Tutorial: Demographic Inference

Ekaterina (Katya) Noskova

29 June 2023

About myself

Junior researcher
UniFR

PhD student
ITMO University

Education

2016 - BSc, Applied Mathematics, St. Petersburg, Russia.
2018 - MSc, Algorithmic Bioinformatics, St. Petersburg, Russia.
Present - PhD, Computer Science, St. Petersburg, Russia.

Current research

Currently live in: Zürich, Switzerland

Junior Researcher, Prof. Wegmann's group,
University of Fribourg, Fribourg, Switzerland.

PopSim consortium

Demographic History

Visualization

drawn by demes [Gower et al. 2022]

Demographic Inference

Starting Tutorial

Open the website for the tutorial that was sent by email
- Login: congen2023-user
- Password: congen2023-password
Go to:
GADMA_workshops/ConGen2023_tutorial_demographic_inference,
select and duplicate: Ekaterina_Noskova_tutorial.ipynb,
open your copy

All those materials (except data) are available in the repository: https://github.com/noscode/GADMA_workshops

Data

The link to data was sent by email
- File clouded_leopard.vcf should be copied to data/ directory
- File example.ped should be copied to outputs/gone_analysis/ directory
- File example.map should be copied to outputs/gone_analysis/ directory
File clouded_leopard.vcf is the main data file, files example.ped and example.map were built from it (how to do it is described in the tutorial's .ipynb file).

Alelle Frequency Spectrum

Allele Frequency Spectrum

Derived allele is a new allele formed by mutation.

Allele frequency spectrum (AFS) of P populations is the joint distribution of the derived allele frequencies of a given set of loci (SNP’s) across P populations.

Allele Frequency Spectrum Example

Reference:	ATACGTC
	1 population	2 population
1 individual	ATCCGAC	ACACTTC
2 individual	ACACGTC	ACACGTT
3 individual	GCACGTC

Position	1	2	3	4	5	6	7
Der. allele	G	C	C	-	T	A	T
Freq. in 1 pop.	1	2	1	-	0	1	0
Freq. in 2 pop.	0	2	0	-	1	0	1

$$ A = \begin{matrix} \scriptsize 3 \\ \scriptsize 2 \\ \scriptsize 1 \\ \scriptsize 0 \\ \\ \end{matrix} \begin{matrix} \begin{pmatrix} 0 & 0 & 0 \\ 0 & 0 & 0 \\ 0 & 0 & 0 \\ 0 & 0 & 0 \end{pmatrix} \\ \begin{matrix} \scriptsize 0 & \scriptsize 1 & \scriptsize 2 \end{matrix} \\ \end{matrix} $$ $$ A = \begin{matrix} \scriptsize 3 \\ \scriptsize 2 \\ \scriptsize \htmlData{class=fragment highlight-current-blue, fragment-index=3}{1} \\ \scriptsize 0 \\ \\ \end{matrix} \begin{matrix} \begin{pmatrix} 0 & 0 & 0 \\ 0 & 0 & 0 \\ 1 & 0 & 0 \\ 0 & 0 & 0 \end{pmatrix} \\ \begin{matrix} \scriptsize \htmlData{class=fragment highlight-current-blue, fragment-index=3}{0} & \scriptsize 1 & \scriptsize 2 \end{matrix} \\ \end{matrix} $$ $$ A = \begin{matrix} \scriptsize 3 \\ \scriptsize \htmlData{class=fragment highlight-current-blue, fragment-index=4}{2} \\ \scriptsize 1 \\ \scriptsize 0 \\ \\ \end{matrix} \begin{matrix} \begin{pmatrix} 0 & 0 & 0 \\ 0 & 0 & 1 \\ 1 & 0 & 0 \\ 0 & 0 & 0 \end{pmatrix} \\ \begin{matrix} \scriptsize 0 & \scriptsize 1 & \scriptsize \htmlData{class=fragment highlight-current-blue, fragment-index=4}{2} \end{matrix} \\ \end{matrix} $$ $$ A = \begin{matrix} \scriptsize 3 \\ \scriptsize 2 \\ \scriptsize \htmlData{class=fragment highlight-current-blue, fragment-index=5}{1} \\ \scriptsize 0 \\ \\ \end{matrix} \begin{matrix} \begin{pmatrix} 0 & 0 & 0 \\ 0 & 0 & 1 \\ 2 & 0 & 0 \\ 0 & 0 & 0 \end{pmatrix} \\ \begin{matrix} \scriptsize \htmlData{class=fragment highlight-current-blue, fragment-index=5}{0} & \scriptsize 1 & \scriptsize 2 \end{matrix} \\ \end{matrix} $$ $$ A = \begin{matrix} \scriptsize 3 \\ \scriptsize 2 \\ \scriptsize 1 \\ \scriptsize \htmlData{class=fragment highlight-current-blue, fragment-index=7}{0} \\ \\ \end{matrix} \begin{matrix} \begin{pmatrix} 0 & 0 & 0 \\ 0 & 0 & 1 \\ 2 & 0 & 0 \\ 0 & 1 & 0 \end{pmatrix} \\ \begin{matrix} \scriptsize 0 & \scriptsize \htmlData{class=fragment highlight-current-blue, fragment-index=7}{1} & \scriptsize 2 \end{matrix} \\ \end{matrix} $$ $$ A = \begin{matrix} \scriptsize 3 \\ \scriptsize 2 \\ \scriptsize \htmlData{class=fragment highlight-current-blue, fragment-index=8}{1} \\ \scriptsize 0 \\ \\ \end{matrix} \begin{matrix} \begin{pmatrix} 0 & 0 & 0 \\ 0 & 0 & 1 \\ 3 & 0 & 0 \\ 0 & 1 & 0 \end{pmatrix} \\ \begin{matrix} \scriptsize \htmlData{class=fragment highlight-current-blue, fragment-index=8}{0} & \scriptsize 1 & \scriptsize 2 \end{matrix} \\ \end{matrix} $$ $$ A = \begin{matrix} \scriptsize 3 \\ \scriptsize 2 \\ \scriptsize 1 \\ \scriptsize \htmlData{class=fragment highlight-current-blue, fragment-index=9}{0} \\ \\ \end{matrix} \begin{matrix} \begin{pmatrix} 0 & 0 & 0 \\ 0 & 0 & 1 \\ 3 & 0 & 0 \\ 0 & 2 & 0 \end{pmatrix} \\ \begin{matrix} \scriptsize 0 & \scriptsize \htmlData{class=fragment highlight-current-blue, fragment-index=9}{1} & \scriptsize 2 \end{matrix} \\ \end{matrix} $$