Examples

This section contains example analyses of local ancestry inference performed on admixed populations from the 1000 Genomes Project. Below, we provide a detailed description of data, preprocessing steps, links to the examples, and the considered demographic models.

Data

Dataset description

Description of the local ancestry datasets used in the examples (1000 Genomes Project).

Data description

Data processing

Preprocessing and formatting steps applied to the data.

Data Processing

Example analyses

ASW population

Example analyses for the ASW population.

ASW population

MXL population

Example analyses for the MXL population.

MXL population

Demographic models

In this section, we consider four demographic models of varying complexity. The corresponding YAML files are specified below.

One pulse model

The following model is written in the file ppp.yaml.

model_name: One_Pulse
description: Represents a population X founded a generations ago by EUR, NAT, and AFR.
time_units: generations
demes:
  - name: EUR
  - name: AFR
  - name: NAT
  - name: X
ancestors: [EUR, NAT, AFR]
proportions: [REUR,RNAT,1-REUR-RNAT]
start_time: t

Two pulses model

The following model is written in the file ppp_pxx.yaml.

model_name: Two pulses
description: A population X founded a generations ago by EUR, AFR, and NAT, then subsequent EUR migration.
time_units: generations
demes:
  - name: EUR
  - name: AFR
  - name: NAT
  - name: X
ancestors: [EUR, NAT, AFR]
proportions: [REUR,RNAT,1-REUR-RNAT]
start_time: t1

pulses:
  - sources: [EUR]
    dest: X
    proportions: [REUR2]
    time: t2

Three pulses model

The following model is written in the file ppp_xxp_pxx.yaml.

model_name: Three pulses
description: A demes model with flexible parameters. Represents a population X founded a generations ago by EUR and NAT, then subsequent AFT migration,
then subsequent EUR migration.
time_units: generations
demes:
  - name: EUR
  - name: NAT
  - name: X
ancestors: [EUR, NAT]
proportions: [REUR,1-REUR]
start_time: t1

pulses:
  - sources: [AFR]
    dest: X
    proportions: [RAFR]
    time: t2
  - sources: [EUR]
    dest: X
    proportions: [REUR2]
    time: t3

Continuous pulse model

The following model is written in the file ccc.yaml.

model_name: One_Pulse
description: Represents a population X founded with a continuous event.
time_units: generations
demes:
  - name: EUR
  - name: NAT
  - name: AFR
  - name: X
ancestors: [EUR, NAT, AFR]
proportions: [REUR, RNAT,RAFR ]
start_time: t1
end_time: t2