Dottorato di Ricerca “Biologia Molecolare, Cellulare ed Ambientale” Corsi dottorali per l’A.A. 2017
“Practical course on Molecular Phylogeny and Population Genetics”
Emiliano Mancini, PhD 22-24 February 2017
AIMS
The purpose of this practical course is to familiarize participants with the basic concepts of molecular phylogeny and population genetics and to offer a first hands-on training on data analysis. Hands-on learning activities are aimed to put concepts into practice and will be conducted using software dedicated to molecular phylogeny and population genetics analyses.
COURSE PROGRAM
Lessons will be held in AULA 7 (Department of Sciences, Viale G. Marconi, 446, 1st floor)
. 22th February 2017 - MOLECULAR PHYLOGENY (THEORY & PRACTICE)
PRINCIPLES. (9.30 - 13.00): Introduction to molecular phylogeny: aims and terminology; Alignment: finding homology among sequences; Genetic distances: modelling substitutions and measuring changes; Inferring trees: Distance, Maximum Parsimony, Likelihood and Bayesian methods; Tree accuracy: bootstrap; Molecular clocks: global and relaxed models.
PRACTICE. (14.30 - 18.00): From chromatograms to dataset preparation; introduction to phylogenetic software; Practice on: i) alignment; ii) substitution models, tree building and molecular clock; iii) Bayesian tree reconstruction; iv) bootstrap and phylogenetic trees congruence.
. 23th February 2017 - POPULATION GENETICS (THEORY)
PRINCIPLES. (9.30 - 13.00): Introduction to population genetics: aims and terminology; Hardy- Weinberg equilibrium: observed vs. expected genotype frequencies; Quantifying genetic diversity: diploid and haploid data; Genetic drift and effective population size (Ne): bottleneck and founder effects; Quantifying loss of heterozygosity: the inbreeding coefficient (FIS); Quantifying population subdivision: the fixation index (FST); Linkage disequilibrium (LD): measuring association among loci; Gene genealogies and molecular evolution: testing neutrality under the coalescent.
. 24th February 2017 - POPULATION GENETICS (PRACTICE)
PRACTICE. (9.30 - 13.00): Dataset preparation, introduction to population genetic software. Practice on: i) Single population bi-allelic data: Hardy Weinberg, FIS and LD; ii): Single population (microsat. data): Hardy Weinberg and FIS; iii) Multiple population (microsat. data): FST computation and interpretation; iv) Haploid data: estimating haplotype and nucleotide diversity, testing neutrality.
BEFORE STARTING THE COURSE
Participants are expected to have installed the following (free) software on their laptops:
MEGA7.0 http://www.megasoftware.net/
MrBAYES3.2.6 http://mrbayes.sourceforge.net/download.php
DnaSP5.10.1 http://www.ub.edu/dnasp/
GenAlEx6.503 http://biology-assets.anu.edu.au/GenAlEx/Download.html
Dataset files and examples for practical activities will be sent via e-mail to all participant before the course starts. Attendants are also encouraged to bring their own data during practical sessions!
Participants are invited to explore some introductory and friendly resources on the web, such as: http://vimeo.com/829413 and http://www.dorak.info/genetics/popgen.html
Find also other software here: http://evolution.genetics.washington.edu/phylip/software.html#methods
OTHER INFO
PhD students from other Universities are invited to join the course! These MUST send an e- mail including their name, surname, affiliation, research field and activities to [email protected] BEFORE 13th February 2017.
COURSE REFERENCES
P. Lemey, M. Salemi, A. M. Vandamme, 2009. The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing.Cambridge University Press, Cambridge, UK.
R. D.M. Page, E. C. Holmes, 1998. Molecular Evolution: A Phylogenetic Approach. Blackwell Scientific, Oxford, UK.
M. Hamilton, 2009. Population genetics. Wiley-Blackwell, Hoboken, NJ, USA.
J. H. Gillespie, 2004. Population genetics: a concise guide. Johns Hopkins Univ Press, Baltimore, Maryland, USA.
J. R. Freeland, S. D. Petersen, H. Kirk, 2011. Molecular Ecology. John Wiley and Sons, Ltd., West Sussex, UK.