TreeBASE Search-Analyses for study 14725

@ARTICLE{TreeBASE2Ref22389, author = {Jack Viljoen and A. Muthama Muasya and Russell L Barrett and Jeremy J Bruhl and Adele K. Gibbs and Jasper Alexander Slingsby and Karen L. Wilson and George Anthony Verboom}, title = {Radiation and repeated transoceanic dispersal of Schoeneae (Cyperaceae) through the Southern Hemisphere}, year = {2013}, keywords = {biogeography; dispersal-extinction-cladogenesis; habitat shift; niche conservatism; polytomy prior; transoceanic dispersal}, doi = {}, url = {http://}, pmid = {}, journal = {American Journal of Botany}, volume = {}, number = {}, pages = {}, abstract = {Premise of the study: The broad austral distribution of Schoeneae is almost certainly a product of long-distance dispersal. Owing to the inadequacies of existing phylogenetic data and a lack of rigorous biogeographic analysis, relationships within the tribe remain poorly resolved and its pattern of radiation and dispersal uncertain. We employ an expanded sampling of taxa and markers and a rigorous analytic approach to address these limitations. We evaluate the roles of geography and ecology in stimulating the initial radiation of the group and in its subsequent dispersal across the Southern Hemisphere. Methods: A dated tree was reconstructed using reversible-jump MCMC with a polytomy prior and molecular dating, applied to data from two nuclear and three cpDNA regions. Ancestral areas and habitats were inferred using dispersal-extinction-cladogenesis models. Key results: Schoeneae originated in Australia in the Pal?ocene. The existence of a "hard" polytomy at the base of the clade reflects the rapid divergence of six principal lineages ca. 50 Ma within Australia. From this ancestral area, Schoeneae have traversed the austral oceans with remarkable frequency, a total of 29 distinct dispersal events reported here. Dispersal rates between landmasses are not explicable by the geographical distances separating them. Transoceanic dispersal generally involved habitat stasis. Conclusions: Although the role of dispersal in explaining global distribution patterns is now widely accepted, the apparent ease with which such dispersal may occur has perhaps been under-appreciated. In Schoeneae, transoceanic dispersal has been remarkably frequent, with ecological opportunity, rather than geography, being most important in dictating dispersal patterns.} }

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Analyses for Study 14725

Citation title: "Radiation and repeated transoceanic dispersal of Schoeneae (Cyperaceae) through the Southern Hemisphere".

Study name: "Radiation and repeated transoceanic dispersal of Schoeneae (Cyperaceae) through the Southern Hemisphere".

This study is part of submission 14725 (Status: Published).

Analyses

Analysis 1

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1 Input object(s)

Analysis step

mrbayes phylogeny reconstruction --

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Commands
BEGIN MRBAYES; CHARSET its =1-844; CHARSET ets =845-1557; CHARSET rbcl=1558-2987; CHARSET rps =2988-4191; CHARSET trn =4192-5476; PARTITION all = 5: its, ets, rbcl, rps, trn; SET partition = all; LSET applyto=(all) nst=mixed rates=gamma ngammacat=4; [GTR+G] PRSET applyto=(all) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,200.0); UNLINK statefreq=(all) tratio=(all) revmat=(all) shape=(all); SET autoclose=yes nowarn=yes; MCMCP ngen=40000000 temp=0.2 nchains=4 nruns=4 printfreq=4000 samplefreq=4000 diagnfreq=40000 relburnin=yes burninfrac=0.5 savebrlens=yes checkpoint=no; MCMC; SUMP burnin=5000; SUMT burnin=5000; END;

Output data

1 Output object(s)

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2 Input object(s)

Analysis step

beast divergence time dating --

Output data

1 Output object(s)

Analysis 2

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1 Input object(s)

Analysis step

phycas phylogeny reconstruction --

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from phycas import * setMasterSeed(192837) mcmc.data_source = 'all.nex' model.type="gtr" model.update_freqs_separately = False model.update_relrates_separately = False model.num_rates = 4 m1 = model() its = subset(1, 844) ets = subset(845, 1557) rbcl = subset(1558, 2987) rps = subset(2988, 4191) trn = subset(4192, 5476) partition.addSubset(its, m1, "its") partition.addSubset(ets, m1, "ets") partition.addSubset(rbcl, m1, "rbcl") partition.addSubset(rps, m1, "rps") partition.addSubset(trn, m1, "trn") partition() mcmc.ncycles = 500000 mcmc.sample_every = 100 mcmc.allow_polytomies = True #mcmc.polytomy_prior = True #mcmc.topo_prior_C = exp(1.0) mcmc.polytomy_prior = False # to use resolution classes (not biased towards resolved trees) mcmc.topo_prior_C = 1.0 # flat mcmc() sump.burnin = 1001 sump() sumt.burnin = 1001 sumt.tree_credible_prob = 0.95 sumt.outgroup_taxon = 'Chrysitrix capensis' sumt()

Output data

1 Output object(s)

Analysis 3

Analysis details

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1 Input object(s)

Analysis step

raxml tree reconstruction --

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Commands
raxmlHPC-HYBRID -T 6 -s infile -n result -q part -p 12345 -b 12345 -N 1000 -m GTRCAT

Output data