Computational protocol: Phylogenetic analyses place the Australian monotypicRevwattsia inDryopteris (Dryopteridaceae)

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Protocol publication

[…] Sequences were edited and aligned using Geneious v5.4.2 () and then manually checked for errors. Markers were analyzed separately using Modeltest v3.06 () to determine the model of evolution that each marker most closely fit () using the Akaike information criterion (AIC). Indels were coded using the program SeqState 1.4.1 () and treated in the matrix as standard data. [...] Bayesian inference was conducted on the concatenated data set (psbA-trnH, rbcL, rbcL-accD, rps4-trnS, trnG-trnR, trnL-trnF, and trnP-petG) using MrBayes v3.2.0 (Ronquist et al. 2011) using the appropriate evolutionary models determined for each. Sampling of all seven loci was primarily within Dryopteris; the remaining taxa, including Revwattsia fragilis, had subsets of the seven loci. The Markov chain Monte Carlo permutation of tree parameters was conducted for 2 runs of 5,000,000 generations, sampling every 100th generation. A plot of generations versus log-likelihood was examined using Tracer v1.5 () to visually assess stationarity and verify that an appropriate burn-in was achieved. The burn-in was 500,000 generations. The 50% majority-rule tree was examined in FigTree v1.3.1 ().Parsimony analyses using the same data set were conducted using TNT (Willi Hennig Society, ) implementing the parsimony ratchet (), with the following search parameters: 1000 ratchets with 200 iterations per replicate, 10% weighting, holding 20 trees per ratchet, followed by tree-bisection-reconnection (TBR) branch swapping to completion. Clade support was assessed by implementing a bootstrap analysis of 1000 replicates with 10 ratchets per replicate and holding 20 trees per ratchet. The max RAM was set at 850 MB allowing for storage of 10,000 trees. […]

Pipeline specifications

Software tools Geneious, ModelTest-NG, MrBayes, FigTree
Application Phylogenetics
Diseases Hepatitis D