Browsing by Author "Mammola, Stefano"
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- Calculating functional diversity metrics using neighbor‐joining treesPublication . Cardoso, Pedro; Guillerme, Thomas; Mammola, Stefano; Matthews, Thomas J.; Rigal, Francois; Graco‐Roza, Caio; Stahls, Gunilla; Carlos Carvalho, JoseThe study of functional diversity (FD) provides ways to understand phenomena as complex as community assembly or the dynamics of biodiversity change under multiple pressures. Different frameworks are used to quantify FD, either based on dissimilarity matrices (e.g. Rao entropy, functional dendrograms) or multidimensional spaces (e.g. convex hulls, kernel-density hypervolumes), each with their own strengths and limits. Frameworks based on dissimilarity matrices either do not enable the measurement of all components of FD (i.e. richness, divergence, and regularity), or result in the distortion of the functional space. Frameworks based on multidimensional spaces do not allow for comparisons with phylogenetic diversity (PD) measures and can be sensitive to outliers. We propose the use of neighbor-joining trees (NJ) to represent and quantify FD in a way that combines the strengths of current frameworks without many of their weaknesses. Importantly, our approach is uniquely suited for studies that compare FD with PD, as both share the use of trees (NJ or others) and the same mathematical principles. We test the ability of this novel framework to represent the initial functional distances between species with minimal functional space distortion and sensitivity to outliers. The results using NJ are compared with conventional functional dendrograms, convex hulls, and kernel-density hypervolumes using both simulated and empirical datasets. Using NJ, we demonstrate that it is possible to combine much of the flexibility provided by multidimensional spaces with the simplicity of tree-based representations. Moreover, the method is directly comparable with taxonomic diversity (TD) and PD measures, and enables quantification of the richness, divergence and regularity of the functional space.
- Functional convergence underground? The scale‐dependency of community assembly processes in European cave spidersPublication . Mammola, Stefano; Graco‐Roza, Caio; Ballarin, Francesco; Hesselberg, Thomas; Isaia, Marco; Lunghi, Enrico; Mouron, Samuel; Pavlek, Martina; Tolve, Marco; Cardoso, PedroAim Quantifying the relative contribution of environmental filtering versus limiting similarity in shaping communities is challenging because these processes often act simultaneously and their effect is scale-dependent. Focusing on caves, island-like natural laboratories with limited environmental variability and species diversity, we tested: (i) the relative contribution of environmental filtering and limiting similarity in determining community assembly in caves; (ii) how the relative contribution of these driving forces changes along environmental gradients. Location Europe. Time period Present. Major taxa studied Subterranean spiders. Methods We used data on distribution and traits for European cave spiders (n = 475 communities). We estimated the trait space of each community using probabilistic hypervolumes, and obtained estimations of functional richness independent of the species richness of each community via null modelling. We model functional diversity change along environmental gradients using generalized dissimilarity modelling. Results Sixty-three percent of subterranean spider communities exhibited a prevalence of trait underdispersion. However, most communities displayed trait dispersion that did not depart significantly from random, suggesting that environmental filtering and limiting similarity were both exerting equally weak or strong, yet opposing influences. Overdispersed communities were primarily concentrated in southern latitudes, particularly in the Dinaric karst, where there is greater subterranean habitat availability. Pairwise comparisons of functional richness across caves revealed these effects to be strongly scale-dependent, largely varying across gradients of cave development, elevation, precipitation, entrance size and annual temperature range. Conversely, geographical distance weakly affected trait composition, suggesting convergence in traits among communities that are far apart. Main conclusions Even systems with stringent environmental conditions maintain the potential for trait differentiation, especially in areas of greater habitat availability. Yet, the relative influence of environmental filtering and limiting similarity change with scale, along clear environmental gradients. The interplay of these processes may explain the assembly of species-poor subterranean communities displaying high functional specialization.
- Fundamental research questions in subterranean biologyPublication . Mammola, Stefano; Amorim, Isabel R.; Bichuette, Maria E.; Borges, P.A.V.; Cheeptham, Naowarat; Cooper, Steven J. B.; Culver, David C.; Deharveng, Louis; Eme, David; Ferreira, Rodrigo Lopes; Fišer, Cene; Fišer, Žiga; Fong, Daniel W.; Griebler, Christian; Jeffery, William R.; Jugovic, Jure; Kowalko, Johanna E.; Lilley, Thomas M.; Malard, Florian; Manenti, Raoul; Martínez, Alejandro; Meierhofer, Melissa B.; Niemiller, Matthew L.; Northup, Diana E.; Pellegrini, Thais G.; Pipan, Tanja; Protas, Meredith; Sofia Reboleira, Ana; Venarsky, Michael P.; Wynne, J. Judson; Zagmajster, Maja; Cardoso, PedroFive decades ago, a landmark paper in Science titled The Cave Environment heralded caves as ideal natural experimental laboratories in which to develop and address general questions in geology, ecology, biogeography, and evolutionary biology. Although the ‘caves as laboratory’ paradigm has since been advocated by subterranean biologists, there are few examples of studies that successfully translated their results into general principles. The contemporary era of big data, modelling tools, and revolutionary advances in genetics and (meta)genomics provides an opportunity to revisit unresolved questions and challenges, as well as examine promising new avenues of research in subterranean biology. Accordingly, we have developed a roadmap to guide future research endeavours in subterranean biology by adapting a well-established methodology of ‘horizon scanning’ to identify the highest priority research questions across six subject areas. Based on the expert opinion of 30 scientists from around the globe with complementary expertise and of different academic ages, we assembled an initial list of 258 fundamental questions concentrating on macroecology and microbial ecology, adaptation, evolution, and conservation. Subsequently, through online surveys, 130 subterranean biologists with various backgrounds assisted us in reducing our list to 50 top-priority questions. These research questions are broad in scope and ready to be addressed in the next decade. We believe this exercise will stimulate research towards a deeper understanding of subterranean biology and foster hypothesis-driven studies likely to resonate broadly from the traditional boundaries of this field.
- Future climate change will severely reduce habitat suitability of the Critically Endangered Chinese giant salamanderPublication . Zhang, Zhixin; Mammola, Stefano; Liang, Zhiqiang; Capinha, César; Wei, Qiwei; Wu, Yuanan; Zhou, Jin; Wang, Chongrui1. Being the largest extant amphibian in the world, the IUCN Critically Endangered Chinese giant salamander Andrias davidianus is a charismatic species with great international public interest. While threats such as commercial overexploitation and habitat degradation have been extensively documented to affect natural populations of A. davidianus, still no information is available about the species sensitivity to climate change. 2. Here, we develop an ensemble of species distribution models (SDMs) for A. davidianus and projected its habitat suitability under present-day and future climate change scenarios. We based our SDMs on bioclimatic and topographic predictors, and recent (2012–2018) field-collected occurrence data across the whole distribution range of the species. 3. The ensemble SDMs exhibited good predictive capacity and suggested that slope, maximum temperature of warmest month, precipitation of driest month, and isothermality are the most influential predictors in determining distribution patterns in this species. The projections of our models point to a pronounced impact of climate changes over A. davidianus, with more than two-thirds of its suitable range expected to be lost in all scenarios of future climates tested. 4. In concert with the numerous other threats that are affecting this species, climate change poses a serious hindrance to the long-term survival of A. davidianus. We emphasise the urgent need of undertaking strict measures to manage this species and safeguard the few remaining available suitable habitats. We suggest that adaptive management strategies including designation of new reserves should be considered to mitigate the impacts of climate change on A. davidianus.
- Groundwater is a hidden global keystone ecosystemPublication . Saccò, Mattia; Mammola, Stefano; Altermatt, Florian; Alther, Roman; Bolpagni, Rossano; Brancelj, Anton; Brankovits, David; Fišer, Cene; Gerovasileiou, Vasilis; Griebler, Christian; Guareschi, Simone; Hose, Grant C.; Korbel, Kathryn; Lictevout, Elisabeth; Malard, Florian; Martínez, Alejandro; Niemiller, Matthew L.; Robertson, Anne; Tanalgo, Krizler C.; Bichuette, Maria Elina; Borko, Špela; Brad, Traian; Campbell, Matthew A.; Cardoso, Pedro; Celico, Fulvio; Cooper, Steven J. B.; Culver, David; Di Lorenzo, Tiziana; Galassi, Diana M. P.; Guzik, Michelle T.; Hartland, Adam; Humphreys, William F.; Ferreira, Rodrigo Lopes; Lunghi, Enrico; Nizzoli, Daniele; Perina, Giulia; Raghavan, Rajeev; Richards, Zoe; Sofia Reboleira, Ana; Rohde, Melissa M.; Fernández, David Sánchez; Schmidt, Susanne I.; van der Heyde, Mieke; Weaver, Louise; White, Nicole E.; Zagmajster, Maja; Hogg, Ian; Ruhi, Albert; Gagnon, Marthe M.; Allentoft, Morten E.; Reinecke, RobertGroundwater is a vital ecosystem of the global water cycle, hosting unique biodiversity and providing essential services to societies. Despite being the largest unfrozen freshwater resource, in a period of depletion by extraction and pollution, groundwater environments have been repeatedly overlooked in global biodiversity conservation agendas. Disregarding the importance of groundwater as an ecosystem ignores its critical role in preserving surface biomes. To foster timely global conservation of groundwater, we propose elevating the concept of keystone species into the realm of ecosystems, claiming groundwater as a keystone ecosystem that influences the integrity of many dependent ecosystems. Our global analysis shows that over half of land surface areas (52.6%) has a medium-to-high interaction with groundwater, reaching up to 74.9% when deserts and high mountains are excluded. We postulate that the intrinsic transboundary features of groundwater are critical for shifting perspectives towards more holistic approaches in aquatic ecology and beyond. Furthermore, we propose eight key themes to develop a science-policy integrated groundwater conservation agenda. Given ecosystems above and below the ground intersect at many levels, considering groundwater as an essential component of planetary health is pivotal to reduce biodiversity loss and buffer against climate change.
- To invade or not to invade? Exploring the niche-based processes underlying the failure of a biological invasion using the invasive Chinese mitten crabPublication . Zhang, Zhixin; Mammola, Stefano; McLay, Colin L.; Capinha, César; Yokota, MasashiInvasive alien species represent a serious threat to global biodiversity, causing considerable damage to native ecosystems. To better assess invasion risks, it is essential to better understand the biological processes that determine the success or failure of invasions. The catadromous Chinese mitten crab Eriocheir sinensis, whose native distribution is the Pacific Coast of China and Korea, has successfully invaded and established populations in North America and Europe. In Japan, where E. sinensis is also regarded as potentially invasive and multiple introduction vectors exist, the species is not yet established. These settings can be used to explore niche-based processes underlying the apparent failure of a biological invasion. We first quantified native and invasive realized niches of E. sinensis in freshwater habitats using geometrical n-dimensional hypervolumes. Based on the assumption of niche conservatism, we then projected habitat suitability of this species in Japan using species distribution models (SDMs) calibrated with distinct sets of distribution data: native occurrences, invasive occurrences, and both. Results showed that E. sinensis has undergone either niche shifts or niche contractions during invasions in different areas of the world. Projections from SDMs indicate that although part of Japan is suitable for E. sinensis, this does not include the freshwater habitats around the Ariake Sea, which is considered to be a suitable marine environment for E. sinensis larvae. The mismatch between suitable freshwater and marine environments provides a possible explanation for the failure of establishment of E. sinensis in Japan to date. Our findings have useful general implications for the interpretation of biological invasions.