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This deliverable reports on Task 2.2 ‘Assembly of observations about microbiomes, plastics, the plastisphere and carbon fluxes’. It used protocols established in task 2.1 ‘Definition of common standards for the assembly of spatially explicit data’ to compile, quality-control and grid existing high-quality observations into a knowledge base of observations (D2.1). Data included into AtlantECO-BASE1 consisted of contributions from the five following data sources and tasks: Task 2.2.1 ‘Microbiome data from traditional microscopy (presence-absence, abundance and biomass)’, Task 2.2.2 ‘Microbiome data from state-of-the-art optical/imaging analysis’, Task 2.2.3 ‘Microbiome and plastisphere data from state-of-the-art genetic analyses’, Task 2.2.4 ‘Nano-, micro and macroplastics data from state-of-the-art sampling methods’, and Task 2.2.5 ‘Carbon flux data from estimated from high resolution bio-optical sensors’. Additional data contributions and mapping efforts from other partners and work packages (Task 2.3) are also included. A comprehensive list and description of all data sets collected can be found in the Appendix Tables to this document.

Aim: The recent recovery of large carnivores in Europe has been explained as resulting from a decrease in human persecution driven by widespread rural land abandonment, paralleled by forest cover increase and the consequent increase in availability of shelter and prey. We investigated whether land cover and human population density changes are related to the relative probability of occurrence of three European large carnivores: the grey wolf (Canis lupus), the Eurasian lynx (Lynx lynx) and the brown bear (Ursus arctos).Location: Europe, west of 64 degrees longitude.Methods: We fitted multi-temporal species distribution models using >50,000 occurrence points with time series of land cover, landscape configuration, protected areas, hunting regulations and human population density covering a 24-year period (1992-2015). Within the temporal window considered, we then predicted changes in habitat suitability for large carnivores throughout Europe.Results: Between 1992 and 2015, the habitat suitability for the three species increased in Eastern Europe, the Balkans, North-West Iberian Peninsula and Northern Scandinavia, but showed mixed trends in Western and Southern Europe. These trends were primarily associated with increases in forest cover and decreases in human population density, and, additionally, with decreases in the cover of mosaics of cropland and natural vegetation.Main conclusions: Recent land cover and human population changes appear to have altered the habitat suitability pattern for large carnivores in Europe, whereas protection level did not play a role. While projected changes largely match the observed recovery of large carnivore populations, we found mismatches with the recent expansion of wolves in Central and Southern Europe, where factors not included in our models may have played a dominant role. This suggests that large carnivores' co-existence with humans in European landscapes is not limited by habitat availability, but other factors such as favourable human tolerance and policy.

When we explore global changes effects over biodiversity it is usually explored the direct effects, while ignoring the indirect effects (biotic), driving to erroneous predictions of how global change impacts biodiversity. Here, we focus on the brown bear (Ursus arctos) to understand how direct and indirect impacts of climate and land use change would affect the future distribution and vulnerability of different populations across Europe. We first conducted a literature search, compiling information on ~100 species consumed by brown bears. We downloaded occurrence data for all species consumed by the brown bear from GBIF. We built species distribution models for all these species, using biomod2 in R, in function of current climate and land use data. We interpolated the spatial variation of energy of each species in the diet, and it was combined with the distribution model resulting in the potential energy for each species. Using different scenarios for climate and land use change, we projected the future distributions of the brown bear diet species. Finally, we calculated the potential current and future suitable habitats of brown bear in function of the potential energy of diet, climate and land use. The range dynamic of the brown bear was best explained by considering both direct and indirect impacts. Accounting for energy (indirect effect) buffered the direct impact of climate and land use change. Our results highlight the importance of taking a food-web ecosystem approach to evaluate the impact of global changes and predict modifications in the distribution and vulnerability of species.

International audience; Asexual taxa often have larger ranges than their sexual progenitors, particularly in areas affected by Pleistocene glaciations. The reasons given for this ‘geographical parthenogenesis’ are contentious, with expansion of the ecological niche or colonisation advantages of uniparental reproduction assumed most important in case of plants. Here, we parameterized a spread model for the alpine buttercup Ranunculus kuepferi and reconstructed the joint Holocene range expansion of its sexual and apomictic cytotype across the European Alps under different simulation settings. We found that, rather than niche broadening or a higher migration rate, a shift of the apomict's niche towards colder conditions per se was crucial as it facilitated overcoming of topographical barriers, a factor likely relevant for many alpine apomicts. More generally, our simulations suggest potentially strong interacting effects of niche differentiation and reproductive modes on range formation of related sexual and asexual taxa arising from their differential sensitivity to minority cytotype disadvantage.

Modelling species distribution is one of the most widely used approaches used by modern ecologists to predict species occurrence as well as to explore the environmental variables that determine the presence of a species in an habitat. Given the outstanding importance of mammals in the context of conservation or management actions, it is not surprising that an ever increasing number of mammalogists have successfully employed species distribution models over the last few years. As a scientific journal devoted to mammal natural history, Hystrix, the Italian Journal of Mammalogy is pleased to present a collection of articles forming a special issue that deals with such an important and timely matter.

Despite its critical conservation status, no formal estimate of the Apennine brown bear (Ursus arctos marsicanus) distribution has ever been attempted, nor a coordinated effort to compile and verify all recent occurrences has ever been ensured. We used 48331 verified bear location data collected by qualified personnel from 2005-2014 in the central Apennines, Italy, to estimate the current distribution of Apennine brown bears. Data sources included telemetry relocations (86%), scats and DNA-verified hair samples (11.3%), sightings (1.1%), indirect signs of presence (1.1%), photos from camera traps (0.3%), and damage to properties (0.3%), both from the central and the peripheral portions of the range. Using a grid-based zonal analysis to transform raw data density, we applied ordinary kriging and estimated a 4923 km2 main bear distribution, encompassing the historical stronghold of the bear population, and including a smaller (1460 km2) area of stable occupancy of reproducing female bears. National and Regional Parks cover 40.5% of the main bear distribution, plus an additional 18% encompassed by the Natura 2000 network alone. Despite some methodological and sampling problems related to spatial and temporal variation in sampling effort at the landscape scale, our approach provides an approximation of the current bear distribution that is suited to frequently update the distribution map. Future monitoring of this bear population would benefit from estimating detectability across a range on environmental and sampling variables, and from intensifying the collection of bear presence data in the peripheral portions of the distribution.

Species distribution models (SDMs) are commonly used to predict potential species distribution in ecology, biogeography, and conservation. However, the lack of consideration for many different aspects of the species’ ecology often result in maps of limited practical value. Yet the wealth of information that is often available (especially for larger vertebrates) could help improve these models. Here, considering the mouflon (Ovis aries) in Sardinia as a case study, we propose a new integrated approach based on different aspects of the species ecology. In particular, we combined an SDM calibrated with an ensemble modelling approach with a morphological spatial pattern analysis and a model of structural connectivity. With this approach it was possible to map at the same time the distribution of potentially suitable habitat patches (and particularly of those being able to host pregnant females) and of the structural corridors connecting these patches. Overall, while the SDM predicted that 14.5% (3480 km2) of Sardinia was suitable for the presence of the mouflon, with our new integrated approach the percentage of areas suitable dropped to a much lower and more realistic 6.6% (1584 km2). Our results have potentially important consequences for the practical conservation and management of the species in Sardinia.

Modelling species distribution is one of the most widely used approaches used by modern ecologists to predict species occurrence as well as to explore the environmental variables that determine the presence of a species in an habitat.Given the outstanding importance of mammals in the context of conservation or management actions, it is not surprising that an ever increasing number of mammalogists have successfully employed species distribution models over the last few years. As a scientific journal devoted to mammal natural history, Hystrix, the Italian Journal of Mammalogy is pleased to present a collection of articles forming a special issue that deals with such an important and timely matter.

The Mediterranean basin, and the Iberian Peninsula in particular, represent an outstanding “hotspot” of biological diversity with a long history of integration between natural ecosystems and human activities. Using deductive distribution models, and considering both Spain and Portugal, we downscaled traditional range maps for terrestrial vertebrates (amphibians, breeding birds, mammals and reptiles) to the finest possible resolution with the data at hand, and we identified hotspots based on three criteria: i) species richness; ii) vulnerability, and iii) endemism. We also provided a first evaluation of the conservation status of biodiversity hotspots based on these three criteria considering both existing and proposed protected areas (i.e., Natura 2000). For the identification of hotspots, we used a method based on the cumulative distribution functions of species richness values. We found no clear surrogacy among the different types of hotspots in the Iberian Peninsula. The most important hotspots (considering all criteria) are located in the western and southwestern portions of the study area, in the Mediterranean biogeographical region. Existing protected areas are not specifically concentrated in areas of high species richness, with only 5.2% of the hotspots of total richness being currently protected. The Natura 2000 network can potentially constitute an important baseline for protecting vertebrate diversity in the Iberian Peninsula although further improvements are needed. We suggest taking a step forward in conservation planning in the Mediterranean basin, explicitly considering the history of the region as well as its present environmental context. This would allow moving from traditional reserve networks (conservation focused on “patterns”) to considerations about the “processes” that generated present biodiversity.

We propose a 3-step methodological approach to identify and classify fish nurseries for fisheries management purposes. We applied our approach to juvenile European hake Merluccius merluccius in the central Mediterranean Sea. Time series of trawl-survey fish-density data were used to map juvenile hake distribution with Bayesian kriging, while geostatistical aggregation curves were used to find density hot-spots. Persistence measures were adopted to identify nurseries on the basis of their spatio-temporal persistence. We found that areas with a high density of juvenile hake showed a high temporal persistence on both a seasonal and annual basis, with the most persistent nursery areas covering about 5% of the study areas while including about 39% of hake recruitment (averaged over 10 yr). We believe the persistence of these areas is indirect evidence of their impor- tance to the productivity of the population, with many potentially important implications for fisheries management. The approach that we developed to identify hake nurseries can be applied to different species and life stages to improve knowledge of the role of habitat for populations and communities.

To address the ongoing global biodiversity crisis, governments have set strategic objectives and have adopted indicators to monitor progress toward their achievement. Projecting the likely impacts on biodiversity of different policy decisions allows decision makers to understand if and how these targets can be met. We projected trends in two widely used indicators of population abundance Geometric Mean Abundance, equivalent to the Living Planet Index and extinction risk (the Red List Index) under different climate and land-use change scenarios. Testing these on terrestrial carnivore and ungulate species, we found that both indicators decline steadily, and by 2050, under a Business-as-usual (BAU) scenario, geometric mean population abundance declines by 18-35% while extinction risk increases for 8-23% of the species, depending on assumptions about species responses to climate change. BAU will therefore fail Convention on Biological Diversity target 12 of improving the conservation status of known threatened species. An alternative sustainable development scenario reduces both extinction risk and population losses compared with BAU and could lead to population increases. Our approach to model species responses to global changes brings the focus of scenarios directly to the species level, thus taking into account an additional dimension of biodiversity and paving the way for including stronger ecological foundations into future biodiversity scenario assessments.

International audience; Aim Climatic niche modelling of species and community distributions implicitly assumes strong and constant climatic determinism across geographical space. We tested this assumption by assessing how stacked-species distribution models (S-SDMs) perform for predicting plant species assemblages along elevation gradients. Location The western Swiss Alps. Methods Using robust presenceabsence data, we first assessed the ability of topo-climatic S-SDMs to predict plant assemblages in a study area encompassing a 2800-m wide elevation gradient. We then assessed the relationships among several evaluation metrics and trait-based tests of community assembly rules. Results The standard errors of individual SDMs decreased significantly towards higher elevations. Overall, the S-SDM overpredicted far more than they underpredicted richness and could not reproduce the humpback curve along elevation. Overprediction was greater at low and mid-range elevations in absolute values but greater at high elevations when standardized by the actual richness. Looking at species composition, overall prediction success, kappa and specificity increased with increasing elevation, while the Jaccard index and sensitivity decreased. The best overall evaluation as driven by specificity occurred at high elevation where species assemblages were shown to be subject to significant environmental filtering of small plants. In contrast, the decreased overall accuracy in the lowlands was associated with functional patterns representing any type of assembly rule (environmental filtering, limiting similarity or null assembly). Main conclusions We provide a thorough evaluation of S-SDM emphasizing the need to carefully interpret standard evaluation metrics, which reflect different aspects of assemblage predictions. We further reported interesting patterns of change in S-SDM errors with changes in assembly rules along elevation. Yet, significant levels of assemblage prediction errors occurred throughout the gradient, calling for further improvement of SDMs, e.g. by adding key environmental filters that act at fine scales and developing approaches to account for variations in the influence of predictors along environmental gradients.

Twenty leading scientists in the field of marine conservation planning attended the first international workshop on conservation planning in the Mediterranean Sea. This globally significant biodiversity hotspot has been subjected to human exploitation and degradation for 1,000s of years. Recently, several initiatives have tried to identify priority areas for conservation across the Mediterranean Sea. However, none of these efforts have led to large-scale actions yet. The aim of the workshop was to establish a network of scientists who are involved in large-scale conservation planning initiatives throughout the Mediterranean basin to promote collaboration and reduce redundancy in conservation initiatives. The three focus groups of the workshop build on existing efforts and intend to deliver: (1) a roadmap for setting conservation priorities, (2) a methodological framework for linking threats, actions and costs to improve the prioritization process, and (3) a systematic conservation planning process tailored to complex environments such as the Mediterranean Sea. Joining forces and involving more scientists (especially from the South-eastern part of the region) in following meetings, the participants endeavour to provide guidelines on how to bridge the science-policy gap and hence aid decision-makers to take efficient conservation actions., JRC.H.1-Water Resources

Substantial investment in climate change research has led to dire predictions of the impacts and risks to biodiversity. The Intergovernmental Panel on Climate Change fourth assessment report(1) cites 28,586 studies demonstrating significant biological changes in terrestrial systems(2). Already high extinction rates, driven primarily by habitat loss, are predicted to increase under climate change(3-6). Yet there is little specific advice or precedent in the literature to guide climate adaptation investment for conserving biodiversity within realistic economic constraints(7). Here we present a systematic ecological and economic analysis of a climate adaptation problem in one of the world's most species-rich and threatened ecosystems: the South African fynbos. We discover a counterintuitive optimal investment strategy that switches twice between options as the available adaptation budget increases. We demonstrate that optimal investment is nonlinearly dependent on available resources, making the choice of how much to invest as important as determining where to invest and what actions to take. Our study emphasizes the importance of a sound analytical framework for prioritizing adaptation investments(4). Integrating ecological predictions in an economic decision framework will help support complex choices between adaptation options under severe uncertainty. Our prioritization method can be applied at any scale to minimize species loss and to evaluate the robustness of decisions to uncertainty about key assumptions.

Maiorano, L., Bartolino, V., Colloca, F., Abella, A., Belluscio, A., Carpentieri, P., Criscoli, A., Jona Lasinio, G., Mannini, A., Pranovi, F., Reale, B., Relini, G., Viva, C., and Ardizzone, G. D. 2009. Systematic conservation planning in the Mediterranean: a flexible tool for the identification of no-take marine protected areas. – ICES Journal of Marine Science, 66: 137–146. We propose the use of systematic conservation planning in the Mediterranean context for the identification of no-take marine protected areas (NTMPAs). We suggest a logical framework that should be used for the identification of areas to be targeted for multispecies, spatially explicit conservation actions. Specifically, we propose seven steps: (i) definition of the study area; (ii) selection of the species or habitats to be considered; (iii) definition of the planning units; (iv) measurement of the fishing effort; (v) definition of the conservation targets; (vi) review of the existing conservation areas; (vii) selection of additional NTMPAs. Moreover, we consider the potential impact of different conservation plans on existing fishing vessels. A working example is presented, focusing on a limited number of species and on a limited study area. This framework can be easily expanded to include datasets of different origin and to accommodate larger spatial scales. Such a process involves major data-collection and capacity-building elements, and conservation of productive commercial fisheries must be a priority.

The Natura 2000 network is the most important conservation effort being implemented in Europe. Nevertheless, no comprehensive and systematic region-or nationwide evaluation of the effectiveness of the network has been conducted. We used habitat suitability models and extent of occurrence of 468 species of vertebrates to evaluate the contribution of the Natura 2000 network to biodiversity conservation in Italy. We also estimated the population size of 101 species inside the Natura 2000 network to assess its capacity to maintain or improve the population status of listed species. In general the Italian Natura 2000 did not seem to integrate existing protected areas well. The Natura 2000 network increased from 11% to 20% the area devoted to conservation in Italy and the coverage provided to areas with high biodiversity. Nevertheless, some areas with high numbers of species were devoid of conservation areas, and more than 50% of the highly irreplaceable areas were not considered in the system. Moreover, the Natura 2000 network cannot maintain 44-80% (depending on the taxa considered) of the species in a "favorable conservation status" under World Conservation Union Red List criteria. The Natura 2000 network is probably stronger than the results of our analyses suggest. The system is based on a site-specific expert-based strategy and is driven by direct and detailed knowledge of local diversity. Nevertheless, if Natura 2000 is taken to represent the final point of all the EU conservation policies, it will inevitably fail. Its role in conservation could be enhanced by integrating the Natura 2000 system into a more general strategy that considers natural processes and the ecological and evolutionary mechanisms underlying these processes.

Aim: Forecasting changes in species distribution under future scenarios is one of the most prolific areas of application for species distribution models (SDMs). However, no consensus yet exists on the reliability of such models for drawing conclusions on species’ distribution response to changing climate. In this study, we provide an overview of common modelling practices in the field and assess the reliability of model predictions using a virtual species approach. Location: Global. Methods: We first review papers published between 2015 and 2019. Then, we use a virtual species approach and three commonly applied SDM algorithms (GLM, MaxEnt and random forest) to assess the estimated and actual predictive performance of models parameterized with different modelling settings and violations of modelling assumptions. Results: Most SDM papers relied on single models (65%) and small samples (N

Kolponomos newportensis is an enigmatic Miocene mammal allied to stem Pinnipedimorpha. It has been suggested that Kolponomos fed on hard-shelled benthic marine invertebrates by using its mandible as a wedge to dislodge its prey from the sea bottom by means of strong pull and torque forces. This unique feeding style was thought to originate from a singular case of mosaic convergence in mandible biomechanics between Kolponomos and the sabretoothed cat Smilodon, which complied with similarly strong torque forces when grappling with prey. As such forces must have reflected on the cranium as well, we hypothesize that the convergence between Kolponomos and the sabretoothed cats could have affected its shape. To test this hypothesis, we looked for patterns of morphological convergence in cranial shape between Kolponomos and sabretoothed cats. We found that Kolponomos is not distinctly closer to Smilodon than a number of other pinnipeds. Yet, local areas of shape convergence with Smilodon are observed in the canine area and the posterior part of the cranium, that is where the bite applies and the temporalis muscle is located, respectively. These results indicate that the mosaic convergence present between the mandibles of Kolponomos and Smilodon is partially reflected in the cranium as well.

Convergence consists in the independent evolution of similar traits in distantly related species. The mammalian craniomandibular complex constitutes an ideal biological structure to investigate ecomorphological dynamics and the carnivorans, due to their phenotypic variability and ecological flexibility, offer an interesting case study to explore the occurrence of convergent evolution. Here, we applied multiple pattern-based metrics to test the occurrence of convergence in the craniomandibular shape of extant carnivorans. To this aim, we tested for convergence in many dietary groups and analyzed several cases of carnivoran convergence concerning either ecologically equivalent species or ecologically similar species of different body sizes described in the literature. Our results validate the occurrence of convergence in ecologically equivalent species in a few cases (as well as in the case of giant and red pandas), but almost never support the occurrence of convergent evolution in dietary categories of living carnivorans. Therefore, convergent evolution in this clade appears to be a rare phenomenon. This is probably the consequence of a complex interplay of one-to-many, many-to-one, and many-to-many relationships taking place between ecology, biomechanics, and morphology., This research received support from the SYNTHESYS programme (ES-TAF-2750 awarded to DT) and the “Avvio alla Ricerca” funds provided by the University of Rome “La Sapienza” (AR11916B48429BEB awarded to DT).

Evolutionary trends (ETs) are traditionally defined as substantial changes in the state of traits through time produced by a persistent condition of directional evolution. ETs might also include directional responses to ecological, climatic or biological gradients and represent the primary evolutionary pattern at high taxonomic levels and over long-time scales. The absence of a well-supported operative definition of ETs blurred the definition of conceptual differences between ETs and other key concepts in evolution such as convergence, parallel evolution, and divergence. Also, it prevented the formulation of modern guidelines for studying ETs and evolutionary dynamics related to them. In phenotypic evolution, the theory of morphodynamics states that the interplay between evolutionary factors such as phylogeny, evo-devo constraints, environment, and biological function determines morphological evolution. After introducing a new operative definition, here we provide a morphodynamics-based framework for studying phenotypic ETs, discussing how understanding the impact of these factors on ETs improves the explanation of links between biological patterns and processes underpinning directional evolution. We envisage that adopting a quantitative, pattern-based, and multifactorial approach will pave the way to new potential applications for this field of evolutionary biology. In this framework, by exploiting the catalysing effect of climate change on evolution, research on ETs induced by global change might represent an ideal arena for validating hypotheses about the predictability of evolution.

Summary At least six different Homo species populated the World during the latest Pliocene to the Pleistocene. The extinction of all but one of them is currently shrouded in mystery, and no consistent explanation has yet been advanced, despite the enormous importance of the matter. Here, we use a recently implemented past climate emulator and an extensive fossil database spanning 2,754 archaeological records to model climatic niche evolution in Homo. We find statistically robust evidence that the three Homo species representing terminating, independent lineages, H. erectus, H. heidelbergensis, and H. neanderthalensis, lost a significant portion of their climatic niche space just before extinction, with no corresponding reduction in physical range. This reduction coincides with increased vulnerability to climate change. In the case of Neanderthals, the increased extinction risk was probably exacerbated by competition with H. sapiens. This study suggests that climate change was the primary factor in the extinction of Homo species.

Monospecific and bispecific genera are of special concern as they represent unique phylogenetic/evolutionary trajectories within larger clades. In addition, as phylogenetically older taxa are supposed to be exposed to higher rarity and extinction risk, monospecific and bispecific genera may be intrinsically more prone to extinction risks than multispecies genera, although extinction risks also depend on the ecological and biological strategy of the species. Here, the distribution across biogeographical zones and the levels of threat to 2 speciose orders of mammals (monospecific and bispecific genera of Rodentia and Soricomorpha) are investigated in order to highlight major patterns at the worldwide scale. In Rodentia, 39.7% of the genera (n = 490) were monospecific and 17.9% were bispecific. In Soricomorpha, 44.4% of the total genera (n = 45) were monospecific and 15% were bispecific. There was a positive correlation between the number of monospecific genera and the total number of genera per family. Peaks of monospecific and bispecific genera richness were observed in Neotropical, Oriental and Afrotropical regions in rodents and in the Palearctic region in soricomorphs. Range size was significantly uneven across biogeographic region in rodents (with larger ranges in Nearctic and Oriental regions and smaller ranges in the Australian region), but there was no difference across biogeographic regions in terms of range size in soricomorphs. Most of the monospecific and bispecific genera occurred in forest habitat in both taxa. The frequency distribution of the monospecific and bispecific genera across IUCN categories did not differ significantly from the expected pattern using the total rodent genera and the multispecies genera.

Aim We sought to assess different megafaunal species responses to the intense climatic changes that characterized the end of the Quaternary. Location Eurasia. Methods We used species distribution modelling, niche overlap tests and co-occurrence analysis to model climatic niche evolution and change in six different megafauna species, including three extinct (woolly mammoth, woolly rhino and steppe bison) and three extant (red deer, wolf and reindeer) species. Results Co-occurrence analysis indicates mammoth, rhino, reindeer and steppe bison to be significantly associated to each other in the fossil record in cold, arid environments. In contrast, red deer and wolf show no evidence for strong habitat requirements, although they both tended to be associated with more humid conditions than the other megafauna. Woolly mammoth and the woolly rhino were the best adapted to the cold, arid conditions dominating the Eurasian landscapes during the Last Glacial Maximum (LGM). Extant species did not exhibit larger climatic niches than extinct species, but changed more from one period to the next than those of extinct species. Main conclusions Although they did not have wider climatic niches, and were the least adapted to cold climates, red deer and the wolf were able to withstand the harsh climatic conditions of the LGM. Conversely, the now extinct mammoth and woolly rhino did not survive the demise of the LGM environment. Although “cold-adapted”, reindeer survived the LGM by occupying a northerly distribution similar to today. Independent evidence indicates the steppe bison lineage might have survived in North America. Our data are consistent with a strong climatic control on the fate of late Quaternary megafauna species in Eurasia. We were unable to exclude a sizeable effect of human intervention by overhunting.