Browsing by Subject "Ecology"

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  • Hardisty, Alex R.; Bacall, Finn; Beard, Niall; Balcazar-Vargas, Maria-Paula; Balech, Bachir; Barcza, Zoltan; Bourlat, Sarah J.; De Giovanni, Renato; de Jong, Yde; De Leo, Francesca; Dobor, Laura; Donvito, Giacinto; Fellows, Donal; Guerra, Antonio Fernandez; Ferreira, Nuno; Fetyukova, Yuliya; Fosso, Bruno; Giddy, Jonathan; Goble, Carole; Guentsch, Anton; Haines, Robert; Ernst, Vera Hernandez; Hettling, Hannes; Hidy, Dora; Horvath, Ferenc; Ittzes, Dora; Ittzes, Peter; Jones, Andrew; Kottmann, Renzo; Kulawik, Robert; Leidenberger, Sonja; Lyytikäinen-Saarenmaa, Paivi; Mathew, Cherian; Morrison, Norman; Nenadic, Aleksandra; de la Hidalga, Abraham Nieva; Obst, Matthias; Oostermeijer, Gerard; Paymal, Elisabeth; Pesole, Graziano; Pinto, Salvatore; Poigne, Axel; Fernandez, Francisco Quevedo; Santamaria, Monica; Saarenmaa, Hannu; Sipos, Gergely; Sylla, Karl-Heinz; Tähtinen, Marko; Vicario, Saverio; Vos, Rutger Aldo; Williams, Alan R.; Yilmaz, Pelin (2016)
    Background: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as "Web services") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust "in silico" science. However, use of this approach in biodiversity science and ecology has thus far been quite limited. Results: BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on- line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible 'virtual laboratory', free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity. Conclusions: Our work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.
  • Hardisty, Alex R; Bacall, Finn; Beard, Niall; Balcázar-Vargas, Maria-Paula; Balech, Bachir; Barcza, Zoltán; Bourlat, Sarah J; De Giovanni, Renato; de Jong, Yde; De Leo, Francesca; Dobor, Laura; Donvito, Giacinto; Fellows, Donal; Guerra, Antonio F; Ferreira, Nuno; Fetyukova, Yuliya; Fosso, Bruno; Giddy, Jonathan; Goble, Carole; Güntsch, Anton; Haines, Robert; Ernst, Vera H; Hettling, Hannes; Hidy, Dóra; Horváth, Ferenc; Ittzés, Dóra; Ittzés, Péter; Jones, Andrew; Kottmann, Renzo; Kulawik, Robert; Leidenberger, Sonja; Lyytikäinen-Saarenmaa, Päivi; Mathew, Cherian; Morrison, Norman; Nenadic, Aleksandra; de la Hidalga, Abraham N; Obst, Matthias; Oostermeijer, Gerard; Paymal, Elisabeth; Pesole, Graziano; Pinto, Salvatore; Poigné, Axel; Fernandez, Francisco Q; Santamaria, Monica; Saarenmaa, Hannu; Sipos, Gergely; Sylla, Karl-Heinz; Tähtinen, Marko; Vicario, Saverio; Vos, Rutger A; Williams, Alan R; Yilmaz, Pelin (BioMed Central, 2016)
    Abstract Background Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as “Web services”) and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust “in silico” science. However, use of this approach in biodiversity science and ecology has thus far been quite limited. Results BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on-line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible ‘virtual laboratory’, free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity. Conclusions Our work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.
  • Rikkinen, Jouko; Meinke, Kristin; Grabenhorst, Heinrich; Gröhn, Carsten; Kobbert, Max; Wunderlich, Jörg; Schmidt, Alexander (2018)
    Calicioid lichens and fungi are a polyphyletic grouping of tiny ascomycetes that accumulate a persistent spore mass (mazaedium) on top of their usually well-stalked ascomata ('mazaediate fungi'). In addition to extant forms, six fossils of the group were previously known from European Paleogene amber. Here we report nine new fossils and analyze the preserved features of all fossils to assess their applicability for dating molecular phylogenies. Many fossils are extremely well preserved, allowing detailed comparisons with modern taxa. SEM investigation reveals that even fine details of ascospore wall ultrastructure correspond to those seen in extant specimens. All fossils can confidently be assigned to modern genera: three to Calicium (Caliciaceae, Lecanoromycetes), five to Chaenotheca (Coniocybaceae, Coniocybomycetes), six to Chaenothecopsis (Mycocaliciaceae, Eurotiales), and one to Phaeocalicium (Mycocaliciaceae, Eurotiales). Several Calicium and Chaenotheca fossils are assignable to specific lineages within their genera, while the Chaenothecopsis fossils demonstrate the extent of intraspecific variation within one such lineage. Some features in the morphology of Chaenotheca succina nov. sp. seem to be ancestral as they have not been reported from modern species of the genus. (C) 2018 Elsevier Masson SAS. All rights reserved.
  • Lukaszewicz, German; Iturburu, Fernando G.; Garanzini, Daniela S.; Menone, Mirta L.; Pflugmacher, Stephan (2019)
    Imidacloprid (IMI) is a neonicotinoid insecticide widely used in agricultural activities all around the world. This compound is transported from croplands to surrounding freshwater ecosystems, producing adverse effects on non-target organisms. Because of the relevance of aquatic macrophytes in the above-mentioned environments and the lack of studies of potential effects of IMI on them, this work aimed to assess the mitotic process and potential genotoxicity in the aquatic macrophyte Bidens laevis L. Although the analysis of the Mitotic Index (MI) showed that IMI was not cytotoxic, the Cell Proliferation Kinetics (CPK) frequencies evidenced modifications in the kinetics of the mitotic process. Indeed, the anaphases ratio decreased at 10 and 100 mu g/L IMI, while at 1000 mu g/L an increase of prophases ratio and a decrease of metaphases ratio were observed. Regarding genotoxicity, IMI produced an increase of the abnormal metaphases frequency from 10 mu g/L to 1000 mu g/L as well as an increase in clastogenic anaphases-telophases frequency at 100 and 1000 mu g/L. In addition, aneugenic anaphases-telophases and C-mitosis frequencies also increased at 1000 mu g/L, confirming the effects on the mitotic spindle. Considering the genotoxic effects on B. laevis through two different mechanisms (aneugenic and clastogenic) and the wide spread use of IMI in agriculture, these mechanisms of toxicity on macrophytes should be considered among other recognized effects of this insecticide on aquatic biota.
  • Weckström, Kaarina; Roche, Benjamin Redmond; Miettinen, Arto; Krawczyk, Diana; Limoges, Audrey; Juggins, Steve; Ribeiro, Sofia; Heikkilä, Maija (2020)
    A long-term perspective is essential for understanding environmental change. To be able to access the past, environmental archives such as marine and lake sediments that store information in the form of diverse proxy records are used. Whilst many analytical techniques exist to extract the information stored in these proxy records, the critical assessment and refinement of current methods in addition to developing new methods is crucial to improving our understanding. This study aims to improve our knowledge on diatom species used for reconstructing ocean surface conditions, especially temperature and sea ice variability over time. We define the distribution and the relationship to sea surface temperature (SST) and sea ice concentrations (SIC) of the species Fragilariopsis oceanica, Fragilariopsis reginae-jahniae and Fossula arctica using diatom training sets from the northern North Atlantic. We further assess the effect of separating these species compared to grouping them under F. oceanica, as has been done in the past. Our results suggest that while these three species share similarities such as the preference for stratified waters induced by sea ice or glacier meltwater, they also exhibit heterogeneous distributions across the northern North Atlantic, with individual optima for SST and SIC. This also affects quantitative reconstructions based on our data, resulting in lower SST and higher SIC estimates when the species are separated in the surface sediment and down-core diatom assemblages.
  • Rikkinen, Jouko Kalevi; Schmidt, Alexander (Academic Press, 2018)
    Amber, fossilized plant resin from gymnosperms and angiosperms, is renowned for preserving a wide range of organisms in microscopic fidelity. These so-called amber inclusions comprise many groups of organisms, ranging from bacteria to arthropods and vertebrates. Calicioid lichens and fungi, which are from now on referred to as “calicioids,” constitute a diverse group of tiny ascomycetes with superficially similar, usually well-stalked ascomata and which often accumulate mature ascospores on top of the apothecial disk to form a true mazaedium. The aim of this study is to use all available information on the morphology and ecology of extant calicioids to reconstruct the substrate and habitat ecology of known fossil calicioids and then to use this information to open new insights into the stand structure and ecological conditions of European Paleogene amber forests. First, we introduce the morphology of extant calicioids and demonstrate that their structural features are intimately linked to habitat ecology and are instrumental for successful dispersal; we also explain the conspicuous morphological convergence between phylogenetically distant calicioid fungi. Then, we show that the adaptive traits of calicioids have not changed since at least the Eocene, and argue that their fundamental niches also have remained unchanged. Finally, we summarize what the diversity and relative abundance of fossil calicioids in amber tells us about the ecological conditions that once prevailed in European amber forests.
  • Moschos, Vaios; Kumar, Nivedita K.; Dällenbach, Kaspar; Baltensperger, Urs; Prevot, Andre S. H.; El Haddad, Imad (2018)
    The impact of brown carbon (BrC) on climate has been widely acknowledged but remains uncertain, because either its contribution to absorption is being ignored in most climate models or the associated mixed emission sources and atmospheric lifetime are not accounted for. In this work, we propose positive matrix factorization as a framework to apportion the contributions of individual primary and secondary organic aerosol (OA) source components of BrC absorption, by combining long-term aerosol mass spectrometry (AMS) data with concurrent ultraviolet-visible (UV-vis) spectroscopy measurements. The former feature time-depend ent factor contributions to OA mass, and the latter consist of wavelength-dependent absorption coefficients. Using this approach for a full-year case study, we estimate for the first time the mass absorption efficiency (MAE) of major light-absorbing water soluble OA components in the atmosphere. We show that secondary biogenic OA contributes negligibly to absorption despite dominating the mass concentration in the summer. In contrast, primary and secondary wood burning emissions are highly absorbing up to 500 nm. The approach allowed us to constrain their MAE within a confined range consistent with previous laboratory work, which can be used in climate models to estimate the impact of BrC from these emissions on the overall absorption.
  • Björklund, Heidi (Helsingin yliopisto, 2015)
    Human-caused habitat changes have led to declines of many species by impairing their occurrence, reproduction and interactions with other species. In Northern Europe, intensive forestry has transformed boreal forests and worsened conditions of species dependent on old forest, but the mechanisms by which habitat changes affect species are often unknown. In my dissertation, I examined habitat changes, their effects and habitat-associated breeding performances of three declining forest-dwelling hawks, the northern goshawk (Accipiter gentilis), the common buzzard (Buteo buteo) and the honey buzzard (Pernis apivorus). These species can compete for nest sites and goshawks can also predate the buzzards. Raptors may lack nest sites in managed forests which is why their nesting has been supported by constructing artificial nests. I analysed the breeding success of the hawks in artificial nests since their benefits as a conservation measure were not previously analysed. Finally, I studied the conditions when dominant species can exclude subordinate ones in competition for suitable nest sites. According to my results, old forests have decreased and young forests increased throughout southern Finland. These changes are adverse for the goshawk whose breeding success improves when old spruce forests are more abundant and young forests scarce around their nests. Breeding performances of the common buzzard and honey buzzard were not significantly associated with habitats. However, common buzzards were reluctant to re-occupy nests surrounded by a vastness of old forest. The breeding success of the goshawk and common buzzard was lower in artificial nests than in natural ones. Thus, this measure aimed at enabling hawk breeding in managed forests seems to conflict with its conservation objectives. I discuss the possible contributing factors and directions for further investigations. Interspecific interactions with other raptors proved to be important when a subordinate hawk decided on territory occupancy. Common buzzards prefer to occupy safe territories, where threats of goshawk predation and interference competition with other raptors are small. Thus, interspecific raptors that are predators or competitors may exclude subordinate raptors from their territories, and thereby contribute to their occurrence. Adverse interactions with other raptors may even impede a subordinate raptor from fully exploiting the periodic food peaks. My dissertation shows that for each species, it is crucial to identify the most relevant spatiotemporal scales in order to identify, how external disturbances affect them most. Long-term data is of paramount importance to detect these scales.
  • Khazaei, Hamid; Street, Kenneth; Bari, Abdallah; Mackay, Michael; Stoddard, Fred (2013)
    Efficient methods to explore plant agro-biodiversity for climate change adaptive traits are urgently required. The focused identification of germplasm strategy (FIGS) is one such approach. FIGS works on the premise that germplasm is likely to reflect the selection pressures of the environment in which it developed. Environmental parameters describing plant germplasm collection sites are used as selection criteria to improve the probability of uncovering useful variation. This study was designed to test the effectiveness of FIGS to search a large faba bean (Vicia faba L.) collection for traits related to drought adaptation. Two sets of faba bean accessions were created, one from moisture-limited environments, and the other from wetter sites. The two sets were grown under well watered conditions and leaf morpho-physiological traits related to plant water use were measured. Machine-learning algorithms split the accessions into two groups based on the evaluation data and the groups created by this process were compared to the original climate-based FIGS sets. The sets defined by trait data were in almost perfect agreement to the FIGS sets, demonstrating that ecotypic differentiation driven by moisture availability has occurred within the faba bean genepool. Leaflet and canopy temperature as well as relative water content contributed more than other traits to the discrimination between sets, indicating that their utility as drought-tolerance selection criteria for faba bean germplasm. This study supports the assertion that FIGS could be an effective tool to enhance the discovery of new genes for abiotic stress adaptation.
  • Logan, Alan C.; Prescott, Susan L.; Haahtela, Tari; Katz, David L. (2018)
    In 1980, Jonas Salk (1914-1995) encouraged professionals in anthropology and related disciplines to consider the interconnections between "planetary health," sociocultural changes associated with technological advances, and the biology of human health. The concept of planetary health emphasizes that human health is intricately connected to the health of natural systems within the Earth's biosphere; experts in physiological anthropology have illuminated some of the mechanisms by which experiences in natural environments (or the built environment) can promote or detract from health. For example, shinrin-yoku and related research (which first emerged from Japan in the 1990s) helped set in motion international studies that have since examined physiological responses to time spent in natural and/or urban environments. However, in order to advance such findings into planetary health discourse, it will be necessary to further understand how these biological responses (inflammation and the collective of allostatic load) are connected to psychological constructs such as nature relatedness, and pro-social/environmental attitudes and behaviors. The exposome refers to total environmental exposures-detrimental and beneficial-that can help predict biological responses of the organism to environment over time. Advances in "omics" techniques-metagenomics, proteomics, metabolomics-and systems biology are allowing researchers to gain unprecedented insight into the physiological ramifications of human behavior. Objective markers of stress physiology and microbiome research may help illuminate the personal, public, and planetary health consequences of "extinction of experience." At the same time, planetary health as an emerging multidisciplinary concept will be strengthened by input from the perspectives of physiological anthropology.
  • Sinai, Iftah; Segev, Ori; Wei, Gilad; Oron, Talya; Merilä, Juha; Templeton, Alan R.; Blaustein, Leon; Greenbaum, Gili; Blank, Lior (2019)
    Genetic studies on core versus peripheral populations have yielded many patterns. This diversity in genetic patterns may reflect diversity in the meaning of peripheral populations as defined by geography, gene flow patterns, historical effects, and ecological conditions. Populations at the lower latitude periphery of a species' range are of particular concern because they may be at increased risk for extinction due to global climate change. In this work we aim to understand the impact of landscape and ecological factors on different geographical types of peripheral populations with respect to levels of genetic diversity and patterns of local population differentiation. We examined three geographical types of peripheral populations of the endangered salamander, Salamandra infraimmaculata, in Northern Israel, in the southernmost periphery of the genus Salamandra, by analyzing the variability in 15 microsatellite loci from 32 sites. Our results showed that: (1) genetic diversity decreases towards the geographical periphery of the species' range; (2) genetic diversity in geographically disjunct peripheral areas is low compared to the core or peripheral populations that are contiguous to the core and most likely affected by a founder effect; (3) ecologically marginal conditions enhance population subdivision. The patterns we found lead to the conclusion that genetic diversity is influenced by a combination of geographical, historical, and ecological factors. These complex patterns should be addressed when prioritizing areas for conservation.
  • Amesbury, Matthew J.; Booth, Robert K.; Roland, Thomas P.; Bunbury, Joan; Clifford, Michael J.; Charman, Dan J.; Elliot, Suzanne; Finkelstein, Sarah; Garneau, Michelle; Hughes, Paul D. M.; Lamarre, Alexandre; Loisel, Julie; Mackay, Helen; Magnan, Gabriel; Markel, Erin R.; Mitchell, Edward A. D.; Payne, Richard J.; Pelletier, Nicolas; Roe, Helen; Sullivan, Maura E.; Swindles, Graeme T.; Talbot, Julie; van Bellen, Simon; Warner, Barry G. (2018)
    Fossil testate amoeba assemblages have been used to reconstruct peatland palaeohydrology for more than two decades. While transfer function training sets are typically of local-to regional-scale in extent, combining those data to cover broad ecohydrological gradients, from the regional-to continental- and hemispheric-scales, is useful to assess if ecological optima of species vary geographically and therefore may have also varied over time. Continental-scale transfer functions can also maximise modern analogue quality without losing reconstructive skill, providing the opportunity to contextualise understanding of purely statistical outputs with greater insight into the biogeography of organisms. Here, we compiled, at moderate taxonomic resolution, a dataset of nearly 2000 modern surface peatland testate amoeba samples from 137 peatlands throughout North America. We developed transfer functions using four model types, tested them statistically and applied them to independent palaeoenvironmental data. By subdividing the dataset into eco-regions, we examined biogeographical patterns of hydrological optima and species distribution across North America. We combined our new dataset with data from Europe to create a combined transfer function. The performance of our North-American transfer function was equivalent to published models and reconstructions were comparable to those developed using regional training sets. The new model can therefore be used as an effective tool to reconstruct peatland palaeohydrology throughout the North American continent. Some eco-regions exhibited lower taxonomic diversity and some key indicator taxa had restricted ranges. However, these patterns occurred against a background of general cosmopolitanism, at the moderate taxonomic resolution used. Likely biogeographical patterns at higher taxonomic resolution therefore do not affect transfer function performance. Output from the combined North American and European model suggested that any geographical limit of scale beyond which further compilation of peatland testate amoeba data would not be valid has not yet been reached, therefore advocating the potential for a Holarctic synthesis of peatland testate amoeba data. Extending data synthesis to the tropics and the Southern Hemisphere would be more challenging due to higher regional endemism in those areas. (C) 2018 The Authors. Published by Elsevier Ltd.
  • Schiesari, Luis; Matias, Miguel G.; Prado, Paulo Inacio; Leibold, Mathew A.; Albert, Cecile H.; Howeth, Jennifer G.; Leroux, Shawn J.; Pardini, Renata; Siqueira, Tadeu; Brancalion, Pedro H. S.; Cabeza, Mar; Coutinho, Renato Mendes; Felizola Diniz-Filho, Jose Alexandre; Fournier, Bertrand; Lahr, Daniel J. G.; Lewinsohn, Thomas M.; Martins, Ayana; Morsello, Carla; Peres-Neto, Pedro R.; Pillar, Valerio D.; Vazquez, Diego P. (2019)
    The complexity of ecological systems is a major challenge for practitioners and decision-makers who work to avoid, mitigate and manage environmental change. Here, we illustrate how metaecology - the study of spatial interdependencies among ecological systems through fluxes of organisms, energy, and matter - can enhance understanding and improve managing environmental change at multiple spatial scales. We present several case studies illustrating how the framework has leveraged decision-making in conservation, restoration and risk management. Nevertheless, an explicit incorporation of metaecology is still uncommon in the applied ecology literature, and in action guidelines addressing environmental change. This is unfortunate because the many facets of environmental change can be framed as modifying spatial context, connectedness and dominant regulating processes - the defining features of metaecological systems. Narrowing the gap between theory and practice will require incorporating system-specific realism in otherwise predominantly conceptual studies, as well as deliberately studying scenarios of environmental change. (C) 2019 Associacao Brasileira de Ciencia Ecologica e Conservacao. Published by Elsevier Editora Ltda.
  • Duplouy, Anne; Hornett, Emily A. (2018)
    The Lepidoptera is one of the most widespread and recognisable insect orders. Due to their remarkable diversity, economic and ecological importance, moths and butterflies have been studied extensively over the last 200 years. More recently, the relationship between Lepidoptera and their heritable microbial endosymbionts has received increasing attention. Heritable endosymbionts reside within the host’s body and are often, but not exclusively, inherited through the female line. Advancements in molecular genetics have revealed that host-associated microbes are both extremely prevalent among arthropods and highly diverse. Furthermore, heritable endosymbionts have been repeatedly demonstrated to play an integral role in many aspects of host biology, particularly host reproduction. Here, we review the major findings of research of heritable microbial endosymbionts of butterflies and moths. We promote the Lepidoptera as important models in the study of reproductive manipulations employed by heritable endosymbionts, with the mechanisms underlying male-killing and feminisation currently being elucidated in moths and butterflies. We also reveal that the vast majority of research undertaken of Lepidopteran endosymbionts concerns Wolbachia. While this highly prevalent bacterium is undoubtedly important, studies should move towards investigating the presence of other, and interacting endosymbionts, and we discuss the merits of examining the microbiome of Lepidoptera to this end. We finally consider the importance of understanding the influence of endosymbionts under global environmental change and when planning conservation management of endangered Lepidoptera species.