I am completely new to the world of evolutionary biology. I would like to model the evolution of a population in presence of sexual selection (female partners select males on the basis of their appearance), estimating if this would lead to the appearance of new species and how much this would ipact on the variability of the sexual character in the population. Has anyone some experience with that?
The first decision you need to make is whether you seek a "backward time" (i.e., coalescent) analysis, or a forward time simulation model. I spend most of my time doing the latter, so I can speak to that. Having written several standalone models and then two frameworks for simulations with the same structure as you discuss (but different goals), I've recently switched to using Bo Peng's superb simuPOP framework (http://simupop.sourceforge.net). After you learn how his framework operates (and there's not just online docs, but a full book from 2012), you can easily write mating operators to implement sexual selection models. The framework already implements populations with and without structure, tracks male and female individuals, and allows you to choose a variety of genome representations to suit your research questions.
Bo is also extremely responsive on the forum/mailing list, and will often fix bugs and implement easy features (in C++, so you can stay coding in python) for folks. Since I study cultural transmission and dual inheritance systems, I needed to do some things with mutation (or innovation) that pop gen folks usually don't need to do, and he was happy to add a hook for me to extract a piece of data easily from the mutator code that otherwise I'd have to implement in a very slow loop in pure python. It is a pleasure to work with someone who's not just concerned about his software, but facilitating *real research* with his software.
Strongly recommended. I hope this helps!
Thanks Mark. I have seen SimuPop and I was not sure if it is worth spending much time to learn it. Your answer is exactly what I needed: I will pursue this direction! Thanks!
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