danielyao12/Fu-s-test

Content

1. Protocols for DNA extraction and library preparation

Ancient DNA damage pattern.
Ancient DNA Assessment.

Here, I did some basic researches on:

Current extraction protocols for ancient DNA, why/how to use UDG treatment (full and partial).
DNA sequencing library preparations and how they related to ancient DNA damage pattern.
Ancient DNA damage pattern.

And I figured out how to use mapDamage2, Mapping-Iterative-Assembler(MIA) and schmutzi to detect ancient DNA damage pattern and contamination. How to use PMDtools to separate endogenous ancient DNA from modern day contamination.

2. Mitochondrial genome analysis

Assignning mtDNA haplogroup from NGS data and how to use snakemake to automate the analysis.

3. Description of ancient samples and archaeological context

Summary all ancient samples used in this paper.
With some backgroud information

4. Sex determination and Y chromosome analysis

5. Principal Component Analysis

How did I format the data.
How did I conduct PCA analysis.
How did I plot the results nicely and my R codes/solutions for that.
Description and Explaination for the PCA plot.

6. ADMIXTURE analysis

How did I format the data.
How did I run the admixture analysis.
R codes/solutions for plotting the results nicely.
Description and Explaination for the admixture plot.

7. Population relationships and admixture using f-statistics

1. Introduction of Outgroup-f3 statistics

Basic about Outgroup-f3 statistics
How to set-up and interpret Outgroup-f3 statistics
How to run Outgroup-f3 test
How to plot Outgroup-f3 test results in R

2. Repeat Outgroup-f3 test in Haak et al. (2015)

3. Repeat f4 test in Haak et al. (2015)

I am working on this and try to finalized it.

8. Phylogenetic relationships of ancient Eurasians

9. Inference of admixture proportions without detailed phylogenetic modeling

10. Number of streams of migration into ancient Europe

11. Relevance of ancient DNA to the problem of Indo-European language dispersals

About myself and this github repository

My name is Mian Li, a PhD student at Binghamton University. This challage (at least to me) is given by Dr. Fu Qiaomei during my post-doc interview.

I am trying to repeat all analyses in the Nature paper named: "Massive migration from the steppe was a source for Indo-European languages in Europe".

Here, I will write down all steps, codes and solutions for the test, and my researches about the backgroud. My solutions, all programs that I used may be different from the orginal paper, but would acheive the same goal or at least do similar work. I can't repeat the whole process perfectly, but I will try my best.

This github is about, here I quote my favorite words from Hansjörg Plieninger:

things I learned, to make it simpler for other people to learn the same thing quicker,
things I learned, to make it simpler for me to do the same thing quicker next time,
things I love, to make it simpler for others to love them, too,
things I do, to make it simpler for you to get in touch with me.

`It was simple, but you know, it's always simple when you've done it.`

Reference: Haak, W., Lazaridis, I., Patterson, N., Rohland, N., Mallick, S., Llamas, B., ... & Fu, Q. (2015). Massive migration from the steppe was a source for Indo-European languages in Europe. Nature, 522(7555), 207. Link

If you have any questions about my codes and steps, feel free to reach out to me through email, limian1987@gmail.com.

My twitter: https://twitter.com/MianLi1987

danielyao12 / Fu-s-test