Species Tree Workshop January 14, 2012 Practice with BEST

1. Species Tree WorkshopJanuary 14, 2012Practice with BEST Please download MrBayes 3.2 for either Windows, Macintos, or UNIX from http://mrbayes.sourceforge.net/

2. Agenda • The MrBayes with BEST (v 3.2) implementation (work in progress) • Run the finch example (download finch.nex) • Run a multiple allele data set • (yeast with 4 genes, 22 taxa, 6 species ) • …or Try your own data

3. Previous Implementation: MrBayes with BEST Step 1: Use MrBayes to propose vectors of joint gene trees (unlinked and rooted with outgroup). Step 2: Given those gene trees, propose a compatible species tree. Step 3: Implement the chain fully within MrBayes using the usual properties of the MCMC as proposed by the user. Program found at www.stat.osu.edu/~dkp/BEST

4. New Implementation: MrBayes 3.2 integrated with BEST Assumes molecular clock for gene trees as part of a full model including Coalescent for gene trees|species tree Program found at http://mrbayes.sourceforge.net/

5. Implementation: MrBayes 3.2 • As always • Wide variety of nucleotide, amino acid, and codon models • Variety of proposal distribution options • Parallel “hot” and “cold” chains to balance efficiency while covering large tree spaces. • Checkpointing to allow stop and starts • New speed improvements • BEST can use MPI for Mac and UNIX • GPU (NVIDIA graphics card) support

6. Steps for any Bayesian Runs • Read the data • Set the model (data|gene tree) • Set the Prior (including gene|species) • Set the MCMC rules • Run the MCMC • Check convergence • Summarize results

7. Files created • ckp (Checkpoint file for restarting) • tree5.run2.t (trees saved loci 5 in run 2) • tree5.parts (partitions seen for tree 5) • tree5.trprobs (tree probabilties) • tree5.con.tre (consensus tree) • tree5.tstat (partition statistics) • tree5.vstat (branch and node statistics)

8. Remember • Use a separate folder for each analysis • Remember the “taxset”and “speciespartition” statements in MrBayes with ≥ one taxa per species • Remember to allow variable population sizes • With n loci, the species tree shows up as files labeled n+1

9. Remember to unlink • Gene tree topologies and branch lengths for sure • unlink topology=(all) brlens=(all); • Parameters of model as approriate • unlink statefreq=(all) revmat=(all);

10. Issues • Gene trees following a molecular clock is too restrictive • Some outputs still need to be modified for species tree use

11. Species Tree Notation Topology, branch lengths, & population sizes: (D: 0.035(C:0.03(A:0.02,B:0.02):0.01#0.3):0.005#0.2)#0.25 0.005 0.01 0.035 0.03 0.02 0.02 A B C D

12. Three lineages of grassfinches (Poephila) Long-tailed (acuticauda) Black-throated (cincta) Long-tailed (hecki)

13. 30 gene trees from Australian finches P. acuticauda P. hecki P. cincta Jennings & Edwards (2005) Evolution 59, 2033-2047.

14. Estimated species tree distribution using BEST

15. Estimated species tree distribution using BEST 1.0 0.94 1.0 0.03 acuticauda c. atropygialis hecki c.atropygialis acuticauda hecki