About the course
Phylogenetic methods are essential for understanding evolutionary relationships among organisms and molecules. They provide the means to study the evolution of biological traits, estimate divergence times, and relate these to relevant evolutionary events. These methods depend on hypotheses of homology, which may be based on morphological or molecular data.
Students will receive theoretical and practical training on how to perform informative phylogenetic analyses based on molecular data. Training includes the selection of terminal taxa and data, running analyses, and making tree-based inferences.
Learning outcomes
At the end of the course, students should be able to reconstruct strong phylogenetic hypotheses for their research by:
- Interpreting evolutionary trees and networks
- Choosing the kinds of data (individual molecular markers, genomic data) and taxa (for tree rooting) that will be informative for their research question
- Understanding molecular homology at different levels, including the concepts of orthology and paralogy
- Performing data mining, running alignment software, and evaluating the quality of alignments by considering homology hypotheses and saturation, including using translation from nucleotide to amino acids for protein-coding genes
- Finding best-fit nucleotide and protein evolutionary models
- Concatenating data from different molecular markers
- Generating maximum likelihood trees with bootstrap branch support
- Running Bayesian methods to generate phylogenetic trees and calculating the posterior probability of different parameters and tree topologies, and summarizing them with consensus trees
- Understanding species trees
- Interpreting and resolving analytical artifacts such as long-branch attraction and rogue taxa
- Performing calibration, applying molecular clocks, and dating tree nodes
- Applying comparative methods (e.g., ancestral state reconstruction).
Language
English
Assignment and credits
The course is equivalent to 2 ECTS. A certificate will be provided by UFRJ.
Students who wish to earn an additional 1 ECTS can complete a written home exam that will be sent after the course. The 3 ECTS certificate will be provided by BIOCORE.
Teachers
- Daniela Takiya, Professor, Biology Institute, Federal University of Rio de Janeiro, Brazil
- Dimitar Dimitrov, Professor, University Museum of Bergen, University of Bergen, Norway
- Fabricius Domingos, Professor, Federal University of Paraná, Brazil
- Joana Zanol, Professor, National Museum, Federal University of Rio de Janeiro, Brazil
- Sonia Andrade, Professor, University of São Paulo, Brazil
- Ricardo Alvarez, Postdoc, University of Campinas, Brazil
Admission and application
Number of students
Maximum 20 students in total
- 12 students from Brazil
- 5 students from Norway
- 3 students from South Africa
Eligibility and prerequisites
Participants should have basic knowledge of biodiversity science and at least a bachelor’s degree in biology. Some experience with molecular data and the use of molecular systematics software is an advantage. Students are expected to read a selection of scientific review papers in advance.
- Norway and South Africa: Only PhD and Master level students associated with MARLIN project partners (UiB, NTNU, UiT, SU, SANBI, CPUT) are eligible for course registration.
- Brazil: Students and non-student participants from any University/Research Institute can apply, but priority and financial support will be given to PhD and Master students from UFRJ, USP, and UFPR.
How to apply
Applications for this course are now closed.
We encourage all course applicants to become Associate Members of BIOCORE to receive updates and information about future events.
Not a member yet? Become a BIOCORE member here.
Selection process
If there are more applicants within each quota than spots, participants will be selected based on their scientific, educational, and/or professional merit, motivation, and the relevance of the course for their career development. MARLIN is committed to providing equal opportunities for all students, independently of their ethnic and socio-economic status.
Results of the selection process will be announced via email shortly after the application deadline.
Financial support
There is no course fee.
Course participants enrolled in a Master’s or PhD program and affiliated with one of the MARLIN project partners (UiB, NTNU, UiT, UFRJ, USP, UFPR, SU, SANBI, CPUT) are eligible for financial support. This includes travel, visa costs, insurance (for students outside Brazil), local transport to the venue, accommodation, and meals.
About the venue
Alto da Figueira Field Station is located about 2.5 hours by car from Rio de Janeiro’s international airport and is the headquarters of ARAÇÁ (Atlantic Forest Research and Conservation Alliance).
Alto da Figueira is a private nature reserve owned and managed by Alexandre and Anna Antonelli since early 2022. The reserve has around 120 hectares of pristine Atlantic Rainforest, with many different forest types, mountains, valleys, streams, and one of the most biodiverse environments on the planet.
Logistics
Transport for course participants will be organised on Friday, 27 November, from Rio de Janeiro to the Alto da Figueira Field Station, with return on Monday, 7 December. The weekends before and after the course will be dedicated to exploring the local surroundings with the station guides and visiting the nearest town.
Rooms and board
The station offers only shared rooms, accommodating 2–4 people per room. Meals for all course participants will be covered by the MARLIN project and include three meals per day as well as coffee breaks. Please note that the station serves only vegetarian food with high nutritional value. There is also the option to cook your own meals in a local kitchen, but this must be arranged privately.
Contact
For questions about the course and local logistics:
For questions about financial support and travel arrangements (MARLIN project):