In the previous course in the Specialization, we learned how to compare genes, proteins, and genomes. One way we can use these methods is in order to construct a "Tree of Life" showing how a large collection of related organisms have evolved over time.
In the first half of the course, we will discuss approaches for evolutionary tree construction that have been the subject of some of the most cited scientific papers of all time, and show how they can resolve quandaries from finding the origin of a deadly virus to locating the birthplace of modern humans.
In the second half of the course, we will shift gears and examine the old claim that birds evolved from dinosaurs. How can we prove this? In particular, we will examine a result that claimed that peptides harvested from a T. rex fossil closely matched peptides found in chickens. In particular, we will use methods from computational proteomics to ask how we could assess whether this result is valid or due to some form of contamination.
Finally, you will learn how to apply popular bioinformatics software tools to reconstruct an evolutionary tree of ebolaviruses and identify the source of the recent Ebola epidemic that caused global headlines.
Overview
Syllabus
- Week 1: Introduction to Evolutionary Tree Construction
Welcome to our class!
In this class, we will consider the following two central biological questions (the computational approaches needed to solve them are shown in parentheses):
- Weeks 1-3: Which Animal Gave Us SARS? (Evolutionary tree construction)
- Weeks 4-5: Was T. rex Just a Big Chicken? (Combinatorial Algorithms)
In Week 6, you will complete a Bioinformatics Application Challenge to apply evolutionary tree construction algorithms in order to determine the origin of the recent ebola outbreak in Africa.
As in previous courses, each of these two chapters is accompanied by a Bioinformatics Cartoon created by talented artist Randall Christopher and serving as a chapter header in the Specialization's bestselling print companion. You can find the first chapter's cartoon at the bottom of this message. What do stick bugs and bats have to do with deadly viruses? And how can bioinformatics be used to stop these viruses in their tracks? Start learning today and find out!
- Week 2: More Algorithms for Constructing Trees from Distance Matrices
Welcome to Week 2 of class!
Last week, we started to see how evolutionary trees can be constructed from distance matrices. This week, we will encounter additional algorithms for this purpose, including the neighbor-joining algorithm, which has become one of the top-ten most cited papers in all of science since its introduction three decades ago.
- Week 3: Constructing Evolutionary Trees from Characters
Welcome to week 3 of class!
Over the last two weeks, we have seen several different algorithms for constructing evolutionary trees from distance matrices.
This week, we will conclude the current chapter by considering what happens if we use properties called "characters" instead of distances. We will also see how to infer the ancestral states of organisms in an evolutionary tree, and consider whether it is possible to define an efficient algorithm for this task.
- Week 4
Welcome to week 4 of the class!
Did birds evolve from dinosaurs? Over the next two weeks, we will see how we could analyze molecular evidence in support of this theory. You can find this week's Bioinformatics Cartoon from Randall Christopher at the bottom of this E-mail. Why does the T. rex look so much like a chicken? And why is the monkey typing frantically? Keep learning to find out!
- Week 5: Resolving the T. rex Peptides Mystery?
Welcome to week 5 of class!
Last week, we asked whether it is possible for dinosaur peptides to survive locked inside of a fossil for 65 million years. This week, we will see what this question has to do with statistics; in the process, we will see how a monkey typing out symbols on a typewriter can be used to address it.
- Week 6: Bioinformatics Application Challenge
Welcome to the sixth and final week of the course!
In this week's Bioinformatics Application Challenge, we will use reconstruct an evolutionary tree of ebolaviruses and use it to determine the origin of the pathogen that caused the recent outbreak in Africa.
Taught by
Pavel Pevzner and Phillip Compeau
