Re: [Swarm-Modelling] population genetics

[Scott Christley]

Thanks for the references Alex.  In my searching, I've seen numerous  
references to coalescent theory, though from my reading on the brief  
summary of it on Wikipedia, it doesn't seem to be what we are  
interested in.

On Oct 27, 2006, at 7:36 PM, Alex Lancaster wrote:

> What exactly do you need to simulate?  i.e. what is your input data,
> do you need to keep track of genotypes as well as allele frequencies?
> what are you trying to measure?  If you trying to estimate parameters
> from data then some prepackaged things may work for you, but if you
> need to introduce some dynamics in each step of the simulation, then
> you probably need to build your own model (perhaps using some existing
> code/algorithms but with additional features that you would probably
> need to write from scratch).  You could do it in Swarm, but it may be
> an overkill if your agents are simply genotypes rather than being
> embedded in organisms with their own dynamics.

We are looking at butterflies of the Colias family; what makes them  
interesting is their sensitivity to temperature.  The biologist that  
I am working with studies global climate change.  We have nucleotide  
sequences for multiple alleles for a particular enzyme, PGI, that is  
in a critical metabolic pathway related to the ability of these  
butterflies to fly.  Ability to fly correlates to their ability to  
mate and lay eggs.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? 
itool=abstractplus&db=pubmed&cmd=Retrieve&dopt=abstractplus&list_uids=16 
292000

What makes the dynamics interesting is that a single allele is not  
the "most fit", so the population does not converge to a single  
allele.  We currently have an agent-based simulation which just two  
alleles, and we have coded dynamics for temperature sensitivity,  
flight probability, mating, etc.

We would like to expand this so that we utilize the actual nucleotide  
sequence data for PGI.  We could then "speed up evolution" through  
recombination and mutation events on the sequences which would imply  
different fitnesses for butterflies in their ability to fly; then  
analyze the population structure under different climates.  So yes,  
the dynamics of the individuals play an important role.

cheers
Scott