setting migration rates when obtaining demography from species tree

[richard-Hobart]

I must not be understanding the logic correctly and was wondering if anyone could enlighten me.

I have the following:

generation_time=500
time_units="myr"

## ancestral population 'TFKOG'
## TFKOG splits OG and TFK - at 3.3 myr 
## TKF splits into TF and K - at 2.3 myr (4600 generations ago)
## TF splits into T and F    - at 1.3 myr (2600 generations ago)
## OG splits into O and G   - at 1 myr (2000 generations ago)

tree = "(((T:1.3,F:1.3)TF:1,K:2.3)TFK:1.0,(O:1.0,G:1.0)OG:2.3)TFKOG"
demography = msprime.Demography.from_species_tree(
    tree, 
    initial_size, 
    growth_rate=0,
    time_units=time_units,
    generation_time=generation_time)

demography.set_symmetric_migration_rate(['T', 'F', 'K'], rate=1e-2)
demography.set_symmetric_migration_rate(['O', 'G'], rate=1e-2)  

This will give me

DemographyDebugger
╠══════════════════════════════════╗
║ Epoch[0]: [0, 2e+03) generations ║
╠══════════════════════════════════╝
╟    Populations (total=9 active=5)
║    ┌──────────────────────────────────────────────────────────────────────┐
║    │   │   start│     end│growth_rate  │  T   │  F   │  K   │  O   │  G   │
║    ├──────────────────────────────────────────────────────────────────────┤
║    │  T│   500.0│   500.0│ 0           │  0   │ 0.01 │ 0.01 │  0   │  0   │
║    │  F│   500.0│   500.0│ 0           │ 0.01 │  0   │ 0.01 │  0   │  0   │
║    │  K│   500.0│   500.0│ 0           │ 0.01 │ 0.01 │  0   │  0   │  0   │
║    │  O│   500.0│   500.0│ 0           │  0   │  0   │  0   │  0   │ 0.01 │
║    │  G│   500.0│   500.0│ 0           │  0   │  0   │  0   │ 0.01 │  0   │
║    └──────────────────────────────────────────────────────────────────────┘
╟    Events @ generation 2e+03
║    ┌────────────────────────────────────────────────────────────────────────────┐
║    │  time│type        │parameters       │effect                                │
║    ├────────────────────────────────────────────────────────────────────────────┤
║    │  2000│Population  │derived=[O, G],  │Moves all lineages from derived       │
║    │      │Split       │ancestral=OG     │populations 'O' and 'G' to the        │
║    │      │            │                 │ancestral 'OG' population. Also set   │
║    │      │            │                 │the derived populations to inactive,  │
║    │      │            │                 │and all migration rates to and from   │
║    │      │            │                 │the derived populations to zero.      │
║    └────────────────────────────────────────────────────────────────────────────┘
╠════════════════════════════════════════╗
║ Epoch[1]: [2e+03, 2.6e+03) generations ║
╠════════════════════════════════════════╝
╟    Populations (total=9 active=4)
║    ┌──────────────────────────────────────────────────────────────┐
║    │    │   start│     end│growth_rate  │  T   │  F   │  K   │ OG │
║    ├──────────────────────────────────────────────────────────────┤
║    │   T│   500.0│   500.0│ 0           │  0   │ 0.01 │ 0.01 │ 0  │
║    │   F│   500.0│   500.0│ 0           │ 0.01 │  0   │ 0.01 │ 0  │
║    │   K│   500.0│   500.0│ 0           │ 0.01 │ 0.01 │  0   │ 0  │
║    │  OG│   500.0│   500.0│ 0           │  0   │  0   │  0   │ 0  │
║    └──────────────────────────────────────────────────────────────┘
╟    Events @ generation 2.6e+03
║    ┌────────────────────────────────────────────────────────────────────────────┐
║    │  time│type        │parameters       │effect                                │
║    ├────────────────────────────────────────────────────────────────────────────┤
║    │  2600│Population  │derived=[T, F],  │Moves all lineages from derived       │
║    │      │Split       │ancestral=TF     │populations 'T' and 'F' to the        │
║    │      │            │                 │ancestral 'TF' population. Also set   │
║    │      │            │                 │the derived populations to inactive,  │
║    │      │            │                 │and all migration rates to and from   │
║    │      │            │                 │the derived populations to zero.      │
║    └────────────────────────────────────────────────────────────────────────────┘

and so forth for other epochs ... which is all well and good. But if I attempt to add something like

demography.add_symmetric_migration_rate_change(1.3, ['F', 'OG'], rate=1e-2)

or

demography.set_symmetric_migration_rate(['TFK', 'OG'], rate=1e-2)  - to model migration between ancestral populations

I invariably get the message:

msprime._msprime.LibraryError: Attempt to move a lineage into an inactive population

Maybe there is a trick to it ..

[jeromekelleher]

Hi @richard-Hobart 👋

I think maybe you've got your time units mixed up?

demography.add_symmetric_migration_rate_change(1.3, ['F', 'OG'], rate=1e-2)

Changes the migration rate at time 1.3 generations ago, but the first event in your demography above happens at 2000 generations ago.

The from_species_tree function provides support for time units as a convenience, but all other times must be in units of generations.