Phylogenetic and Systematics Analysis

Code:

BIOL4124

Acronym:

BIOL4124

Level:

400

Keywords
Classification	Keyword
OFICIAL	Biology

Instance: 2024/2025 - 1S

Active?	Yes
Responsible unit:	Department of Biology
Course/CS Responsible:	Master in Biodiversity, Genetics and Evolution

Cycles of Study/Courses

Acronym	No. of Students	Study Plan	Curricular Years	Credits UCN	Credits ECTS	Contact hours	Total Time
M:BBC	7	The study plan since 2018	2	-	6	42	162
M:BGE	20	Official study plan since 2024/2025	1	-	6	42	162
M:GF	0	plano de estudos do Mestrado em Genética Forense a partir de 2013_2014.	1	-	6	42	162

Teaching language

English

Objectives

The course aims to give students an understanding of the importance of phylogenetics for systematics, comparative biology, biomedical issues and conservation planning. Widely used methodologies are discussed and compared, along with the relative philosophies behind each method. 

Learning outcomes and competences

The aim is that by the end of the course students can take data from the web and analyse it in a phylogenetic framework, while appreciating the differences between alternative methods.

Working method

Presencial

Pre-requirements (prior knowledge) and co-requirements (common knowledge)

NA

Program

Introduction to phylogenetics. Why is it so important?

A brief history. From Darwin and the first "trees", through debates of
cladistics vs phenetics, to parsimony vs likelihood and to the present
situation.
 
Methodologies. Maximum Parsimony, Distance methods (minimum evolution,
neighbor-joining and UPGMA), Maximum Likilhood and Bayesian Inferences.
The pros and cons of different methods.
 
Consensus methods. How to combine sources of information.
 
Support methods. Bootstrapping, Bayesian Posterior Probabilities, Decay
Index. What do they mean and how to compare them.
 
Philosophy. If Popper was right, are we barking up the wrong tree?
 
An assessment of the interplay between population genetics and
phylogenetics. Why use networks instead of trees? Comparing the methodologies above and below the species level.

Mandatory literature

Wiley E. O.; Phylogenetics. ISBN: 978-0-471-05975-2 (As an example. Bibliography (scientific papers) will be supplied with the lectures.)

Teaching methods and learning activities

Theoretical and practical classes. During the practical classes students will obtain and analyse real data obtained from GeneBank and other molecular databases.

Evaluation Type

Distributed evaluation without final exam

Assessment Components

designation	Weight (%)
Participação presencial	20,00
Trabalho escrito	80,00
Total:	100,00

Amount of time allocated to each course unit

designation	Time (hours)
Estudo autónomo	60,00
Frequência das aulas	42,00
Trabalho escrito	60,00
Total:	162,00

Eligibility for exams

Attendance to the practical component and report delivery.

Calculation formula of final grade

Final report: 80%
Attendance and participation: 20%

Classification improvement

Final report.