Phylogenetic workshop: From morphology and total-evidence analyses to macroevolutionary patterns 1400-PhW-en
The course consists of two thematic blocks covering phylogenetics and modelling, with a focus on paleobiological research and the evolution of morphology. Each class will be preceded by a brief theoretical introduction.
Data acquisition and evaluation:
• Introduction to morphological data acquisition and matrix building
• Character coding
• Interpretation and evaluation of morphological phylogenetic trees
• Age constraints
• Introduction to statistical modelling and RevBayes
• Preparing phylogenetic data for RevBayes
Phylogenetic and modelling block:
• Introduction to Bayesian phylogenetics and MCMC inference
• Substitution models & Bayesian Tree inference
• Models of morphological evolution
• Tutorials and project work (tree inference)
• Bayesian tree inference and the fossilized birth-death model
• Tutorials and project work (time tree inference)
• Comparative phylogenetic methods
• Project work and presentation preparation
• Cophylogenetics methods
• Synthesis and presentation of project results
Rodzaj przedmiotu
Koordynatorzy przedmiotu
Efekty kształcenia
KNOWLEDGE:
1. The graduate understands the mutual relationships of all living organisms. They know advanced phylogenetic methodology that allows establishing relationships between organisms (K_W07 BI2).
2. The graduate recognizes the need for advanced statistical methods to describe phenomena and analyze data in biological sciences (K_W08 BI2).
3. The graduate knows specialized bioinformatics tools used in phylogenetics, with particular emphasis on the specifics of evolutionary (paleo)biology (K_W09 BI2).
4. The graduate knows molecular methods used in biological sciences and environmental research (K_W08 Os2).
SKILLS:
1. The graduate applies appropriate statistical methods as well as computer algorithms and techniques to describe biological phenomena and analyze biological data (K_U06 BI2).
2. The graduate uses advanced statistical methods and tools to analyze empirical data and describe natural processes (K_U01 Os2).
3. The graduate predicts phylogenetic relationships and evolutionary patterns based on analytical data (K_U02 Os2).
4. The graduate has the ability to prepare a research project based on their own scientific research and a short scientific presentation in a foreign language (K_U11 Os2).
SOCIAL COMPETENCES:
1. Demonstrates the need for constant updating and deepening of knowledge in the field of phylogenetics (K_K02 Os2).
2. Expands interests in the direction of exact sciences (K_K03 Os2).
3. Demonstrates the need for constant updating of knowledge in the field of mathematical and natural sciences (K_K04 Os2).
4. Feels the need for constant self-education and updating of knowledge, using scientific sources related to phylogenetics and genomics (K_K07 BI2).
Kryteria oceniania
Based on points for tasks performed
Literatura
Barido-Sottani, J., Justison, J. A., Wright, A. M., Warnock, R. C., Pett, W., & Heath, T. A. (2020). Estimating a time-calibrated phylogeny of fossil and extant taxa using RevBayes. Phylogenetics in the genomic era, 5-2.
Bromham, L., Duchêne, S., Hua, X., Ritchie, A. M., Duchêne, D. A., & Ho, S. Y. (2018). Bayesian molecular dating: opening up the black box. Biological Reviews, 93(2), 1165-1191.
Dismukes, W., Braga, M. P., Hembry, D. H., Heath, T. A., & Landis, M. J. (2022). Cophylogenetic methods to untangle the evolutionary history of ecological interactions. Annual Review of Ecology, Evolution, and Systematics, 53, 275-298.
Mulvey, L. P., May, M. R., Brown, J. M., Hoehna, S., Wright, A. M., & Warnock, R. C. (2024). Assessing the Adequacy of Morphological Models used in Palaeobiology. bioRxiv, 2024-01.
Revell, L. J., & Harmon, L. J. (2022). Phylogenetic comparative methods in R. Princeton University Press.
Warnock, R. C., & Wright, A. M. (2020). Understanding the tripartite approach to Bayesian divergence time estimation. Cambridge University Press.
Uwagi
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W cyklu 2023L:
The Workshops is planned at the Faculty of Biology. The planned date of the workshops is from July 24 to August 3 |
W cyklu 2024L:
The Workshops is planned at the Faculty of Biology. The planned date of the workshops is from July 24 to August 3 |
Więcej informacji
Dodatkowe informacje (np. o kalendarzu rejestracji, prowadzących zajęcia, lokalizacji i terminach zajęć) mogą być dostępne w serwisie USOSweb: