View source for Molecular Evolution 27615 - 2016

== '''Lecture Schedule 2016''' ==

===Week 1 (February 3): Introduction to evolutionary theory and population genetics. Models of growth, selection and mutation===

:; Online lectures
:* [https://class.coursera.org/molevol-003/lecture/11 Common descent (11:52)]
:* [https://class.coursera.org/molevol-003/lecture/15 Natural selection (14:57)]
:* [https://class.coursera.org/molevol-003/lecture/17 Evidence for evolution (part 1) (9:34)] 
:* [https://class.coursera.org/molevol-003/lecture/19 Evidence for evolution (part 2) (20:54)]
:* [https://class.coursera.org/molevol-003/lecture/35 Population growth and selection (18:13)]

:; Course material
:* [http://wiki.bio.dtu.dk/~agpe/course_material/27615/PDFs/lecturenotebook.pdf Lecture notes]
:* [http://wiki.bio.dtu.dk/~agpe/course_material/27615/PDFs/slides_week1.pdf Slides, week 1]

:; Computer exercise
:* [http://www.cbs.dtu.dk/courses/27615/exercises/simulation1_courseraversion.php Population Growth, Fitness, and Selection]

----

===Week 2 (February 10): Neutral mutations and genetic drift. Tree reconstruction by parsimony===

:; Online lectures
:* [https://class.coursera.org/molevol-003/lecture/21 Neutral Theory of Molecular Evolution (11:28)]
:* [https://class.coursera.org/molevol-003/lecture/23 Genetic Drift (9:35)]
:* [https://class.coursera.org/molevol-003/lecture/25 Trees: Terminology and Representation (9:41)]
:* [https://class.coursera.org/molevol-003/lecture/27 Homology and Homoplasy (9:07)]
:* [https://class.coursera.org/molevol-003/lecture/29 Maximum Parsimony (7:48)]
:* [https://class.coursera.org/molevol-003/lecture/31 The Fitch Algorithm (10:31)]
:* [https://class.coursera.org/molevol-003/lecture/33 Searching Tree Space (14:01)]

:; Course material
:* [http://wiki.bio.dtu.dk/~agpe/course_material/27615/PDFs/slides_week2.pdf Slides, week 2]

:; Computer exercise
:* [http://www.cbs.dtu.dk/courses/27615/exercises/parsimony1_courseraversion.php Phylogenetic Analysis using Parsimony]

----

===Week 3+4 (February 17+24): Mini project 1===

Building a tree from scratch: What are the closest relatives of whales?

The mini project should be submitted and assessed via the [https://www.peergrade.io/login peergrade.io] interface. 

----

===Week 5 (March 2): Consensus trees. Distance matrix methods===

:; Online lectures
:* [https://class.coursera.org/molevol-003/lecture/39 Consensus Trees (16:27)]
:* [https://class.coursera.org/molevol-003/lecture/41 Distance Matrix Methods, part 1 (6:07)]
:* [https://class.coursera.org/molevol-003/lecture/43 Distance Matrix Methods, part 2 (22:28)]
:* [https://class.coursera.org/molevol-003/lecture/45 Neighbour Joining (15:28)]

:; Course material
:* [[Media:Consensus.pdf|Handout exercise: Consensus Trees]]
:* [[Media:Distance handout.pdf|Handout exercise: Distance Matrix Methods]]
:* [[Media:Slides week3.pdf|Slides, week 5]]

:; Computer exercises
:* [http://www.cbs.dtu.dk/courses/27615/exercises/consensustrees_courseraversion.php Consensus Trees]
:* [http://www.cbs.dtu.dk/courses/27615/exercises/distance1_courseraversion.php Distance Matrix Methods]

----

===Week 6 (March 9): Models of sequence evolution. Likelihood methods===

:; Online lectures
:* [https://class.coursera.org/molevol-003/lecture/49 Models of evolution (28:48)]
:* [https://class.coursera.org/molevol-003/lecture/51 Maximum likelihood (22:06)]
:* [https://class.coursera.org/molevol-003/lecture/53 Ancestral reconstruction (10:45)]

:; Course material
:* [[Media:Handout real exp change.pdf|Handout exercise: Real, Observed, and Expected Change]]
:* [[Media:Handout likelihood.pdf|Handout exercise: Computation of Likelihood]]
:* [[Media:Slides week4.pdf|Slides, week 6]]

:; Computer exercises
:* [http://www.cbs.dtu.dk/courses/27615/exercises/distance2_courseraversion.php Models of Evolution]
:* [http://www.cbs.dtu.dk/courses/27615/exercises/likelihood1_courseraversion.php Maximum Likelihood]

----

===Week 7+8 (March 16 + 30): Mini project 2===

----

===Week 9 (April 6): Bayesian inference of phylogeny===

:; Online lectures
:* [https://class.coursera.org/molevol-003/lecture/55 Bayesian Inference (23:48)]
:* [https://class.coursera.org/molevol-003/lecture/57 Markov chain Monte Carlo (19:54)]

:; Course material
:* [[Media:Handout.class08.pdf|Handout exercise: Bayesian estimation of model parameter value]]
:* [[Media:Slides week5.pdf|Slides, week 9]]
:* [http://mgel.env.duke.edu/wp-content/publicuploads/eguchi-2008-intro-to-baysian-statistics.pdf Background reading: "An Introduction to Bayesian Statistics Without Using Equations"]
:* [http://www.nature.com/nbt/journal/v22/n9/pdf/nbt0904-1177.pdf Background reading: "What is Bayesian statistics?"]
:* [http://rsta.royalsocietypublishing.org/content/roypta/361/1813/2681.full.pdf Background reading: "Bayesian computation: a statistical revolution"]

:; Computer exercise
:* [http://www.cbs.dtu.dk/courses/27615/exercises/bayes1_courseraversion.php Bayesian Phylogeny]

----

===Week 10 (April 13): Testing hypotheses in a phylogenetic context===

:; Online lectures
:* [https://class.coursera.org/molevol-003/lecture/59 Model selection, part 1 (15:19)]
:* [https://class.coursera.org/molevol-003/lecture/61 Model selection, part 2 (17:20)]
:* [https://class.coursera.org/molevol-003/lecture/63 Introduction to exercise (15:24)]

:; Course material
:* [[Media:Slides week6.pdf|Slides, week 10]]

:; Computer exercise
:* [http://www.cbs.dtu.dk/courses/27615/exercises/modelselect_courseraversion.php Model selection]



----

===Week 11 + 12 (April 20 + 27): Mini project 3===

----

===Week 13 (May 4): Mini project 3 finished + questions for exam ===

----

===Old exam sets===

* [http://wiki.bio.dtu.dk/teaching/index.php/27615-2011 Mini project exam]
* [http://www.cbs.dtu.dk/courses/27615/exam_examples/exam_2004.pdf Exam 2004] ([http://www.cbs.dtu.dk/courses/27615/exam_examples/exam_2004_withanswers.pdf Answers])
* [http://www.cbs.dtu.dk/courses/27615/exam_examples/exam2005.pdf Exam 2005]
* [http://www.cbs.dtu.dk/courses/27615/exam_examples/exam2006.pdf Exam 2006]
* [http://www.cbs.dtu.dk/courses/27615/exam_examples/exam2007.pdf Exam 2007]
* [http://www.cbs.dtu.dk/courses/27615/exam_examples/exam2008.pdf Exam 2008]
* [http://www.cbs.dtu.dk/courses/27615/exam_examples/exam2009.pdf Exam 2009] ([[Media:Exam2009 answers.pdf|Answers]])
* [[Media:Exam2015.pdf|Exam 2015]] ([[Media:Exam2015 answers.pdf|Answers]])