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_episodes/00a-background.md

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+---
+title: "Background and Metadata"
+teaching: 15
+questions:
+- "What data are we using?"
+- "Why is this experiment important?"
+objectives:
+- "Why study *E. coli*?"
+- "Understand the data set"
+- "What is hypermutability?"
+---
+
+# Background
+
+We are going to use a long-term sequencing dataset from a population of *Escherichia coli* (designated *Ara-3*). 
+
+ - **What is *E. coli*?**
+    - *E. coli* are rod-shaped bacteria can survive under a wide variety of conditions including variable temperatures, nutrient availability, and oxygen levels. Most strains are harmless, but some are associated with food-poisoning. 
+
+![ [Wikimedia](https://species.wikimedia.org/wiki/Escherichia_coli#/media/File:EscherichiaColi_NIAID.jpg) ](../img/172px-EscherichiaColi_NIAID.jpg)
+
+<!-- https://species.wikimedia.org/wiki/Escherichia_coli#/media/File:EscherichiaColi_NIAID.jpg -->
+
+ - **Why is *E. coli* important?**
+    - *E. coli* are one of the most well-studied model organisms in science. As a single-celled organism, *E. coli* reproduces rapidly, typically doubling its population every 20 minutes, which means it can be manipulated easily in experiments. In addition, most naturally occurring strains of *E. coli* are harmless. Most importantly, the genetics of *E. coli* are fairly well understood and can be manipulated to study adaptation and evolution.
+
+# The Data
+
+ - The data we are going to use is part of a long-term evolution experiment led by [Richard Lenski](https://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment).
+
+ - The experiment was designed to assess adaptation in *E. coli*. A population (designated **Ara-3**) were propagated for more than 40,000 generations in a glucose-limited minimal medium (in most conditions glucose is the best carbon source for *E. coli*, providing faster growth than other sugars). This medium was supplemented with citrate which *E. coli* cannot metabolize in the aerobic conditions of the experiment. Sequencing of the populations at regular time points reveals that spontaneous citrate-using variant (**Cit+**) appeared between 31,000 and 31,500 generations causing an increase in population size and diversity. In addition, this experiment showed hypermutability in certain regions. Hypermutability is important and can help accelerate adaptation to novel environments, but also can be selected against in well-adapted populations.
+
+ - To see a timeline of the experiment to date, check out this [figure](https://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment#/media/File:LTEE_Timeline_as_of_May_28,_2016.png), and this paper [Blount et al. 2008: Historical contingency and the evolution of a key innovation in an experimental population of *Escherichia coli*](http://www.pnas.org/content/105/23/7899).
+
+
+## View the Metadata
+
+We will be working with three sample events from the **Ara-3** strain of this experiment, one from 5,000 generations, one from 15,000 generations, and one from 50,000 generations. The population changed substantially during the course of the experiment, and we will be exploring how (the evolution of a **Cit+** mutant) with our variant calling workflow. The metadata file required for this lesson can be [downloaded directly here](ADD LINK) or [viewed in Github](./data/REPLACE.csv).
+
+<!-- add link to metadat file above. Add text to state how it was downloaded (via ENA or otherwise. Best to include something that can be manipulated/filtered/subset for either shell or R demos.) See here for an example: https://raw.githubusercontent.com/datacarpentry/R-genomics/gh-pages/data/Ecoli_metadata.csv--> 
+
+This metadata describes information on the *Ara-3* clones and the columns represent:
+
+| Column           | Description                                |
+|------------------|--------------------------------------------|
+| sample           | clone name					|
+| generation       | generation when sample frozen		|
+| clade            | based on parsimony-based tree		|
+| strain           | ancestral strain				|
+| cit              | citrate-using mutant status		|
+| run              | Sequence read archive sample ID		|
+| genome_size      | size in Mbp (made up data for this lesson) |
+
+
+
+### Challenge
+
+Based on the metadata, can you answer the following questions?
+
+* How many different **Ara-3** generations exist in the data?
+* How many rows and how many columns are in this data?
+* How many citrate+ mutants have been recorded in **Ara-3**?
+
+
+<!-- can add some additional info relevant to interplay of hypermutability and Cit+ adaptations, but keep it simple for now -->
+