Simulating a reintroduction programme (ex situ to in situ)

[João Pedro Meireles]

Hello Everyone. 

I am working on a project to try to simulate the genetic impact that the reintroduction of some ex situ individuals might have in an isolated wild population. 

So far I am just simulating the demographic history of the set-up based on literature: the history of the wild population and its bottlenecks, the formation of an isolated subpopulation, the creation of an ex situ population with founders from the wild population, etc... 

I am running everything as a Non-WrightFisher model. It is a medium-sized carnivore mammal species. Each tick is assumed to be one year in time. 

A couple of questions:

1. I am simulating bottlenecks. For this, I am just changing the carrying capacity of the population to force the population to remain that size. Is this a correct approach? 
2. Is there a way to pick x founders from the population randomly to create the ex situ population? For nonWF models, the only thing I found in the manual was to pick up random parents from the wild population and generate offspring into the ex situ population. Is this an acceptable approach?

Thank you. 

[Víctor Muñoz]

Hi João,
Here is the link to one of our articles where we simulated a genetic rescue for a brown bear population. The methodology is very similar to what you want to do, so you might find some useful ideas there.

https://conbio.onlinelibrary.wiley.com/doi/full/10.1111/cobi.14133

For the bottleneck, I think adjusting the population size with fitnessScaling using a smaller carrying capacity is a good approach, we used that in our study, but let's say it's a very basic approach.
Regarding your second question, if you want to randomly select individuals from population 1, you can use “p1.sampleIndividuals();”. Whether this approach is suitable depends on your goal. If you want your ex-situ population founders to be random individuals, this method works. If you want them to have specific age or fitness characteristics, you'll need to specify these parameters in the sampling.

I hope these suggestions help you.

Greetings,
Victor

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SLiM forward genetic simulation: http://messerlab.org/slim/
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Víctor Hugo Muñoz Mora 

Research fellow

University of Ferrara

Group site: https://is.gd/popgg

Site of the project "genomics of five italian endemics": https://endemixit.com/

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[Peter Ralph]

Two additional notes:

1. I am simulating bottlenecks. For this, I am just changing the carrying capacity of the population to force the population to remain that size. Is this a correct approach?
   

I don't know what "correct" is, but that sounds perfectly reasonable to me. However, you should probably check that this is doing what you want - for instance, check whether actual population (census) size is doing what you expect? (The population size changes will lag the carrying capacity changes, although it depends how you're implementing carrying capacity.)

1. Is there a way to pick x founders from the population randomly to create the ex situ population? For nonWF models, the only thing I found in the manual was to pick up random parents from the wild population and generate offspring into the ex situ population. Is this an acceptable approach?

Again, that sounds reasonable - but, perhaps you would also like to know about the takeMigrants() function, that directly moves individuals (not offspring) to a new subpopulation?

Sounds like a great project, and that you're going about it in a good way!

--peter

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[João Pedro Meireles]

Hello Peter and Victor!

Thank you so much for your tips and insights! 

The manipulation of the carrying capacity is working as I expected since it shapes the census population to the desirable sizes I set up. I will see if genetically it will have the desirable effect of a bottleneck. But so far, I am just trying to create a demographic model that fits the history of that species before stepping into genetics. 

I will keep working on it and I will update you on the situation at a later point! 

Cheers!