Working notes for 2016

2016-02-05. Tests on priors for STACEY 1.1. Tests of operators StaceyNodeReheight, NodesNudge, FocusedScaler, and CoordinatedPruneRegraft, ThreeBranchAdjuster. Also see previous tests.

2016-02-24. BEAST2 and Intellij. How to make a new version of STACEY for a new version of BEAST. Also, list of BEAST 2.4 vs STACEY 1.1.1 errors.

2016-03-14. Alternative to SNAPP model. See Possible projects.

2016-04-18. Priors for species delimitation. See Possible projects.

2016-05-12. R scripts for running simulations of AlloppNET. This is a snapshot of R code used for the simulations for Bengt's review of polyploid phylogenies.

2016-10-31. Introgression. See Possible projects.

Possible projects - Nov 2016

Simulation of large hybridization networks

For example, auto- and allo-polyploidy as well as ordinary speciation, among 300k angiosperms. I have written a simulator, but currently the results are more curious than useful. The process can 'explode', that is, produce an infinite number of species in a finite amount of time. There are several possible limiting factors such as number of chromosomes, amount of DNA, cell size, competition between similar species.

Introgression. Model with migrating gtree branches

The rough idea is described here. Started implementing something like this.

Priors for species delimitation.

The Kirchhoff matrix tree method. The mathematics is cute, but the approach doesn't seem to provide very 'sensible' results. I also have an idea using distances to clusterings.

Alternative to SNAPP model

My notes. I think too similar to De Maio, 2015. Maybe some variants interesting.

A few more ideas

• Origins of replication initiation (ORIs). See Lynch (2007), p102-107. ORIs can be located via strand symmetry - or rather, lack of it - in prokaryotes. Can ORIs be located in eukaryotes? Can they be used to inform substitution models?
• Estimating effective population sizes of organelles vs nuclear. See Lynch (2007), p323-326. If ploidy becomes a parameter, could estimate thius. Should be easy to implement, but not clear how interesting.
• Recombination (See handwritten notes Jan 2016).
• Developmental plasticity and evolution. Some simulations along the lines of Frank (2011) could be done, but the most interesting aspects are very hard.
• Laplacian approximation instead of MCMC. Hard, lots of work.
• Modelling extinct species (in context of hybridization or introgression).
• Gradual speciation and/or introgression. Model with time-slices and demes.

References

• Michael Lynch, 2007. The Origins of Genome Architecture.
• De Maio et al, 2015. PoMo: An Allele Frequency-Based Approach for Species Tree Estimation. Systematic Biology.
• S A Frank, 2011. Natural selection. II. Developmental variability and evolutionary rate. Journal of evolutionary biology 24 (11), 2310-2320