, Miguel Escuer, Bryan S. Griffiths, Carmen Gutiérrez, Karin Hohberg, Daria Kalinkina, Paul Kardol, Alan Kergunteuil, Gerard Korthals, Valentyna Krashevska, Alexey A. Kudrin, Qi Li, Wenju Liang, Matthew Magilton, Mariette Marais, José Antonio Rodríguez Martín, Elizaveta Matveeva, El Hassan Mayad, Christian Mulder, Peter Mullin, Roy Neilson, T. A. Duong Nguyen, Uffe N. Nielsen, Hiroaki Okada, Juan Emilio Palomares Rius, Kaiwen Pan, Vlada Peneva, Loïc Pellissier, Julio Carlos Pereira da Silva, Camille Pitteloud, Thomas O. Powers, Kirsten Powers, Casper W. Quist, Sergio Rasmann, Sara Sánchez Moreno, Stefan Scheu, Heikki Setälä, Anna Sushchuk, Alexei V. Tiunov, Jean Trap, Wim H. van der Putten, Mette Vestergård, Cecile Villenave, Lieven Waeyenberge, Diana H. Wall, Rutger Wilschut, Daniel G. Wright, Jiue-in Yang, and Thomas Ward Crowther

Published
2019
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7. The effect of community‐wide phytochemical diversity on herbivory reverses from low to high elevation

Author

Camille Pitteloud, Adrien Delavallade, Gaétan Glauser, Sergio Rasmann, Loïc Pellissier, Patrice Descombes, Pilar Fernandez-Conradi, and Emmanuel Defossez

Subjects
0106 biological sciences, Herbivore, Ecology, food and beverages, Plant Science, 15. Life on land, Biology, 010603 evolutionary biology, 01 natural sciences, Phytochemical, 13. Climate action, High elevation, alpine environment, biodiversity-ecosystem functioning, chemical defences, common garden experiment, plant–climate interactions, plant–herbivore interactions, secondary metabolites, untargeted HPLC-MS, human activities, Ecology, Evolution, Behavior and Systematics, 010606 plant biology & botany, Diversity (business)
Abstract

1. Theory predicts that a large fraction of phytochemical diversity—the richness of individual chemical compounds produced by plants—governs the complexity of interactions between plants and their herbivores. While the effect of specific classes of chemical compounds on plant resistance against herbivores has been largely documented, the effect of community-level variation in phytochemical diversity on plant–herbivore interactions has so far received minimal consideration. 2. We hypothesized that plant communities bearing on average higher levels of phytochemical diversity should sustain lower herbivory rates, overall. Yet, the magnitude of this effect could vary across different environmental conditions, potentially because of climate-mediated effects on phytochemical production and changes in herbivore community richness and composition. 3. To address these hypotheses, we used previous knowledge of species-level phytochemical make-up for more than 400 plant species of the Swiss Alps. Using common garden experiments, we estimated season-wide herbivore damage on low (average 3,500 unique molecules) and high (average 4,500 unique molecules) phytochemical diversity plant communities that were planted in the colline, mountain and alpine vegetation sites along two elevation transects in the Alps. 4. We found that high phytochemical diversity plant communities showed reduced levels of herbivore damage in the colline (low elevation) sites, but this pattern reversed in the alpine (high elevation) sites. Our results suggest that the outcome of phytochemical diversity on plant–herbivore interactions depends on the characteristics of the local herbivore communities, together with trade-offs between chemical defences and other plant traits (i.e. physical defences and plant palatability). 5. Synthesis. Phytochemical diversity is a key component of functional diversity, influencing community composition and dynamics. We show that the effect of phytochemical diversity on herbivory is environmental-dependent, generating ecological switches when moving from low to high elevation. Through upward movement of plants under climate change, phytochemical community structure will be likely modified, ultimately disrupting local community assembly processes. ISSN:0022-0477

Published
2021
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8. The structure of plant–herbivore interaction networks varies along elevational gradients in the European Alps

Author

Charles Novaes de Santana, Jean-Claude Walser, Loïc Pellissier, Camille Pitteloud, Sergio Rasmann, and Patrice Descombes

Subjects
0106 biological sciences, 0303 health sciences, Herbivore, Generality, Ecology, Robustness (evolution), DNA metabarcoding, Keystone species, Nestedness, Null models, Robustness, Trophic networks, 15. Life on land, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract

Aim Ecological gradients are expected to be associated with structural rewiring of species interaction networks. The study of network structures along geographic and ecological gradients, however, remains marginal because documenting species interactions at multiple sites is a methodological challenge. Here, we aimed to study the structural variation in plant–herbivore interaction networks along elevational gradients using molecular metabarcoding. Location European Alps. Taxon Plant and Orthopteran herbivores. Methods We used a standardized DNA metabarcoding method applied to Orthopteran faeces to document the structure of 48 networks of species interactions across six elevational gradients. We examined how structural properties of plant–Orthoptera networks reflecting specialization and robustness vary with elevation. We compared observed variation to null models to account for differences in network size. Results We found an increase in the levels of generality and nestedness with decreasing temperature, and the correlation was stronger than in null models. These relationships corresponded to greater robustness and reduced the importance of specific keystone species in alpine habitats compared to lowland grasslands. Main conclusions In cold environments, plant–herbivore networks are wired in a way that may reinforce the resilience of the system to species extinction. Documenting ecological networks along ecological gradients allows a better understanding of the influence of climate on the structure of ecological communities. © 2020 John Wiley & Sons Ltd. ISSN:0305-0270 ISSN:1365-2699

Published
2020
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9. DNA-based networks reveal the ecological determinants of plant-herbivore interactions along environmental gradients

Author

Camille Pitteloud, Emmanuel Defossez, Camille Albouy, Patrice Descombes, Sergio Rasmann, and Loïc Pellissier

Subjects
orthopteran herbivore, phylogenetic position, Genetics, trait matching, temperature, plant, metabolomics, Ecology, Evolution, Behavior and Systematics, DNA metabarcoding, resource abundance
Abstract

Understanding the ecological rules structuring the organization of species interactions is a prerequisite to predicting how ecosystems respond to environmental changes. While the ecological determinants of single networks have been documented, it remains unclear whether network ecological rules are conserved along spatial and environmental gradients. To address this gap, we reconstructed 48 plant–herbivore interaction networks along six elevation gradients in the Central European Alps in Switzerland, using DNA metabarcoding on orthoptera feces. We developed hypotheses on the ecological mechanisms expected to structure interaction networks, based on plant phylogeny, plant abundance, leaf toughness, leaf nitrogen content and plant metabolomics. We show that plant phylogenetic relationships and species abundance have the greatest explanatory power regarding the structure of the ecological networks. Moreover, we found that leaf nitrogen content is a key determinant of interactions in warmer environments, while phenolic compounds and terpenoids are more important in colder environments, suggesting that determinants of species interactions can shift along environmental gradients. With this work, we propose an approach to study the mechanisms that structure the way species interact with each other between bioregions and ecosystems.

Published
2022

10. Hybridization fuelled diversification in Spialia butterflies

Author

Joan C. Hinojosa, Leonardo Dapporto, Camille Pitteloud, Darina Koubínová, Juan Hernández‐Roldán, Juan Carlos Vicente, Nadir Alvarez, Roger Vila, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), and Generalitat de Catalunya

Subjects
Gene Flow, Male, ddRADseq, Genomics, DNA, Mitochondrial, Phylogeography, Reproductive character displacement, Genetics, Animals, Hybridization, Genetic, Hybridization, Butterflies, Ecology, Evolution, Behavior and Systematics, Phylogeny
Abstract

The importance of hybridization and introgression is well documented in the evolution of plants but, in insects, their role is not fully understood. Given the fact that insects are the most diverse group of organisms, assessing the impact of reticulation events on their evolution may be key to comprehend the emergence of such remarkable diversity. Here, we used an insect model, the Spialia butterflies, to gather genomic evidence of hybridization as a promoter of novel diversity. By using double-digest RADseq (ddRADseq), we explored the phylogenetic relationships between Spialia orbifer, S. rosae and S. sertorius, and documented two independent events of interspecific gene flow. Our data support that the Iberian endemism S. rosae probably received genetic material from S. orbifer in both mitochondrial and nuclear DNA, which could have contributed to a shift in the ecological preferences of S. rosae. We also show that admixture between S. sertorius and S. orbifer probably occurred in Italy. As a result, the admixed Sicilian populations of S. orbifer are differentiated from the rest of populations both genetically and morphologically, and display signatures of reproductive character displacement in the male genitalia. Additionally, our analyses indicated that genetic material from S. orbifer is present in S. sertorius along the Italian Peninsula. Our findings add to the view that hybridization is a pervasive phenomenon in nature and in butterflies in particular, with important consequences for evolution due to the emergence of novel phenotypes., Financial support was provided by projects PID2019-107078GB-I00 funded by MCIN/AEI/10.13039/501100011033 and 2017-SGR-991 funded by Generalitat de Catalunya to R.V., by grant BES-2017-080641, funded by MCIN/AEI/10.13039/501100011033 and by “ESF Investing in your future” to J.C.H. and by the project “Ricerca e conservazione sugli Impollinatori dell’Arcipelago Toscano e divulgazione sui Lepidotteri del parco” to L.D. Computational resources used by D.K. were supplied by the project "e-Infrastruktura CZ" (e-INFRA LM2018140) provided within the program Projects of Large Research, Development and Innovations Infrastructures.

Published
2022

12. Spatial and evolutionary predictability of phytochemical diversity

Author

Camille Pitteloud, Loïc Pellissier, Pierre-Marie Allard, Gaétan Glauser, Pilar Fernandez-Conradi, Sergio Rasmann, Jean-Luc Wolfender, Tom W. N. Walker, Patrice Descombes, and Emmanuel Defossez

Subjects
Vascular plant, Conservation of Natural Resources, Range (biology), Climate, Phytochemicals, Soil, Drug Discovery, plant secondary metabolites, landscape ecology, diversity hotspots, chemical ecology, alpine habitat, Endemism, Ecosystem, Phylogeny, Multidisciplinary, biology, Ecology, Altitude, Temperature, food and beverages, Species diversity, Plant community, Edaphic, Biodiversity, Biological Sciences, Hydrogen-Ion Concentration, Plants, respiratory system, biology.organism_classification, Europe, Habitat, Metabolome, Landscape ecology, human activities
Abstract

To cope with environmental challenges, plants produce a wide diversity of phytochemicals, which are also the source of numerous medicines. Despite decades of research in chemical ecology, we still lack an understanding of the organization of plant chemical diversity across species and ecosystems. To address this challenge, we hypothesized that molecular diversity is not only related to species diversity, but also constrained by trophic, climatic, and topographical factors. We screened the metabolome of 416 vascular plant species encompassing the entire alpine elevation range and four alpine bioclimatic regions in order to characterize their phytochemical diversity. We show that by coupling phylogenetic information, topographic, edaphic, and climatic variables, we predict phytochemical diversity, and its inherent composition, of plant communities throughout landscape. Spatial mapping of phytochemical diversity further revealed that plant assemblages found in low to midelevation habitats, with more alkaline soils, possessed greater phytochemical diversity, whereas alpine habitats possessed higher phytochemical endemism. Altogether, we present a general tool that can be used for predicting hotspots of phytochemical diversity in the landscape, independently of plant species taxonomic identity. Such an approach offers promising perspectives in both drug discovery programs and conservation efforts worldwide. (© 2021 National Academy of Sciences.) ISSN:0027-8424 ISSN:1091-6490

Published
2021
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13. Novel trophic interactions under climate change promote alpine plant coexistence

Author

Alan Kergunteuil, Patrice Descombes, Emmanuel Defossez, Gaétan Glauser, Sergio Rasmann, Camille Pitteloud, Loïc Pellissier, Pierre-Marie Allard, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Department of Environmental Systems Science [ETH Zürich] (D-USYS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Neuchâtel Platform of Analytical Chemistry (NPAC), Université de Neuchâtel (UNINE), Institute of Biology of the University of Neuchâtel, Laboratoire Agronomie et Environnement (LAE), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and University of Geneva [Switzerland]

Subjects
0106 biological sciences, Alpine plant, Climate Change, Introduced species, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Plant defense against herbivory, Animals, Ecosystem, Biomass, Herbivory, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Trophic level, 2. Zero hunger, 0303 health sciences, Biomass (ecology), Herbivore, Multidisciplinary, Ecology, fungi, food and beverages, 15. Life on land, Plants, Grassland, 13. Climate action, Species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Introduced Species
Abstract

Mountain ecology under climate change Climate warming causes shifts in the distributions of organisms and different organisms may move at different rates, resulting in changes in the composition and functioning of ecological communities. These effects are rarely considered in forecasts about the effects of climate change on biodiversity. Using experimental translocations, Descombes et al. investigated how differential upslope migration in alpine plants and their insect herbivores affects community interactions. Lowland herbivores modify the three-dimensional vegetation structure at higher altitudes, and this modified vegetation structure favors the coexistence of plant species, especially by favoring small-stature species. Reorganized trophic interactions will play an important role in driving plant community changes under future climate change. Science , this issue p. 1469

Published
2020
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14. SoilTemp: A global database of near-surface temperature

Author

Juha M. Alatalo, Ilya M. D. Maclean, Ivan Nijs, Pascal Boeckx, Ronja E. M. Wedegärtner, Josefine Walz, Sergiy Medinets, Jonas Ardö, Martin Wilmking, Aníbal Pauchard, Onur Candan, Joseph Okello, Miguel Portillo-Estrada, Christian Rossi, Francesco Malfasi, Robert G. Björk, Tim Seipel, Pekka Niittynen, Kristoffer Hylander, Simone Cesarz, Michael B. Ashcroft, Dany Ghosn, T'Ai Gladys Whittingham Forte, Andrew D. Thomas, Nina Buchmann, Pavel Dan Turtureanu, Marcello Tomaselli, Martin Svátek, Luca Vitale, Christian Rixen, Valter Di Cecco, Pascal Vittoz, Jan Wild, Hans J. De Boeck, M. Rosa Fernández Calzado, Khatuna Gigauri, Haydn J.D. Thomas, Josef Brůna, Patrice Descombes, Robert Kanka, Roman Plichta, Julia Boike, Juan J. Jiménez, Mihai Pușcaș, James D. M. Speed, Tudor-Mihai Ursu, Maaike Y. Bader, Jian Zhang, Shengwei Zong, Marko Smiljanic, Ben Somers, Toke T. Høye, Martin Macek, Rebecca Finger Higgens, Jürgen Homeier, Fatih Fazlioglu, Ana Clara Mazzolari, Katja Tielbörger, Marek Čiliak, Sanne Govaert, Matěj Man, Loïc Pellissier, Bente J. Graae, Mana Gharun, Juan Lorite, Jhonatan Sallo Bravo, Thomas Scholten, Ian Klupar, Jonathan Lenoir, Martin Kopecký, Angela Stanisci, Joseph J. Bailey, Stuart W. Smith, Gergana N. Daskalova, Andrej Varlagin, Radim Matula, Meelis Pärtel, Ann Milbau, Peter Barančok, Jörg G. Stephan, Marijn Bauters, Jan Dick, Zuzana Sitková, Alistair S. Jump, Felix Gottschall, Fernando Moyano, Mario Trouillier, Filip Hrbáček, Eduardo Fuentes-Lillo, Nicoletta Cannone, Koenraad Van Meerbeek, Miska Luoto, Christopher Andrews, Charly Geron, Lisa J. Rew, Michael Stemkovski, Rafaella Canessa, Lucia Hederová, Peter Haase, Klaus Steinbauer, Keith W. Larson, Mats P. Björkman, Edoardo Cremonese, Lore T. Verryckt, Aud H. Halbritter, Jiri Dolezal, František Máliš, William D. Pearse, Zhaochen Zhang, Christian D. Larson, Sylvia Haider, Robert Weigel, Harald Pauli, Romina D. Dimarco, Nico Eisenhauer, Agustina Barros, Shyam S. Phartyal, Liesbeth van den Brink, Edmund W. Basham, Adrian V. Rocha, Mauro Guglielmin, Rafael A. García, Andrej Palaj, Josef Urban, Austin Koontz, Brett R. Scheffers, Mia Vedel Sørensen, Isla H. Myers-Smith, Camille Meeussen, Lena Muffler, Krystal Randall, Volodymyr I. Medinets, Sonia Merinero, Laurenz M. Teuber, Salvatore R. Curasi, José Luis Benito Alonso, Pieter De Frenne, Kamil Láska, Jonas Schmeddes, Martin A. Nuñez, Amanda Ratier Backes, Alessandro Petraglia, Miroslav Svoboda, Ellen Dorrepaal, Sonja Wipf, Juha Aalto, Masahito Ueyama, Benjamin Blonder, Jonas J. Lembrechts, Esther R. Frei, Lukas Siebicke, Bernard Heinesch, C. Johan Dahlberg, Juergen Kreyling, Camille Pitteloud, Florian Zellweger, Rebecca A. Senior, David H. Klinges, Miguel Ángel de Pablo, Elizabeth G. Simpson, George Kazakis, Jozef Kollár, Pallieter De Smedt, Olivier Roupsard, Jan Altman, Michele Carbognani, Julia Kemppinen, Manuela Winkler, Valeria Aschero, Pieter Vangansbeke, Andrea Lamprecht, Stef Haesen, University of Antwerp (UA), Finnish Meteorological Institute (FMI), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, University of Wollongong [Australia], Australian Museum [Sydney], Universiteit Gent = Ghent University (UGENT), Institute of Botany of the Czech Academy of Sciences (IB / CAS), Czech Academy of Sciences [Prague] (CAS), Czech University of Life Sciences Prague (CZU), Ecologie et Dynamique des Systèmes Anthropisés - UMR CNRS 7058 (EDYSAN), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), University of Exeter, Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), LMI IESOL Intensification Ecologique des Sols Cultivés en Afrique de l’Ouest [Dakar] (IESOL), Institut de recherche pour le développement (IRD [Sénégal]), Universidad de Concepción - University of Concepcion [Chile], Instituto de Ecología y Biodiversidad (IEB), Universidad Adventista de Chile - Adventist University of Chile (UNACH), Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Qatar University, Norwegian University of Science and Technology [Trondheim] (NTNU), Norwegian University of Science and Technology (NTNU), Nanyang Technological University [Singapour], University of Gothenburg (GU), Universität Greifswald - University of Greifswald, Georg-August-University = Georg-August-Universität Göttingen, Martin-Luther-University Halle-Wittenberg, German Centre for Integrative Biodiversity Research (iDiv), Leipzig University, Mountains of the Moon University, Laboratory of Applied Physical Chemistry - ISOFYS (Gent, Belgium), Mendel University in Brno (MENDELU), Siberian Federal University (SibFU), Nalanda University, Hemvati Nandan Bahuguna Garhwal University (HNBGU), Babes-Bolyai University [Cluj-Napoca] (UBB), A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences [Moscow] (RAS), Instituto de Investigaciones Forestales y Agropecuarias Bariloche (IFAB), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Instituto Nacional de Tecnología Agropecuaria (INTA), University of Stirling, Umeå University, Istituto per i Sistemi Agricoli e Forestali del Mediterraneo (ISAFOM), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Dartmouth College [Hanover], University of Bergen (UiB), University of Notre Dame [Indiana] (UND), Utah State University (USU), Imperial College London, Arctic Research Centre [Aarhus] (ARC), Aarhus University [Aarhus], Universidad de Granada = University of Granada (UGR), Università degli studi di Parma = University of Parma (UNIPR), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Stockholm University, University of South Bohemia, Aberystwyth University, York St John University, Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Chania (CIHEAM-IAMC), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM), Universidad de Alcalá - University of Alcalá (UAH), Montana State University (MSU), Lund University [Lund], Universitá degli Studi dell’Insubria = University of Insubria [Varese] (Uninsubria), Philipps Universität Marburg = Philipps University of Marburg, Università degli Studi del Molise = University of Molise (UNIMOL), Universidad Nacional de Cuyo [Mendoza] (UNCUYO), Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales [Mendoza] (CONICET-IANIGLA), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional de Cuyo [Mendoza] (UNCUYO), Technical University in Zvolen (TUZVO), Georgian Institute of Public Affairs (GIPA), Austrian Academy of Sciences (OeAW), Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), Osaka Prefecture University, Instituto Nacional de Investigaciones en Biodiversidad y Medioambiente [Bariloche] (INIBIOMA-CONICET), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional del Comahue [Neuquén] (UNCOMA), National Institute of Research and Development for Biological Sciences [Bucarest] (INCDSB), Université de Lausanne = University of Lausanne (UNIL), University of Tartu, Institute of Landscape Ecology of the Slovak Academy of Sciences, Slovak Academy of Sciences (SAS), Jolube Consultor Botánico, Northeast Normal University, Majella National Park - Parco Nazionale della Majella, National Forest Centre - Národné lesnícke centrum [Zvolen], University of Tübingen, County Administrative Board of Västra Götaland, Odessa National I.I.Mechnikov University, Research Institute for Nature and Forest (INBO), University of Edinburgh, University of California [Berkeley] (UC Berkeley), University of California (UC), Arizona State University [Tempe] (ASU), Swedish University of Agricultural Sciences (SLU), Gembloux Agro-Bio Tech [Gembloux], Université de Liège, Centre for Ecology and Hydrology [Bangor] (CEH), Natural Environment Research Council (NERC), Princeton University, Fundación Agencia Aragonesa para la Investigación y el Desarrollo (ARAID), Alfred Wegener Institute [Potsdam], Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Humboldt University Of Berlin, University of Florida [Gainesville] (UF), East China Normal University [Shangaï] (ECNU), Ordu University - Ordu Üniversitesi, Universidad Nacional de San Antonio Abad del Cusco (UNSAAC), Masaryk University [Brno] (MUNI), Aosta Valley Regional Environmental Protection Agency (ARPA), Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung, Leibniz Association, Universität Duisburg-Essen = University of Duisburg-Essen [Essen], Swiss National Park - Parc Naziunal Svizzer, Universität Zürich [Zürich] = University of Zurich (UZH), ANR-19-CE32-0005,IMPRINT,IMpacts des PRocessus mIcroclimatiques sur la redistributioN de la biodiversiTé forestière en contexte de réchauffement du macroclimat(2019), University of Helsinki, Universiteit Gent = Ghent University [Belgium] (UGENT), Centre National de la Recherche Scientifique (CNRS)-Université de Picardie Jules Verne (UPJV), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Georg-August-University [Göttingen], Consiglio Nazionale delle Ricerche [Roma] (CNR), University of Granada [Granada], University of Parma = Università degli studi di Parma [Parme, Italie], Universitá degli Studi dell’Insubria, Philipps University of Marburg, Università degli Studi del Molise (Unimol), Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), University of Lausanne (UNIL), University of California [Berkeley], University of California, Humboldt-Universität zu Berlin, and University of Duisburg-Essen

Subjects
0106 biological sciences, 010504 meteorology & atmospheric sciences, Biome, Biodiversity & Conservation, Microclimate, computer.software_genre, 01 natural sciences, topoclimate, Snow, HETEROGENEITY, SCALE, database, General Environmental Science, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Global and Planetary Change, CLIMATE-CHANGE, Database, Ecology, Spatial database, Vegetation, Biological Sciences, Chemistry, soil climate, climate change, species distributions, Biodiversity Conservation, ecosystem processes, microclimate, temperature, Life Sciences & Biomedicine, Biologie, [SDE.MCG]Environmental Sciences/Global Changes, Climate change, Environmental Sciences & Ecology, [SDV.BID]Life Sciences [q-bio]/Biodiversity, MOISTURE, 010603 evolutionary biology, soil, LITTER DECOMPOSITION, species 19 distributions, Environmental Chemistry, DISTRIBUTIONS, SCALE SOIL, Biology, climate, Ecosystem, 0105 earth and related environmental sciences, Science & Technology, Global warming, SPECIES DISTRIBUTION MODELS, 15. Life on land, Radiative forcing, MACROCLIMATE, Agriculture and Soil Science, 13. Climate action, SNOW, Earth and Environmental Sciences, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, computer, Environmental Sciences
Abstract

Current analyses and predictions of spatially explicit patterns and processes in ecology most often rely on climate data interpolated from standardized weather stations. This interpolated climate data represents long-term average thermal conditions at coarse spatial resolutions only. Hence, many climate-forcing factors that operate at fine spatiotemporal resolutions are overlooked. This is particularly important in relation to effects of observation height (e.g. vegetation, snow and soil characteristics) and in habitats varying in their exposure to radiation, moisture and wind (e.g. topography, radiative forcing or cold-air pooling). Since organisms living close to the ground relate more strongly to these microclimatic conditions than to free-air temperatures, microclimatic ground and near-surface data are needed to provide realistic forecasts of the fate of such organisms under anthropogenic climate change, as well as of the functioning of the ecosystems they live in. To fill this critical gap, we highlight a call for temperature time series submissions to SoilTemp, a geospatial database initiative compiling soil and near-surface temperature data from all over the world. Currently, this database contains time series from 7,538 temperature sensors from 51 countries across all key biomes. The database will pave the way toward an improved global understanding of microclimate and bridge the gap between the available climate data and the climate at fine spatiotemporal resolutions relevant to most organisms and ecosystem processes. ispartof: GLOBAL CHANGE BIOLOGY vol:26 issue:11 pages:6616-6629 ispartof: location:England status: published

Published
2020
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15. Contrasting responses of above- and below-ground herbivore communities along elevation

Author

Alan Kergunteuil, Sergio Rasmann, Sara Sánchez-Moreno, Camille Pitteloud, Loïc Pellissier, Sébastien Ibanez, Patrice Descombes, Department of Environmental Systems Science [ETH Zürich] (D-USYS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Laboratoire Agronomie et Environnement (LAE), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute of Biology of the University of Neuchâtel, Université de Neuchâtel (UNINE), Laboratoire d'Ecologie Alpine (LECA ), and Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)

Subjects
0106 biological sciences, Nematoda, Biodiversity, Environmental gradient, Species richness, Herbivory, Functional traits, Ecological interactions, Biology, 010603 evolutionary biology, 01 natural sciences, Soil, Abundance (ecology), Animals, Ecosystem, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Herbivore, Ecology, Elevation, Edaphic, Ecosystem Ecology–Original Research, 15. Life on land, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 010606 plant biology & botany
Abstract

Above- and below-ground herbivory are key ecosystem processes that can be substantially altered by environmental changes. However, direct comparisons of the coupled variations of above- and below-ground herbivore communities along elevation gradients remain sparse. Here, we studied the variation in assemblages of two dominant groups of herbivores, namely, aboveground orthoptera and belowground nematodes, in grasslands along six elevation gradients in the Swiss Alps. By examining variations of community properties of herbivores and their food plants along montane clines, we sought to determine whether the structure and functional properties of these taxonomic groups change with elevation. We found that orthoptera decreased in both species richness and abundance with elevation. In contrast with aboveground herbivores, the taxonomic richness and the total abundance of nematode did not covary with elevation. We further found a stronger shift in above- than below-ground functional properties along elevation, where the mandibular strength of orthoptera matched a shift in leaf toughness. Nematodes showed a weaker pattern of declined sedentary behavior and increased mobility with elevation. In contrast to the direct exposal of aboveground organisms to the surface climate, conditions may be buffered belowground, which together with the influence of edaphic factors on the biodiversity of soil biota, may explain the differences between elevational patterns of above- and below-ground communities. Our study emphasizes the necessity to consider both the above- and below-ground compartments to understand the impact of current and future climatic variation on ecosystems, from a functional perspective of species interactions. Electronic supplementary material The online version of this article (10.1007/s00442-020-04778-7) contains supplementary material, which is available to authorized users.

Published
2020
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17. A global database of soil nematode abundance and functional group composition

Author

Qi Li, Byron J. Adams, Christian Mulder, Larissa de Brito Caixeta, Bryan S. Griffiths, Roy Neilson, Karin Hohberg, Thomas O. Powers, Daniel G. Wright, Camille Pitteloud, Mette Vestergård, Richard D. Bardgett, David A. Wardle, Aidan M. Keith, Sergio Rasmann, Tancredi Caruso, Alan Kergunteuil, Devin Routh, Alexei V. Tiunov, Djibril Djigal, Juvenil Enrique Cares, Alexey A. Kudrin, Juan E. Palomares Rius, Rachid Bouharroud, Jean Trap, Gerard W. Korthals, Stefan Scheu, Kirsten Powers, José Mauro da Cunha e Castro, Lieven Waeyenberge, Marie Dam, Wasim Ahmad, Paul Kardol, E. Mzough, Walter Traunspurger, Cécile Villenave, El Hassan Mayad, Michael Bonkowski, Carmen Gutiérrez, Stefan Geisen, Rachel Creamer, Olaf Schmidt, Zahra Ferji, Uffe N. Nielsen, Valentyna Krashevska, Miguel Escuer, Xiaoyun Chen, Júlio Carlos Pereira da Silva, Ron G.M. de Goede, Sofia R. Costa, Loïc Pellissier, Matthew Magilton, Vlada Peneva, Wim H. van der Putten, Peter Mullin, Daria Kalinkina, E. M. Matveeva, Thomas W. Crowther, Rutger A. Wilschut, José Antonio Rodríguez Martín, Mariette Marais, Diana H. Wall, Hiroaki Okada, Anna Sushchuk, Johan van den Hoogen, Heikki Setälä, Raquel Campos-Herrera, Jiue-in Yang, Casper W. Quist, Wenju Liang, Kaiwen Pan, Sara Sanchez Moreno, Howard Ferris, T. A. Duong Nguyen, Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Netherlands Institute of Ecology - NIOO-KNAW (NETHERLANDS), Department of Biology [Fort Collins], Colorado State University [Fort Collins] (CSU), Nanyang Technological University [Singapour], Universität Bielefeld = Bielefeld University, Wageningen University and Research [Wageningen] (WUR), Brigham Young University (BYU), Aligarh Muslim University, University of California [Davis] (UC Davis), University of California (UC), University of Manchester [Manchester], University of Cologne, Instituto de Ciencias de la Vid y el Vino (ICVV), Universidad de La Rioja (UR)-Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Institute of Biology of the University of Neuchâtel, Université de Neuchâtel (UNINE), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), This research was supported by a grant from DOB Ecology to T.W.C., a grant from the Netherlands Organization for Scientific Research (grant 016.Veni.181.078) to S.G., grants from NSF (OPP 1115245, 1341736, 0840979) to B.J.A., by a Ramon y Cajal fellow award (RYC-2016-19939) to R.C.H., a grant from UNEP & Global Environment Facility to J.E.C., grants from NERC’s Soil Security Programme to R.D.B. (NE/M017028/1) T.C. (NE/M017036/1), a grant from FAPEMIG/FAPESP/VALE S.A.(CRA-RDP-00136-10) to L.B.C., through the strategic programme UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569) awarded to S.R.C., a grant from CNPq PROTAX (562346/2010-4) to J.M.d.C.C., a grant from DFG (CRC990) to V.K. and S.S., a grant from the MSHE of Russia (AAAA-A17-117112850234-5) to A.A.K., grants from the Chinese Academy of Sciences (XDB15010402) and the National Natural Science Foundation of China (41877047) to Q.L., grants from the National Natural Science Foundation of China (31330011, 31170484) to W.L., grants from NERC (NE/M017036/1) to M.M., grants from the Spanish Ministry of Innovation (CGL2009-14686-C02-01/02, CGL2013-43675-P) to J.A.R.M., grant from the Spanish Ministry of Innovation (RYC-2016-19939) to R.C.H., grants from NSF (DEB-0450537, DEB-1145440) to P.M., T.O.P. and K. Powers, grants from the German Academic Exchange Service (PKZ 91540366) and NAFOSTED (106.05–2017.330) to T.A.D.N., by an ARC Discovery project (DP150104199) to U.N.N., by the National Key Research and Development Program of China (2016YFC0502101) and the National Natural Science Foundation of China (31370632) to K. Pan, a ERC Research Council Advanced grant (ERC-Adv 323020 SPECIALS) to W.H.v.d.P, a grant from the Natural Environment Research Council (NERC) to D.G.W., a grant from BAPHIQ (106AS-9.5.1-BQ-B3) to J.-i.Y., a grant from the Russian Foundation for Basic Research (18-29-05076) to A.V.T. The James Hutton Institute receives financial support from the Scottish Government Rural and Environment Science and Analytical Services (RESAS) division. Investigations in Northwest Russia were carried out under state order for IB KarRC RAS and are partially supported by the Russian Foundation for Basic Research (18-34-00849)., DOB Ecology, Netherlands Organization for Scientific Research, Ministerio de Economía y Competitividad (España), National Science Foundation (US), European Commission, Natural Environment Research Council (UK), Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), German Research Foundation, Ministry of Science and Higher Education of the Russian Federation, Chinese Academy of Sciences, National Natural Science Foundation of China, German Academic Exchange Service, National Foundation for Science and Technology Development (Vietnam), National Key Research and Development Program (China), European Research Council, Bureau of Animal and Plant Health Inspection and Quarantine (Taiwan), Russian Foundation for Basic Research, James Hutton Institute, Scottish Government's Rural and Environment Science and Analytical Services, University of California, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
0106 biological sciences, Data Descriptor, Nematoda, Ecosystem ecology, Biome, 010501 environmental sciences, computer.software_genre, 01 natural sciences, Soil, Abundance (ecology), Data and Information, lcsh:Science, biology, Ecology, Biodiversity, Soil Biology, PE&RC, Biosystematiek, Computer Science Applications, Biogeography, 1181 Ecology, evolutionary biology, Composition (visual arts), Statistics, Probability and Uncertainty, Information Systems, Statistics and Probability, Biogeochemical cycle, EXTRACTION, Geospatial analysis, Soil test, Library and Information Sciences, Education, Life Science, Animals, Functional group (ecology), Life Below Water, Bodembiologie, Ecosystem, 0105 earth and related environmental sciences, 15. Life on land, biology.organism_classification, Nematode, Biology and Microbiology, 13. Climate action, Nematoda/classification, Biosystematics, lcsh:Q, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, computer, Animal Distribution, 010606 plant biology & botany
Abstract

As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns., This research was supported by a grant from DOB Ecology to T.W.C., a grant from the Netherlands Organization for Scientific Research (grant 016.Veni.181.078) to S.G., grants from NSF (OPP 1115245, 1341736, 0840979) to B.J.A., by a Ramon y Cajal fellow award (RYC-2016-19939) to R.C.H., a grant from UNEP & Global Environment Facility to J.E.C., grants from NERC’s Soil Security Programme to R.D.B. (NE/M017028/1) T.C. (NE/M017036/1), a grant from FAPEMIG/FAPESP/VALE S.A.(CRA-RDP-00136-10) to L.B.C., through the strategic programme UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569) awarded to S.R.C., a grant from CNPq PROTAX (562346/2010-4) to J.M.d.C.C., a grant from DFG (CRC990) to V.K. and S.S., a grant from the MSHE of Russia (AAAA-A17-117112850234-5) to A.A.K., grants from the Chinese Academy of Sciences (XDB15010402) and the National Natural Science Foundation of China (41877047) to Q.L., grants from the National Natural Science Foundation of China (31330011, 31170484) to W.L., grants from NERC (NE/ M017036/1) to M.M., grants from the Spanish Ministry of Innovation (CGL2009-14686-C02-01/02, CGL2013- 43675-P) to J.A.R.M., grant from the Spanish Ministry of Innovation (RYC-2016-19939) to R.C.H., grants from NSF (DEB-0450537, DEB-1145440) to P.M., T.O.P. and K. Powers, grants from the German Academic Exchange Service (PKZ 91540366) and NAFOSTED (106.05–2017.330) to T.A.D.N., by an ARC Discovery project (DP150104199) to U.N.N., by the National Key Research and Development Program of China (2016YFC0502101) and the National Natural Science Foundation of China (31370632) to K. Pan, a ERC Research Council Advanced grant (ERC-Adv 323020 SPECIALS) to W.H.v.d.P, a grant from the Natural Environment Research Council (NERC) to D.G.W., a grant from BAPHIQ (106AS-9.5.1-BQ-B3) to J.-i.Y., a grant from the Russian Foundation for Basic Research (18-29-05076) to A.V.T. The James Hutton Institute receives financial support from the Scottish Government Rural and Environment Science and Analytical Services (RESAS) division. Investigations in Northwest Russia were carried out under state order for IB KarRC RAS and are partially supported by the Russian Foundation for Basic Research (18-34-00849).

Published
2020
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18. Soil nematode abundance and functional group composition at a global scale

Author

Lieven Waeyenberge, Mariette Marais, Stefan Geisen, Diana H. Wall, Roy Neilson, Kaiwen Pan, Matthew Magilton, Devin Routh, Sara Sanchez Moreno, Wasim Ahmad, Daria Kalinkina, Juan E. Palomares Rius, Karin Hohberg, Miguel Escuer, Vlada Peneva, Walter S. Andriuzzi, Michael Bonkowski, Peter Mullin, Anna Sushchuk, Johan van den Hoogen, Heikki Setälä, Thomas W. Crowther, El Hassan Mayad, Qi Li, José Mauro da Cunha e Castro, Rutger A. Wilschut, Alexey A. Kudrin, Thomas O. Powers, Carmen Gutiérrez, Daniel G. Wright, David A. Wardle, Djibril Djigal, Camille Pitteloud, Howard Ferris, Juvenil Enrique Cares, José Antonio Rodríguez Martín, Cécile Villenave, Sofia R. Costa, Jiue-in Yang, Christian Mulder, E. M. Matveeva, Casper W. Quist, Byron J. Adams, Larissa de Brito Caixeta, Bryan S. Griffiths, Tancredi Caruso, T. A. Duong Nguyen, Sergio Rasmann, Paul Kardol, Alan Kergunteuil, Stefan Scheu, Kirsten Powers, Ron G.M. de Goede, Valentyna Krashevska, Gerard W. Korthals, Rachel Creamer, Loïc Pellissier, Richard D. Bardgett, Raquel Campos-Herrera, Júlio Carlos Pereira da Silva, Jean Trap, Marie Dam, Walter Traunspurger, Mette Vestergård, Wenju Liang, Alexei V. Tiunov, Wim H. van der Putten, Uffe N. Nielsen, Xiaoyun Chen, Hiroaki Okada, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Netherlands Institute for Ecology (NIOO-KNAW), Dept Entomol & Nematol, University of California [Davis] (UC Davis), University of California-University of California, Universität Bielefeld = Bielefeld University, Nanyang Technological University (NTU), Wageningen University and Research Centre (WUR), Brigham Young University (BYU), Aligarh Muslim University, Colorado State University [Fort Collins] (CSU), Sch Earth & Environm Sci, University of Adelaide, University of Cologne, Universidad de La Rioja (UR), Universidade de Brasília (UnB), The Queen’s University of Belfast, Nanjing Agricultural University, Universidade do Minho, Ctr Pesquisa Agr Trop Semi Arido, Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Ministério da Agricultura, Pecuária e Abastecimento [Brasil] (MAPA), Governo do Brasil-Governo do Brasil-Ministério da Agricultura, Pecuária e Abastecimento [Brasil] (MAPA), Governo do Brasil-Governo do Brasil, Zealand Inst Business & Techno, Partenaires INRAE, Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Scotland's Rural College (SRUC), Senckenberg Research Institute and Natural History Museum, Russian Academy of Sciences [Moscow] (RAS), Department of Forest Ecology and Management, Swedish University of Agricultural Sciences (SLU), Université de Neuchâtel (UNINE), Georg-August-University [Göttingen], Chinese Academy of Sciences (CAS), Agricultural Research Council (ARC), Inst Nacl Invest & Tecnol Agr & Alimentaria, Université Ibn Zohr [Agadir], University of Catania [Italy], University of Nebraska [Lincoln], University of Nebraska System, The James Hutton Institute, Vietnam Academy of Science and Technology (VAST), Western Sydney University, National Agriculture and Food Research Organization (NARO), Bulgarian Academy of Sciences (BAS), Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Universidade Federal de Lavras (UFLA), University of Helsinki, Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA), Aarhus University [Aarhus], Elisol Environnement, Research Institute for Agricultural, Fisheries and Food (ILVO), Ctr Ecol & Hydrol, Dept Plant Pathol & Microbiol, University of California [Riverside] (UCR), DOB Ecology, Netherlands Organization for Scientific Research (NWO) : 016, National Science Foundation (NSF) : DEB-0450537 et DEB-1145440, UNEP & Global Environment Facility, NERC Natural Environment Research Council (NE/M017036/1), FAPEMIG/FAPESP/VALE S.A. : CRA-RDP-00136-10, UID/BIA/04050/2013, POCI-01-0145-FEDER-007569, National Council for Scientific and Technological Development (CNPq) : 562346/2010-4, German Research Foundation (DFG) : CRC990, MSHE of Russia : AAAA-A17-117112850234-5, Chinese Academy of Sciences : XDB15010402, National Natural Science Foundation of China : 31370632, Spanish Ministry of Innovation : CGL2009-14686-C02-01/02 et CGL2013-43675-P, Deutscher Akademischer Austausch Dienst (DAAD) : PKZ 91540366, National Foundation for Science & Technology Development (NAFOSTED) : 106.05 -2017.330, Australian Research Council : DP150104199, National Key Research and Development Program of China : 2016YFC0502101, NERC Natural Environment Research Council, BAPHIQ : 106AS-9.5.1-BQ-B3, Scottish Government Rural and Environment Science and Analytical Services (RESAS) division, Russian Foundation for Basic Research (RFBR) : 18-34-00849, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Wageningen University and Research [Wageningen] (WUR), Department of Animal Ecology (Morgenbreede, Germany), Germany), Universität Bielefeld, School of Earth and Environmental Sciences [Manchester] (SEES), University of Manchester [Manchester], Department of Terrestrial Ecology, Institut of Zoology, Johnstown Castle, Environment Research Centre, Teagasc - The Agriculture and Food Development Authority (Teagasc), CDH, Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Environment Research Centre, Irish Agriculture and Food Development Authority, Georg-August-Universität Göttingen = University of Göttingen, Iowa State University (ISU), National Institute for Public Health and the Environment [Bilthoven] (RIVM), Centre for Telecommunications and Micro-Electronics (CTME), Victoria University [Melbourne], National Institute of Agro-Environmental Sciences (NIAES), Unit of Ecology and Evolution, Albert-Ludwigs-Universität Freiburg, George August University Goettingen, Faculty of Biological and Environmental Sciences [Helsinki], A.N. Severtsov Institute of Ecology and Evolution, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Wageningen University and Research Centre [Wageningen] (WUR), Institute of Geology and Geophysics [Beijing] (IGG), Chinese Academy of Sciences [Beijing] (CAS), UR SEQBIO, Institut de Recherche pour le Développement (IRD), Laboratoire d'Energétique, d'Electronique et Procédés (LE2P), Université de La Réunion (UR), National Agriculture and Food Research Organization, Johann-Friedrich Blumenbach Institut für Zoologie und Anthropologie, University of Copenhagen = Københavns Universitet (KU), JOHAN VAN DEN HOOGEN, HOWARD FERRIS, BRYAN S. GRIFFITHS, KARIN HOHBERG, DARIA KALINKINA, PAUL KARDOL, ALAN KERGUNTEUIL, GERARD KORTHALS, MARIETTE MARAIS, DANIEL G. WRIGHT, JIUE-IN YANG, THOMAS WARD CROWTHER., SERGIO RASMANN, WALTER TRAUNSPURGER, DAVID A. WARDLE, RON G. M. DE GOEDE, BYRON J. ADAMS, WASIM AHMAD, WALTER S. ANDRIUZZI, RICHARD D. BARDGETT, MICHAEL BONKOWSKI, RAQUEL CAMPOS HERRERA, JUVENIL E. CARES, TANCREDI CARUSO, LARISSA DE BRITO CAIXETA, XIAOYUN CHEN, SOFIA R. COSTA, RACHEL CREAMER, JOSE MAURO DA CUNHA E CASTRO, CPATSA, MARIE DAM, DJIBRIL DJIGAL, MIGUEL ESCUER, CARMEN GUTIÉRREZ, VALENTYNA KRASHEVSKA, ALEXEY A. KUDRIN, QI LI, WENJU LIANG, MATTHEW MAGILTON, JOSÉ ANTONIO RODRÍGUEZ MARTÍN, ELIZAVETA MATVEEVA, EL HASSAN MAYAD, CHRISTIAN MULDER, PETER MULLIN, ROY NEILSON, T. A. DUONG NGUYEN, UFFE N. NIELSEN, HIROAKI OKADA, KAIWEN PAN, JUAN EMILIO PALOMARES RIUS, VLADA PENEVA, LOÏC PELLISSIER, JULIO CARLOS PEREIRA DA SILVA, CAMILLE PITTELOUD, THOMAS O. POWERS, KIRSTEN POWERS, CASPER W. QUIST, SARA SÁNCHEZ MORENO, STEFAN SCHEU, HEIKKI SETÄLÄ, ANNA SUSHCHUK, ALEXEI V. TIUNOV, JEAN TRAP, WIM VAN DER PUTTEN, METTE VESTERGÅRD, CECILE VILLENAVE, LIEVEN WAEYENBERGE, DIANA H. WALL, RUTGER WILSCHUT, STEFAN GEISEN, DEVIN ROUTH, Netherlands Organization for Scientific Research, National Science Foundation (US), Global Environment Facility, Natural Environment Research Council (UK), Fundação de Amparo à Pesquisa do Estado de São Paulo Minas Gerais, Fundação de Amparo à Pesquisa do Estado de São Paulo, Fundação para a Ciência e a Tecnologia (Portugal), European Commission, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), German Research Foundation, Chinese Academy of Sciences, National Natural Science Foundation of China, Ministerio de Economía y Competitividad (España), German Academic Exchange Service, National Foundation for Science and Technology Development (Vietnam), Australian Research Council, Scottish Government's Rural and Environment Science and Analytical Services, Russian Foundation for Basic Research, Campos-Herrera, R., Campos-Herrera, R. [0000-0003-0852-5269], and Terrestrial Ecology (TE)

Subjects
0106 biological sciences, Nematoda, DIVERSITY, Geographic Mapping, 01 natural sciences, Mudança Climática, BIOMASS, CARBON, Soil, Abundance (ecology), Nematoides no solo, Biomass, Directie, ComputingMilieux_MISCELLANEOUS, SDG 15 - Life on Land, Biomass (ecology), Multidisciplinary, Ecology, Uncertainty, Biosphere, 04 agricultural and veterinary sciences, Soil Biology, PE&RC, Biogeografia global, Biosystematiek, Phylogeography, Biogeography, international, BACTERIA, RIBOSOMAL-RNA, Soil biology, 010603 evolutionary biology, Nematóide, Machine learning, Soil food web, Animals, Life Science, Ecosystem, General, Laboratorium voor Nematologie, Bodembiologie, Ecological modelling, Soil nematodes, Reproducibility of Results, 15. Life on land, MATURITY INDEX, Carbon, OXYGEN-CONSUMPTION, Solo, 13. Climate action, Soil water, 040103 agronomy & agriculture, PATTERNS, 0401 agriculture, forestry, and fisheries, Environmental science, Biosystematics, BIODIVERSITY, Soil fertility, EPS, Laboratory of Nematology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, COMMUNITIES
Abstract

Soil organisms are a crucial part of the terrestrial biosphere. Despite their importance for ecosystem functioning, few quantitative, spatially explicit models of the active belowground community currently exist. In particular, nematodes are the most abundant animals on Earth, filling all trophic levels in the soil food web. Here we use 6,759 georeferenced samples to generate a mechanistic understanding of the patterns of the global abundance of nematodes in the soil and the composition of their functional groups. The resulting maps show that 4.4 ± 0.64 × 1020 nematodes (with a total biomass of approximately 0.3 gigatonnes) inhabit surface soils across the world, with higher abundances in sub-Arctic regions (38% of total) than in temperate (24%) or tropical (21%) regions. Regional variations in these global trends also provide insights into local patterns of soil fertility and functioning. These high-resolution models provide the first steps towards representing soil ecological processes in global biogeochemical models and will enable the prediction of elemental cycling under current and future climate scenarios., This research was supported by a grant from DOB Ecology to T.W.C., a grant from the Netherlands Organization for Scientific Research (grant 016.Veni.181.078) to S.G., grants from NSF (OPP 1115245, 1341736, 0840979) to B.J.A., by a Ramon y Cajal fellow award (RYC-2016-19939) to R.C.H., a grant from UNEP & Global Environment Facility to J.E.C., a grant from NERC (NE/M017036/1) to T.C., a grant from FAPEMIG/FAPESP/VALE S.A.(CRA-RDP-00136-10) to L.B.C., through the strategic programme UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569) awarded to S.R.C., a grant from CNPq PROTAX (562346/2010-4) to J.M.d.C.C., a grant from DFG (CRC990) to V.K. and S.S., a grant from the MSHE of Russia (AAAA-A17-117112850234-5) to A.A.K., grants from the Chinese Academy of Sciences (XDB15010402) and the National Natural Science Foundation of China (41877047) to Q.L., grants from the National Natural Science Foundation of China (31330011, 31170484) to W.L., grants from NERC (NE/M017036/1) to M.M., grants from the Spanish Ministry of Innovation (CGL2009-14686-C02-01/ 02, CGL2013-43675-P) to J.A.R.M., grants from NSF (DEB-0450537, DEB-1145440) to P.M., T.O.P. and K. Powers, grants from the German Academic Exchange Service (PKZ 91540366) and NAFOSTED (106.05 – 2017.330) to T.A.D.N., by an ARC Discovery project (DP150104199) to U.N.N., by the National Key Research and Development Program of China (2016YFC0502101) and the National Natural Science Foundation of China (31370632) to K. Pan, a grant from the Natural Environment Research Council (NERC) to D.G.W., a grant from BAPHIQ (106AS-9.5.1-BQ-B3) J.-i.Y. The James Hutton Institute receives financial support from the Scottish Government Rural and Environment Science and Analytical Services (RESAS) division. Investigations in northwest Russia were carried out under state order for IB KarRC RAS and are partially supported by the Russian Foundation for Basic Research (18-34-00849). We thank E. Clark and A. Orgiazzi for review of the manuscript; and R. Bouharroud, Z. Ferji, L. Jackson and E. Mzough for providing data.

Published
2019
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19. Comparing species interaction networks along environmental gradients

Author

Dominique Gravel, Guy Woodward, Niklaus E. Zimmermann, Tomas Roslin, Serguei Saavedra, Nina Farwig, Michel Loreau, Catherine H. Graham, Rudolf P. Rohr, Carlos J. Melián, María Alejandra Maglianesi, Loïc Pellissier, Camille Albouy, Wilfried Thuiller, Jordi Bascompte, and Camille Pitteloud

Subjects
0106 biological sciences, Standardization, Null model, 010604 marine biology & hydrobiology, Network structure, 15. Life on land, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Ecological network, Trait, General Agricultural and Biological Sciences, Biological system, Environmental gradient
Abstract

Knowledge of species composition and their interactions, in the form of interaction networks, is required to understand processes shaping their distribution over time and space. As such, comparing ecological networks along environmental gradients represents a promising new research avenue to understand the organization of life. Variation in the position and intensity of links within networks along environmental gradients may be driven by turnover in species composition, by variation in species abundances and by abiotic influences on species interactions. While investigating changes in species composition has a long tradition, so far only a limited number of studies have examined changes in species interactions between networks, often with differing approaches. Here, we review studies investigating variation in network structures along environmental gradients, highlighting how methodological decisions about standardization can influence their conclusions. Due to their complexity, variation among ecological networks is frequently studied using properties that summarize the distribution or topology of interactions such as number of links, connectance, or modularity. These properties can either be compared directly or using a procedure of standardization. While measures of network structure can be directly related to changes along environmental gradients, standardization is frequently used to facilitate interpretation of variation in network properties by controlling for some co-variables, or via null models. Null models allow comparing the deviation of empirical networks from random expectations and are expected to provide a more mechanistic understanding of the factors shaping ecological networks when they are coupled with functional traits. As an illustration, we compare approaches to quantify the role of trait matching in driving the structure of plant-hummingbird mutualistic networks, i.e. a direct comparison, standardized by null models and hypothesis-based metaweb. Overall, our analysis warns against a comparison of studies that rely on distinct forms of standardization, as they are likely to highlight different signals. Fostering a better understanding of the analytical tools available and the signal they detect will help produce deeper insights into how and why ecological networks vary along environmental gradients.

Published
2017
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20. Genomic signatures accompanying the dietary shift to phytophagy in polyphagan beetles

Author

Seunggwan Shin, Julien Roux, Robert M. Waterhouse, Mathieu Seppey, Bernhard Misof, Xin Zhou, Duane D. McKenna, Brent C. Emerson, Camille Pitteloud, Hermes E. Escalona, Nadir Alvarez, Panagiotis Ioannidis, Marc Robinson-Rechavi, National Science Foundation (US), Department of Agriculture (US), European Commission, German Research Foundation, BGI Group, China National GeneBank, Swiss National Science Foundation, Ministerio de Economía y Competitividad (España), and Muséum national d'Histoire naturelle (France)

Subjects
0106 biological sciences, lcsh:QH426-470, Gene family evolution, media_common.quotation_subject, Adaptation, Biological, Beetle-plant trophic interactions, Genomics, Beetle diversification, Detoxification enzymes, 010603 evolutionary biology, 01 natural sciences, Adephaga, 03 medical and health sciences, Animals, Biological Evolution, Coleoptera/enzymology, Coleoptera/genetics, Herbivory, Models, Genetic, Multigene Family, 0302 clinical medicine, Genetic, Models, Gene family, ddc:576.5, Adaptation, lcsh:QH301-705.5, Gene, Polyphaga, media_common, 030304 developmental biology, Trophic level, 2. Zero hunger, 0303 health sciences, Herbivore, biology, Research, Coleoptera/enzymology/genetics, biology.organism_classification, Biological, Coleoptera, lcsh:Genetics, Speciation, lcsh:Biology (General), Evolutionary biology, 030217 neurology & neurosurgery
Abstract

© The Author(s). 2019, [Background] The diversity and evolutionary success of beetles (Coleoptera) are proposed to be related to the diversity of plants on which they feed. Indeed, the largest beetle suborder, Polyphaga, mostly includes plant eaters among its approximately 315,000 species. In particular, plants defend themselves with a diversity of specialized toxic chemicals. These may impose selective pressures that drive genomic diversification and speciation in phytophagous beetles. However, evidence of changes in beetle gene repertoires driven by such interactions remains largely anecdotal and without explicit hypothesis testing., [Results] We explore the genomic consequences of beetle-plant trophic interactions by performing comparative gene family analyses across 18 species representative of the two most species-rich beetle suborders. We contrast the gene contents of species from the mostly plant-eating suborder Polyphaga with those of the mainly predatory Adephaga. We find gene repertoire evolution to be more dynamic, with significantly more adaptive lineage-specific expansions, in the more speciose Polyphaga. Testing the specific hypothesis of adaptation to plant feeding, we identify families of enzymes putatively involved in beetle-plant interactions that underwent adaptive expansions in Polyphaga. There is notable support for the selection hypothesis on large gene families for glutathione S-transferase and carboxylesterase detoxification enzymes., [Conclusions] Our explicit modeling of the evolution of gene repertoires across 18 species identifies putative adaptive lineage-specific gene family expansions that accompany the dietary shift towards plants in beetles. These genomic signatures support the popular hypothesis of a key role for interactions with plant chemical defenses, and for plant feeding in general, in driving beetle diversification., This work was supported by the United States National Science Foundation (DEB 1355169) and the United States Department of Agriculture (cooperative agreement 8130-0547-CA) to DDM, the Spanish grant CGL2013-42589-P awarded by the MINECO and co-financed by FEDER to BCE, the Science Foundation DFG grant BA2152/11-1, 2, the BGI-Shenzhen, the China National Genebank, and the following Swiss National Science Foundation grants: 31003A_143936 (PI), 31003A_173048 (MRR), PP00P3_170664 (RMW), and PP00P3_172899 (NA). Funding for open access charge: Geneva Natural History Museum.

Published
2019

21. Bacterial communities within Phengaris (Maculinea) alcon caterpillars are shifted following transition from solitary living to social parasitism of Myrmica ant colonies

Author

Luca Pietro Casacci, Lucie Kešnerová, Nadi Alvarez, Melissa R. L. Whitaker, Roger Vila, Camille Pitteloud, Mark A. Szenteczki, Philipp Engel, Swiss National Science Foundation, Ministerio de Economía y Competitividad (España), European Commission, Agencia Estatal de Investigación (España), and National Science Foundation (US)

Subjects
0106 biological sciences, 16S amplicon sequencing, Phengaris alcon, Spiroplasma, butterflies, Lepidoptera, Lycaenidae, myrmecophily, Zoology, Parasitism, Myrmecophily, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Phengaris, Myrmica, Ecology, Evolution, Behavior and Systematics, Original Research, 030304 developmental biology, Nature and Landscape Conservation, 0303 health sciences, Ecology, biology, fungi, food and beverages, Ant colony, biology.organism_classification, Butterflies, Trophallaxis
Abstract

Bacterial symbionts are known to facilitate a wide range of physiological processes and ecological interactions for their hosts. In spite of this, caterpillars with highly diverse life histories appear to lack resident microbiota. Gut physiology, endogenous digestive enzymes, and limited social interactions may contribute to this pattern, but the consequences of shifts in social activity and diet on caterpillar microbiota are largely unknown. Phengaris alcon caterpillars undergo particularly dramatic social and dietary shifts when they parasitize Myrmica ant colonies, rapidly transitioning from solitary herbivory to ant tending (i.e., receiving protein‐rich regurgitations through trophallaxis). This unique life history provides a model for studying interactions between social living, diet, and caterpillar microbiota. Here, we characterized and compared bacterial communities within P. alcon caterpillars before and after their association with ants, using 16S rRNA amplicon sequencing and quantitative PCR. After being adopted by ants, bacterial communities within P. alcon caterpillars shifted substantially, with a significant increase in alpha diversity and greater consistency in bacterial community composition in terms of beta dissimilarity. We also characterized the bacterial communities within their host ants (Myrmica schencki), food plant (Gentiana cruciata), and soil from ant nest chambers. These data indicated that the aforementioned patterns were influenced by bacteria derived from caterpillars’ surrounding environments, rather than through transfers from ants. Thus, while bacterial communities are substantially reorganized over the life cycle of P. alcon caterpillars, it appears that they do not rely on transfers of bacteria from host ants to complete their development., Ecology and Evolution, 9 (8), ISSN:2045-7758

Published
2019

22. Spatial and temporal genetic dynamics of the grasshopper

Author

Sarah, Schmid, Samuel, Neuenschwander, Camille, Pitteloud, Gerald, Heckel, Mila, Pajkovic, Raphaël, Arlettaz, and Nadir, Alvarez

Subjects
conservation genetics, hybridization capture RAD, population genetics, phylogeography, Original Research
Abstract

Analyzing genetic variation through time and space is important to identify key evolutionary and ecological processes in populations. However, using contemporary genetic data to infer the dynamics of genetic diversity may be at risk of a bias, as inferences are performed from a set of extant populations, setting aside unavailable, rare, or now extinct lineages. Here, we took advantage of new developments in next‐generation sequencing to analyze the spatial and temporal genetic dynamics of the grasshopper Oedaleus decorus, a steppic Southwestern‐Palearctic species. We applied a recently developed hybridization capture (hyRAD) protocol that allows retrieving orthologous sequences even from degraded DNA characteristic of museum specimens. We identified single nucleotide polymorphisms in 68 historical and 51 modern samples in order to (i) unravel the spatial genetic structure across part of the species distribution and (ii) assess the loss of genetic diversity over the past century in Swiss populations. Our results revealed (i) the presence of three potential glacial refugia spread across the European continent and converging spatially in the Alpine area. In addition, and despite a limited population sample size, our results indicate (ii) a loss of allelic richness in contemporary Swiss populations compared to historical populations, whereas levels of expected heterozygosities were not significantly different. This observation is compatible with an increase in the bottleneck magnitude experienced by central European populations of O. decorus following human‐mediated land‐use change impacting steppic habitats. Our results confirm that application of hyRAD to museum samples produces valuable information to study genetic processes across time and space.

Published
2017

23. Climatic niche evolution is faster in sympatric than allopatric lineages of the butterfly genus

Author

Camille Pitteloud, Vlad Dincă, Sven Buerki, Loïc Pellissier, Nadir Alvarez, Tomasz Suchan, Juan L. Hernández-Roldán, Alicia Mastretta-Yanes, Yannick Chittaro, Nils Arrigo, Roger Vila, Luca Fumagalli, Ernst Brockmann, and Irena Kleckova

Subjects
0106 biological sciences, 0301 basic medicine, Sympatry, Asia, Genetic Speciation, Evolution, Climate, Allopatric speciation, Biology, Parapatric speciation, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Africa, Northern, Animals, Ecosystem, Phylogeny, General Environmental Science, Ecological niche, General Immunology and Microbiology, Ecology, Niche differentiation, General Medicine, Reproductive isolation, 15. Life on land, Biological Evolution, Europe, 030104 developmental biology, Sympatric speciation, General Agricultural and Biological Sciences, Butterflies
Abstract

Understanding how speciation relates to ecological divergence has long fascinated biologists. It is assumed that ecological divergence is essential to sympatric speciation, as a mechanism to avoid competition and eventually lead to reproductive isolation, while divergence in allopatry is not necessarily associated with niche differentiation. The impact of the spatial context of divergence on the evolutionary rates of abiotic dimensions of the ecological niche has rarely been explored for an entire clade. Here, we compare the magnitude of climatic niche shifts between sympatric versus allopatric divergence of lineages in butterflies. By combining next-generation sequencing, parametric biogeography and ecological niche analyses applied to a genus-wide phylogeny of Palaearctic Pyrgus butterflies, we compare evolutionary rates along eight climatic dimensions across sister lineages that diverged in large-scale sympatry versus allopatry. In order to examine the possible effects of the spatial scale at which sympatry is defined, we considered three sets of biogeographic assignments, ranging from narrow to broad definition. Our findings suggest higher rates of niche evolution along all climatic dimensions for sister lineages that diverge in sympatry, when using a narrow delineation of biogeographic areas. This result contrasts with significantly lower rates of climatic niche evolution found in cases of allopatric speciation, despite the biogeographic regions defined here being characterized by significantly different climates. Higher rates in allopatry are retrieved when biogeographic areas are too widely defined—in such a case allopatric events may be recorded as sympatric. Our results reveal the macro-evolutionary significance of abiotic niche differentiation involved in speciation processes within biogeographic regions, and illustrate the importance of the spatial scale chosen to define areas when applying parametric biogeographic analyses.

Published
2017

24. Hybridization capture using RAD probes (hyRAD), a new tool for performing genomic analyses on museum collection specimens

Author

Anna Kostikova, Mila Pajkovic, Nils Arrigo, Camille Pitteloud, Nadir Alvarez, Sarah Schmid, Michał Ronikier, N. S. Gerasimova, and Tomasz Suchan

Subjects
0106 biological sciences, 0301 basic medicine, Research Facilities, Restriction Mapping, DNA cloning, Artificial Gene Amplification and Extension, Museum Collections, 01 natural sciences, Genome, Polymerase Chain Reaction, chemistry.chemical_compound, Genomic library, Genetics, 0303 health sciences, Multidisciplinary, Phylogenetic tree, Shotgun sequencing, Nucleic Acid Hybridization, Genomics, Amplicon, Data Accuracy, Restriction site, Medicine, Butterflies, Research Article, Science, Molecular Probe Techniques, Computational biology, Grasshoppers, Biology, Research and Analysis Methods, 010603 evolutionary biology, Polymorphism, Single Nucleotide, Specimen Handling, 03 medical and health sciences, Restriction map, Animals, Molecular Biology Techniques, Sequencing Techniques, Molecular Biology, 030304 developmental biology, Gene Library, Shotgun Sequencing, Sequence Assembly Tools, Computational Biology, Biology and Life Sciences, DNA, Sequence Analysis, DNA, Genome Analysis, Genomic Libraries, Probe Hybridization, Restriction enzyme, 030104 developmental biology, chemistry, Genetic Loci, Amplified fragment length polymorphism, Cloning
Abstract

In the recent years, many protocols aimed at reproducibly sequencing reduced-genome subsets in non-model organisms have been published. Among them, RAD-sequencing is one of the most widely used. It relies on digesting DNA with specific restriction enzymes and performing size selection on the resulting fragments. Despite its acknowledged utility, this method is of limited use with degraded DNA samples, such as those isolated from museum specimens, as these samples are less likely to harbor fragments long enough to comprise two restriction sites making possible ligation of the adapter sequences (in the case of double-digest RAD) or performing size selection of the resulting fragments (in the case of single-digest RAD). Here, we address these limitations by presenting a novel method called hybridization RAD (hyRAD). In this approach, biotinylated RAD fragments, covering a random fraction of the genome, are used as baits for capturing homologous fragments from genomic shotgun sequencing libraries. This simple and cost-effective approach allows sequencing of orthologous loci even from highly degraded DNA samples, opening new avenues of research in the field of museum genomics. Not relying on the restriction site presence, it improves among-sample loci coverage. In a trial study, hyRAD allowed us to obtain a large set of orthologous loci from fresh and museum samples from a non-model butterfly species, with a high proportion of single nucleotide polymorphisms present in all eight analyzed specimens, including 58-year-old museum samples. The utility of the method was further validated using 49 museum and fresh samples of a Palearctic grasshopper species for which the spatial genetic structure was previously assessed using mtDNA amplicons. The application of the method is eventually discussed in a wider context. As it does not rely on the restriction site presence, it is therefore not sensitive to among-sample loci polymorphisms in the restriction sites that usually causes loci dropout. This should enable the application of hyRAD to analyses at broader evolutionary scales., PLoS ONE, 11 (3), ISSN:1932-6203

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