Gallery

This page includes examples that illustrate various features of Demes models, including some well-known and more complicated models of human history.

Zigzag model

description: A single population model with epochs of exponential growth and decay.
doi:
  - https://doi.org/10.1038/ng.3015
time_units: generations
demes:
  - name: generic
    epochs:
    - {end_time: 34133.31, start_size: 7156}
    - {end_time: 8533.33, end_size: 71560}
    - {end_time: 2133.33, end_size: 7156}
    - {end_time: 533.33, end_size: 71560}
    - {end_time: 133.33, end_size: 7156}
    - {end_time: 33.333, end_size: 71560}
    - {end_time: 0, end_size: 71560}

Gutenkunst et al. (2009) Out-of-Africa expansion

description: The Gutenkunst et al. (2009) OOA model.
doi:
- https://doi.org/10.1371/journal.pgen.1000695
time_units: years
generation_time: 25

demes:
- name: ancestral
  description: Equilibrium/root population
  epochs:
  - {end_time: 220e3, start_size: 7300}
- name: AMH
  description: Anatomically modern humans
  ancestors: [ancestral]
  epochs:
  - {end_time: 140e3, start_size: 12300}
- name: OOA
  description: Bottleneck out-of-Africa population
  ancestors: [AMH]
  epochs:
  - {end_time: 21.2e3, start_size: 2100}
- name: YRI
  description: Yoruba in Ibadan, Nigeria
  ancestors: [AMH]
  epochs:
  - start_size: 12300
- name: CEU
  description: Utah Residents (CEPH) with Northern and Western European Ancestry
  ancestors: [OOA]
  epochs:
  - {start_size: 1000, end_size: 29725}
- name: CHB
  description: Han Chinese in Beijing, China
  ancestors: [OOA]
  epochs:
  - {start_size: 510, end_size: 54090}

migrations:
- {demes: [YRI, OOA], rate: 25e-5}
- {demes: [YRI, CEU], rate: 3e-5}
- {demes: [YRI, CHB], rate: 1.9e-5}
- {demes: [CEU, CHB], rate: 9.6e-5}

Jacobs et al. (2019) Denisovan admixture

description: |
  A ten population model of out-of-Africa, including two pulses of
  Denisovan admixture into Papuans, and several pulses of Neandertal
  admixture into non-Africans.
  Most parameters are from Jacobs et al. (2019), Table S5 and Figure S5.
  This model is an extension of one from Malaspinas et al. (2016), thus
  some parameters are inherited from there.
time_units: generations
doi:
- https://doi.org/10.1016/j.cell.2019.02.035
- https://doi.org/10.1038/nature18299

demes:
- name: YRI
  epochs:
  - {end_time: 20225.0, start_size: 32671.0}
  - {end_time: 2218.0, start_size: 41563.0}
  - {end_time: 0, start_size: 48433.0}
- name: DenA
  ancestors: [YRI]
  start_time: 20225.0
  epochs:
  - {end_time: 15090.0, start_size: 13249.0}
  - {end_time: 12500.0, start_size: 100.0}
  - {end_time: 9750.0, start_size: 100.0}
  - {end_time: 0, start_size: 5083.0}
- name: NeaA
  ancestors: [DenA]
  start_time: 15090.0
  epochs:
  - {end_time: 3375.0, start_size: 13249.0}
  - {end_time: 0, start_size: 826.0}
- name: Den2
  ancestors: [DenA]
  start_time: 12500.0
  epochs:
  - start_size: 13249.0
- name: Den1
  ancestors: [DenA]
  start_time: 9750.0
  epochs:
  - start_size: 13249.0
- name: Nea1
  ancestors: [NeaA]
  start_time: 3375.0
  epochs:
  - start_size: 13249.0
- name: Ghost
  ancestors: [YRI]
  start_time: 2218.0
  epochs:
  - {end_time: 2119.0, start_size: 1394.0}
  - {end_time: 0, start_size: 8516.0}
- name: Papuan
  ancestors: [Ghost]
  start_time: 1784.0
  epochs:
  - {end_time: 1685.0, start_size: 243.0}
  - {end_time: 0, start_size: 8834.0}
- name: CHB
  ancestors: [Ghost]
  start_time: 1758.0
  epochs:
  - {end_time: 1659.0, start_size: 2231.0}
  - {end_time: 1293.0, start_size: 12971.0}
  - {end_time: 0, start_size: 9025.0}
- name: CEU
  ancestors: [CHB]
  start_time: 1293.0
  epochs:
  - start_size: 6962.0

migrations:
- {demes: [YRI, Ghost], rate: 0.000179, start_time: 1659.0}
- {demes: [CHB, Papuan], rate: 0.000572, start_time: 1659.0, end_time: 1293.0}
- {demes: [CHB, Papuan], rate: 5.72e-05, start_time: 1293.0}
- {demes: [CHB, Ghost], rate: 0.000442, start_time: 1659.0, end_time: 1293.0}
- {demes: [CEU, CHB], rate: 3.14e-05}
- {demes: [CEU, Ghost], rate: 0.000442}

pulses:
- {sources: [Nea1], dest: Ghost, time: 1853.0, proportions: [0.024]}
- {sources: [Den2], dest: Papuan, time: 1575.8620689655172, proportions: [0.018]}
- {sources: [Nea1], dest: CHB, time: 1566.0, proportions: [0.011]}
- {sources: [Nea1], dest: Papuan, time: 1412.0, proportions: [0.002]}
- {sources: [Den1], dest: Papuan, time: 1027.5862068965516, proportions: [0.022]}
- {sources: [Nea1], dest: CHB, time: 883.0, proportions: [0.002]}