The course introduces advanced experimental designs, including block and nested designs and repeated measurements, and their statistical analysis. This includes an introduction to univariate methods, focusing on mixed-effects linear models as an extension of standard linear models. The main focus of the course is multivariate analysis of species composition, covering the principles of ordination and commonly used methods such as PCA, RDA, DCA, and CCA. Students also learn basic and advanced permutation tests suitable for different experimental designs. Lectures are complemented by computer practicals, in which students gain hands-on experience analyzing real ecological datasets in R, mainly using the vegan package. This is an intermediate-level statistics course that assumes prior basic knowledge of linear regression and analysis of variance, including experience with the lm and aov functions in R.

• lecturers: Aleš Lisner, Petr Blažek,
• credits: 6

The course introduces the main concepts and methods of community ecology, focusing on quantifying and interpreting community diversity, its relationships with environmental conditions, and its effects on ecosystem functioning. Topics include community assembly, species coexistence and competition, food webs and trophic interactions, functional traits and life-history strategies, ecological succession, and spatial and temporal variation in community composition. Students also explore the use of null models and other analytical approaches to understand ecological patterns and processes, as well as applications in nature conservation and biological control. The course begins with a three-day field trip in September, during which students collect ecological data for subsequent analysis in computer practicals. Field participation is not compulsory but is highly recommended. To complete the course, students must participate in data analysis practicals, give a presentation on a topic of their choice in community ecology at the concluding seminar, and pass an oral examination.

• lecturers: Jan Lepš, Vojtěch Novotný, Lars Götzenberger
• credits: 6

The course introduces the main concepts related to the use of species traits to understand ecological processes, such as niche differentiation, species interactions, and community assembly, and how these feed into ecosystem processes and services. In practical sessions, the students will discuss the prominent trait schemes of Grime and Westoby, get an understanding of how to optimise trait sampling campaigns, and calculate essential community level trait indices such as community weighted means (CWM) and functional diversity (FD) in the statistical software R. To pass the course with a grade, students need to hand in an assignment that demonstrates that they can apply the theoretical background and methodological tools learned in the course on a data set of their own choosing.

• lecturers: Francesco de Bello, Lars Götzenberger
• credits: 5

This course introduces several important families of basic and advanced regression models, with particular emphasis on generalized linear models (GLMs), generalized additive models (GAMs), linear mixed-effects models (LMEs), and their integration into complex path models (structural equation modelling; SEM). The course also covers models for categorical response variables (e.g., logistic or ordinal regression), as well as the basics of classification and regression trees (CART) and survival analysis. The course focuses on the analysis of real-world datasets and the practical application of these methods using the widely used statistical software R.

• lecturers: Aleš Lisner, Petr Koutecký
• credits: 6

Main aspects of invasive behavior of alien organisms, especially vascular plants, are explained. Theoretical principles of invasive ecology are accompanied by examples from central Europe as well as other parts of the World. Not only processes of invasion but also eradication of noxious alien organisms and restoration of native communities are considered.

• lecturers: Karel Prach, Ondřej Mudrák
• credits: 3

The course provides an overview of current approaches to using molecular data in ecological, phylogenetic, and evolutionary research. It covers key methods used at the genealogical and population levels, including haplotype networks, multilocus analyses, and coalescent-based inferences of demographic history, selection, and other evolutionary processes, as well as the basic principles of molecular phylogenetics (maximum parsimony, maximum likelihood, and Bayesian inference). Topics also include population genetic structure, speciation, and applications of molecular methods in biodiversity research and conservation. Lectures are complemented by computer practicals, in which students learn to use phylogenetic and population genetic software to investigate ecological and evolutionary questions. Assessment is based on participation in lectures and practicals, demonstrated proficiency with the software, and a written exam.

• lecturer: Václav Hypša
• credits: 6

The course introduces the ecology of tropical ecosystems, with a focus on their functional and evolutionary aspects and the processes shaping their biodiversity. Topics include the origin and maintenance of tropical species diversity, the structure of food webs and interspecific interactions, tropical vegetation, and ecological gradients across regions and continents. The course also explores ecological succession, the evolution and ecology of tropical islands, and the effects of human activities on tropical ecosystems. Conservation of tropical biodiversity and methods of ecological research in the tropics provide links between ecological theory and practical challenges. Lectures are complemented by seminars in which students read, discuss, and critically analyze selected key research papers in tropical ecology.

• lecturer: Vojtěch Novotný
• credits: 5

The course introduces the main concepts and classic methods of evolutionary ecology, focusing on the feedbacks between ecological and evolutionary processes and the adaptations of organisms to their environment. Topics include natural selection and evolutionary responses, fitness, life-history strategies, trade-offs, phenotypic plasticity, and the evolution of behaviour, mating systems, cooperation, and interactions between species. Case studies illustrate links between theoretical concepts and empirical observations, including adaptations to predators, dormancy, parental care, and the evolution of drug resistance. Lectures are complemented by discussions of classical and recent scientific papers or computer practicals depending on the students' choice. The practicals introduce simulation tools and data analysis and visualization in R, providing hands-on experience with quantitative approaches to ecological and evolutionary problems. Students also design and carry out a small project in R individually or in pairs, based on an eco-evolutionary topic of their choice. Assessment is based on an essay/project report summarizing the selected topic and a short written test.

• lecturer: David Boukal
• credits: 6

The course consists of a one-week field trip exploring the landscape around Mohelno, including the diverse habitats, plants, and animals of the Jihlava and Oslava river canyons. During excursions to different habitats, students carry out simple field projects involving the sampling of plant or animal communities. They then process the collected data and present their results, together with the ecological background and aims of their projects, to their fellow students.

• tutors: Petr Blažek, Jan Lepš
• credits: 3

The course focus on writing and publishing scientific papers. It introduces the principles of scientific publishing, including publication strategies, scientific writing, and the creative use of ecological data to address research questions. The main focus is hands-on experience: students work in groups using provided field data to develop research questions, analyze the data, draw conclusions, and write a manuscript with support from tutors. The course culminates in submitting the manuscript to a scientific journal, with one of the students usually taking the lead as first author. The tutors are (or recently used to be) editors of respected journals, such as Journal of Applied Ecology, Journal of Ecology, Journal of Vegetation Science, or PLoS One. Read the posts in Vegetation Science Blog about writing the Pan et al. 2024 paper and Habencyus et al. 2024 paper.

• tutors: Jan Lepš, Francesco de Bello, Lars Götzenberger, Jan Hrček, Aleš Lisner
• credits: 4

From previous runs of the module, we managed to publish more than ten papers in respected international journals:

• Gracia, C., Lisner, A., Applová, M., Chondol, T., Dolejšek, V., Janíkova, E., ... & Segrestin, J. (2025). Plant diversity loss has limited effects on below-ground biomass and traits but alters community short-term root production in a species-rich grassland. Journal of Ecology, 113, 662–671.
• Pan, X., Ferris, N. D., Applová, M., Gresse, J., Iamba, K. S., Khum, W., Švancárová, T., Wipulasena, A. Y. A., Hrček, J., & Lepš, J. (2024). The convex relationship between plant cover and biomass: Implications for assessing species and community properties. Journal of Vegetation Science, 35, e13288.
• Hábenczyus, A. A., Weiterová, I., Foremnik, K., Jakob, A., Khopkar, S., Kumar, A., Lazar, A., Paganeli, B., Samraoui, K. R., Sidwell, J., Hrček, J., & Lepš, J. (2024). Long-term effects of meadow management on seed bank diversity and composition. Journal of Vegetation Science, 35, e13282.
• Mugnai, M., Trindade, D. P., Thierry, M., Kaushik, K., Hrček, J., & Götzenberger, L. (2022). Environment and space drive the community assembly of Atlantic European grasslands: Insights from multiple facets. Journal of Biogeography, 49, 699–711.
• Tammaru, K., Košnar, J., Abbas, A. F., Barta, K. A., de Bello, F., Harrison, S., ... & Lepš, J. (2021). Ecological differentiation of Carex species coexisting in a wet meadow: Comparison of pot and field experiments. Acta Oecologica, 110, 103692.
• Backhaus, L., Albert, G., Cuchietti, A., Jaimes Nino, L. M., Fahs, N., Lisner, A., ... & García Medina, N. (2021). Shift from trait convergence to divergence along old-field succession. Journal of Vegetation Science, 32, e12986.
• Galland, T., Adeux, G., Dvořáková, H., E.-Vojtkó, A., Orbán, I., Lussu, M., Puy, J., Blažek, P., Lanta, V., Lepš, J., de Bello, F., Carmona, C. P., Valencia, E., & Götzenberger, L. (2019). Colonization resistance and establishment success along gradients of functional and phylogenetic diversity in experimental plant communities. Journal of Ecology, 107, 2090–2104.
• Brown, J. B., Mennicken, S., Massante, J. C., Dijoux, S., Telea, A., Benedek, A. M., Götzenberger, L., Májeková, M., Lepš, J., Šmilauer, P., Hrček, J., & de Bello, F. (2019). A novel method to predict dark diversity using unconstrained ordination analysis. Journal of Vegetation Science, 30, 610–619.
• E.-Vojtkó, A., Freitag, M., Bricca, A., Martello, F., Moreno Compañ, J., Küttim, M., Kun, R., de Bello, F., Klimešová, J., & Götzenberger, L. (2017). Clonal vs leaf-height-seed (LHS) traits: Which are filtered more strongly across habitats? Folia Geobotanica, 52, 269–281.
• Szefer, P., Carmona, C. P., Chmel, K., Konečná, M., Libra, M., Molem, K., Novotný, V., Segar, S. T., Švamberková, E., Topliceanu, T.-S., & Lepš, J. (2017). Determinants of litter decomposition rates in a tropical forest: Functional traits, phylogeny and ecological succession. Oikos, 126, 1101–1111.
• Volf, M., Redmond, C., Albert, Á. J., Le Bagousse-Pinguet, Y., Biella, P., Götzenberger, L., Hrázský, Z., Janeček, Š., Klimešová, J., Lepš, J., Šebelíková, L., Vlasatá, T., & de Bello, F. (2016). Effects of long- and short-term management on the functional structure of meadows through species turnover and intraspecific trait variability. Oecologia, 180, 941–950.
• Májeková, M., Paal, T., Plowman, N. S., Bryndová, M., Kasari, L., Norberg, A., Weiss, M., Bishop, T. R., Luke, S. H., Sam, K., Le Bagousse-Pinguet, Y., Lepš, J., Götzenberger, L., & de Bello, F. (2016). Evaluating functional diversity: Missing trait data and the importance of species abundance structure and data transformation. PLOS ONE, 11, e0149270.
• Kelemen, A., Lazzaro, L., Besnyői, V., Albert, Á.-J., Konečná, M., Dobay, G., Memelink, I., Adamec, V., Götzenberger, L., de Bello, F., Le Bagousse-Pinguet, Y., & Lepš, J. (2015). Net outcome of competition and facilitation in a wet meadow changes with plant’s life stage and community productivity. Preslia, 87, 347–361.

Jan Lepš

Author of the Cambridge book Analysis of ecological data using CANOCO (with Petr Šmilauer, two editions), former Associate Editor of J. Appl. Ecol. and J. Veg. Sci.

Vojtěch Novotný

Tropical ecologist studying plant-insect food webs in the rainforests of Papua New Guinea (and teaching about them in Europe), Associate Editor of Ecology Letters. Read more.

Karel Prach

Author of Cambridge Univ. Press book [with R.L. Walker] Plant succession among terrestrial biomes of the world. Member of editorial boards of Restoration Ecology and Preslia. Read more.

Francesco de Bello

Author of a Cambridge Univ. Press book on trait-based ecology. Associate Editor at the J. of Ecology and Forum Editor at the J. of Vegetation Science and Applied Vegetation Science. Read more.

Václav Hypša

Author of various publications on evolutionary and phylogenetic issues connected to parasitism and symbiosis. Read more.

David Boukal

Studies responses of (freshwater) ecosystems to anthropogenic disturbance. Associate Editor of The American Naturalist. Read more.

Lars Götzenberger

Studies traits (mainly plants) to understand community assembly, ecosystem processes, vegetation dynamics, and plant strategies. Has a particular interest in floral traits and trait data bases. Together with lecturer Francesco de Bello, author of a text book on using traits in ecology published by Cambridge University Press. Associated editor for Journal of Vegetation Science. Read more.

• Information for incoming Erasmus students

Erasmus+ funding may be available for students attending the module as part of a semester study stay at the University of South Bohemia. Students interested in this option should contact the International office at their home university well in advance to discuss eligibility and funding possibilities.

Students participating through Erasmus+ should be nominated by their home institution by 30 April and submit all required application documents by 15 May. Early communication is particularly important for students who require a visa, as immigration procedures may take several months in some countries.

For questions regarding Erasmus+ mobility, please contact Barbora Okosy (This email address is being protected from spambots. You need JavaScript enabled to view it.).