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From: | Scott Christley |
Subject: | Re: [Swarm-Modelling] population genetics |
Date: | Fri, 27 Oct 2006 20:15:40 -0400 |
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
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