37627 - Evolution Theory

Learning outcomes

This course gives advanced knowledge of the scientific progresses of Evolutionary Biology, as well as of patterns, processes and mechanisms of Evolution. In particular, the course starts from a detailed analysis of neodarwinism and punctuated equilibria, and it will indroduce students to some of the modern research frontiers of Evolutionary Biology thereafter (Evo-Devo, Evolutionary genomics, Game theory, etc.).

Course contents

Part 1 – Advanced evolutionary biology
Epistemology and Evolutionary Biology. The concept of Scientific Theory. Falsificationism. Occam's Razor.
Introduction to Evolutionary Biology. Applications. Proofs of Evolution. Homology.
Introduction to the Modern Synthesis. Origin of genetic variability. The population. Genetic structure of populations (Hardy-Weinberg, genetic drift, genetic flow). Natural selection and fitness. Examples of selection. Species and species concepts. Reproductive isolation. Sibling species. Ring species. Clines. Models of speciation: allopatric, sympatric, stasipatric. Chromosomal speciation. Speciation by hybridization. Polyploidy, parthenogenesis, hybridogenesis, androgenesis.
Neutral theory. Molecular clock.
The altruism problem. Group selection. Inclusive fitness. Kin selection. Game theory.
The selfish gene.
Punctuated equilibria. Mass extinctions. Burgess fauna.
Macroevolution and macromutations.
Origin and evolution of Life on Earth. Pre-biotic chemistry. The experiment of Miller. The "primordial soup" hypothesis and other hypotheses. The RNA world. First unicellular organisms. Archea. Procariota. Origin of Eukaryothes and the pluricellularity. Origin and evolutionary radiation of the principal animal Phyla.

Part 2 – Evolutionary genomics

INTRODUCTION: brief history of Genomics, Human Genome Project, ENCODE.
MATERIALS AND METHODS IN GENOMICS: Sanger sequencing, Massive Parallel Sequencing (MPS), pyrosequencing (Roche 454), reversible-dye terminator sequencing-by-synthesis (Illumina), semiconductor sequencing (Ion Torrent & Ion Proton), Single-Molecule Real-Time Sequencing (SMRT sequencing, PacBio), primer walking, hierarchical shotgun sequencing, whole-genome shotgun sequencing,genetic maps and mapping, sequencing strategies, workflow and outputs, sequence quality (Phred score), de novo assembly, paired-ends and mate-pairs, reads, contigs, scaffolds, assembly quality (N50, N90), SNP and variant calling, annotation, why sequencing a genome/transcriptome?, MPS applications, transcript quantification (RPKM/FPKM), Moore's Law, problems with "Big Data".
FUNDAMENTALS OF EVOLUTION: Fisher's theorem, effective population size and genetic drift, allele fixation probability, neutral evolution, fitness landscape, genetic draft, linkage, neutral and nearly-neutral theories of molecular evolution, punctuated equilibria, exaptation.
COMPARATIVE GENOMICS: genome diversity (composition, structure, dimension), the evolutionary stability of genes, orthology and paralogy, Clusters of Orthologous Genes (COGs), genomescapes and evolutionary regimes, genome evolutionary constraints, the minimal gene set, Non-Orthologous Gene Displacement, the functional content of minimal gene sets, genome fluidity.
PROKARYOTIC GENOMES: genome size and gene density, prokaryote evolution, evolution of prokaryotic genome architecture, the operon, the selfish operon concept, universal scaling laws, bureaucratic ceiling of genomic complexity, horizontal gene transfer, the prokaryotic mobilome, the central role of horizontal gene transfer in prokaryotes, fundamental processes in prokaryote evolution, tree-like evolution vs network-like evolution, the Forest of Life.
THE ORIGIN OF EUKARYOTES: Woesian tree, theories about eukaryote origin, structural and functional differences between prokaryotes and eukaryotes, endosymbiosis, archezoan tree and the root of the eukaryotic tree, Last Eukaryote Common Ancestor (LECA), RNA continuity model and reductive evolution, stem phase, the ancestors of eukaryotes, the symbiogenesis model, origin of cell nucleus and introns.
EUKARYOTIC GENOMES: genome size and number of genes, C-value enigma, mutation pressure theories, optimal DNA theories, phenotypic effects of genome size, function of non-genic DNA, genetic load, non-adaptive hypothesis of genome evolution, mutational equilibrium model.
ORIGIN AND EVOLUTION OF BIOLOGICAL INNOVATIONS: origin of new genes, protein domains, multidomain proteins, evolution by gene duplication, the evolutionary fate of duplicated genes, speciation by divergent resolution, gene families, neofunctionalization (e.g. trichromatic vision in primates), vertebrate genome duplications (1R, 2R e FSGD).
MITOCHONDRIA: structure, chemiosmotic mechanism of ATP production, mitochondrial genome, endosymbiotic gene transfer, mtDNA encoded proteins, nucleus-mitochondrion coevolution, mitochondrial bottleneck, prokaryote complexity ceiling (replication time and gene loss, cell surface-to-volume ratio, phagocytosis, energetic limits), why do mitochondria need a genome?, CoRR hypothesis, mitochondrial theory of ageing.
GENIC AND GENOMIC CONFLICTS: multilevel selection and asymmetric heredity, replication advantage, "petite" mutation, segregation advantage, segregation distorters, meiotic drive, conflicts between cytoplasmic and nuclear genes, conflicts among cytoplasmic genes and uniparental inheritance, Doubly Uniparental Inheritance (DUI) of mitochondria.

Readings/Bibliography

Ferraguti M., Castellacci C. Evoluzione, modelli e processi. Pearson.

Douglas J. Futuyma. L'evoluzione. Zanichelli.

Mark Ridley. Evoluzione. La storia della vita e i suoi meccanismi. Ed. McGraw-Hill

Teaching methods

During lectures and exercises, open discussions with the teacher will be strongly stimulated.

Assiduous participation to lessons is mandatory, given to the strict concatenation of the arguments.

Assessment methods

The examination, at the end of the course, aims to assess the achievement of the learning objectives of Module 1:

• knowledge and understanding of the Theory of Evolution, including its theoretical basis and the most recent developments.

The final score is defined by an oral examination together with the program of Module 2.

Teaching tools

Lectures, with powerpoint presentations and exercises. Powerpoint presentations used during the lessons will be available to students.

Office hours

See the website of Marco Passamonti

See the website of Fabrizio Ghiselli