Evolutionism

obligatory courses

Classroom

The course "Evolutionism" is intended for students of Bioinformatics and Systems Biology and includes both lectures and practicals. The lectures include an outline of the history of life on Earth and of the basic mechanisms of evolution. The practicals are devoted primarily to phylogenetic and evolutionary analyzes using open/free software.

Lectures:

1. Evolution as a historical fact and as a theory. Sources of knowledge about evolution. The history of evolutionary thought. Charles Darwin and the theory of natural selection. Illustrative metaphors: survival of fittest (fitness), replicators and their vehicles, selfish gene.

2. Reconstructing phylogenetic trees based on morphological and molecular data. Maximum Parsimony, Maximum Likelihood and Bayesian methods. Inconsistency issues (Felsenstein and Farris zones).

3. Gene trees and species trees, horizontal transfer and incomplete lineage sorting. Estimating the internal support of the tree.

4. The pace and patterns of evolution. Gradualism and punctualism. The emergence of evolutionary novelties and the increase in biological complexity.

5. History of life on Earth. The origin of life.

6. Geography of life. Dispersion and vicariance. Historical phylogeography and biogeography. Evolution of biodiversity.

7. Genetic and phenetic variation. Elements of population genetics (Hardy-Weinberg law, linkage, genetic drift). Neutral evolution.

8. Natural selection and adaptations. Fitness.

9. Sex and sexual selection. Evolution in sexual and asexual populations, evolutionary costs of sex.

10. Conflict and cooperation. Kin selection and the evolution of altruism and social behavior. Game theory in the analyses of evolutionary strategies.

11. Species and speciation. Problems with the definition, allopatric and sympatric speciation; reproductive barriers (pre- and post-zygotic).

12. Evolutionary arms race - the evolution of interspecies antagonistic relationships.

13. Evolution of genes and genomes.

14. Human evolution.

15. Evolution in social perception. Creationism, "intelligent design theory".

Practicals

1. Sequence analyses using data from GenBank (BLAST, Dotplot): BLAST search and interpretation of results; potential errors in sequences deposited in databases (reversed sequences, chimeras); distinguishing ortho- and paralogous sequences based on trees, detecting orthologs within genomes, databases of orthologs.

2. Preparation of alignments for phylogenetic analyzes (Clustal, Mesquite, Trimal, Bmge etc.): alignments of nucleotide and protein sequences; analysis of the suitability of the 3rd position in the codon for phylogenetic analyses; assessing the reliability of alignment and selection of sequence ranges for the analyses.

3. Phylogenetic analyses: Maximum parsimony method (MEGA); selection of nucleotide substitution model in phylogenetic analyzes (JModeltest, IQtree etc.); distance methods (MEGA); maximum likelihood method (MEGA, PHYML, RAxML, IQtree, FastTree); Bayesian analyses (MrBayes).

4. Tree parameters and internal branch support assessments: bootstrap, jack-knifing, different methods of branch reliability estimation, posterior probability; tree topology testing (IQtree, Mesquite etc.).

5. Phylogenomics and genome evolution: detection of large genome rearrangements, comparison of genomes (synthenia), analyses of protein family expansion, gene acquisition and loss; horizontal gene transfer.

6. Detection of adaptive evolution in molecular data (PAML, especially codeml).

7. Bayesian dating of phylogeny - calibration points as prior assumptions.

8. Estimation of ancestral states of morphological traits - the method of maximum parsimony and maximum likelihood; evolution models for continuous and categorical characters; the problem of arbitrary coding and character weighting.

9. Historical biogeography - reconstruction of the distribution and dispersal of taxa in time and space. Comparison of home range inheritance models (DIVA, DEC, DEC + J etc.).

10. Phylogenetic comparative methods – assessing coevolution of traits.

1. Futuyma, D.J & Kirkpatrick, M. 2018. Evolution. 4th ed. Sinauer Associates.

2. Hall, B.G. 2008. Phylogenetic trees made easy: a how-to manual. W.H. Freeman.

3. Avise, J.C. 1994. Molecular markers, natural history and evolution. Kluver Academic Publishers.

KNOWLEDGE. Student:

- understands the relationships among organisms; knows the methodology enabling to infer the relationships between genes and between organisms

- knows the history of life on Earth and describes the mechanisms of evolution including their molecular basis

- understands the importance of biogeography and phylogeny in understanding the structure of the living word and the biodiversity

SKILLS. Student:

- is able to analyze the obtained results and to discuss them based on the available literature

- is able to present the obtained results in the form of a written work or multimedia presentation

SOCIAL COMPETENCE. Student:

- acknowledges the need for constant training and for updating his/her knowledge of mathematics and natural sciences

The practicals are graded based on a project that includes selected evolutionary analyzes (e.g., sequence and phylogenetic analyses). The lectures end with a written examination consisting of multiple-choice questions. The final grade is the average of the grades from the practicals and the lectures - both must be positive. Students who pass the practicals with a grade of at least 4.0 may take the exam on the zero date. In this case, the exam is oral and consists of five open questions. The examination in the second term is also oral.