HU Credits: 4

Degree/Cycle: 2nd degree (Master)

Responsible Department: Ecology, Evolution & Behavior

Semester: 2nd Semester

Teaching Languages: Hebrew

Campus: E. Safra

Course/Module Coordinator: Dr Efrat Gavish-Regev

Coordinator Email: efrat.gavish-regev@mail.huji.ac.il

Coordinator Office Hours: Monday 16:00- 18:00

Teaching Staff:
Prof CHIPMAN ARIEL,
Dr. Efrat Gavish-Regev,
Dr. Neta Manela,
Mr.

Course/Module description:
An introductory course to biological systematics (including taxonomy and phylogenetics). The course will present the principles of biological systematics, hypothesis testing about species boundaries and species delimitation, understanding evolutionary relationships among taxa and applying systematics methods to understanding evolutionary patterns and processes.
The course will include a review of the history of the field, key concepts, different methodological approaches, types of data, and statistical methods for tree building and tree optimization.

Course/Module aims:
Understanding the importance of taxonomic research and its key position in organismic biology and in comparative research in general. Understanding the scientific basis of the taxonomic method, acquiring tools for using taxonomic and systematic methodology for a range of biological questions.

Learning outcomes - On successful completion of this module, students should be able to:
On completion of the course students will be able to describe a species, to test scientific hypotheses of species delimitation and to use phylogenetic tools to analyze and map evolutionary patterns at different taxonomic levels and in different biological processes.

Attendance requirements(%):
70% lectures. 80% tutorials

Teaching arrangement and method of instruction: 50% lectures, 50% tutorials and exercises.

Course/Module Content:
1) History of taxonomy and systematics. Exercise – Guided data collecting for species delimitation projects 1: Types of data. 2) Basic terminology – species, homology, characters, character states. Exercise – Guided data collecting for species delimitation projects 2: Vouchers, metadata, using spreadsheets to prepare “Examined material” lists and specimen descriptions. 3) Homology – definitions, types of homology. Exercise – Start work on final project. 4) Species I – speciation. Exercise – Species concepts. 5) Species II – identifying, describing and defining species. Exercise – Geometric morphometrics, within and between population variances. 6) Types of characters, informative and non-informative characters and character coding (morphological). Exercise – Building morphological character matrices with different character coding methods, creating keys using Delta/ Xper/ LucID. 7) Introduction to trees – Different types of trees. Approaches to tree building. Outgroups and rooting. Exercise – Building trees from morphological characters using tree visualization software. 8) Introduction to molecular approaches. Sources of molecular data. Phylogenetic algorithms and Phylogenomics. Exercise – Handling molecular datasets (including alignment). 9) Different approaches to systematics and hypothesis testing. Exercise – Tree Statistics. 10) Mapping and tracing evolutionary characters on trees. Exercise – Character mapping and ancestral state reconstruction. 11) Time and systematics – Incorporating fossils. Fossil based calibrations. Time trees. Exercise – Fossil trees. 12) Integrated approaches – total evidence trees. Unusual datasets (behavior, development). Exercise – Work on final project. 13) Presentations of final projects.

Required Reading:
1) Baum D.A. & Smith S.D. 2013. TREE THINKING – AN INTRODUCTION TO PHYLOGENETIC BIOLOGY. Roberts & Co. Pub. 476 Pp.
2) Schuh R.T. & Brower A.V.Z. 2009. BIOLOGICAL SYSTEMATICS - PRINCIPLES AND APPLICATIONS. 2nd Edition. Comstock Pub. Associates/Cornell University Press 311 Pp.
3) Wheeler W.C. 2012. SYSTEMATICS – A COURSE OF LECTURES. Wiley-Blackwell 426 Pp.
4) Wiley E.O. & Lieberman B.S. 2011. PHYLOGENETICS: THEORY AND PRACTICE OF PHYLOGENETIC SYSTEMATICS. 2nd Edition. Wiley-Blackwell 432 Pp.
5) Winston Judith. 1999. DESCRIBING SPECIES – PRACTICAL TAXONOMIC PROCEDURE FOR BIOLOGISTS. Revised Edition. Columbia University Press 512 Pp.

Additional Reading Material:

Course/Module evaluation:
End of year written/oral examination 0 %
Presentation 5 %
Participation in Tutorials 5 %
Project work 70 %
Assignments 20 %
Reports 0 %
Research project 0 %
Quizzes 0 %
Other 0 %

Additional information:
Students can use data from their own projects for exercises and for the final paper. If they do not have relevant data, they will be able to use data from the Collections (either published data or if they are interested they can generate new data during the course).

We will encourage students who carry out novel analyses (from their own data or from unpublished collections data) to publish their projects in the scientific literature.