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 between sequences
  • Complexity of the search space, distance matrix methods, maximum parsimony
  • Heuristics based on tree alterations, maximum likelihood, Bayesian methods, statistical confidence 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

finches_images
galapagos_map
darwin_finches
lack_beak_depth_distribs
20. Module6_Session2_qu_of_the_day
1. Module6_Session2_part1
2. Module6_Session2_part2
3. Module6_Session2_part3
4. Module6_Session2_part4
5. Module6_Session2_part5
6. Module6_Session2_part6
7. Module6_Session2_part7
8. Module6_Session2_part8
9. Module6_Session2_prac
Module6_Session2_Module6_Session2_prac

seven_seqs.fa
30. Module6_Session3_qu_of_the_day
1. Module6_Session3_part1
2. Module6_Session3_part2
3. Module6_Session3_part3
4. Module6_Session3_part4
5. Module6_Session3_part5
6. Module6_Session3_prac
Module6_Session3Module6_Session3_prac
40. Module6_Session4_qu_of_the_day
1. Module6_Session4_part1
2. Module6_Session4_part2
3. Module6_Session4_part3
4. Module6_Session4_part4
5. Module6_Session4_part5
6. Module6_Session4_prac
Module6_Session4Module6_Session4_prac_

seven_seqs.fa
274s.mit12.phys
smaller2_mit12_58seqs_fasta

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.