The course On the Evolution and Ecology expands the biological concepts beyond the level of the individual and
focuses on the evolutionary basis of the recent snapshot of biological diversity. Individual species will be perceived
as a product of long term evolution under complex constraints, including the ecological and ethological ones. The
course will benefit from the information base provided in the first year and use it in the higher hierarchical level of
biological complexity. The individuals will be an actors in the play of life which is complex, mutually
interconnected, combining biotic and abiotic factors, nowadays highly affected by our civilization. General
knowledge from the first year will be challenged by the diversity of adaptations reflecting the evolution,
developmental constrains and particular ecological limits.
The course On the Evolution and Ecology will set the stage for follow-up courses, particularly Biological
techniques. The course will follow the prerequisite From molecules to cells and From cells to organisms.
The course is built from topical blocks (see Syllabus) each of them consisting of lecture (3h) and workshop focused
on primary literature as a Q&A session (2h).
Poslední úprava: Rubešová Jana, RNDr., Ph.D. (07.02.2022)
Literatura - angličtina
1. Ecology: From Individuals to Ecosystems, 5th Edition, ISBN-13: 978-1119279358 2021
2. Ecology: Concepts and Applications, 8th Edition, ISBN-13: 978-1260085150 2018
4. Evolution, Second Edition, ISBN-13: 978-0393690118 2019
5. Genetics: Genes, genomes, and evolution, 978-0198712558 2017
6. Lecture notes
7. Pre-recorded lectures
8. Problem sets
Poslední úprava: Rubešová Jana, RNDr., Ph.D. (08.06.2022)
Požadavky ke zkoušce - angličtina
Final mark is based on the oral examination (67%) and results of tests taken during the course (33%). Oral examination takes place during the examination period and students must first obtain the evaluation for Q&A sessions, workshops and take-home exercises.
Poslední úprava: Rubešová Jana, RNDr., Ph.D. (07.02.2022)
Sylabus - angličtina
1) Introduction to the course and evolutionary biology
Evolutionary biology as both historical and nomothetic science, historical contingency, predicting evolutionary changes and limits of predictability, adaptation, constraints, levels of selection, relationship between evolutionary biology, ecology and other disciplines, role of phenotypic plasticity in evolution (eco-devo).
Characters vs. character states, sequence alignment, Needleman-Wunch, strategies for multiple sequence alignment, advantages of molecular characters, substitution saturation, genetic distance, phylogenetic tree, heuristic search through a topology space, neighbour-joining, scoring the trees by least squares, maximum parsimony, maximum likelihood or Bayesian statistics, bootstrapping, rooting the tree.
Practical: Aligning DNA sequences, editing the alignment, calculation of the phylogenetic tree by neighbour-joining and maximum likelihood, visualising the trees.
10 key terms: character, character state, alignment, substitution saturation, genetic distance, phylogenetic tree, heuristic search, maximum parsimony, maximum likelihood, bootstrapping.
4) Evolution of sex and asexuality
Sexual systems, sex determination, sex-specific heritability (mtDNA, sex chromosomes).
Practical part: Discussions about meaning of key terms and reasons for their evolution (or lack of).
10 key terms: sexual reproduction, costs and benefits of sex, mating types, anisogamy,
hermaphroditism, sex determination, sex chromosomes, sex-limited inheritance, genomic imprinting, parthenogenesis.
What species are and how species arise with and without presence of gene flow. Mechanisms and evolution of reproductive isolation. Evolutionary consequences of hybridization and interspecific gene flow. Methods of measuring gene flow. The role of sex chromosomes in speciation. How species originate in asexually reproducing organisms.
10 key terms: Species concepts, reproductive isolation, sympatric vs. allopatric speciation, speciation with gene flow, reinforcement, coupling of reproductive barriers, origin of intrinsic postzygotic isolation, Haldane's rule, large X-effect, evolutionary consequences of interspecific gene flow, hybrid speciation.
8) Tracing Earth's Biological Evolution: A Historical Perspective
Does macroevolution exist, and how is it different from microevolution? How do evolutionary novelties arise, and when are they truly new? What is evolvability, and is it subject to evolution itself? What were the major transitions in evolution? Are there macroevolutionary trends? How do mass extinctions influence the evolution of life?
Practical part: Examining the evolution of evolvability, the origin of novelties, and evolutionary trends in computer simulations of evolution. Some simulations will be freeware, while others will be presented upfront.
Key terms: Macroevolution, Adaptive radiation, Species selection, Mass extinctions, Evolutionary trends, Evolutionary constraints, Evolution of evolvability, Evolutionary innovations, Major transitions in evolution, Symbiogenesis.
9) What limits species' ecological niches and geographic ranges?
Eco-evolutionary feedbacks. The lesson will highlight the importance of considering evolution (population genetics) and ecology (sensu population dynamics) jointly. Main topic: What limits species' ecological niches and geographic ranges? From the ideas of Joseph Grinnell, JBS Haldane and Ernst Mayer to the modern theory of limits to adaptation and evolutionary rescue. Second topic: the “other” eco-evo feedback, focusing on the effect of evolution on ecological communities.
Key terms: eco-evo feedback, hard and soft selection, gene flow, genetic drift, evolutionary rescue, cost of selection, shifting balance theory, character displacement, maintenance of variability, metapopulation, neighbourhood size, effective population size (note: Ne was not on my slides yet was discussed).
Tutorial: student-led paper discussion. Haldane 1957 (cost of selection); Farkas et al 2013 (eco-evo feedback); Angert et al. 2020 (range edges review).
10) Heredity: from genes to continuous traits and back
Fisher's synthesis of Mendelism and biometric inheritance, and Galton's fallacy and regression to mean, heritability (both narrow and broad sense) and contrast twin studies to GWAS, genetic interactions.
Practical part: "how are traits stored in genes". Each student picks an interesting quantitative trait (conformity, IQ, muscle strength, adiposity...) and tries to find out what is known about "how this is coded" from genes and epigenetic regulation to proteins, cellular level features, tissues to behavioural manifestation.
11) Evolution of biodiversity across phylogeny, communities, and worldwide
(1) Evolution of ecological communities: Introducing phylogenetic diversity of the community, phylogenetic betadiversity, and evolutionary distinctiveness, with connections to biodiversity hotspots worldwide and biodiversity conservation. Community phylogenetic structure, the rules of community assembly and null models. (2) Evolution of diversity patterns: Explanations for the latitudinal diversity gradient, the diversification process, tropics as the cradle and museum of diversity, adaptive radiations and evolution of species niches
Practical part: discussions, and/or R exercises. Studying the phylogenetic structure of ecological communities, calculating phylogenetic diversity, phylogenetic betadiversity, species relatedness, implementing null models. Hummingbirds serve as the model system. The exercise investigates their diversification and tests whether tropics act as the engine of global diversity. It implements models of trait evolution for hummingbirds (Brownian motion, adaptive radiation, selection model) and trait co-evolution (phylogenetic independent contrasts).
