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Prof. Gentile Francesco Ficetola
Univ. Milano

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0 Amphibians
0 Reptiles
0 Species Distribution Modelling
0 Biodiversity conservation
0 environmental DNA

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Amphibians
Reptiles
environmental DNA
Biodiversity conservation
Species Distribution Modelling

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Short Biography

G. Francesco Ficetola is a researcher combining multiple approaches (field activities, landscape ecology, macroecology, evolutionary ecology and environmental DNA) to improve knowledge on biodiversity. His research focuses on the determinants of biodiversity patterns, and on the long-term effects of human activities at multiple scales, from micro-habitat to global.

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Article
Published: 15 July 2021 in Nature Ecology & Evolution
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Long-term studies are essential to understand the impacts of global changes on the multiple facets of biological diversity. Here, we use distribution data for over 600 species of arthropods collected over 150 years from locations across Italy and test how multiple environmental stressors (climate, land use and human population density) influenced assemblage composition and functionality. By carefully reconstructing the temporal changes in these stressors, we explicitly tested how environmental changes can determine the observed changes in taxonomic and functional diversity. We found that rapid changes in precipitation destabilize the assemblages and maximize colonization and extinction rates, especially when coupled with changes in human population density (for taxonomy) or temperature (for functionality). Higher microclimatic heterogeneity increases the stability of biodiversity by reducing taxonomic and functional loss. Finally, changes in natural habitats increased colonization, influencing taxonomic nestedness and functional replacement. The integration of long-term datasets combining distributions, climate and traits may deepen our understanding of the processes underlying biodiversity responses to global-scale drivers. Using a 150-year time series of data on arthropod species richness in Italy, the authors identify the main drivers of assemblage compositional turnover, finding that turnover is highest in locations with rapid changes in precipitation, particularly when human population density also increased rapidly.

ACS Style

Silvio Marta; Michele Brunetti; Raoul Manenti; Antonello Provenzale; Gentile Francesco Ficetola. Climate and land-use changes drive biodiversity turnover in arthropod assemblages over 150 years. Nature Ecology & Evolution 2021, 1 -10.

AMA Style

Silvio Marta, Michele Brunetti, Raoul Manenti, Antonello Provenzale, Gentile Francesco Ficetola. Climate and land-use changes drive biodiversity turnover in arthropod assemblages over 150 years. Nature Ecology & Evolution. 2021; ():1-10.

Chicago/Turabian Style

Silvio Marta; Michele Brunetti; Raoul Manenti; Antonello Provenzale; Gentile Francesco Ficetola. 2021. "Climate and land-use changes drive biodiversity turnover in arthropod assemblages over 150 years." Nature Ecology & Evolution , no. : 1-10.

Research article
Published: 01 July 2021 in Global Ecology and Biogeography
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Aim Worldwide distribution patterns of living animals are structured in multiple zoogeographical regions, characterized by faunas with homogeneous composition that are separated by sharp boundaries. These zoogeographical regions can differ depending on the considered animal group, probably because they have distinct characteristics such as dispersal, metabolism, or evolutionary history, and thus divergent responses to major biogeographical drivers, such as tectonic movements, abrupt climate transitions and orographic barriers. Here, we tested if the drivers of biogeographical boundaries are different between vertebrate classes with strongly divergent traits and evolutionary history. Location Global. Time period Present. Major taxa studied Amphibians, birds and mammals. Methods We focused on terrestrial biogeographical boundaries, considering multiple potential drivers: spatial heterogeneity of present-day climate, altitudinal variation, long-term tectonic movements and past climate change (temperature). We used spatially explicit regression models and geographically weighted regressions to select and quantify the factors explaining the position of the biogeographical boundaries between vertebrate classes. Results For mammals, tectonic movements, abrupt climatic transitions and orographic barriers jointly determined extant biogeographical boundaries, with tectonic movements being the most important. For birds, abrupt climatic transitions played the strongest role, while the effect of orographic barriers was weak. For amphibians, biogeographical boundaries mostly corresponded to areas with abrupt climatic transitions. The strongest transitions of amphibian faunas occur in areas with abrupt shifts of temperature and precipitation regimes. Main conclusions Our analyses confirmed that different drivers have jointly shaped the global vertebrate biogeographical regions, and highlight that taxa with different features show heterogeneous responses across the globe. Eco-physiological constraints likely increase the importance of spatial heterogeneity of climate, while dispersal limitations magnify the relevance of physical barriers (mountain chains and long-term tectonic instability). Integrating among-taxa heterogeneity into analyses thus provides a more complete view of how different processes determine biodiversity variation across the globe.

ACS Style

Gentile Francesco Ficetola; Florent Mazel; Mattia Falaschi; Silvio Marta; Wilfried Thuiller. Determinants of zoogeographical boundaries differ between vertebrate groups. Global Ecology and Biogeography 2021, 30, 1796 -1809.

AMA Style

Gentile Francesco Ficetola, Florent Mazel, Mattia Falaschi, Silvio Marta, Wilfried Thuiller. Determinants of zoogeographical boundaries differ between vertebrate groups. Global Ecology and Biogeography. 2021; 30 (9):1796-1809.

Chicago/Turabian Style

Gentile Francesco Ficetola; Florent Mazel; Mattia Falaschi; Silvio Marta; Wilfried Thuiller. 2021. "Determinants of zoogeographical boundaries differ between vertebrate groups." Global Ecology and Biogeography 30, no. 9: 1796-1809.

Journal article
Published: 23 June 2021 in Diversity
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Speleomantes are the only plethodontid salamanders present in Europe. Multiple studies have been performed to investigate the trophic niche of the eight Speleomantes species, but none of these studies included hybrid populations. For the first time, we studied the trophic niche of five Speleomantes hybrid populations. Each population was surveyed twice in 2020, and stomach flushing was performed on each captured salamander; stomach flushing is a harmless technique that allows stomach contents to be inspected. We also assessed the potential divergence in size and body condition between natural and introduced hybrids, and their parental species. Previously collected data on Speleomantes were included to increase the robustness of these analyses. In only 33 out of 134 sampled hybrid Speleomantes we recognized 81 items belonging to 11 prey categories. The frequency of empty stomachs was higher in females and individuals from natural hybrid populations, whereas the largest number of prey was consumed by males. We compared the total length and body condition of 685 adult salamanders belonging to three types of hybrids and three parental (sub)species. Three group of salamanders (one hybrid and two parental species) showed significantly larger size, whereas no difference in body condition was observed. This study provided novel ecological information on Speleomantes hybrid populations. We also provided insights into the potential divergence between hybrids and parental species in terms of size and body condition. We discuss our findings, and formulate several hypotheses that should be tested in the future.

ACS Style

Enrico Lunghi; Fabio Cianferoni; Stefano Merilli; Yahui Zhao; Raoul Manenti; Gentile Ficetola; Claudia Corti. Ecological Observations on Hybrid Populations of European Plethodontid Salamanders, Genus Speleomantes. Diversity 2021, 13, 285 .

AMA Style

Enrico Lunghi, Fabio Cianferoni, Stefano Merilli, Yahui Zhao, Raoul Manenti, Gentile Ficetola, Claudia Corti. Ecological Observations on Hybrid Populations of European Plethodontid Salamanders, Genus Speleomantes. Diversity. 2021; 13 (7):285.

Chicago/Turabian Style

Enrico Lunghi; Fabio Cianferoni; Stefano Merilli; Yahui Zhao; Raoul Manenti; Gentile Ficetola; Claudia Corti. 2021. "Ecological Observations on Hybrid Populations of European Plethodontid Salamanders, Genus Speleomantes." Diversity 13, no. 7: 285.

Data descriptor
Published: 09 June 2021 in Scientific Data
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European plethodontid salamanders (genus Speleomantes; formerly Hydromantes) are a group of eight strictly protected amphibian species which are sensitive to human-induced environmental changes. Long-term monitoring is highly recommended to evaluate their status and to assess potential threats. Here we used two low-impact methodologies to build up a large dataset on two mainland Speleomantes species (S. strinatii and S. ambrosii), which represents an update to two previously published datasets, but also includes several new populations. Specifically, we provide a set of 851 high quality images and a table gathering stomach contents recognized from 560 salamanders. This dataset offers the opportunity to analyse phenotypic traits and stomach contents of eight populations belonging to two Speleomantes species. Furthermore, the data collection performed over different periods allows to expand the potential analyses through a wide temporal scale, allowing long-term studies.

ACS Style

Enrico Lunghi; Fabio Cianferoni; Simone Giachello; Yahui Zhao; Raoul Manenti; Claudia Corti; Gentile Francesco Ficetola. Updating salamander datasets with phenotypic and stomach content information for two mainland Speleomantes. Scientific Data 2021, 8, 1 -6.

AMA Style

Enrico Lunghi, Fabio Cianferoni, Simone Giachello, Yahui Zhao, Raoul Manenti, Claudia Corti, Gentile Francesco Ficetola. Updating salamander datasets with phenotypic and stomach content information for two mainland Speleomantes. Scientific Data. 2021; 8 (1):1-6.

Chicago/Turabian Style

Enrico Lunghi; Fabio Cianferoni; Simone Giachello; Yahui Zhao; Raoul Manenti; Claudia Corti; Gentile Francesco Ficetola. 2021. "Updating salamander datasets with phenotypic and stomach content information for two mainland Speleomantes." Scientific Data 8, no. 1: 1-6.

Research article
Published: 17 May 2021 in Biodiversity
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Changes in human activities caused by the COVID-19 pandemic can have multiple effects on biodiversity but there is limited knowledge of how this can impact invasive alien species (IAS). Societal measures against the spread of COVID-19 can have both short-term and long-term consequences on IAS. In the short-term, reduced human disturbance on natural habitats can increase the activity of IAS and accelerate their spread. Furthermore, management agencies have reduced control activities, sometimes allowing IAS to thrive, and ongoing monitoring programs have been interrupted, hindering rapid identification and management of biological invasions. Long-term impacts could include global modifications to wildlife trade and increased releases of captive-bred species because of the fear of zoonotic diseases and also greater public awareness of the risks of pathogens being spread among animal populations. Long-term collection and sharing of data are crucial to modulate IAS management during and after the lockdowns.

ACS Style

Elia Lo Parrino; Mattia Falaschi; Raoul Manenti; Gentile Francesco Ficetola. Lockdown policy effects on invasive species: a perspective. Biodiversity 2021, 1 -6.

AMA Style

Elia Lo Parrino, Mattia Falaschi, Raoul Manenti, Gentile Francesco Ficetola. Lockdown policy effects on invasive species: a perspective. Biodiversity. 2021; ():1-6.

Chicago/Turabian Style

Elia Lo Parrino; Mattia Falaschi; Raoul Manenti; Gentile Francesco Ficetola. 2021. "Lockdown policy effects on invasive species: a perspective." Biodiversity , no. : 1-6.

Commentary
Published: 27 April 2021 in Biodiversity and Conservation
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The cryosphere (i.e. glaciers and permafrost) and its related landforms offer a wide range of ecosystem services, thus they have strong relationships with human population. Even if these harsh environments have often been regarded as inhospitable, there is a growing amount of literature on glacial biodiversity, specifically concerning European mountains. Glaciers and permafrost-related landforms (e.g. rock glaciers) host a variety of cold-adapted taxa, from bacteria to vertebrates. They have been included in the Natura 2000 network, specifically in the habitat type: Permanent Glaciers (code 8340), but their biodiversity is still poorly known. Even if local extinctions and population reductions of cold-adapted species due to glacier and permafrost shrinking have been already documented, none of the species living in this habitat type are listed in the Habitat Directive Annexes. With this commentary, we call for urgent actions for an ecological characterization of this habitat type in order to plan monitoring and management of the biodiversity hosted by them. An increased knowledge of this no longer permanent habitat appears particularly urgent, because it is not replaceable and is likely to go extinct in the next decades.

ACS Style

M. Gobbi; R. Ambrosini; C. Casarotto; G. Diolaiuti; G. F. Ficetola; V. Lencioni; R. Seppi; C. Smiraglia; D. Tampucci; B. Valle; M. Caccianiga. Vanishing permanent glaciers: climate change is threatening a European Union habitat (Code 8340) and its poorly known biodiversity. Biodiversity and Conservation 2021, 30, 2267 -2276.

AMA Style

M. Gobbi, R. Ambrosini, C. Casarotto, G. Diolaiuti, G. F. Ficetola, V. Lencioni, R. Seppi, C. Smiraglia, D. Tampucci, B. Valle, M. Caccianiga. Vanishing permanent glaciers: climate change is threatening a European Union habitat (Code 8340) and its poorly known biodiversity. Biodiversity and Conservation. 2021; 30 (7):2267-2276.

Chicago/Turabian Style

M. Gobbi; R. Ambrosini; C. Casarotto; G. Diolaiuti; G. F. Ficetola; V. Lencioni; R. Seppi; C. Smiraglia; D. Tampucci; B. Valle; M. Caccianiga. 2021. "Vanishing permanent glaciers: climate change is threatening a European Union habitat (Code 8340) and its poorly known biodiversity." Biodiversity and Conservation 30, no. 7: 2267-2276.

Journal article
Published: 18 March 2021 in Animals
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Since 2016, a feral population of llama Lama glama has been present in Central Italy after escaping from a zoological garden and starting to reproduce. We updated demographic status and distribution of this population and investigated societal perception towards the llama presence and management in the area through a standard questionnaire. Field data were collected through direct (transects traveled by car and on foot) and indirect (newspapers, social networks and online platforms) research. The feral population appears to be declining. In July 2020, the population was represented by three individuals (one male and two females), identified also through photoidentification, most likely located within a 40-hectare area. The majority of citizens are aware of the presence of feral llamas and show a positive attitude toward them and a negative one toward management actions. The case of feral llamas in Italy is an evident example of unsafe management of a species which should have kept in a zoo and which, once set free, was able to catalyze the attention of the general public. The decline of this population limits the need of drastic management actions that, given the appreciation expressed by people and press toward these animals, would have been at risk of conflict with the public opinion. Removal action should be rapidly taken, i.e., before any demographic rebound and before the population becomes a stable feature of the local landscape.

ACS Style

Carlo Gargioni; Andrea Monaco; Gentile Francesco Ficetola; Lorenzo Lazzeri; Emiliano Mori. From the Andes to the Apennines: Rise and Fall of a Free-Ranging Population of Feral Llamas. Animals 2021, 11, 857 .

AMA Style

Carlo Gargioni, Andrea Monaco, Gentile Francesco Ficetola, Lorenzo Lazzeri, Emiliano Mori. From the Andes to the Apennines: Rise and Fall of a Free-Ranging Population of Feral Llamas. Animals. 2021; 11 (3):857.

Chicago/Turabian Style

Carlo Gargioni; Andrea Monaco; Gentile Francesco Ficetola; Lorenzo Lazzeri; Emiliano Mori. 2021. "From the Andes to the Apennines: Rise and Fall of a Free-Ranging Population of Feral Llamas." Animals 11, no. 3: 857.

Research
Published: 25 February 2021 in Ecography
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The species–area relationship (SAR) is one of the most well‐established scaling patterns in ecology. Its implications for understanding how communities change across spatial gradients are numerous, including the effects of habitat loss on biodiversity. However, ecological communities are not mere collections of species. They are the result of interactions between these species forming complex networks that tie them together. Should we aim to grasp the spatial scaling of biodiversity as a whole, it is fundamental to understand the changes in the structure of interaction networks with area. In spite of a few empirical and theoretical studies that address this challenge, we still do not know much about how network structure changes with area, or what are the main environmental drivers of these changes. Here, using the meta‐network of potential interactions between all terrestrial vertebrates in Europe (1140 species and 67 201 feeding interactions), we analysed network–area relationships (NARs) that summarize how network properties scale with area. We do this across ten biogeographical regions, which differ in environmental characteristics. We found that the spatial scaling of network complexity strongly varied across biogeographical regions. However, once the variation in SARs was accounted for, differences in the shape of NARs vanished. On the other hand, the proportion of species across trophic levels remained remarkably constant across biogeographical regions and spatial scales, despite the great variation in species richness. Spatial variation in mean annual temperature and habitat clustering were the main environmental determinants of the shape of both SARs and NARs across Europe. Our results suggest new avenues in the exploration of the effects of environmental factors on the spatial scaling of biodiversity. We argue that NARs can provide new insights to analyse and understand ecological communities.

ACS Style

Núria Galiana; Ceres Barros; João Braga; Gentile Francesco Ficetola; Luigi Maiorano; Wilfried Thuiller; José M. Montoya; Miguel Lurgi. The spatial scaling of food web structure across European biogeographical regions. Ecography 2021, 44, 653 -664.

AMA Style

Núria Galiana, Ceres Barros, João Braga, Gentile Francesco Ficetola, Luigi Maiorano, Wilfried Thuiller, José M. Montoya, Miguel Lurgi. The spatial scaling of food web structure across European biogeographical regions. Ecography. 2021; 44 (5):653-664.

Chicago/Turabian Style

Núria Galiana; Ceres Barros; João Braga; Gentile Francesco Ficetola; Luigi Maiorano; Wilfried Thuiller; José M. Montoya; Miguel Lurgi. 2021. "The spatial scaling of food web structure across European biogeographical regions." Ecography 44, no. 5: 653-664.

Review
Published: 13 February 2021 in Quaternary
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The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.

ACS Style

Eric Capo; Charline Giguet-Covex; Alexandra Rouillard; Kevin Nota; Peter Heintzman; Aurèle Vuillemin; Daniel Ariztegui; Fabien Arnaud; Simon Belle; Stefan Bertilsson; Christian Bigler; Richard Bindler; Antony Brown; Charlotte Clarke; Sarah Crump; Didier Debroas; Göran Englund; Gentile Ficetola; Rebecca Garner; Joanna Gauthier; Irene Gregory-Eaves; Liv Heinecke; Ulrike Herzschuh; Anan Ibrahim; Veljo Kisand; Kurt Kjær; Youri Lammers; Joanne Littlefair; Erwan Messager; Marie-Eve Monchamp; Fredrik Olajos; William Orsi; Mikkel Pedersen; Dilli Rijal; Johan Rydberg; Trisha Spanbauer; Kathleen Stoof-Leichsenring; Pierre Taberlet; Liisi Talas; Camille Thomas; David Walsh; Yucheng Wang; Eske Willerslev; Anne van Woerkom; Heike Zimmermann; Marco Coolen; Laura Epp; Isabelle Domaizon; Inger G. Alsos; Laura Parducci. Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations. Quaternary 2021, 4, 6 .

AMA Style

Eric Capo, Charline Giguet-Covex, Alexandra Rouillard, Kevin Nota, Peter Heintzman, Aurèle Vuillemin, Daniel Ariztegui, Fabien Arnaud, Simon Belle, Stefan Bertilsson, Christian Bigler, Richard Bindler, Antony Brown, Charlotte Clarke, Sarah Crump, Didier Debroas, Göran Englund, Gentile Ficetola, Rebecca Garner, Joanna Gauthier, Irene Gregory-Eaves, Liv Heinecke, Ulrike Herzschuh, Anan Ibrahim, Veljo Kisand, Kurt Kjær, Youri Lammers, Joanne Littlefair, Erwan Messager, Marie-Eve Monchamp, Fredrik Olajos, William Orsi, Mikkel Pedersen, Dilli Rijal, Johan Rydberg, Trisha Spanbauer, Kathleen Stoof-Leichsenring, Pierre Taberlet, Liisi Talas, Camille Thomas, David Walsh, Yucheng Wang, Eske Willerslev, Anne van Woerkom, Heike Zimmermann, Marco Coolen, Laura Epp, Isabelle Domaizon, Inger G. Alsos, Laura Parducci. Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations. Quaternary. 2021; 4 (1):6.

Chicago/Turabian Style

Eric Capo; Charline Giguet-Covex; Alexandra Rouillard; Kevin Nota; Peter Heintzman; Aurèle Vuillemin; Daniel Ariztegui; Fabien Arnaud; Simon Belle; Stefan Bertilsson; Christian Bigler; Richard Bindler; Antony Brown; Charlotte Clarke; Sarah Crump; Didier Debroas; Göran Englund; Gentile Ficetola; Rebecca Garner; Joanna Gauthier; Irene Gregory-Eaves; Liv Heinecke; Ulrike Herzschuh; Anan Ibrahim; Veljo Kisand; Kurt Kjær; Youri Lammers; Joanne Littlefair; Erwan Messager; Marie-Eve Monchamp; Fredrik Olajos; William Orsi; Mikkel Pedersen; Dilli Rijal; Johan Rydberg; Trisha Spanbauer; Kathleen Stoof-Leichsenring; Pierre Taberlet; Liisi Talas; Camille Thomas; David Walsh; Yucheng Wang; Eske Willerslev; Anne van Woerkom; Heike Zimmermann; Marco Coolen; Laura Epp; Isabelle Domaizon; Inger G. Alsos; Laura Parducci. 2021. "Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations." Quaternary 4, no. 1: 6.

Research paper
Published: 27 January 2021 in Journal of Experimental Zoology Part A: Ecological and Integrative Physiology
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Tris(1‐chloro‐2‐propyl)phosphate (TCPP) is the most common chlorinated organophosphorus flame retardant in seawater. Due to its chemical features and abundance, TCPP has been classified as a high hazard, and restrictions of use have been set in multiple countries. Despite TCPP being highly present in the marine environment, only a few studies have explored the TCPP impact on the development of marine invertebrates. Ascidians are important invertebrate members of benthic marine communities and reliable model systems for ecotoxicological research. The aim of this study was to assess the adverse effects of TCPP exposure on the embryogenesis of the ascidian Ciona intestinalis. Our results showed that this pollutant affected both muscles and nervous system development. Malformations appeared similar to those reported in other animal models for other flame retardants, suggesting that these molecules could share a common mechanism of action and induce a mixture effect when simultaneously present in the aquatic environment even at sub‐teratogenic concentrations.

ACS Style

Silvia Mercurio; Silvia Messinetti; Raoul Manenti; Gentile Francesco Ficetola; Roberta Pennati. Embryotoxicity characterization of the flame retardant tris(1‐chloro‐2‐propyl)phosphate (TCPP) in the invertebrate chordate Ciona intestinalis. Journal of Experimental Zoology Part A: Ecological and Integrative Physiology 2021, 335, 339 -347.

AMA Style

Silvia Mercurio, Silvia Messinetti, Raoul Manenti, Gentile Francesco Ficetola, Roberta Pennati. Embryotoxicity characterization of the flame retardant tris(1‐chloro‐2‐propyl)phosphate (TCPP) in the invertebrate chordate Ciona intestinalis. Journal of Experimental Zoology Part A: Ecological and Integrative Physiology. 2021; 335 (3):339-347.

Chicago/Turabian Style

Silvia Mercurio; Silvia Messinetti; Raoul Manenti; Gentile Francesco Ficetola; Roberta Pennati. 2021. "Embryotoxicity characterization of the flame retardant tris(1‐chloro‐2‐propyl)phosphate (TCPP) in the invertebrate chordate Ciona intestinalis." Journal of Experimental Zoology Part A: Ecological and Integrative Physiology 335, no. 3: 339-347.

Meeting review
Published: 12 January 2021 in Molecular Ecology
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High‐throughput sequencing (HTS) is increasingly being used for the characterisation and monitoring of biodiversity. If applied in a structured way, across broad geographic scales, it offers the potential for a much deeper understanding of global biodiversity through the integration of massive quantities of molecular inventory data generated independently at local, regional and global scales. The universality, reliability, and efficiency of HTS data can potentially facilitate the seamless linking of data among species assemblages from different sites, at different hierarchical levels of diversity, for any taxonomic group and regardless of prior taxonomic knowledge. However, collective international efforts are required to optimally exploit the potential of site‐based HTS data for global integration and synthesis, efforts that at present are limited to the microbial domain. To contribute to the development of an analogous strategy for the non‐microbial terrestrial domain, an international symposium entitled ‘Next Generation Biodiversity Monitoring’ was held in November 2019, in Nicosia (Cyprus). The symposium brought together evolutionary geneticists, ecologists, and biodiversity scientists involved in diverse regional and global initiatives using HTS as a core tool for biodiversity assessment. In this review, we summarise the consensus that emerged from the three‐day symposium. We converged on the opinion that an effective terrestrial Genomic Observatories network for global biodiversity integration and synthesis should be spatially‐led and strategically united under the umbrella of the metabarcoding approach. Subsequently, we outline an HTS‐based strategy to collectively build an integrative framework for site‐based biodiversity data generation.

ACS Style

Paula Arribas; Carmelo Andújar; Martin I. Bidartondo; Kristine Bohmann; Éric Coissac; Simon Creer; Jeremy R. Dewaard; Vasco Elbrecht; Gentile Francesco Ficetola; Marta Goberna; Susan Kennedy; Henrik Krehenwinkel; Florian Leese; Vojtech Novotny; Fredrik Ronquist; Douglas W. Yu; Lucie Zinger; Thomas J. Creedy; Emmanouil Meramveliotakis; Víctor Noguerales; Isaac Overcast; Hélène Morlon; Alfried P. Vogler; Anna Papadopoulou; Brent C. Emerson. Connecting high‐throughput biodiversity inventories: Opportunities for a site‐based genomic framework for global integration and synthesis. Molecular Ecology 2021, 30, 1120 -1135.

AMA Style

Paula Arribas, Carmelo Andújar, Martin I. Bidartondo, Kristine Bohmann, Éric Coissac, Simon Creer, Jeremy R. Dewaard, Vasco Elbrecht, Gentile Francesco Ficetola, Marta Goberna, Susan Kennedy, Henrik Krehenwinkel, Florian Leese, Vojtech Novotny, Fredrik Ronquist, Douglas W. Yu, Lucie Zinger, Thomas J. Creedy, Emmanouil Meramveliotakis, Víctor Noguerales, Isaac Overcast, Hélène Morlon, Alfried P. Vogler, Anna Papadopoulou, Brent C. Emerson. Connecting high‐throughput biodiversity inventories: Opportunities for a site‐based genomic framework for global integration and synthesis. Molecular Ecology. 2021; 30 (5):1120-1135.

Chicago/Turabian Style

Paula Arribas; Carmelo Andújar; Martin I. Bidartondo; Kristine Bohmann; Éric Coissac; Simon Creer; Jeremy R. Dewaard; Vasco Elbrecht; Gentile Francesco Ficetola; Marta Goberna; Susan Kennedy; Henrik Krehenwinkel; Florian Leese; Vojtech Novotny; Fredrik Ronquist; Douglas W. Yu; Lucie Zinger; Thomas J. Creedy; Emmanouil Meramveliotakis; Víctor Noguerales; Isaac Overcast; Hélène Morlon; Alfried P. Vogler; Anna Papadopoulou; Brent C. Emerson. 2021. "Connecting high‐throughput biodiversity inventories: Opportunities for a site‐based genomic framework for global integration and synthesis." Molecular Ecology 30, no. 5: 1120-1135.

Contributed paper
Published: 23 December 2020 in Conservation Biology
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Many organisms live in networks of local populations connected by dispersing individuals, called spatially structured populations (SSPs), where the long‐term persistence of the entire network is determined by the balance between two processes acting at the scale of local populations: extinction and colonization. When multiple threats act on an SSP, a comparison of the different factors determining local extinctions and colonizations is essential to plan sound conservation actions. Here we assessed the drivers of long‐term population dynamics of multiple amphibian species at the regional scale. We used dynamic occupancy models within a Bayesian framework to identify the factors determining persistence and colonization of local populations. Since connectivity among patches is fundamental for SSPs dynamics, we considered two measures of connectivity acting on each focal patch: incidence of the focal species and incidence of invasive crayfish. We used meta‐analysis to summarize the effect of different drivers at the community level. Persistence and colonization of local populations were jointly determined by factors acting at different scales. Persistence probability was positively related to the area and the permanence of wetlands, while it showed a negative relationship with the occurrence of fish. Colonization probability was highest in semi‐permanent wetlands and in sites with a high incidence of the focal species in nearby sites, while it showed a negative relationship with the incidence of invasive crayfish in the landscape. By analyzing long‐term data on amphibian population dynamics, we found a strong effect of some classic features commonly used in SSP studies, such as patch area and focal species incidence. The presence of an invasive alien species at the landscape‐scale emerged as one of the strongest drivers of colonization dynamics, suggesting that studies on SSPs should consider different connectivity measures more frequently, such as the incidence of predators, especially when dealing with biological invasions. Article impact statement: The negative impact of invasive alien species at the landscape level is pervasive across the entire community of semi‐aquatic amphibians. This article is protected by copyright. All rights reserved

ACS Style

Mattia Falaschi; Simone Giachello; Elia Lo Parrino; Martina Muraro; Raoul Manenti; Gentile Francesco Ficetola. Long‐term drivers of persistence and colonization dynamics in spatially structured amphibian populations. Conservation Biology 2020, 1 .

AMA Style

Mattia Falaschi, Simone Giachello, Elia Lo Parrino, Martina Muraro, Raoul Manenti, Gentile Francesco Ficetola. Long‐term drivers of persistence and colonization dynamics in spatially structured amphibian populations. Conservation Biology. 2020; ():1.

Chicago/Turabian Style

Mattia Falaschi; Simone Giachello; Elia Lo Parrino; Martina Muraro; Raoul Manenti; Gentile Francesco Ficetola. 2020. "Long‐term drivers of persistence and colonization dynamics in spatially structured amphibian populations." Conservation Biology , no. : 1.

Journal article
Published: 16 December 2020 in Science of The Total Environment
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Environmental factors are well known to affect spatio-temporal patterns of infectious disease outbreaks, but whether the rapid spread of COVID-19 across the globe is related to local environmental conditions is highly debated. We assessed the impact of environmental factors (temperature, humidity and air pollution) on the global patterns of COVID-19 early outbreak dynamics during January–May 2020, controlling for several key socio-economic factors and airport connections. We showed that during the earliest phase of the global outbreak (January–March), COVID-19 growth rates were non-linearly related to climate, with fastest spread in regions with a mean temperature of ca. 5 °C, and in the most polluted regions. However, environmental effects faded almost completely when considering later outbreaks, in keeping with the progressive enforcement of containment actions. Accordingly, COVID-19 growth rates consistently decreased with stringent containment actions during both early and late outbreaks. Our findings indicate that environmental drivers may have played a role in explaining the early variation among regions in disease spread. With limited policy interventions, seasonal patterns of disease spread might emerge, with temperate regions of both hemispheres being most at risk of severe outbreaks during colder months. Nevertheless, containment measures play a much stronger role and overwhelm impacts of environmental variation, highlighting the key role for policy interventions in curbing COVID-19 diffusion within a given region. If the disease will become seasonal in the next years, information on environmental drivers of COVID-19 can be integrated with epidemiological models to inform forecasting of future outbreak risks and improve management plans.

ACS Style

Gentile Francesco Ficetola; Diego Rubolini. Containment measures limit environmental effects on COVID-19 early outbreak dynamics. Science of The Total Environment 2020, 761, 144432 -144432.

AMA Style

Gentile Francesco Ficetola, Diego Rubolini. Containment measures limit environmental effects on COVID-19 early outbreak dynamics. Science of The Total Environment. 2020; 761 ():144432-144432.

Chicago/Turabian Style

Gentile Francesco Ficetola; Diego Rubolini. 2020. "Containment measures limit environmental effects on COVID-19 early outbreak dynamics." Science of The Total Environment 761, no. : 144432-144432.

Journal article
Published: 07 December 2020 in Birds
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The Barn Owl Tyto alba is commonly reported as a non-selective predator of small mammals, and its diet has been thoroughly analyzed also to assess the small mammal assembly composition in many study areas. The aim of this work was to analyze the diet of the Barn Owl in the Elba island through the analysis of 161 pellets collected in September 2020. Undigested fragments were isolated and compared with reference collections. We confirmed that the Barn Owl is a typical predator of field mice (62% of relative frequency), with synanthropic murid rodents as the second category of prey. The frequency of consumption of shrews increased by 9% with respect to the previous work, suggesting that the natural environment of Elba island is still in a good health status. Moreover, fragments of two newborn hares were detected, increasing the knowledge on the local trophic spectrum of the Barn Owl. Finally, the skull of a Geoffroy’s Myotis Myotis emarginatus confirmed the presence of this species in Elba island after over 60 years from the first unconfirmed record. Repeated studies conducted in the same study site may provide useful information on prey population trends and local environmental status.

ACS Style

Miriam Viganò; Leonardo Ancillotto; Paolo Agnelli; Gentile Francesco Ficetola; Emiliano Mori. Frequency of Occurrence and Ingested Biomass of Different Prey of the Barn Owl Tyto alba in an Island Ecosystem. Birds 2020, 1, 5 -12.

AMA Style

Miriam Viganò, Leonardo Ancillotto, Paolo Agnelli, Gentile Francesco Ficetola, Emiliano Mori. Frequency of Occurrence and Ingested Biomass of Different Prey of the Barn Owl Tyto alba in an Island Ecosystem. Birds. 2020; 1 (1):5-12.

Chicago/Turabian Style

Miriam Viganò; Leonardo Ancillotto; Paolo Agnelli; Gentile Francesco Ficetola; Emiliano Mori. 2020. "Frequency of Occurrence and Ingested Biomass of Different Prey of the Barn Owl Tyto alba in an Island Ecosystem." Birds 1, no. 1: 5-12.

Special issue
Published: 04 November 2020 in Molecular Ecology
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Macroinvertebrate assemblages are the most common bioindicators used for stream biomonitoring, yet the standard approach exhibits several time‐consuming steps, including the sorting and identification of organisms based on morphological criteria. In this study, we examined if DNA metabarcoding could be used as an efficient molecular‐based alternative to the morphology‐based monitoring of stream using macroinvertebrates. We compared results achieved with the standard morphological identification of organisms sampled in 18 sites located on 15 French wadeable streams to results obtained with the DNA metabarcoding identification of sorted bulks of the same macroinvertebrate samples, using read numbers (expressed as relative frequencies) as a proxy for abundances. We especially evaluated how combining and filtering metabarcoding data obtained from three different markers (COI: BF1‐BR2, 18S: Euka02 and 16S: Inse01) could improve the efficiency of bioassessment. One hundred and forty taxa were identified based on morphological criteria, and 127 were identified based on DNA metabarcoding using the three markers, with an overlap of 99 taxa. The threshold values used for sequence filtering based on the “best identity” criterion and the number of reads had an effect on the assessment efficiency of data obtained with each marker. Compared to single marker results, combining data from different markers allowed improving the match between biotic index values obtained with the bulk‐DNA versus morphology‐based approaches. Both approaches assigned the same ecological quality class to a majority (86%) of the site sampling events, highlighting both the efficiency of metabarcoding as a biomonitoring tool but also the need for further research to improve this efficiency.

ACS Style

Albin Meyer; Frédéric Boyer; Alice Valentini; Aurélie Bonin; Gentile Francesco Ficetola; Jean‐Nicolas Beisel; Jonathan Bouquerel; Philippe Wagner; Coline Gaboriaud; Florian Leese; Tony Dejean; Pierre Taberlet; Philippe Usseglio‐Polatera. Morphological vs. DNA metabarcoding approaches for the evaluation of stream ecological status with benthic invertebrates: Testing different combinations of markers and strategies of data filtering. Molecular Ecology 2020, 30, 3203 -3220.

AMA Style

Albin Meyer, Frédéric Boyer, Alice Valentini, Aurélie Bonin, Gentile Francesco Ficetola, Jean‐Nicolas Beisel, Jonathan Bouquerel, Philippe Wagner, Coline Gaboriaud, Florian Leese, Tony Dejean, Pierre Taberlet, Philippe Usseglio‐Polatera. Morphological vs. DNA metabarcoding approaches for the evaluation of stream ecological status with benthic invertebrates: Testing different combinations of markers and strategies of data filtering. Molecular Ecology. 2020; 30 (13):3203-3220.

Chicago/Turabian Style

Albin Meyer; Frédéric Boyer; Alice Valentini; Aurélie Bonin; Gentile Francesco Ficetola; Jean‐Nicolas Beisel; Jonathan Bouquerel; Philippe Wagner; Coline Gaboriaud; Florian Leese; Tony Dejean; Pierre Taberlet; Philippe Usseglio‐Polatera. 2020. "Morphological vs. DNA metabarcoding approaches for the evaluation of stream ecological status with benthic invertebrates: Testing different combinations of markers and strategies of data filtering." Molecular Ecology 30, no. 13: 3203-3220.

Special issue
Published: 08 October 2020 in Molecular Ecology
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Environmental DNA metabarcoding is becoming a key tool for biodiversity monitoring over large geographical or taxonomic scales and for elusive taxa like soil organisms. Increasing sample sizes and interest in remote or extreme areas often require the preservation of soil samples and thus deviations from optimal standardized protocols. However, we still ignore the impact of different methods of soil sample preservation on the results of metabarcoding studies and there is no guideline for best practices so far. Here, we assessed the impact of four methods of soil sample preservation that can be conveniently used also in metabarcoding studies targeting remote or difficult to access areas. Tested methods include: preservation at room temperature for 6h, preservation at 4°C for three days, desiccation immediately after sampling and preservation for 21 days, and desiccation after 6h at room temperature and preservation for 21 days. For each preservation method, we benchmarked resulting estimates of taxon diversity and community composition of three different taxonomic groups (bacteria, fungi and eukaryotes) in three different habitats (forest, river bank and grassland) against results obtained under ideal conditions (i.e. extraction of eDNA right after sampling). Overall, the different preservation methods only marginally impaired results and only under certain conditions. When rare taxa were considered, we detected small but significant changes in MOTU richness of bacteria, fungi and eukaryotes across treatments, but MOTUs richness was similar across preservation methods if rare taxa were not considered. All the approaches were able to identify differences in community structure among habitats, and the communities retrieved using the different preservation conditions were extremely similar. We propose guidelines on the selection of the optimal soil sample preservation conditions for metabarcoding studies, depending on the practical constraints, costs and ultimate research goals.

ACS Style

Alessia Guerrieri; Aurélie Bonin; Tamara Münkemüller; Ludovic Gielly; Wilfried Thuiller; Gentile Francesco Ficetola. Effects of soil preservation for biodiversity monitoring using environmental DNA. Molecular Ecology 2020, 1 .

AMA Style

Alessia Guerrieri, Aurélie Bonin, Tamara Münkemüller, Ludovic Gielly, Wilfried Thuiller, Gentile Francesco Ficetola. Effects of soil preservation for biodiversity monitoring using environmental DNA. Molecular Ecology. 2020; ():1.

Chicago/Turabian Style

Alessia Guerrieri; Aurélie Bonin; Tamara Münkemüller; Ludovic Gielly; Wilfried Thuiller; Gentile Francesco Ficetola. 2020. "Effects of soil preservation for biodiversity monitoring using environmental DNA." Molecular Ecology , no. : 1.

Special issue
Published: 13 September 2020 in Molecular Ecology
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Metabarcoding of bulk or environmental DNA has great potential for biomonitoring freshwater environments. However, successful application of metabarcoding to biodiversity monitoring requires universal primers with high taxonomic coverage that amplify highly variable, short metabarcodes with high taxonomic resolution. Moreover, reliable and extensive reference databases are essential to match the outcome of metabarcoding analyses with the available taxonomy and biomonitoring indices. Benthic invertebrates, particularly insects, are key taxa for freshwater bioassessment. Nevertheless, few studies have so far assessed markers for metabarcoding of freshwater macrobenthos. Here we combined in silico and laboratory analyses to test the performance of different markers amplifying regions in the 18S rDNA (Euka02), 16S rDNA (Inse01), and COI (BF1_BR2‐COI) genes, and developed an extensive database of benthic macroinvertebrates of France and Europe, with a special focus on key insect orders (Ephemeroptera, Plecoptera and Trichoptera). Analyses on 1514 individuals representing different taxa of benthic macroinvertebrates showed very different amplification success across primer combinations. The Euka02 marker showed the highest universality, while the Inse01 marker showed excellent performance for the amplification of insects. BF1_BR2‐COI showed the highest resolution, while the resolution of Euka02 was often limited. By combining our data with GenBank information, we developed a curated database including sequences representing 822 genera. The heterogeneous performance of the different primers highlights the complexity of the identification of the best markers, and advocates for the integration of multiple metabarcodes for a more comprehensive and accurate understanding of ecological impacts on freshwater biodiversity.

ACS Style

Gentile Francesco Ficetola; Frédéric Boyer; Alice Valentini; Aurélie Bonin; Albin Meyer; Tony Dejean; Coline Gaboriaud; Philippe Usseglio‐Polatera; Pierre Taberlet. Comparison of markers for the monitoring of freshwater benthic biodiversity through DNA metabarcoding. Molecular Ecology 2020, 1 .

AMA Style

Gentile Francesco Ficetola, Frédéric Boyer, Alice Valentini, Aurélie Bonin, Albin Meyer, Tony Dejean, Coline Gaboriaud, Philippe Usseglio‐Polatera, Pierre Taberlet. Comparison of markers for the monitoring of freshwater benthic biodiversity through DNA metabarcoding. Molecular Ecology. 2020; ():1.

Chicago/Turabian Style

Gentile Francesco Ficetola; Frédéric Boyer; Alice Valentini; Aurélie Bonin; Albin Meyer; Tony Dejean; Coline Gaboriaud; Philippe Usseglio‐Polatera; Pierre Taberlet. 2020. "Comparison of markers for the monitoring of freshwater benthic biodiversity through DNA metabarcoding." Molecular Ecology , no. : 1.

Journal article
Published: 31 August 2020 in Diversity
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Usually, biospeleological studies focus on cave-specialist taxa showing strong adaptation to the subterranean environment, as their unusual morphological and ecological features represent intriguing case studies. On the other hand, species occurring in subterranean environments but without marked adaptations have been generally overlooked, probably because they are thought to be accidental and not very important for the ecosystem. Particularly exemplificative is the case of Tipuloidea crane flies (Diptera), which although abundant, are rarely considered in biospeleological studies. Here, by analyzing the crane fly occupancy, we observed that individuals occur within the shallowest areas of subterranean environments throughout the year, with a peak of presence during hot season. Crane flies occupy dark and warm areas close to the connection with surface and with smoother walls. Furthermore, we observed that the presence of crane flies is positively related to the abundance and the richness of cave predators, highlighting their importance for the sustainment of the local community. With this study we aim to stimulate future researches on these important, but still neglected cave species.

ACS Style

Enrico Lunghi; Gentile Francesco Ficetola; Yahui Zhao; Raoul Manenti. Are the Neglected Tipuloidea Crane Flies (Diptera) an Important Component for Subterranean Environments? Diversity 2020, 12, 333 .

AMA Style

Enrico Lunghi, Gentile Francesco Ficetola, Yahui Zhao, Raoul Manenti. Are the Neglected Tipuloidea Crane Flies (Diptera) an Important Component for Subterranean Environments? Diversity. 2020; 12 (9):333.

Chicago/Turabian Style

Enrico Lunghi; Gentile Francesco Ficetola; Yahui Zhao; Raoul Manenti. 2020. "Are the Neglected Tipuloidea Crane Flies (Diptera) an Important Component for Subterranean Environments?" Diversity 12, no. 9: 333.

Biodiversity research
Published: 26 August 2020 in Diversity and Distributions
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Aim Climate change is expected to cause mountain species to shift their ranges to higher elevations. Due to the decreasing amounts of habitats with increasing elevation, such shifts are likely to increase their extinction risk. Heterogeneous mountain topography, however, may reduce this risk by providing microclimatic conditions that can buffer macroclimatic warming or provide nearby refugia. As aspect strongly influences the local microclimate, we here assess whether shifts from warm south‐exposed aspects to cool north‐exposed aspects in response to climate change can compensate for an upward shift into cooler elevations. Location Switzerland, Swiss Alps. Methods We built ensemble distribution models using high‐resolution climate data for two mountain‐dwelling viviparous ectotherms, the Alpine salamander and the Common lizard, and projected them into various future scenarios to gain insights into distributional changes. We further compared elevation and aspect (northness) of current and predicted future locations to analyse preferences and future shifts. Results Future ranges were consistently decreasing for the lizard, but for the salamander they were highly variable, depending on the climate scenario and threshold rule. Aspect preferences were elevation‐dependent: warmer, south‐exposed microclimates were clearly preferred at higher compared to lower elevations. In terms of presence and future locations, we observed both elevational upward shifts and northward shifts in aspect. Under future conditions, the shift to cooler north‐exposed aspects was particularly pronounced at already warmer lower elevations. Main conclusions For our study species, shifts in aspect and elevation are complementary strategies to mitigate climatic warming in the complex mountain topography. This complements the long‐standing view of elevational upward shift being their only option to move into areas with suitable future climate. High‐resolution climate data are critical in heterogeneous environments to identify microrefugia and thereby improving future impact assessments of climate change.

ACS Style

Stephan Feldmeier; Benedikt R. Schmidt; Niklaus E. Zimmermann; Michael Veith; Gentile Francesco Ficetola; Stefan Lötters. Shifting aspect or elevation? The climate change response of ectotherms in a complex mountain topography. Diversity and Distributions 2020, 26, 1483 -1495.

AMA Style

Stephan Feldmeier, Benedikt R. Schmidt, Niklaus E. Zimmermann, Michael Veith, Gentile Francesco Ficetola, Stefan Lötters. Shifting aspect or elevation? The climate change response of ectotherms in a complex mountain topography. Diversity and Distributions. 2020; 26 (11):1483-1495.

Chicago/Turabian Style

Stephan Feldmeier; Benedikt R. Schmidt; Niklaus E. Zimmermann; Michael Veith; Gentile Francesco Ficetola; Stefan Lötters. 2020. "Shifting aspect or elevation? The climate change response of ectotherms in a complex mountain topography." Diversity and Distributions 26, no. 11: 1483-1495.

Journal article
Published: 17 July 2020 in Nature Communications
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Invasive predators can exert strong selection on native populations. If selection is strong enough, populations could lose the phenotypic variation caused by adaptation to heterogeneous environments. We compare frog tadpoles prior to and 14 years following invasion by crayfish. Prior to the invasion, populations differed in their intrinsic developmental rate, with tadpoles from cold areas reaching metamorphosis sooner than those from warm areas. Following the invasion, tadpoles from invaded populations develop faster than those from non-invaded populations. This ontogenetic shift overwhelmed the intraspecific variation between populations in a few generations, to the point where invaded populations develop at a similar rate regardless of climate. Rapid development can have costs, as fast-developing froglets have a smaller body size and poorer jumping performance, but compensatory growth counteracts some costs of development acceleration. Strong selection by invasive species can disrupt local adaptations by dampening intraspecific phenotypic variation, with complex consequences on lifetime fitness.

ACS Style

Andrea Melotto; Raoul Manenti; Gentile Francesco Ficetola. Rapid adaptation to invasive predators overwhelms natural gradients of intraspecific variation. Nature Communications 2020, 11, 1 -10.

AMA Style

Andrea Melotto, Raoul Manenti, Gentile Francesco Ficetola. Rapid adaptation to invasive predators overwhelms natural gradients of intraspecific variation. Nature Communications. 2020; 11 (1):1-10.

Chicago/Turabian Style

Andrea Melotto; Raoul Manenti; Gentile Francesco Ficetola. 2020. "Rapid adaptation to invasive predators overwhelms natural gradients of intraspecific variation." Nature Communications 11, no. 1: 1-10.