Methods in Systematics

Objectives

1. Knowledge:

1.1. Knowing the theoretical bases and methods involved in the identification, naming and classification of living things (taxonomy), and the reconstruction of their evolutionary relationships (phylogenetics).

2. Skills and competences:

2.1 Build morphological data matrices;

2.2. Build molecular matrixes using sequences;

2.3. Use molecular databases available on the Internet;

2.4. Analyse molecular data in systematics, applying methods of maximum parsimony, maximum likelihood, Bayesian inference and molecular clock dating, using specific software;

2.5. Critically analyse published case studies;

2.6. Participate actively in group work;

2.7. Verbally present published case studies in a scientifically accurate and visually appealing way.

Program

1. Science of systematics

2. Identification, naming and classification of living things

2.1. Biological collections: sampling methods and associated ethical issues

2.2. Differentiating characters: 1) Types of characters and definition of states; 2) Morphological and molecular characters: conflict, compromise or complementarity?

2.3. The bases of biological nomenclature

2.4. Classification and systems: historical perspective and present time

3. Reconstruction of the evolutionary relationships among living things: phylogenetic methods

3.1. Cladistics and maximum parsimony: 1) Basic concepts: homology, homoplasy, syn/aut/apomorphy, sim/plesiomorphy, polarization, monophyletic, paraphyletic and polyphyletic groups; 2) Matrices and polarization of characters; 3) Construction of cladograms and the search for the most parsimonious tree

3.2. Maximum likelihood analysis and estimation of evolutionary models

3.3. Methods of Bayesian inference

3.4. Molecular clock dating; clocks and calibration

Teaching Methodologies

Active learning methods promote the acquisition of skills and competencies that relate to key objectives of this course. In order to meet these objectives, students will carry out a wide range of exercises using computers, in order to familiarize them with the analytical procedures and computer programs commonly used by systematicians. It is intended that students are proficient in all steps involved in the methods studied.

Bibliography

Avise J. C., 1994. Molecular Markers, Natural History and Evolution. Springer, US.

Felsenstein J., 2004. Inferring Phylogenies. Sinauer Associates, Inc., Sutherland, Massachusetts.

Forey P. L., C. J. Humphries, I. J. Kitching, R. W. Scotland, D. J. Siebert & D. M. Williams, 1993. Cladistics: A Practical Course in Systematics. Clarendon Press, Oxford.

Hall B. G., 2011. Phylogenetic Trees Made Easy: A How-To Manual. Sinauer Associates, Inc., Sutherland, Massachusetts.

Judd W. S., C. S. Campbell, E. A. Kellogg, P. F. Stevens & M. J. Donoghue, 2002. Plant systematics: A Phylogenetic Approach. Sinauer associates, Inc., Sutherland, Massachusetts.

Patterson C., 1987. Molecules and Morphology in Evolution: Conflict Or Compromise? Cambridge University Press, Cambridge.

Salemi M. & A. M.Vandamme, 2003. The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny. Cambridge University Press, Cambridge.