First cycle
degree courses
Second cycle
degree courses
Single cycle
degree courses
School of Science
EVOLUTIONARY BIOLOGY
Course unit
MOLECULAR PHYLOGENY
SCP8084997, A.A. 2019/20

Information concerning the students who enrolled in A.Y. 2019/20

Information on the course unit
Degree course Second cycle degree in
EVOLUTIONARY BIOLOGY
SC1179, Degree course structure A.Y. 2018/19, A.Y. 2019/20
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Number of ECTS credits allocated 8.0
Type of assessment Mark
Course unit English denomination MOLECULAR PHYLOGENY
Website of the academic structure http://biologia.scienze.unipd.it/2019/laurea_magistrale_biologiaevoluzionistica
Department of reference Department of Biology
Mandatory attendance
Language of instruction Italian
Branch PADOVA
Single Course unit The Course unit can 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
Other lecturers OMAR ROTA STABELLI

ECTS: details
Type Scientific-Disciplinary Sector Credits allocated
Core courses BIO/01 General Botanics 2.0
Core courses BIO/05 Zoology 1.0
Core courses BIO/11 Molecular Biology 5.0

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

Type of hours Credits Teaching
hours
Hours of
Individual study
Shifts
Laboratory 2.0 32 18.0 No turn
Lecture 6.0 48 102.0 No turn

Calendar
Start of activities 02/03/2020
End of activities 12/06/2020
Show course schedule 2019/20 Reg.2018 course timetable

Examination board
Board From To Members of the board
2 FILOGENESI MOLECOLARE 2019-2020 01/10/2019 27/11/2020 GRAPPUTO ALESSANDRO (Presidente)
PILASTRO ANDREA AUGUSTO (Membro Effettivo)
ROTA STABELLI OMAR (Membro Effettivo)
1 FILOGENESI MOLECOLARE 2018-2019 01/10/2018 30/11/2019 GRAPPUTO ALESSANDRO (Presidente)
PILASTRO ANDREA AUGUSTO (Membro Effettivo)
ROTA STABELLI OMAR (Membro Effettivo)
ZANE LORENZO (Supplente)

Syllabus
Prerequisites: It would be useful to have acquired basic knowledge of Genetics, Evolutionary Biology, Systematics and Bioinformatics
Target skills and knowledge: The course is aimed for the student to acquire extensive knowledge on molecular phylogenetic analysis with particular focus on:

1) the methods of phylogenetic tree reconstruction with molecular data
2) the molecular evolution
3) the practical use of the molecular phylogeny in other discipline (food industries, safety, biodiversity, health)
4) the use of the correct terminology.

By class lectures and practical activity in the laboratory at the end of the course the student will be able to:

1) produce phylogenetic trees from molecular data
2) be able to analyse molecular data under a evolutionary perspective
3) Identify species by molecular analysis
4) to develop amity of synthesis and critical thinking
Examination methods: The student assessment will be achieved by a written examination on a PC using the e-learning platform. The test will consist of 6 questions:

4 questions with open answer to assess the acquired knowledge, comprehension and ability to synthetize the concepts developed during the course

2 more focused questions on the interpretation of examples of phylogenetic relationships of specific taxonomic groups and the methods to reconstruct the tree.
Assessment criteria: The student will be assessed 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: The course is subdivided in two parts; one of a series of frontal lectures (48 hours) and one of practical experience in a laboratory (32 hours).

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;
trees and supertrees;
the positive selection at the molecular level and the methods to identified it,
genome sequencing projects and phylogenomics;
Phylogeny of key taxonomic groups and examples of recent phylogenetic works.

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, MrBayes and Fasttree.
Use of the software BEAST to date with molecular data evolutionary events.
Planned learning activities and teaching methods: The course is subdivided in 48 hours of lectures (1) and 32 hours of laboratory (2).

1) The argument developed during the course are presented with the aids of ppt with images, tables and short descriptions. The work in class is interactive with questions and presentation of key studies taken from the literature to develop the discussion and critical thinking;

2) The laboratory is subdivided in a practical molecular part (8 h), with DNA extraction, PCR and sequencing of biological samples, and a bioinformatics lab (24 h). 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: All material presented in class, ppts, articles used as examples, experimental protocols used in the laboratory, datasets and software links, is available on the e-learning platform at https://elearning.unipd.it/biologia
Textbooks (and optional supplementary readings)
  • Lemey P., Salemi M., Vadamme A., The phylogenetic handbook. II edition. Cambridge UK: Cambridge, 2009. In inglese Cerca nel catalogo
  • Lindell Bromham, An Introduction to Molecular Evolution and Phylogenetics. 2nd Ed.. Oxford: Oxford University Press, 2016. In Inglese Cerca nel catalogo

Innovative teaching methods: Teaching and learning strategies
  • Lecturing
  • Laboratory
  • Case study
  • Interactive lecturing
  • Working in group
  • Questioning
  • Work-integrated learning
  • Use of online videos
  • Loading of files and pages (web pages, Moodle, ...)

Innovative teaching methods: Software or applications used
  • Moodle (files, quizzes, workshops, ...)

Sustainable Development Goals (SDGs)
Life Below Water Life on Land