First cycle
degree courses
Second cycle
degree courses
Single cycle
degree courses
School of Science
EVOLUTIONARY BIOLOGY
Course unit
MOLECULAR PHYLOGENY
SCN1031435, A.A. 2013/14

Information concerning the students who enrolled in A.Y. 2013/14

Information on the course unit
Degree course Second cycle degree in
EVOLUTIONARY BIOLOGY
SC1179, Degree course structure A.Y. 2009/10, A.Y. 2013/14
N0
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Number of ECTS credits allocated 6.0
Type of assessment Mark
Course unit English denomination MOLECULAR PHYLOGENY
Website of the academic structure http://biologia.scienze.unipd.it/2013/laurea_magistrale_biologiaevoluzionistica
Department of reference Department of Biology
Mandatory attendance No
Language of instruction Italian
Branch PADOVA
Single Course unit The Course unit CANNOT be attended under the option Single Course unit attendance
Optional Course unit The Course unit can be chosen as Optional Course unit

Lecturers
Teacher in charge ALESSANDRO GRAPPUTO BIO/05

ECTS: details
Type Scientific-Disciplinary Sector Credits allocated
Educational activities in elective or integrative disciplines BIO/05 Zoology 1.0
Core courses BIO/11 Molecular Biology 5.0

Course unit organization
Period First semester
Year 1st Year
Teaching method frontal

Type of hours Credits Teaching
hours
Hours of
Individual study
Shifts
Laboratory 1.0 16 9.0 No turn
Lecture 5.0 40 85.0 No turn

Calendar
Start of activities 01/10/2013
End of activities 25/01/2014
Show course schedule 2019/20 Reg.2018 course timetable

Examination board
Board From To Members of the board
7 FILOGENESI MOLECOLARE PROROGA 2017 01/10/2018 30/11/2019 GRAPPUTO ALESSANDRO (Presidente)
PILASTRO ANDREA AUGUSTO (Membro Effettivo)
ZANE LORENZO (Supplente)
6 FILOGENESI MOLECOLARE 2017/2018 01/10/2017 25/11/2018 GRAPPUTO ALESSANDRO (Presidente)
PILASTRO ANDREA AUGUSTO (Membro Effettivo)
ZANE LORENZO (Supplente)
5 FILOGENESI MOLECOLARE 2016-2017 01/10/2016 30/11/2017 GRAPPUTO ALESSANDRO (Presidente)
PILASTRO ANDREA AUGUSTO (Membro Effettivo)
ZANE LORENZO (Supplente)
4 Filogenesi Molecolare 2015-2016 01/10/2015 30/09/2016 GRAPPUTO ALESSANDRO (Presidente)
PILASTRO ANDREA AUGUSTO (Membro Effettivo)
ZANE LORENZO (Supplente)
3 FILOGENESI MOLECOLARE 2014-2015 01/10/2014 30/09/2015 GRAPPUTO ALESSANDRO (Presidente)
PILASTRO ANDREA AUGUSTO (Membro Effettivo)
ZANE LORENZO (Supplente)
2 FILOGENESI MOLECOLARE 01/10/2013 30/09/2014 GRAPPUTO ALESSANDRO (Presidente)
PILASTRO ANDREA AUGUSTO (Membro Effettivo)
ZANE LORENZO (Supplente)

Syllabus
Prerequisites: It would be useful to have acquired basic knowledge in genetics, evolutionary biology and bioinformatics
Target skills and knowledge: By following this course students should acquire the basic elements to carry out an analysis and the interpretation of sequencing data in an evolutionary perspective.
Examination methods: Written
Assessment criteria: The student will be evaluated on the bases of the acquired knowledge and his/her ability to use the molecular and bioinformatics tools in the analysis of data and interpretation of phylogenetic trees.
Course unit contents: Lectures:

The study of molecular evolution is a field of research that merge the most recent progress in molecular biology with those in bioinformatics. In the course will be shown the principal of molecular evolution ad phylogeny, In particular will be considered:
the diverse type of molecular data and the techniques for their acquisition;
the alignment of sequences;
the comparison of DNA and protein sequences to calculate the genetic distance;
the mechanisms of molecular evolution and the theory of neutrality;
the models of nucleotide substitution;
the molecular identification of species (barcoding of life);
The phylogenetic reconstruction methods of maximum parsimony, genetic distance, maximum likelihood and Bayesian inference;
the concept of molecular clock and its application in the molecular phylogenies;
trees and supertrees;
the positive selection at the molecular level and the methods to identified it,
genome sequencing projects and the phylogenomics.

Laboratory:

Molecular identification of species (barcoding); genomic DNA extraction from unidentified samples, PCR and sequencing of mitochondrial genes;

Bioinformatics lab:

chromatogram reading and analysis; use of GenBank and the barcode database BOLD to identify species;
phylogenetic reconstruction with the main algorithms using MEGA.
Planned learning activities and teaching methods: The course include 40 hours of lectures and 16 hours of laboratory. The laboratory is subdivided in a practical molecular part, with DNA extraction, PCR and sequencing of biological samples, and a bioinformatics lab. The laboratory will include individual and /or group work in which the student will analyse and apply the phylogenetic methods to example data sets.
Additional notes about suggested reading: Slides showed in class and suggested articles also available on the elearning platform at http://elearning.unipd.it/biologia/
Textbooks (and optional supplementary readings)
  • Hall Barry G., Phylogenetic tree made easy: A how to manual. IV edition. Massachusetts USA: Sinauer, 2011. In inglese Cerca nel catalogo
  • Lemey P., Salemi M., Vadamme A., The phylogenetic handbook. II edition. Cambridge UK: Cambridge, 2009. In inglese; solo per chi desidera approfondire gli argomenti Cerca nel catalogo