Module 6: Molecular Evolution and Phylogenetics

Module topics

  • Historical perspective on the development of the theory of evolution. Mechanisms of molecular evolution and speciation.
  • Traits, phylogenies, evolutionary models and divergence times.
  • Complexity of the space of phylogenetic models, heuristics to map it. Tree building with distance matrix methods. Parsimony approaches.
  • Tree building with maximum likelihood approaches. Bayesian viewpoint. Branch support measures.

Resources

SessionLecture RecordingsLecture SlidesPractical Assignment
10. Meet_the_trainer_Jean-Baka
00. Module6_Session1_qu_of_the_day
1. Module6_Session1_part1
2. Module6_Session1_part2
3. Module6_Session1_part3
4. Module6_Session1_part4
5. Module6_Session1_part5
6. Module6_Session1_prac
Module6_Session1_Module6_Session1_prac

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galapagos_map
darwin_finches
lack_beak_depth_distribs
2coming soonModule6_Session2coming soon
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Trainers

Jean-Baka

 

 

Jean-Baka Domelevo Entfellner

Primary trainer

Affiliation: University of the Western Cape

My formal education took place in France, mainly in Mathematics, Physics and Computer Science at undergrad level. After completing a BSc and a MSc in Computer Science (Ecole Normale Supérieure de Cachan and University of Rennes, France), my PhD in bioinformatics (University of Montpellier, France, PhD supervisor: O. Gascuel) was about the combination of longitudinal and phylogenetic models to identify remote homologous proteins. I successfully completed that PhD in 2011. Since 2012, I am a postdoctoral fellow at the South African National Bioinformatics Institute (SANBI) with the H3ABioNet project (part of the H3Africa initiative) and since 2016, I am also Senior Lecturer in Computer Science at the University of the Western Cape (Cape Town, South Africa).

Jonathan_Kayondo

 

Jonathan Kayondo

Co-trainer

Affiliation: Ugandan Virus Research Institute

I am a Senior Research Officer (SRO) at the Uganda Virus Research Institute (UVRI), with a molecular genetic training background. My research encompasses investigations on disease vectors and pathogens with a focus on the genetics of malaria transmitting mosquitoes and HIV drug resistance. I am currently involved in research exploring controlling malaria vectors using engineered endonucleases, and the design of more sensitive assays for detection of HIV-drug resistance minority variants. I also contribute to Bioinformatics capacity development at the institute where various analysis pipelines, e.g. for NGS-based metagenomics and variant calling, are being developed to enhance pathogen detection for research purposes or disease outbreak investigations. The Uganda Virus Research Institute is a reference centre for various viral infections and is involved in investigations on communicable and also non-communicable diseases to generate information that will help initiate new or to improve on existing control and prevention strategies.