Genome wide scans reveal cryptic lineages in a dry‐adapted eucalypt 

 

Tree Genetics & Genomes 

 

Dorothy A. Steane1,2,3, Brad M. Potts, Elizabeth McLean, Lesley Collins, Suzanne M. Prober, William D. Stock, René E. Vaillancourt and Margaret 

Byrne 

1 School of Biological Sciences and National Centre for Future Forest Industries, University of Tasmania, Private Bag 55, Hobart, Tasmania 7000, 

Australia  

2 Faculty of Science, Health, Education and Engineering and Collaborative Research Network, University of the Sunshine Coast, Locked Bag 4, 

Maroochydore, Queensland, 4558,Australia 

3 Corresponding author: Dorothy.Steane@utas.edu.au 

 Online Resource 4 When it became apparent that E. salubris comprised two distinct genetic lineages, we checked the result in a phylogenetic context using a variety of algorithms.  (A) A distance matrix was calculated using the Additive Dollo Distance algorithm (Woodhams et al. 2013) that was developed for dominant binary data, particularly DArT; from this distance matrix, a tree was found by minimum evolution using FastME (Desper and Gascuel 2002) and was plotted using the Interactive Tree Of Life (Letunic and Bork 2011).  (B) A Neighbornet network was constructed using Splitstree 4.13.1 (Huson and Bryant 2006), using uncorrected P values and 1000 bootstrap replicates.  (C) One of two most parsimonious trees from maximum parsimony analysis.  Numbers above branches show bootstrap support for major clades.  Star indicates branch that collapsed in strict consensus.  (D) A MrBayes (Altekar et al. 2004; Huelsenbeck and Ronquist 2001; Ronquist and Huelsenbeck 2003) analysis was conducted using two parallel runs of eight chains, heating set to 0.2, run for 12,420,000 generations, sampling every 5000 generations.  This yielded 2484 trees per run.  Stationarity was reached after about 5 million generations (Tracer; Rambaut et al. 2014), so a conservative burnin of 6 million generations resulted in the removal of 1200 trees per run.  The remaining trees were used to compute a 

consensus.  The tree was built using FigTree (http://tree.bio.ed.ac.uk/software/figtree/).  Numbers above branches are posterior probability values.  References Altekar G, Dwarkadas S, Huelsenbeck JP, Ronquist F (2004) Parallel metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic 

inference. Bioinformatics 20:407‐415. doi:10.1093/bioinformatics/btg427 Desper R, Gascuel O (2002) Fast and accurate phylogeny reconstruction algorithms based on the minimum‐evolution principle. Journal of 

Computational Biology 9:687‐705. doi:10.1089/106652702761034136 Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754‐755. 

doi:10.1093/bioinformatics/17.8.754 Huson D, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23:254‐267 Letunic I, Bork P (2011) Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Research 

39:W475‐W478. doi:10.1093/nar/gkr201 Rambaut A, Suchard MA, Xie D, Drummond AJ (2014) Tracer v1.6.  Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572‐1574. 

doi:10.1093/bioinformatics/btg180 Woodhams M, Steane DA, Jones RC, Nicolle D, Moulton V, Holland BR (2013) Novel Distances for Dollo Data. Syst Biol 62:62‐77. 

doi:10.1093/sysbio/sys071  

 

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9_RT16_SWP

1_QV18_E

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9_RT19_SWP

6_BR5_SWP

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8_LR9_SWP

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1_QV5_E

9_RT6_SWP

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6_BR10_SWP

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