Population Genetics and Molecular Evolution

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Credits
6
Types
Compulsory
Requirements
This subject has not requirements
Department
UB;UAB
This course offers a comprehensive introduction to the key principles governing the evolution of DNA and protein sequences within and between populations. It covers essential topics such as the study of genetic variation, linkage disequilibrium, the effects of different evolutionary forces on evolutionary change, the neutral theory of molecular evolution, and the role of adaptation in species divergence. Emphasis is also placed on computational approaches, including the algorithms and software commonly used to analyze gene and genome evolution. The course combines in-person theoretical lectures, problem-solving sessions, and hands-on practicals, supported by short assignments designed to reinforce core concepts.

Teachers

Person in charge

  • Alejandro Sánchez Gracia ( )
  • Julio Rozas Liras ( )
  • Marta Puig Font ( )

Others

  • Marta Coronado Zamora ( )
  • Olga Dolgova Konjushenko ( )
  • Sara Guirao Rico ( )

Weekly hours

Theory
2
Problems
2
Laboratory
0
Guided learning
0
Autonomous learning
6

Objectives

  1. Acquire a foundational understanding of the evolution of biological sequences.
    Related competences: K1, S1, S3, S8, C2, C3, C4,
  2. Acquire practical skills in applying computational tools to analyze molecular population genetics and divergence data.
    Related competences: K3, K7, S2, S5, S7, C3,
  3. Gain a basic understanding of the theoretical, mathematical, and algorithmic principles involved in population genetics and molecular evolution.
    Related competences: K2, K3, S3, C3,

Contents

  1. Genetic variation
    Types of genetic variation. Allele and genotype frequencies. Hardy-Weinberg equilibrium.
  2. Genetic drift and mutation
    Genetic drift. Mutation. Neutral genetic variation.
  3. Natural selection
    Basic model of natural selection. Fitness and selection coefficient. Balancing selection.
  4. Migration and population structure
    Continent-island model. Fixation indices.
  5. Extension of population genetics: molecular population genetics
    Measuring DNA polymorphism. Linkage disequilibrium. Genetic hitchhiking. Gene mapping. GWAS.
  6. Molecular adaptation and neutrality tests
    Inferring natural selection from sequence data: neutrality-based tests: Tajima¿s D, HKA and MK
  7. Molecular clocks and the neutral theory of molecular evolution
    Theoretical basis and key concepts. Predicted consequences and examples from biological data
  8. Modelling sequence evolution
    Estimation of sequence divergence and evolutionary rates. Application of computational simulations in the study of molecular evolution. Backward- and forward-time simulations.
  9. Molecular adaptation and functional divergence
    Inferring natural selection from divergence data. Codon substitution models. Changes in amino acid substitution rates after gene duplication and speciation.

Activities

Activity Evaluation act





Mid-term exam


Objectives: 1
Week: 9
Theory
2h
Problems
0h
Laboratory
0h
Guided learning
0h
Autonomous learning
0h

Final exam


Objectives: 1 3
Week: 17
Theory
2h
Problems
0h
Laboratory
0h
Guided learning
0h
Autonomous learning
0h

Teaching methodology

Classroom teaching will include a combination of theoretical lectures, interactive seminars, and practical sessions in the computer lab.

Theoretical lectures will provide the core knowledge and key concepts of the course, offering students the opportunity to ask questions and engage in discussions to deepen their understanding.

Seminars will focus on active learning, where students will analyze real research studies in greater depth.

Practical sessions in the computer lab will offer hands-on experience in specialized software and tools to analyze data, run simulations, and apply concepts in real-research data scenarios.

Evaluation methodology

In order to successfully complete the course, the student must participate in all evaluated activities and obtain a final grade greater than 5/10.

The final grade will be calculated as follows (maximum final grade is 10):

4 points: Final exam
4 point: Midterm exam
2 points: Evaluation of practical sessions

Re-evaluation Information
Students who do not reach a final grade of 5.0 must take the re-evaluation exam.
Only the theoretical part of the course can be retaken in this exam. Practical work and assignments will not be re-evaluated.

Bibliography

Basic:

  • Bioinformatics and Molecular Evolution - HIGGS, Paul G., ATTWOOD, Teresa K., Wiley-Blackwell, 2005. ISBN: 978-1-405-10683-2
  • Practical Computing for Biologists - HADDOCK, Steven H. D., DUNN, Casey W., Sinauer Associates, 2010. ISBN: 9780878933914
  • Estimating Species Trees: Practical and Theoretical Aspects - KNOWLES, L. L., KUBATKO, L. S., Wiley-Blackwell, 2010. ISBN: 978-0-470-52685-9
  • An introduction to population genetics : Theory and Applications - NIELSEN, R., SLATKIN, M., Sinauer Associates, 2013. ISBN: 1605351539
  • Understanding Population Genetics - SÄll, Torbjörn, BENGTSSON, Bengt O., Wiley-Blackwell, 2017. ISBN: 978-1-119-12407-8
  • Molecular Evolution: A Statistical Approach - YANG, Ziheng, OXFORD University Press, 2014. ISBN: 978-0-19-960261-2

Complementary:

  • Molecular Population Genetics - CASILLA, S., BARBADILLA, A., GENETICS , 2017. 205:1003-1035.
    https://doi.org/10.1534/genetics.116.196493
  • Reconstruction of Phylogenetic Trees. In: The Tree of Life (Chapter 54; pp: 651-661) - POSADA, D., Sinauer Associates , 2014. ISBN: 9781605352299
  • Nucleotide Variability Analysis and Intraespecific phylogenies. In: The Tree of Life (Chapter 55; pp: 663-673) - ROZAS, J., SÁNCHEZ-GRACIA, A., Sinauer Associates , 2014. ISBN: 9781605352299

Web links