Interpreting GADMA migration rates for demes YAML

[dmacguigan]

Hello,

I'm attempting to make a demes YAML by hand using using the results from a GADMA analysis. However, demes has a very specific definition of migration rate. From https://popsim-consortium.github.io/demes-spec-docs/main/specification.html#migration

Continuous asymmetric migration over the half-open time interval (start_time, end_time], from the deme with name source to the deme with name dest. Rates are defined as the probability that parents in the “destination” population are chosen from the “source” population. Migration rates are thus per generation and must be less than or equal to one. There must be at most one migration specified per source/destination pair for any given time interval. Furthermore, if more than one source population have continuous migration into the same destination population, the sum of those migration rates must also be less than or equal to one, as rates define probabilities. The probability that parents come from the same population is just one minus the sum of incoming migration rates.

I want to make sure I'm correctly specifying the migration rates for demes. For example, GADMA's estimated migration rate (in genetic units) between two populations is 0.05973, how would I transform that for demes? I apologize if there is an obvious answer; I'm still a bit new to interpreting demographic results.

Thank you,
Dan

[noscode]

Hi Dan,

Are you using genetic units for your model? If so, then there can be some issues with demes, even for the population size. Typically, demes requires demographic parameters in physical units.
What is your aim? Do you want to draw a picture or report a yaml file as a result? If it is just for a picture, then migration rates do not matter so much: demesdraw pictures migration as a set of random arrows between populations. If I remember correctly, the values of migration do not matter as well, just the presence or absence of migration.

[dmacguigan]

Hello again @noscode!

Yes, the goal of this is to just visualize the model. I think demesdraw draws lines proportional to the migration rate. See the APR ref for demesdraw.tubes.

https://grahamgower.github.io/demesdraw/latest/api.html

num_lines_per_migration (int) – The number of lines to draw per migration. For symmetric migrations, this number of lines will be drawn in each direction.

I've converted most of my model params from genetic units to individuals or generations. I'm just not sure how to convert the migration rates to the demes format.

[dmacguigan]

Sorry, did not mean to close the issue.

[noscode]

Sorry, I totally missed your last comment. If it is still relevant I can help with that:

I've converted most of my model params from genetic units to individuals or generations. I'm just not sure how to convert the migration rates to the demes format.

In order to convert genetic units to physical, you need to divide migration rates by 2*Nanc. That will transform m12 to the fraction of population 1 that comes from population 2 (m12 is basically migration from population 2 to population 1).