@article{FigueiredoKraussSteffanDewenteretal.2019, author = {Figueiredo, Ludmilla and Krauss, Jochen and Steffan-Dewenter, Ingolf and Cabral, Juliano Sarmento}, title = {Understanding extinction debts: spatio-temporal scales, mechanisms and a roadmap for future research}, series = {Ecography}, volume = {42}, journal = {Ecography}, number = {12}, doi = {10.1111/ecog.04740}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-204859}, pages = {1973-1990}, year = {2019}, abstract = {Extinction debt refers to delayed species extinctions expected as a consequence of ecosystem perturbation. Quantifying such extinctions and investigating long-term consequences of perturbations has proven challenging, because perturbations are not isolated and occur across various spatial and temporal scales, from local habitat losses to global warming. Additionally, the relative importance of eco-evolutionary processes varies across scales, because levels of ecological organization, i.e. individuals, (meta)populations and (meta)communities, respond hierarchically to perturbations. To summarize our current knowledge of the scales and mechanisms influencing extinction debts, we reviewed recent empirical, theoretical and methodological studies addressing either the spatio-temporal scales of extinction debts or the eco-evolutionary mechanisms delaying extinctions. Extinction debts were detected across a range of ecosystems and taxonomic groups, with estimates ranging from 9 to 90\% of current species richness. The duration over which debts have been sustained varies from 5 to 570 yr, and projections of the total period required to settle a debt can extend to 1000 yr. Reported causes of delayed extinctions are 1) life-history traits that prolong individual survival, and 2) population and metapopulation dynamics that maintain populations under deteriorated conditions. Other potential factors that may extend survival time such as microevolutionary dynamics, or delayed extinctions of interaction partners, have rarely been analyzed. Therefore, we propose a roadmap for future research with three key avenues: 1) the microevolutionary dynamics of extinction processes, 2) the disjunctive loss of interacting species and 3) the impact of multiple regimes of perturbation on the payment of debts. For their ability to integrate processes occurring at different levels of ecological organization, we highlight mechanistic simulation models as tools to address these knowledge gaps and to deepen our understanding of extinction dynamics.}, language = {en} } @article{LewerentzHoffmannSarmentoCabral2021, author = {Lewerentz, Anne and Hoffmann, Markus and Sarmento Cabral, Juliano}, title = {Depth diversity gradients of macrophytes: Shape, drivers, and recent shifts}, series = {Ecology and Evolution}, volume = {11}, journal = {Ecology and Evolution}, number = {20}, doi = {10.1002/ece3.8089}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-260280}, pages = {13830-13845}, year = {2021}, abstract = {Investigating diversity gradients helps to understand biodiversity drivers and threats. However, one diversity gradient is rarely assessed, namely how plant species distribute along the depth gradient of lakes. Here, we provide the first comprehensive characterization of depth diversity gradient (DDG) of alpha, beta, and gamma species richness of submerged macrophytes across multiple lakes. We characterize the DDG for additive richness components (alpha, beta, gamma), assess environmental drivers, and address temporal change over recent years. We take advantage of yet the largest dataset of macrophyte occurrence along lake depth (274 depth transects across 28 deep lakes) as well as of physiochemical measurements (12 deep lakes from 2006 to 2017 across Bavaria), provided publicly online by the Bavarian State Office for the Environment. We found a high variability in DDG shapes across the study lakes. The DDGs for alpha and gamma richness are predominantly hump-shaped, while beta richness shows a decreasing DDG. Generalized additive mixed-effect models indicate that the depth of the maximum richness (Dmax) is influenced by light quality, light quantity, and layering depth, whereas the respective maximum alpha richness within the depth gradient (Rmax) is significantly influenced by lake area only. Most observed DDGs seem generally stable over recent years. However, for single lakes we found significant linear trends for Rmax and Dmax going into different directions. The observed hump-shaped DDGs agree with three competing hypotheses: the mid-domain effect, the mean-disturbance hypothesis, and the mean-productivity hypothesis. The DDG amplitude seems driven by lake area (thus following known species-area relationships), whereas skewness depends on physiochemical factors, mainly water transparency and layering depth. Our results provide insights for conservation strategies and for mechanistic frameworks to disentangle competing explanatory hypotheses for the DDG.}, language = {en} } @article{VedderLeidingerSarmentoCabral2021, author = {Vedder, Daniel and Leidinger, Ludwig and Sarmento Cabral, Juliano}, title = {Propagule pressure and an invasion syndrome determine invasion success in a plant community model}, series = {Ecology and Evolution}, volume = {11}, journal = {Ecology and Evolution}, number = {23}, doi = {10.1002/ece3.8348}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-259107}, pages = {17106-17116}, year = {2021}, abstract = {The success of species invasions depends on multiple factors, including propagule pressure, disturbance, productivity, and the traits of native and non-native species. While the importance of many of these determinants has already been investigated in relative isolation, they are rarely studied in combination. Here, we address this shortcoming by exploring the effect of the above-listed factors on the success of invasions using an individual-based mechanistic model. This approach enables us to explicitly control environmental factors (temperature as surrogate for productivity, disturbance, and propagule pressure) as well as to monitor whole-community trait distributions of environmental adaptation, mass, and dispersal abilities. We simulated introductions of plant individuals to an oceanic island to assess which factors and species traits contribute to invasion success. We found that the most influential factors were higher propagule pressure and a particular set of traits. This invasion trait syndrome was characterized by a relative similarity in functional traits of invasive to native species, while invasive species had on average higher environmental adaptation, higher body mass, and increased dispersal distances, that is, had greater competitive and dispersive abilities. Our results highlight the importance in management practice of reducing the import of alien species, especially those that display this trait syndrome and come from similar habitats as those being managed.}, language = {en} } @article{BowlerBjorkmanDornelasetal.2020, author = {Bowler, Diana E. and Bjorkman, Anne D. and Dornelas, Maria and Myers-Smith, Isla H. and Navarro, Laetitia M. and Niamir, Aidin and Supp, Sarah R. and Waldock, Conor and Winter, Marten and Vellend, Mark and Blowes, Shane A. and B{\"o}hning-Gaese, Katrin and Bruelheide, Helge and Elahi, Robin and Ant{\~a}o, Laura H. and Hines, Jes and Isbell, Forest and Jones, Holly P. and Magurran, Anne E. and Cabral, Juliano Sarmento and Bates, Amanda E.}, title = {Mapping human pressures on biodiversity across the planet uncovers anthropogenic threat complexes}, series = {People and Nature}, volume = {2}, journal = {People and Nature}, number = {2}, doi = {10.1002/pan3.10071}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-213634}, pages = {380 -- 394}, year = {2020}, abstract = {Climate change and other anthropogenic drivers of biodiversity change are unequally distributed across the world. Overlap in the distributions of different drivers have important implications for biodiversity change attribution and the potential for interactive effects. However, the spatial relationships among different drivers and whether they differ between the terrestrial and marine realm has yet to be examined. We compiled global gridded datasets on climate change, land-use, resource exploitation, pollution, alien species potential and human population density. We used multivariate statistics to examine the spatial relationships among the drivers and to characterize the typical combinations of drivers experienced by different regions of the world. We found stronger positive correlations among drivers in the terrestrial than in the marine realm, leading to areas with high intensities of multiple drivers on land. Climate change tended to be negatively correlated with other drivers in the terrestrial realm (e.g. in the tundra and boreal forest with high climate change but low human use and pollution), whereas the opposite was true in the marine realm (e.g. in the Indo-Pacific with high climate change and high fishing). We show that different regions of the world can be defined by Anthropogenic Threat Complexes (ATCs), distinguished by different sets of drivers with varying intensities. We identify 11 ATCs that can be used to test hypotheses about patterns of biodiversity and ecosystem change, especially about the joint effects of multiple drivers. Our global analysis highlights the broad conservation priorities needed to mitigate the impacts of anthropogenic change, with different priorities emerging on land and in the ocean, and in different parts of the world.}, language = {en} } @article{VedderLensMartinetal.2022, author = {Vedder, Daniel and Lens, Luc and Martin, Claudia A. and Pellikka, Petri and Adhikari, Hari and Heiskanen, Janne and Engler, Jan O. and Sarmento Cabral, Juliano}, title = {Hybridization may aid evolutionary rescue of an endangered East African passerine}, series = {Evolutionary Applications}, volume = {15}, journal = {Evolutionary Applications}, number = {7}, doi = {10.1111/eva.13440}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-287264}, pages = {1177-1188}, year = {2022}, abstract = {Abstract Introgressive hybridization is a process that enables gene flow across species barriers through the backcrossing of hybrids into a parent population. This may make genetic material, potentially including relevant environmental adaptations, rapidly available in a gene pool. Consequently, it has been postulated to be an important mechanism for enabling evolutionary rescue, that is the recovery of threatened populations through rapid evolutionary adaptation to novel environments. However, predicting the likelihood of such evolutionary rescue for individual species remains challenging. Here, we use the example of Zosterops silvanus, an endangered East African highland bird species suffering from severe habitat loss and fragmentation, to investigate whether hybridization with its congener Zosterops flavilateralis might enable evolutionary rescue of its Taita Hills population. To do so, we employ an empirically parameterized individual-based model to simulate the species' behaviour, physiology and genetics. We test the population's response to different assumptions of mating behaviour and multiple scenarios of habitat change. We show that as long as hybridization does take place, evolutionary rescue of Z. silvanus is likely. Intermediate hybridization rates enable the greatest long-term population growth, due to trade-offs between adaptive and maladaptive introgressed alleles. Habitat change did not have a strong effect on population growth rates, as Z. silvanus is a strong disperser and landscape configuration is therefore not the limiting factor for hybridization. Our results show that targeted gene flow may be a promising avenue to help accelerate the adaptation of endangered species to novel environments, and demonstrate how to combine empirical research and mechanistic modelling to deliver species-specific predictions for conservation planning.}, language = {en} } @article{VedderAnkenbrandSarmentoCabral2021, author = {Vedder, Daniel and Ankenbrand, Markus and Sarmento Cabral, Juliano}, title = {Dealing with software complexity in individual-based models}, series = {Methods in Ecology and Evolution}, volume = {12}, journal = {Methods in Ecology and Evolution}, number = {12}, doi = {10.1111/2041-210X.13716}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-258214}, pages = {2324-2333}, year = {2021}, abstract = {Individual-based models are doubly complex: as well as representing complex ecological systems, the software that implements them is complex in itself. Both forms of complexity must be managed to create reliable models. However, the ecological modelling literature to date has focussed almost exclusively on the biological complexity. Here, we discuss methods for containing software complexity. Strategies for containing complexity include avoiding, subdividing, documenting and reviewing it. Computer science has long-established techniques for all of these strategies. We present some of these techniques and set them in the context of IBM development, giving examples from published models. Techniques for avoiding software complexity are following best practices for coding style, choosing suitable programming languages and file formats and setting up an automated workflow. Complex software systems can be made more tractable by encapsulating individual subsystems. Good documentation needs to take into account the perspectives of scientists, users and developers. Code reviews are an effective way to check for errors, and can be used together with manual or automated unit and integration tests. Ecological modellers can learn from computer scientists how to deal with complex software systems. Many techniques are readily available, but must be disseminated among modellers. There is a need for further work to adapt software development techniques to the requirements of academic research groups and individual-based modelling.}, language = {en} } @article{WohlwendCravenWeigeltetal.2021, author = {Wohlwend, Michael R. and Craven, Dylan and Weigelt, Patrick and Seebens, Hanno and Winter, Marten and Kreft, Holger and Zurell, Damaris and Sarmento Cabral, Juliano and Essl, Franz and van Kleunen, Mark and Pergl, Jan and Pyšek, Petr and Knight, Tiffany M.}, title = {Anthropogenic and environmental drivers shape diversity of naturalized plants across the Pacific}, series = {Diversity and Distributions}, volume = {27}, journal = {Diversity and Distributions}, number = {6}, doi = {10.1111/ddi.13260}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-239925}, pages = {1120 -- 1133}, year = {2021}, abstract = {Aim The Pacific exhibits an exceptional number of naturalized plant species, but the drivers of this high diversity and the associated compositional patterns remain largely unknown. Here, we aim to (a) improve our understanding of introduction and establishment processes and (b) evaluate whether this information is sufficient to create scientific conservation tools, such as watchlists. Location Islands in the Pacific Ocean, excluding larger islands such as New Zealand, Japan, the Philippines and Indonesia. Methods We combined information from the most up-to-date data sources to quantify naturalized plant species richness and turnover across island groups and investigate the effects of anthropogenic, biogeographic and climate drivers on these patterns. In total, we found 2,672 naturalized plant species across 481 islands and 50 island groups, with a total of 11,074 records. Results Most naturalized species were restricted to few island groups, and most island groups have a low number of naturalized species. Island groups with few naturalized species were characterized by a set of widespread naturalized species. Several plant families that contributed many naturalized species globally also did so in the Pacific, particularly Fabaceae and Poaceae. However, many families were significantly over- or under-represented in the Pacific naturalized flora compared to other regions of the world. Naturalized species richness increased primarily with increased human activity and island altitude/area, whereas similarity between island groups in temperature along with richness differences was most important for beta diversity. Main conclusions The distribution and richness of naturalized species can be explained by a small set of drivers. The Pacific region contains many naturalized plant species also naturalized in other regions in the world, but our results highlight key differences such as a stronger role of anthropogenic drivers in shaping diversity patterns. Our results establish a basis for predicting and preventing future naturalizations in a threatened biodiversity hotspot.}, language = {en} } @article{LeidingerVedderCabral2021, author = {Leidinger, Ludwig and Vedder, Daniel and Cabral, Juliano Sarmento}, title = {Temporal environmental variation may impose differential selection on both genomic and ecological traits}, series = {Oikos}, volume = {130}, journal = {Oikos}, number = {7}, doi = {10.1111/oik.08172}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-238945}, pages = {1100 -- 1115}, year = {2021}, abstract = {The response of populations and species to changing conditions determines how community composition will change functionally, including via trait shifts. Selection from standing variation has been suggested to be more efficient than acquiring new mutations. Yet, studies on community trait composition and trait selection largely focus on phenotypic variation in ecological traits, whereas the underlying genomic traits remain understudied. Using a genome-explicit, niche- and individual-based model, we address the potential interactions between genomic and ecological traits shaping communities under an environmental selective forcing, namely temporal positively autocorrelated environmental fluctuation. In this model, all ecological traits are explicitly coded by the genome. For our experiments, we initialized 90 replicate communities, each with ca 350 initial species, characterized by random genomic and ecological trait combinations, on a 2D spatially explicit landscape with two orthogonal gradients (temperature and resource use). We exposed each community to two contrasting scenarios: without (i.e. static environments) and with temporal variation. We then analyzed emerging compositions of both genomic and ecological traits at the community, population and genomic levels. Communities in variable environments were species poorer than in static environments, and populations more abundant, whereas genomes had lower genetic linkage, mean genetic variation and a non-significant tendency towards higher numbers of genes. The surviving genomes (i.e. those selected by variable environments) coded for enhanced environmental tolerance and smaller biomass, which resulted in faster life cycles and thus also in increased potential for evolutionary rescue. Under temporal environmental variation, larger, less linked genomes retained more variation in mean dispersal ability at the population level than at genomic level, whereas the opposite trend emerged for biomass. Our results provide clues to how sexually-reproducing diploid plant communities might react to variable environments and highlights the importance of genomic traits and their interaction with ecological traits for eco-evolutionary responses to changing climates.}, language = {en} }