Theory & Methods of Ecology

I am very interested in theory of ecology, or rather conceptual ecology (e.g. terminology and conceptual frameworks). Also, I am interested in how ecology works as a science, and whether there are ways for improvement. In my point of view, ecology could profit much from a closer integration of single-study results into theory, and from closer interaction with other fields like computer sciences and philosophy.

Together with Jonathan Jeschke, I developed the hierarchy-of-hypotheses (HoH) approach, and us and several colleagues applied it to uncover the level of empirical evidence for major hypotheses in invasion ecology. At hi-knowledge.org, the result are summarized in a hierarchical network. It is our vision that if combined with natural language processing and other techniques, this web tool could be developed into an interactive atlas of knowledge for invasion ecology. Similar tools could be developed in other fields as well, e.g. restoration ecology or urban ecology.

Philosophy of science in my point of view offers a wealth of knowledge and methods we as ecologists could draw from for improving how we do our science. I am very interested in exploring these possibilities, and found out that philosophers often are highly interested in interacting with ecologists (the same holds for computer scientists).

Projects

enKORE - Towards an open, zoomable atlas for invasion science and beyond

Invasive species and other non-native species are on the rise, and their global impacts on ecosystems, economies and human health are highly problematic. Invasion science, the study of these species, is critical to mitigate their impacts, yet due to the strong increase of data and information in this area, it has become difficult to acquire and maintain an overview of the field. As a result, existing evidence is often not found, knowledge is not transferred to practice, and research is conducted in pursuit of dead ends. We propose to address these challenges by developing an interactive atlas of invasion science that can be extended to other disciplines in the future. This knowledge portal will be called enKORE, EvolviNg KnOwledge REsource. It will be open for anyone to use, including researchers, citizen scientists, practitioners and policy makers. Users will be able to zoom into the major research questions and hypotheses of invasion science, which are connected to the relevant studies published in the field and, if available, the underlying raw data. enKORE will apply cutting-edge visualization techniques, artificial intelligence and novel methods for knowledge synthesis.

Funded by Volkswagen Foundation, project start: September 2021, project proposal

Project partners: Jonathan Jeschke, Peter Kraker, Daniel Mietchen

INAS - Interactive Argumentation Support in the Invasion Biology Domain

This project is funded as part of the Robust Argumentation Machines program by the DFG. We will develop an argumentation machine that supports users in and during the argumentation process in a scientific context. The goal is to enable users to follow ongoing argumentation in a scientific community and to develop their own arguments. The project collaborates closely with other initiatives that work on mapping and organizing scientific knowledge, such as the hi-knowledge project. Our interdisciplinary team brings together people from Natural Language Processing, Biology, Semantic Web and Knowledge Representation. Check out our project website!

Funded by DFG, project start: Septemer 2021, project proposal

Project partners: Sina Zarrieß, Birgitta König-Ries, Jonathan Jeschke, Alsayed Algergawy

Cooperation:

• Alsayed Algergawy

• Jonathan Jeschke

• Birgitta König-Ries

• Peter Kraker, Open Knowledge Maps

• Daniel Mietchen

• Sina Zarrieß

Essays

Jeschke, J., Bartram, I., Heger, T., Lokatis, S. & Tockner, K. (2020): Dark Knowledge ans Licht holen. Laborjournal 7-8: 34-37. [link to pdf]

Publications

Heger, T., Jeschke, J. M., Bernard-Verdier, M., Musseau, C. L., Mietchen, D. (2024): Hypothesis Description: Enemy Release Hypothesis. Research Ideas and Outcomes, 10: e107393. https://doi.org/10.3897/rio.10.e107393

* Heger, T., Mietchen, D., Jeschke, J. M. (2024): Template for a Hypothesis Description paper. Research Ideas and Outcomes, 10: e119808. https://doi.org/10.3897/rio.10.e119808

* Mietchen, D., Jeschke, J. M., Heger, T. (2024): Introducing Hypothesis Descriptions. Research Ideas and Outcomes, 10, e119805. https://doi.org/10.3897/rio.10.e119805

* Bernard-Verdier, M., Heger, T., Mietchen, D., Musseau, C. L., Brinner, M., Hillig, A., Kraker, P., Lokatis, S., Nunes, A. L., Scheidweiler, N., Stocker, M., Vial, R., Vogt, L., Bacher, S., Baklouti, E., Gupta, H. B., Beisel, J.-N., Bertolino, S., Briski, E., Castellanos-Galindo, G. A., Courchamp, F., Daly, E., Dawson, W., Dickey, J., Evans, T., Itescu, Y., Koenig-Ries, B., Kumar, L., Kumschick, S., Meyerson, L. A., Pattison, Z., Pfadenhauer, W., Renault, D., Rickowski, F., Ruland, F., Schittko, C., Straka, T., Yannelli, F., Jeschke, J. M. (2023): Building an atlas of knowledge for invasion biology and beyond! 2nd enKORE-INAS Workshop. Research Ideas and Outcomes 9. https://doi.org/10.3897/rio.9.e115395

* Bernard-Verdier, M., Heger, T., Jeschke, J. M., Mietchen, D., Musseau, C. (2023): Summary report of the 1st enKORE-INAS workshop. In: Zenodo. https://doi.org/10.5281/zenodo.8421054

Lokatis, S., Jeschke, J. M., Bernard-Verdier, M., Buchholz, S., Grossart, H.-P., Havemann, F., Hölker, F., Itescu, Y., Kowarik, I., Kramer-Schadt, S., Mietchen, D., Musseau, C., Planillo, A., Schittko, C., Straka, T., Heger, T. (2023): Hypotheses in urban ecology: building a common knowledge base. Biological Reviews 98, 1530-1547. DOI: 10.1111/brv.12964

Daly, E. Z., Chabrerie, O., Massol, F., Facon, B., Hess, M. C. M., Tasiemski, A., Grandjean, F., Chauvat, M., Viard, F., Forey, E., Folcher, L., Buisson, E., Boivin, T., Baltora-Rosset, S., Ulmer, R., Gibert, P., Thiébaut, G., Pantel, J. H., Heger, T., Richardson, D. M., Renault, D. (2023): A synthesis of biological invasion hypotheses associated with the introduction–naturalisation–invasion continuum. Oikos 2023: e09645. DOI: 10.1111/oik.09645

Brinner, M., Heger, T., Zarriess, S. (2022): Linking a Hypothesis Network From the Domain of Invasion Biology to a Corpus of Scientific Abstracts: The INAS Dataset. In: Proceedings of the first Workshop on Information Extraction from Scientific Publications. Association for Computational Linguistics, pp. 32-42. [link to pdf]

Synodinos, A. D., Karnatak, R., Aguilar-Trigueros, C. A., Gras, P., Heger, T., Ionescu, D., Maaß, S., Musseau, C. L., Onandia, G., Planillo, A., Weiss, L., Wollrab, S., Ryo, M. (2023): The rate of environmental change as an important driver across scales in ecology. Oikos 2023: e09616. DOI: 10.1111/oik.09616

* Algergawy, A., Gänßinger, M., Heger, T., Jeschke, J., & König-Ries, B. (2022): The Invasion Biology Ontology (INBIO) [Data set]. Zenodo. DOI: 10.5281/zenodo.6826848

Heger, T., Jeschke, J. M., Febria, C., Kollmann, J., Murphy, S., Rochefort, L., Shackelford, N., Temperton, V.M., Higgs, E. (2022): Mapping and assessing the knowledge base of ecological restoration. Restoration Ecology. DOI: 10.1111/rec.13676; Blogpost with summary

Stocker, M., Heger, T., Schweidtmann, A.M., Ćwiek-Kupczyńska, H., Penev, L., Dojchinovski, M., Willighagen, E., Vidal, M.-E., Turki, H.A., Balliet, D., Tiddi, I., Kuhn, T., Mietchen, D., Karras, O., Vogt, L., Hellmann, S., Jeschke, J.M., Krajewski, P., Auer, S. (2022): SKG4EOSC - Scholarly Knowledge Graphs for EOSC: Establishing a backbone of knowledge graphs for FAIR Scholarly Information in EOSC. Research Ideas and Outcomes 8: e83789. DOI: 10.3897/rio.8.e83789 [link to pdf]

Heger, T. (2022): What are ecological mechanisms? Suggestions for a fine-grained description of causal mechanisms in invasion ecology. Biology & Philosophy 37:9. DOI: 10.1007/s10539-022-09838-1 [link to pdf]

Heger, T., Zarrieß, S., Algergawy, A., Jeschke, J.M. & König-Ries, B. (2022): INAS: Interactive Argumentation Support for the Scientific Domain of Invasion Biology. Research Ideas and Outcomes, 8, e80457. DOI: 10.3897/rio.8.e80457 [link to pdf]

Jeschke, J.M., Heger, T., Kraker, P., Schramm, M., Kittel, C. & Mietchen, D. (2021). Towards an open, zoomable atlas for invasion science and beyond. NeoBiota, 68: 5-18. DOI: 10.3897/neobiota.68.66685 [link to pdf]

Heger, T. (2021). Philosophy of Science for Biologists, edited by K. Kampourakis & T. Uller, Cambridge University Press (2020). 340pp., €33,20 (Paperback), ISBN: 9781108740708. Basic and Applied Ecology, 56: 176-177. DOI: 10.1016/j.baae.2021.07.012

Heger, T., Aguilar, C., Bartram, I., Braga, R. R., Dietl, G. P., Enders, M., Gibson, D. J., Gómez-Aparicio, L., Gras, P., Jax, K., Lokatis, S., Lortie, C. J., Mupepele, A.-C., Schindler, S., Starrfelt, J., Synodinos, A. & Jeschke, J. M. (2021): The hierarchy-of-hypotheses approach: A synthesis method for enhancing theory development in ecology and evolution. BioScience 71: 337-349. DOI: 10.1093/biosci/biaa130 [link to pdf]

Algergawy, A., Stangneth, R., Heger, T., Jeschke, J. M. & König-Ries, B. (2020): Towards a Core Ontology for Hierarchies of Hypotheses in Invasion Biology. The Semantic Web. ESWC 2020 Satellite Events (LNCS Series). [link to pdf]

Enders, M., Havemann, F., Ruland, F., Bernard-Verdier, M., Catford, J. A., Gómez Aparicio, L., Haider, S., Heger, T., Kueffer, C., Kühn, I., Meyerson, L. A., Musseau, C., Novoa, A., Ricciardi, A., Sagouisa, A., Schittko, C., Strayer, D. L., Vilà, M., Essl, F., Hulme, P. E., van Kleunen, M., Kumschick, S., Lockwood, J. L., Mabey, A., McGeoch, M. A., Palma, E., Pyšek, P., Saul, W.-C., Yannelli, F. & Jeschke, J. M. (2020): A conceptual map of invasion biology: integrating hypotheses into a consensus network. Global Ecology and Biogeography 29: 978-991. DOI: 10.1111/geb.13082 [link to pdf]

Ryo, M., Jeschke, J. M., Rillig, M. & Heger, T. (2020): Machine learning with the hierarchy-of-hypotheses (HoH) approach discovers novel pattern in studies on biological invasions. Research Synthesis Methods 11: 66-73. DOI: 10.1002/jrsm.1363 [link to pdf]

Heger, T. & Jeschke, J. M. (2018): The hierarchy-of-hypotheses approach. –  Jeschke, J. M. & Heger, T. (eds). Invasion Biology. Hypotheses and Evidence. CAB International: 14-18.

Heger, T. & Jeschke, J. M. (2018): The hierarchy-of-hypotheses approach updated - a toolbox for structuring and analysing theory, research and evidence. –  Jeschke, J. M. & Heger, T. (eds). Invasion Biology. Hypotheses and Evidence. CAB International: 38-47.

Heger, T. & Jeschke, J. M. (2018): Enemy release hypothesis. –  Jeschke, J. M. & Heger, T. (eds). Invasion Biology. Hypotheses and Evidence. CAB International: 92-102.

Heger, T. & Jeschke, J. M. (2018): Conclusions and outlook. –  Jeschke, J. M. & Heger, T. (eds). Invasion Biology. Hypotheses and Evidence. CAB International: 167-172.

Jeschke, J. M. & Heger, T. (2018):  Synthesis. –  Jeschke, J. M. & Heger, T. (eds). Invasion Biology. Hypotheses and Evidence. CAB International: 157-166.

Heger, T. & Jeschke, J. M. (2014): The enemy release hypothesis as a hierarchy of hypotheses. Oikos 123: 741-750. DOI: 10.1111/j.1600-0706-2013.01263.x

Heger, T., Pahl, A. T., Botta-Dukát, Z., Gherardi, F., Hoppe, C., Hoste, I., Jax, K., Lindström, L., Boets, P., Haider, S., Kollmann, J., Wittmann, M. & Jeschke, J. M. (2013): Conceptual frameworks and methods for advancing invasion ecology. AMBIO 42: 527–540. DOI: 10.1007/s13280-012-0379-x

Heger, T., Saul, W.-C. & Trepl, L. (2013): What biological invasions 'are' is a matter of perspective. Journal for Nature Conservation 21: 93-96. DOI: 10.1016/j.jnc.2012.11.002

Jeschke, J. M., Gómez Aparicio, L., Haider, S., Heger, T., Lortie, C. J., Pyšek, P. & Strayer, D. L. (2012): Support for major hypotheses in invasion biology is uneven and declining. NeoBiota 14: 1-20. DOI: 10.3897/neobiota.14.3435 [link to pdf]