Computational protocol: Moorean tree snail survival revisited: a multi-island genealogical perspective

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Protocol publication

[…] The resulting chromatograms were edited by comparing both strands using Sequence Navigator 1.0.1 (Applied Biosystems, Foster City, CA). COI sequences were aligned easily due to an absence of indels. Maximum likelihood (ML) analyses were performed using PAUP*4.0b10 [] under the TVM+I+G model of sequence evolution, the best-fit model selected by Akaike Information Criterion implemented in Modeltest 3.7 []. Likelihood parameters [base frequencies (A = 0.3300, C = 0.1064, G = 0.1354, T = 0.4282); rate matrix (1.1933, 27.6197, 1.8944, 0.4618, 27.6197, 1); shape of gamma distribution = 1.2494; proportion of invariable sites = 0.5742] found in Modeltest were used and heuristic searches were employed by using a neighbor-joining starting tree and nearest neighbor interchange (NNI) branch swapping. The partulid genus Eua, restricted to central Pacific islands in Samoa, American Samoa and Tonga, was used as the outgroup []. Initial searches found two ML trees with a log-likelihood (ln L) value of -9968.9197. Both trees were further used as starting trees for another round of heuristic search and a single ML tree (ln L = -9967.6214) was recovered.Bayesian posterior probabilities and parsimony bootstrap were employed to measure nodal support. Parsimony bootstrapping [] was done with the "fast" stepwise-addition option for heuristic searches (1000 replicates) using PAUP*. Bayesian analyses were performed using MrBayes 3.1.2 [] set for the GTR+Γ+I model. Model parameters were treated as unknown and were estimated for each analysis. Four chains were run simultaneously for 1,000,000 generations and trees were sampled every 100 cycles. Posterior probability values were estimated by generating a 50% majority rule consensus tree after the burn-in period of 2,000 using PAUP*. […]

Pipeline specifications

Software tools ModelTest-NG, MrBayes
Application Phylogenetics