Unveiling the factors shaping the distribution of widely distributed alpine vertebrates, using multi-scale ecological niche modelling of the bat Plecotus macrobullaris

Several alpine vertebrates share a distribution pattern that extends across the South-western Palearctic but is limited to the main mountain massifs. Although they are usually regarded as cold-adapted species, the range of many alpine vertebrates also includes relatively warm areas, suggesting that factors beyond climatic conditions may be driving their distribution. In this work we first recognize the species belonging to the mentioned biogeographic group and, based on the environmental niche analysis of Plecotus macrobullaris, we identify and characterize the environmental factors constraining their ranges. Distribution overlap analysis of 504 European vertebrates was done using the Sorensen Similarity Index, and we identified four birds and one mammal that share the distribution with P. macrobullaris. We generated 135 environmental niche models including different variable combinations and regularization values for P. macrobullaris at two different scales and resolutions. After selecting the best models, we observed that topographic variables outperformed climatic predictors, and the abruptness of the landscape showed better predictive ability than elevation. The best explanatory climatic variable was mean summer temperature, which showed that P. macrobullaris is able to cope with mean temperature ranges spanning up to 16°C. The models showed that the distribution of P. macrobullaris is mainly shaped by topographic factors that provide rock-abundant and open-space habitats rather than climatic determinants, and that the species is not a cold-adapted, but rather a cold-tolerant eurithermic organism. P. macrobullaris shares its distribution pattern as well as several ecological features with five other alpine vertebrates, suggesting that the conclusions obtained from this study might be extensible to them. We concluded that rock-dwelling and open-space foraging vertebrates with broad temperature tolerance are the best candidates to show wide alpine distribution in the Western Palearctic. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12983-014-0077-6) contains supplementary material, which is available to authorized users

A global initiative for ecological and evolutionary hologenomics

Acknowledgements The Earth Hologenome Initiative could not be conceived without the trust and economic support provided by the Danish National Research Foundation through the grant DNRF143, and the Carlsberg Foundation through the grant CF20-0460. The authors also acknowledge the NERC (grant NE/M018660/1), and University of Exeter Europe Network Fund for the economic support provided to ongoing projects embedded within the EHI. M. Denoël is a Research Director at F.R.S.-FNRS (Fonds de la Recherche Scientifique). C. Rodríguez Fernandes thanks the support of cE3c through an assistant researcher contract (FCiência.ID contract #366) and FCT (Fundação para a Ciência e a Tecnologia) for Portuguese National Funds attributed to cE3c within the projects UIDB/00329/2020, UIDP/00329/2020, and LA/P/0121/2020. We also thank all the researchers who participated in the fieldwork, as well as the support people who facilitated the administrative paperwork, with a special mention for the Head of the Globe Institute Anders J. Hansen, who has signed dozens of participation agreements. Finally, we acknowledge that some of the elements included in the figures have been obtained and modified from the Integration and Application Network, University of Maryland—Center for Environmental Science (https://ian.umces.edu/media-library/symbols).Peer reviewe

Insight on how fishing bats discern prey and adjust their mechanic and sensorial features during the attack sequence

Several insectivorous bats have included fish in their diet, yet little is known about the processes underlying this trophic shift. We performed three field experiments with wild fishing bats to address how they manage to discern fish from insects and adapt their hunting technique to capture fish. We show that bats react only to targets protruding above the water and discern fish from insects based on prey disappearance patterns. Stationary fish trigger short and shallow dips and a terminal echolocation pattern with an important component of the narrowband and low frequency calls. When the fish disappears during the attack process, bats regulate their attack increasing the number of broadband and high frequency calls in the last phase of the echolocation as well as by lengthening and deepening their dips. These adjustments may allow bats to obtain more valuable sensorial information and to perform dips adjusted to the level of uncertainty on the location of the submerged prey. The observed ultrafast regulation may be essential for enabling fishing to become cost-effective in bats, and demonstrates the ability of bats to rapidly modify and synchronise their sensorial and motor features as a response to last minute stimulus variations.This study was part of the Ministerio de Ciencia e Innovacion (MICINN) project CGL2009-12393. The University of The Basque Country (UPV/EHU) (INF09/15) and the Basque Government (IT385-07 and IT301-10) funded this study and provided grant support to O.A. and A.A (BFI-2009-252, BFI-2010-190, Doktore berriak eta Ikertzaile doktoreak espezializatzeko kontratatzeko laguntzak)

Unveiling the factors shaping the distribution of widely distributed alpine vertebrates, using multi-scale ecological niche modelling of the bat Plecotus macrobullaris

Several alpine vertebrates share a distribution pattern that extends across the South-western Palearctic but is limited to the main mountain massifs. Although they are usually regarded as cold-adapted species, the range of many alpine vertebrates also includes relatively warm areas, suggesting that factors beyond climatic conditions may be driving their distribution. In this work we first recognize the species belonging to the mentioned biogeographic group and, based on the environmental niche analysis of Plecotus macrobullaris, we identify and characterize the environmental factors constraining their ranges. Distribution overlap analysis of 504 European vertebrates was done using the Sorensen Similarity Index, and we identified four birds and one mammal that share the distribution with P. macrobullaris. We generated 135 environmental niche models including different variable combinations and regularization values for P. macrobullaris at two different scales and resolutions. After selecting the best models, we observed that topographic variables outperformed climatic predictors, and the abruptness of the landscape showed better predictive ability than elevation. The best explanatory climatic variable was mean summer temperature, which showed that P. macrobullaris is able to cope with mean temperature ranges spanning up to 16 degrees C. The models showed that the distribution of P. macrobullaris is mainly shaped by topographic factors that provide rock-abundant and open-space habitats rather than climatic determinants, and that the species is not a cold-adapted, but rather a cold-tolerant eurithermic organism. P. macrobullaris shares its distribution pattern as well as several ecological features with five other alpine vertebrates, suggesting that the conclusions obtained from this study might be extensible to them. We concluded that rock-dwelling and open-space foraging vertebrates with broad temperature tolerance are the best candidates to show wide alpine distribution in the Western Palearctic.We wish to thank Orly Razgour for her insightful comments on the manuscript and for proofreading the text. The Basque Government (research projects IT385-07, IT301-10 and IT754-13, and predoctoral grants BFI-2010-190 and BFI-2009-252) and the University of the Basque Country UPV/EHU supported this work

Fishing long-fingered bats (<i>Myotis capaccinii</i>) prey regularly upon exotic fish

7 p.The long-fingered bat Myotis capaccinii is a European trawling bat reported to feed on fish in several Mediterranean locations, but the ecological circumstances of this behavior have not yet been studied. To elucidate the importance of fishing in this bat's diet, we evaluated the frequency and seasonal variation of fish remains in 3,000 fecal pellets collected from M. capaccinii at a nursery roost in Dénia (Eastern Iberian Peninsula) in 2008, 2009, and 2010. Fish consumption occurred evenly throughout the year. All otoliths found in feces were identified as belonging to the surface-feeding fish Gambusia holbrooki. Measuring otoliths, we estimated that the mean size of consumed fish was significantly smaller than the mean measured for available fish, suggesting that the long-fingered bat's relatively small body may constrain its handling of larger prey. Of note, one bat had eaten 15 fish, showing that fish may be a locally or seasonally important trophic resource for this species. By capturing 15 bats and radio-tracking the four with the most fish remains in their droppings, we also identified fishing areas, including a single fishing ground comprising several ponds within a golf course. Ponds hold a high density of G. holbrooki, suggesting that the amount of fish at the water surface may be the principal factor triggering fishing. The observed six-fold increase in percentage of consumed fish across the study period may be related to recent pond-building in the area. We discuss whether this quick behavioral response is a novel feature of M. capaccinii or an intrinsic feature that has erupted and faded locally along the species' history.This study was part of the MICINN project CGL2009-12393 coordinated by J. Aihartza, UPV/EHU. The Basque Government provided grant support to O. Aizpurua and A. Alberdi (BFI-2009-252 and BFI-2010-190). Support was also provided by the University of The Basque Country UPV/EHU (INF09/15) and the Basque Government (IT385-07 and IT301-10). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. This study was performed with the permission of the Valencian Government

An integrated framework to identify wildlife populations under threat from climate change

Climate change is a major threat to global biodiversity that will produce a range of new selection pressures. Understanding species responses to climate change requires an interdisciplinary perspective, combining ecological, molecular and environmental approaches. We propose an applied integrated framework to identify populations under threat from climate change based on their extent of exposure, inherent sensitivity due to adaptive and neutral genetic variation and range shift potential. We consider intraspecific vulnerability and population-level responses, an important but often neglected conservation research priority. We demonstrate how this framework can be applied to vertebrates with limited dispersal abilities using empirical data for the bat Plecotus austriacus. We use ecological niche modelling and environmental dissimilarity analysis to locate areas at high risk of exposure to future changes. Combining outlier tests with genotype–environment association analysis, we identify potential climate-adaptive SNPs in our genomic data set and differences in the frequency of adaptive and neutral variation between populations. We assess landscape connectivity and show that changing environmental suitability may limit the future movement of individuals, thus affecting both the ability of populations to shift their distribution to climatically suitable areas and the probability of evolutionary rescue through the spread of adaptive genetic variation among populations. Therefore, a better understanding of movement ecology and landscape connectivity is needed for predicting population persistence under climate change. Our study highlights the importance of incorporating genomic data to determine sensitivity, adaptive potential and range shift potential, instead of relying solely on exposure to guide species vulnerability assessments and conservation planning

Holo-Omics:Integrated Host-Microbiota Multi-omics for Basic and Applied Biological Research

From ontogenesis to homeostasis, the phenotypes of complex organisms are shaped by the bidirectional interactions between the host organisms and their associated microbiota. Current technology can reveal many such interactions by combining multi-omic data from both hosts and microbes. However, exploring the full extent of these interactions requires careful consideration of study design for the efficient generation and optimal integration of data derived from (meta)genomics, (meta) transcriptomics, (meta)proteomics, and (meta)metabolomics. In this perspective, we introduce the holo-omic approach that incorporates multi-omic data from both host and microbiota domains to untangle the interplay between the two. We revisit the recent literature on biomolecular host-microbe interactions and discuss the im-plementation and current limitations of the holo-omic approach. We anticipate that the application of this approach can contribute to opening new research avenues and discoveries in biomedicine, biotechnology, agricultural and aquacultural sciences, nature conservation, as well as basic ecological and evolutionary research.The authors thank the following for funding their research: The Danish National Research Foundation award to M.T.P.G. (DNRF143), Villum Fonden grant to M.T. P.G. (17417), Lundbeckfonden grant to A.A. (R250-2017-1351), Danish Council for Independent Research grants to A.A. (DFF 5051-00033) and M.T.L. (DFF 8022-00005), ERC Consolidator Grant toM. T.P.G. (681396-Extinction Genomics), The Norwegian Seafood Research Fund -FHF grant to M.T.P.G. and M.T.L. (901436-HoloFish), H2020 Marie Sklodowska-Curie Individual Fellowship grant toM.T.L. (745723-HappyFish) and the European Union's Horizon 2020 Research and Innovation Programme grant to M.T.P.G., A.A. and M.T.L. (Grant Agreement No 817729 -HoloFood). Furthermore, the authors would like to thank Rob Dunn for his input and discussions

Considering adaptive genetic variation in climate change vulnerability assessment reduces species range loss projections

Local adaptations can determine the potential of populations to respond to environmental changes, yet adaptive genetic variation is commonly ignored in models forecasting species vulnerability and biogeographical shifts under future climate change. Here we integrate genomic and ecological modeling approaches to identify genetic adaptations associated with climate in two cryptic forest bats. We then incorporate this information directly into forecasts of range changes under future climate change and assessment of population persistence through the spread of climate-adaptive genetic variation (evolutionary rescue potential). Considering climate-adaptive potential reduced range loss projections, suggesting that failure to account for intraspecific variability can result in overestimation of future losses. On the other hand, range overlap between species was projected to increase, indicating that interspecific competition is likely to play an important role in limiting species’ future ranges. We show that although evolutionary rescue is possible, it depends on a population’s adaptive capacity and connectivity. Hence, we stress the importance of incorporating genomic data and landscape connectivity in climate change vulnerability assessments and conservation management