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

NOTE: This is a rough program. The level of detail will be established each Academic Year with the participants, based on their preferences and the numerosity of the class (in order to leave enough time for the interactive part of the course).


0. Introduction

General information about the course: logistics, structure, definition of the program, teaching material, resources. Introduction to genomics.


1. Evolution by DNA Duplication

Types of DNA duplications. Mechanisms of DNA duplication. Molecular homology. Gene duplications and gene families. Origin and evolution of duplicated genes: divergent evolution, nonfunctionalization, retention of original function, neofunctionalization, subfunctionalization. Concerted evolution. Birth-and-death evolution: expansion and contraction of gene families. Polyploidy: polyploidization, autopolyploidy, allopolyploidy, consequences of polyploidy, rediploidization.


2. Evolution by Molecular Tinkering

Exaptation, evolution by tinkering. Protein domains. Multidomain proteins. Orthology and domain shuffling. Internal gene duplications. Exon-domain correspondence. Mosaic proteins. Exon shuffling, domain mobility. Gene fusion and fission. Domain accretion. Multidomain gene assembly. Alternative splicing. De novo origin of genes. Gene loss. Molecular tinkering: suboptimality and gratuitous complexity.


3. Mobile Elements in Evolution

Mobile elements, transposable elements and transposition. Classification of transposable elements. DNA-mediated transposable elements. Retroelements. LINEs and SINEs. Retrosequences. The “ecology” of transposable elements. Genetic and evolutionary effects of transposition. Horizontal gene transfer. Intracellular DNA transfer.


4. The origin of eukaryotes

The “Tree of Life” hypothesis. Tree vs network. “Forest of Life”, “Ring of Life”. Vertical and horizontal components of prokaryote evolution. The origin of eukaryotes: “Archezoa Hypothesis”, “Hydrogen Hypothesis”, “Fateful Encounter Hypothesis”. The ancestors of eukaryotes. The origin of introns.


5. Genomic conflicts

Multilevel selection and asymmetric heredity, replication advantage, segregation advantage, segregation distorters, meiotic drive, cytonuclear conflicts. Genomic conflicts and evolution of sex chromosomes. Detour: cooperation, evolution of eusociality, inclusive fitness and kin selection vs multilevel selection.


6. Mitonuclear evolution

Mitochondria. ATP production by chemiosmosis. The complexity ceiling of prokaryotes, surface/volume ratio and cell size limits, phagocytosis, “the energetics of genome complexity”. The mitochondrial genome, endosymbiotic gene transfer. Mitonuclear coevolution. Why do mitochondria have a genome? The CoRR hypothesis. “Mitochondrial Theory of Ageing”, “Division of Labour Hypothesis”. Mitochondrial bottleneck, selection, drift. Mitochondria and the evolution of sex. “The Mother’s Curse”. Mitonuclear speciation. Mitonuclear adaptation.


7. Origins of Evolutionary Innovations

Metabolic innovation. Innovation through regulation. Novel molecules. Genotype networks, self organization, and natural selection. A synthesis of neutralism and selectionism. The role of robustness for innovation. Gene duplications and innovation. The role of recombination. Environmental change in adaptation and innovation. Evolutionary constraints and genotype spaces. Phenotypic plasticity and innovation.


8. Case studies

Flipped classroom, group discussion.

Readings/Bibliography

• Dan Graur “Molecular and Genome Evolution”, Sinauer Associates (Parts 1-4).

• Geoffrey Hill “Mitonuclear Ecology”, Oxford University Press (Part 6).

• Andreas Wagner “The Origins of Evolutionary Innovations”, Oxford University Press (Part 7).

• Scientific articles and online material.

Teaching methods

The first part of the course consists of classic frontal teaching, and it will introduce concepts, mechanisms, and methods of analysis. Seminars by international scientists are also planned.

The second part is carried out in "flipped classroom" mode, and its purpose is to delve into some case-studies and discuss state-of-the-art works. Each student choose a scientific publication dealing with evolutionary genomics, and presents it to the class. A discussion will follow, in which the teacher acts as the moderator.

Before taking this course, it is highly recommended to have attended the following courses:

• 91360 - Genetica di Popolazione ed Evoluzione Molecolare
• 91789 - Evoluzione e Filogenesi (C.I.).

 

Assessment methods

The final exam consists of a simulation of the scientific publication process.
Each student will write a review paper (in english) about a topic of their choice, and submit it to the teacher that will act as an Editor and will send the manuscript to two reviewers (other students in the class). The reviewers will send their reviews to the teacher that will add his own comments and will send everything back to the author that will revise the manuscript. The revised manuscript will be submitted to the teacher that will proceed with a final evaluation.
The peer-review process will be subject to evaluation as well, and each student will have to review 2 papers.

Detailed informations about the evaluation process will be given during the introductory lesson.

Teaching tools

Slides, scientific publications, online multimedia.

Office hours

See the website of Fabrizio Ghiselli