
27615 
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


 F5B (Wed 1317)
 Location:  Campus Lyngby  Scope and form:  Lectures and computer exercizes  Duration of Course:  13 weeks   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 indepth knowledge of modelbased 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 proteinencoding 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 nonparametric
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
(gammadistributed 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
Department:  27 Department of
Systems Biology  Home page:   Registration Sign up:  At CampusNet 
Last updated: 05. maj, 2014 No result







