Meta-Community Phylogeny Simulation 101


Example meta-community phylogeny. Circles are proportional to the number of individuals at the end of the run. Look! The species that died out isn’t anywhere at the end! I used rainbow to make this look slightly more appealing; I admit it’s not the prettiest figure in history.

Following on from the last post, I wrote a quick function that (sort of) simulates individuals of species moving through a meta-community (sim.meta.comm), and then added something on top that simulates the evolution of those species (including generating a phylogeny; sim.meta.phy.comm). I also neatened up the creation of a phylogeny from what I’ve been calling an ‘edge matrix’ in my code (edge2phylo). The meta-community has different environmental conditions throughout it, and individuals can migrate at each time-step. There’s no competition in the model yet.

I expected this to be a nightmare, but as long as you use the steps that monitor the ecology of the species as a check for whether you need to do anything with the phylogeny, it actually turns out that simulating the phylogeny is easier when you’ve got ecological information than when you’re just doing the phylogeny alone. In this version, I don’t have any effect of species traits – that’s for next time.

The main conceptual point I took from this is the difficulty in deciding how to model stochasticity. It’s hard to get the environmental parameters on the same scale as the stochasticity and species abundance parameters, and as such I ended up doing everything with Poisson distributions which seemed rather strange to me. It’s quite worrying how easy it was to make environments where species all headed to extinction, apart from in very, very small patches of the environment before I got my head around it all.

Next time – competition and trait evolution within the same model! Then, and only then, will I move on to actually trying to estimate parameters of interest from all this…


Phylogeny simulation 101

Species across a landscape, as simulate by Boucher et al. It's this pretty stained-glass-esque diagram that inspired me to do this!

Species across a landscape, as simulate by Boucher et al. It’s this pretty stained-glass-esque diagram that inspired me to do this!

Lots of people have written code to simulate phylogenies, and yet more have written code that simulate traits across phylogenies. I’m not claiming any great novelty in what I’ve just done, but simulates a phylogeny under given speciation and extinction rates, and simulates a phylogeny, and a trait that affects speciation and extinction rate.

What I like about this is that the dependence on trait values is actually a dependence on what values of that trait other species have – in other words, it’s a niche-packing kind of model. Again, I’m not claiming any great novelty in these sorts of models (read this excellent paper, for example), but this was my first stab in what I hope will be a long stream of work. This is very raw code (a quick skim of it makes me realise a refactor would more than halve its length) but it does get the job done (I hope!).

My first impression is that this stuff isn’t very hard, so if you have any interest you should definitely give it a go. Moreover, the insight I gained from it was quite important – the shape and size of a phylogeny changes a great deal over different simulations, and while on some level I knew this it was only while checking to see if I’d messed something up that I really gathered a true appreciation for it.

Next post… either a model incorporating communities/biogeography (–> some model of allopatric speciation), or a vague attempt at fitting estimting the parameters I set once the phylogeny/traits are calculated. I have a feeling those two will be much harder!…