PHYLOGENETICS AND PHYLOGENOMICS
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- Versione italiana
- Academic year
- 2018/2019
- Teacher
- SILVIA GHIROTTO
- Credits
- 6
- Didactic period
- Secondo Semestre
- SSD
- BIO/18
Training objectives
- Phylogenetics and Phylogenomics is of fundamental importance to Evolutionary Biology studies in the genomic era. During the course, the students will i) understand why having a resolved phylogeny is essential in many fields of biological investigation, ii) comprehend the theoretical bases of the major methods for phylogenetic inference, and iii) apply such methods with genetic and genomic data using widely used bioinformatic implementations.
In particular, the student will acquire the knowledge concerning:
- the representation of the evolution of a taxonomic group, of a group of populations, of a group of individuals or of a group of genes, through a phylogenetic tree;
- the concepts of analogy and homology, with a focus on the analysis
of molecular data (orthology);
- the different computational approaches for phylogenetic reconstruction;
- the bases of the coalescence theory, and therefore the difference between gene trees and species trees, and the bases of species delimitation methods;
- the concept of molecular clock and the calibration of phylogenetic trees;
- the concepts underlying the inference of selective processes based on phylogenetic reconstructions;
- phylogenomics, ie the integration of information from many genes or recombination blocks using mutational and evolutionary models specific for different DNA stretches;
- phylogenetic networks based on multiple genes;
Furthermore, the student will develop the following skills (ability to use the acquired knowledge):
- reading and manipulation of the main file formats for molecular data analysis;
- analysis of molecular data with specific software (for example, MAFFT, Aliview, jModelTest, RAxML, BEAST2, FigTree), useful for aligning sequences, reconstructing phylogenies, estimating their robustness and making their graphic visualization;
- tackling the computational issues coming from the use of genomic data: mapping, identification of orthologues and local alignments; methods for identifying linkage blocks and local topologies along a genomic alignment (for example, Saguaro and TWISST); phylogeny of species using multiple gene trees (for example, starBEAST2, ASTRAL, SNAPP); reconstruction of phylogenetic networks (for example, Splitstree, Phylonet, PhylonetHMM). Prerequisites
- Basic knowledge of evolutionary theory and computer sciences. Experience with bash/command line applications is not required but will make software learning easier.
Course programme
- The 48-hour course will consist of 32 hours of theoretical lessons and 16 hours of bioinformatics lab.
During the theoretical lessons the following main topics will be presented:
- the representation of biological evolution with a phylogenetic tree at different levels (genes, populations, species): what is its meaning;
- basic concepts and nomenclature in phylogenetic studies;
- computational approaches for phylogenetic reconstructions based on genetic distances, maximum parsimony, maximum likelihood, and Bayesian methods;
- methods for estimating the robustness of a phylogenetic reconstruction;
- molecular evolution models and methods to determine the most suitable model for available data;
- bases of coalescence theory, and applications in phylogeny and taxonomy;
- dating a phylogenetic reconstruction: calibration of the nodes using fossils and/or a substitution rate (fixed or relaxed molecular clocks);
- issues with orthology when aligning genomes of different species: the structural evolution of the genome (e.g., duplications, multiple-copy genes, pseudogenizations, hotspots and recombination coldspots, etc);
- how to integrate genes trees to build species trees: incomplete lineage sorting, admixture and random or adaptive introgression for some genomic genes/regions;
- from trees to phylogenetic networks;
- some examples shwoing the use of phylogenetics in the study of viruses, adaptation, taxonomy, and in conservation genetics.
Practical exercises will mainly focus on the use of software for the alignment of sequences of genes or extended genomic regions, the research of ortholog genes in genomes of different species, the calculation of genetic distances, the reconstruction of genes trees and species trees with maximum likelihood and Bayesian methods, analysis of their robustness, the reconstruction of a temporal calibrated phylogeny, the visualization and editing of phylogenetic trees. Didactic methods
- Lectures with slides and bioinformatics labs with practical exercises about the different methods presented in the theoretical lessons and about widely-used software applications. Such exercises will be an essential part of the course.
Learning assessment procedures
- The written exam will consist of four questions both open-ended and multiple-choice on the topics dealt with during the theoretical lectures and a practical test consisting of two bioinformatics exercises to be carried out using the skills acquired during the labs. For each application or exercise a maximum of 5 points will be given for a total of 30/30 in the overall evaluation.
Reference texts
- Slides and handouts provided by the teacher
