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27615 Molecular Evolution

Danish title:

Molekylær evolution

Language:

Point( ECTS )

5

Course type:

MSc
Taught under open university
Technological specialization course, MSc. Eng., Bioinformatics Systems Biology

Schedule:

F5B (wed 13-17)

Location:

Campus Lyngby

Scope and form:

Lectures and computer exercizes

Duration of Course:

13 weeks

Date of examination:

F5B, E5B

Type of assessment:

Exam duration:

Aid:

Evaluation:

Qualified Prerequisites:

,

Participants restrictions:

Minimum 10

General course objectives:

To provide the student with broad knowledge in the field of molecular evolution (i.e., the evolution of DNA, RNA, and proteins), and with in-depth knowledge of model-based methods for phylogenetic tree reconstruction and hypothesis testing in an evolutionary context. Although the study of molecular evolution does require a certain level of mathematical understanding, this course has been designed to attract a diverse range of students.

Learning objectives:

A student who has met the objectives of the course will be able to:
  • Account for natural selection and the neutral theory of molecular evolution.
  • Solve simple population genetic problems.
  • Account for important properties of phylogenetic tree plots.
  • Construct phylogenetic trees under the parsimony, distance, and maximum likelihood criteria (using the PAUP* program); construct Bayesian phylogenetic trees (using the MrBayes program).
  • Use the Fitch algorithm to manually compute the length of a tree given an alignment; use this as the basis for selecting the most parsimonious tree(s).
  • Manually compute the likelihood for a phylogenetic model given a set of parameter values and an alignment.
  • Manually compute the posterior probabilities for a set of phylogenetic models, given a set of parameter values and prior model probabilities; use this as the basis for selecting the best model.
  • Use the program modeltest to choose a suitable nucleotide substitution model for a phylogenetic analysis.
  • Use the PAML program package to detect positively selected sites in a protein-encoding gene.
  • Use likelihood ratio testing for manually selecting the best of two alternative phylogenetic models.
  • Use the PAUP* program for investigating the degree of uncertainty in a phylogenetic tree by non-parametric bootstrapping.
  • Use the PAML program package for comparing alternative phylogenetic hypotheses by parametric bootstrapping.

Content:

Brief introduction to evolutionary theory and population genetics.
Mechanisms of molecular evolution. Models of DNA and protein substitution. Reconstruction of phylogenetic trees using distance based methods, parsimony, maximum likelihood, and Bayesian techniques. Advanced models of nucleotide substitution (gamma-distributed mutation rates, molecular clock models, codon models and analysis of selective pressure). Statistical analysis of biological hypotheses (likelihood ratio tests, parametric bootstrapping, Bayesian statistics).

The student will acquire practical experience in the use of computational methods by analyzing sequences from the scientific literature.

Green challenge participation:

Please contact the teacher for information on whether this course gives the student the opportunity to prepare a project that may participate in DTU´s Study Conference on sustainability, climate technology, and the environment (GRØN DYST). More infor http://www.groendyst.dtu.dk/english

Responsible:

Anders Gorm Pedersen , Building 208, Ph. (+45) 4525 2484 , gorm@cbs.dtu.dk

Department:

27 Department of Systems Biology

Home page:

http://www.cbs.dtu.dk/courses/27615.mol/

Registration Sign up:

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Last updated: 05. maj, 2014