Journal Club 1 - Ancestry

For this assignment, you should read the assigned papers and answer the questions below.  To ease into things, the questions consist of a beginning of the year survey and some short questions about the readings. 

Overview

Our first course module will be about inferring ancestry from genomes. For our first journal club, we will read the following to get some background about the history of human populations:

• Ancient Genomics of Modern Humans: The First Decade Download Ancient Genomics of Modern Humans: The First Decade
• A global reference for human genetic variation Download A global reference for human genetic variation

The first paper is an overview of what analysis of ancient human (and human relative) genomes have taught us about the history of human populations. Our goal in reading this paper is to get a broad understanding of how different population groups have arisen (e.g. African, European, Native American, etc.) and their relationship with each other. Do not get bogged down in specifics of some of the ancient genomes or populations mentioned. We'll talk in more detail about ancient human populations in Week 8.

The second paper describes the "1000 Genomes Project", a major effort to sequence several thousand human genomes from diverse present-day populations. This dataset has served as an extremely valuable resource for many human genetics studies, and also will be used frequently for assignments in this course. The paper gives an overview of the genetic variation found in a typical human genome and a summary of genetic variation across world populations. Again, do not get bogged down in methods details. Many of the methods presented (imputation, GWAS, and more) will be covered in depth in future lectures.

Questions (1 pt each)

You can answer the questions in the text box provided.

Survey

1. What is your primary motivation for taking this course?

2. Which of the following do you have experience using: UNIX command line, bash scripting, Python, Jupyter Notebooks? What is your relative comfort level in each?

3. Have you take a genetics or similar course before? Describe your comfort level talking about terms such as genomes, variants, alleles, haplotypes, pedigrees, recombination.

4. Are there any particular topics or tools you're most interested in learning about this quarter?

Journal club questions

5. Describe genetic evidence supporting the "Out of Africa" hypothesis.

6. About how many years ago did African and non-African populations split? What about east vs. west Eurasian populations? About how many years ago did gene flow from Neanderthals occur? Note Neanderthal admixing is thought to have occurred before the divergence of non-African populations.

7. Many present-day populations can be described as recently admixed between two or more historically distinct population groups. Which ancestral populations contributed to present-day African-Americans? What about present-day Mexican individuals? See Figure 2a and Extended Data Fig. 5 of the 1000 Genomes paper, and population codes here: https://www.internationalgenome.org/category/population Links to an external site.to help answer this question. 

Questions 8-10: Write down three questions you had about the assigned readings that you would like to discuss in class.