91399 - Genome Evolution

Learning outcomes

The aim of this course is to provide advanced knowledge about the structure and evolution of prokaryotic and eukaryotic genomes. The course will take into consideration the origin of the genetic code, the origin of eukaryotes, the elements that characterize genomes and the molecular mechanisms underlying their evolution, and will deal with the concepts of function and complexity. Moreover, a consistent section of the course is dedicated to the discussion of the principal evolutionary models and the contribution of selection, genetic drift, mutation rate, recombination, robustness, and canalization in different groups of organisms. Each student have the opportunity to present recent publications in the field of evolutionary genomics, and discuss them with the class.

Course contents

The course is organized into 7 core thematic blocks, each mapped to a dedicated workspace on  Gemini Notebook to optimize study focus and eliminate digital "noise":

Notebook 1: Complex Systems, Constraints, and Innovation

• The Genome as a Historical Object: Interplay of mutation, selection, genetic drift, and recombination; structural suboptimality, redundancy, and robustness.
• Molecular Tinkering and Exaptation: Evolution by recycling existing components; protein domain shuffling, exon shuffling, de novo gene origin, gene fusion/fission, and gene loss.
• Complexity, Chaos, and Networks: Introduction to Complex Adaptive Systems (CAS); deterministic chaos, the logistic map, and the "edge of chaos"; emergent properties and the topology of Gene Regulatory Networks (GRN).

Notebook 2: Genomes in Conflict and Metastable Equilibria

• Mobile Elements and Genome Defense: Ecology of transposable elements; host-parasite arms races, epigenome defense (DNA methylation, small RNAs, piRNAs), and domestication of parasitic sequences.
• Intragenomic Conflicts and Enforcement: The genome as an unharmonious coalition; transmission advantage vs. organismal fitness; meiotic drive, B chromosomes, and cytonuclear conflicts. Enforcement mechanisms, genomic imprinting, and greenbeard genes.

Notebook 3: Cooperation, Evolutionary Transitions, and Cooperation Breakdown

• Eukaryogenesis and Multicellularity: Tree of Life vs. Ring of Life debates; endosymbiotic gene transfer (EGT) and the origin of eukaryotes. Genetic basis of cooperation among clonal cells, soma/germline segregation, and the organism paradox.
• The Breakdown of Cooperation: Biological cooperation as temporarily stabilized conflict; enforcement mechanisms (apoptosis, immune surveillance) and the emergence of "cheaters"; cancer interpreted as a macroevolutionary breakdown of multicellular cooperation and reversion of biological individuality.

Notebook 4: Mitonuclear Coevolution

• Energetics and Complexity: Physical constraints in prokaryotes; ATP production by chemiosmosis as the engine for genome expansion; CoRR and Division of Labour hypotheses.
• Mitonuclear Ecology: The chimeric nature of the OXPHOS system; nucleo-mitochondrial epistasis and mitonuclear speciation; consequences of strict maternal inheritance (Mother's Curse); heteroplasmy dynamics, mitochondrial bottlenecks, and purifying selection.

Notebook 5: Altruism and Eusociality

• The Selection Debate: The evolution of altruism; historical and mathematical comparisons between Kin Selection / Inclusive Fitness and Multilevel Selection Theory (MLS1 and MLS2); the Price Equation.
• Genomics of Eusociality: Social insects as superorganisms; supergenes (chromosomal inversions) regulating social phenotypes; epigenetic plasticity in caste differentiation.

Notebook 6: Origins of Evolutionary Innovations

• Navigating Fitness Landscapes: Metabolic vs. regulatory innovations; navigating genotype spaces and adaptive valleys through epistasis, pleiotropy, and path-dependence; synthesis of neutralism and selectionism.
• Theory of Major Evolutionary Transitions: Jumps in biological complexity analyzed through nestedness; the universal transition cycle: conflict, enforcement, stabilization, and potential breakdown.

Notebook 7: Seminars, Case Studies & Flipped Classroom

• Active Research: Guest seminars from alumni and ERGA (European Reference Genome Atlas) researchers.
• Flipped Classroom: Student-led presentations and active peer-discussions of modern genomic papers.

Readings/Bibliography

Cutting-edge scientific articles, reviews, and slides provided by the lecturer and uploaded to the Virtuale and Gemini Notebook platforms.

Textbooks and popular science books will also be recommended for those wishing to delve deeper into specific topics.

Teaching methods

The course balances different instructional approaches:

1. Frontal lectures: Deep conceptual analysis of genomic systems and mathematical models.

2. Flipped Classroom and Seminars: Active-learning sessions where students present and critically dissect landmark papers.

3. Digital AI-Tutoring: Ongoing interaction with Gemini Notebook to test concepts, draft texts, and experiment with interdisciplinary connections.

 

Students with learning disorders and\or temporary or permanent disabilities: please, contact the office responsible as soon as possible so that they can propose acceptable adjustments. The request for adaptation must be submitted in advance (15 days before the exam date) to the lecturer, who will assess the appropriateness of the adjustments, taking into account the teaching objectives. Please do not contact professors or Department staff, but make an appointment with the Service. The Service will then determine what adjustments are specifically appropriate, and get in touch with the professor.

Assessment methods

The final exam is a complete simulation of the scientific publication and peer-review process.

1. Submission: Each student writes a review paper (in English) on a genomic topic of their choice and submits it to the teacher (Journal Editor).

2. Peer-Review: Each student performs two critical but constructive reviews of colleagues' papers.

3. Revision: Authors receive their reviews, edit their papers, and write a rebuttal letter.

4. Final interview: A brief discussion focusing on the final paper.

Regarding learning assessments, limited, declared, and non-substantial use of AI is permitted for supportive tasks (such as summarizing and paraphrasing). Substantial use of AI to complete any part of the assessment is strictly prohibited.

Teaching tools

PowerPoint slides, scientific papers, Google Workspace tools, and Google's Gemini Notebook platform.

Office hours

See the website of Fabrizio Ghiselli