91401 - Laboratory of Phylogenesis

Learning outcomes

At the end of the course the student will acquire knowledge on the main methods of analysis for the study of phylogenetics, at several taxonomic levels. More in detail, the student will gain the know-how for the building and analyzing standard data matrices (binary, morphological data, etc), molecular data (nucleotides or amino acids) and combined data sets. Furthermore, the student will learn the use of specific algorithm for phylogentic tree building/search. Finally, the student will acquire the ability to critically read and interpret results within the relevant theoretical-experimental framework.

Course contents

Diversity, evolution and phylogenetics. Anatomy of a phylogenetic tree: operational taxonomic unit (OTU); hypothetical taxonomic unit (HTU) - nodes; branches; root. Rooted and unrooted trees; cladograms, phylograms and chronograms. Monophyletic, paraphyletic and polyphyletic groups. Crown and stem groups. Definition of taxonomy, systematics and phylogeny. Phylogenetic or cladistic systematics.

Character evolution. Concept of homology and homoplasy; apomorphic, plesiomorphic, synapomorphic and symplesiomorphic characters. Phylogeny on morphological and molecular characters: differences, interpretation, advantages and disadvantages. Incongruence in phylogenetics and the "species tree and gene tree" problem. Next Generation Sequencing (NGS) and phylogenomics. Strict and relaxed molecular clock. Chronograms and tree calibration using fossil records, biogeographical events, and secondary calibrations.

The tree of Life; focus on metazoan and plant phylogeny.

Morphological (standard data or presence/absence) and molecular (nucleotides or amino acids) data matrices; mixed matrices. Phylogenetic reconstructions: algorithmic approach (distance-based - UPGMA, Neighbor-Joining) and best tree search methods (character-based). Optimality criteria: Maximum Parsimony and Maximum Likelihood trees. Node support: resampling techniques (Bootstrap; Jackknife) and character-based techniques (Bremer support). Bayesian inference and posterior probability. Search using the Markov chain Monte Carlo (MCMC) method.

Methods for the study of molecular data. Alignment of coding and non-coding sequences (progressive alignments and approaches with iterations); structural alignments. Concatenated data; phylogenomic matrices. Observed genetic divergence. Multiple substitutions and models of nucleotide and amino acid substitutions. Heterogeneity of substitutions between sites and proportion of invariant sites.

Systematic bias in phylogenetic inference: nucleotide compositional bias, signal saturation, long branch attraction.

Comparative methods in phylogeny and study of the evolution of characters: reconstruction of the ancestral state.

Exercises in the computer laboratory for the analysis of morphological and molecular matrices. The students, individually, will carry out a phylogeny project which will be part of the evaluation.

Readings/Bibliography

David A. Baum & Stacey D. Smith. Tree Thinking. An introduction to phylogenetic biology. WH Freeman & Company.
Barry G. Hall. Phylogenetic Trees Made Easy: A How-To Manual. Sinauer Associates.

Teaching methods

Public letures and computer exercises. Presentation, analysis and discussion of cases study; elaboration and individual presentation of phylogenetic analyses.

Due to the kind of activity and didactical methods, attending the present course requires the prior participation of all students to the following e-learning Modules 1 and 2:

Module 1 [https://elearning-sicurezza.unibo.it/course/view.php?id=23] – Safety General Training

Module 2 [https://elearning-sicurezza.unibo.it/course/view.php?id=43] – Safety Specific Training (part I)

Assessment methods

The exam at the end of the course aims to assess the achievement of the following learning objectives:

• deep knowledge of evolutionary theories and processe, and their study
• deep knowledge of morphological and molecular characters for phylogenetic inference at different taxonomic level
• understanding of the theoretical basis of the methods of phylogenetic and filogenomic inferences;
• correct interpretation of the data and results
  

The exam involves the presentation and discussion of an original phylogenetic analysis project, designed and conducted by the student, with an in-depth discussion of main topics.

To participate to exams is necessary to subscribe the list on AlmaEsami, within the indicated deadline. Those unable to subscribe are invited to communicat as soon as possible (and before the official closure of the exam list subscription) the problem to studend segretary. The teacher will eventually decide about the admission. Evaluation will be recorded with 5 days from the exam date, even in absence of the student according to the guidelines published at http://www.unibo.it/Portale/Guida/AlmaEsamiInformazioniDocenti.htm .

Teaching tools

Theoretical lessons, with power point presentations and practical exercises with computers.

All slides, files, tutorials and other material used during the course will be provided to students

Office hours

See the website of Andrea Luchetti