MOLECULAR EVOLUTION
Academic year and teacher
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- Versione italiana
- Academic year
- 2015/2016
- Teacher
- SILVIA GHIROTTO
- Credits
- 6
- Curriculum
- Biologia evoluzionistica e genetica
- Didactic period
- Primo Semestre
- SSD
- BIO/18
Training objectives
- The purpose of this course is to describe the dynamics of evolutionary change at the molecular level, the extent and the meaning of these changes within and between species, the driving forces behind the evolutionary process, and the effects of the various molecular mechanisms on the long-term evolution of genomes, genes and their products. Part of the course will involve the discussion of both classical and recent papers and hand-on analysis of case studies.
Prerequisites
- Knowledge of genetics, mathematics, biostatistics. Basic knowledge of population genetics are also appreciated.
Course programme
- This course will deal with the following topics:
Introduction. What is molecular evolution, its mechanisms and applications.2h
Biological molecules. RNA ans DNA. Genotype and phenotype. Genes, genetic codes and mutations. Molecular markers (SNPs, micro-minisatellites, indels and CNVs).4h
Genome evolution. Genome's architecture and differences between species. Structure and function of genes, gene expression and epigenetic modifications. Origin, evolution and phenotypic impact of new genes. Gene duplication, horizontal gene transfer and gene fusion. Duplication of entire genomes (2R and 3R hypotheses). 4h
Basic knowledge of evolutionary biology. History of evolutionary biology. Evolutionary thoughts before Darwin. Lamarckian theory of evolution, and the inheritance of acquired characters. Brief Brief biography of Charles Darwing and the trip of the Beagle. Malthus' influence on Darwin, and the developement of his evolutionary theory. Natural selection as a matter of the reproductive success. Modern synthesis of evolution. Evidence of darwinian evolution from different fields. 4h
Dynamics of genes in populations. Hardy-Weinberg equilibrium and its assumptions. Violations of any of the five major assumptions, with particular focus to:
Natural Selection. Fitness and adaptation. Selection coefficient and estimation of allele frequencies after a generation of natural selection for different dominance models (complete dominance, codominance and overdominance) 6h
Genetic Drift: Stochastic nature of evolution and genetics. Change in the frequency of an allele in a population due to random sampling. Concept of effective population size.4h
Gene substitution. Fixation probability, fixation time and rate of genetic substitution under the effect of natural selection and/or genetic drift.4h
From populations to species: molecular phylogenetics. Relationships between species: from systematics to molecular genetics. Genetic data to study the molecular phylogenetics. Common ancestor and homologous sequences. Difference between paralogous and orthologous sequences. Phylogenetic tree reconstruction: methods based on genetic distance, maximum parsimony methods and methods of maximum likelihood. 4h
Genetic distance and nucleotide substitution model. Nucleotide substitution in a DNA sequence, and estimate of the genetic distance between two sequences from the proportion of observed differences. Evolutionary changes in nucleotide sequences, Jukes-Cantor's one-parameter model, Kimura's two-parameter model. Applications. 6h
Rates and patterns of nucleotide substitution. Rates of nucleotide substitution in coding and noncoding regions. Synonymous versus nonsynonymous rates. Variation among genes and different gene regions. Causes of variation in substitution rates: functional constraints. Application to the alpha a-crystallin in Spalax ehrenbergi.4h
Positive or Darwinian Selection. Detecting positive selection. McDonald-Kreitman test and its significance. Applications. Estimates of dN/dS through approximated and maximum likelihood methods. Detecting positive selection on a particular branch of a phylogenetic tree: compare models via likelihood 6h Didactic methods
- The course is structured in 48 hours of theoretical lessons (6CFU). The teacher will use slides and hand-outs of the lessons that will make available to students.
Learning assessment procedures
- The learning test consists in a written exam. This exam is composed by 14 T/F questions (0.5 points/question, 7 points in total), 3 multiple choice (1.5 point/question, 4.5 points in total), 1 execise (6.5 points), 3 open questions (5 point/question, 15 points in total). The students will pass the exam with a score not lower than 18 points.
Reference texts
- Slides and hand-outs of the lessons.
Chapters from the following books:
Fundamentals of Molecular Evolution di Dan Graur e Wen-Hsiung Li, SINAUER
L'evoluzione di Douglas J Futuyma, Zanichelli
Evoluzione, modelli e processi a cura di Marco Ferraguti e Carla Castellacci, PEARSON
