Genome Evolution Course 2009-2010

www.yanaiweb.com/genome

Itai Yanai, Technion – Israel Institute of Technology

 

Problem Set #1 assigned October 18th, 2009

 

To be submitted as hard-copy in English or Hebrew on October 25th, 2009 (at the beginning of class, 9:30am).

E-mail submissions will not be accepted.

 

Problem 1: Evolutionary games

A)    A lucky lineage? Can you prove that at some point in past a woman gave birth to a daughter who in turn had a daughter, who had a daughter (repeat 300 times), who then had a son, who had a son (repeat 300 times)?

B)    More ancestors than atoms in the universe? You have two parents, four grandparents, eight great-grandparents, etc. Did you have 2^10,000 great-great-…-great grandparents 10,000 generations ago? What’s going on here?

 

Problem 2: Experimental evolution. Humans have a lifespan of ~80 years. Describe a ‘new society’ in which after 1,000 years the average age is 120?

 

Problem 3: Lamarckian evolution. Explain what Lamarck’s and Darwin’s theories of evolution have in common and where they differ.

 

Problem 4: Evolution and Progress. It is a common error to equate evolution with progress. Describe a scenario where evolution proceeds in a circuitous route instead of a straight line. A population of giraffes evolving an increasingly longer neck may be thought of as an evolutionary straight line. 

 

Problem 5: Hands-on Genomics

The Genome Bioinformatics Group of UC Santa Cruz has put together a very useful genome browser. For this exercise, I suggest that you learn to use the browser by choosing a gene of interest or a random one (see below) and describe its genomic neighborhood. The questions are:

·         How many genes are located in the 1MB upstream and downstream of it.

·         Are CpG islands found upstream of its transcription?

·         Does the gene appear to undergo alternative splicing according to EST’s?

 

How to get started:

  1. Choose a random gene from this file.
    1. Use the 3rd, 5th and 6th columns (corresponding to the chromosome number, start of transcription, and end of transcription, respectively) to construct ‘position tag’ in the following format:
    2. For example, the tag for one gene is: chr6:31583788-31584796
  2. Go to: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=145272516&clade=mammal&org=Human&db=hg19
  3. In the ‘position or search term’ box, enter in the tag and submit. The browser will open to this gene’s area.
  4. Zoom out 10X to get a look at the surrounding region. The button is at the upper right end of the screen.
  5. Set to ‘full’ the tracks you wish to examine. For example, CpG Islands (under Regulation) and Spliced ESTs.