Computational protocol: Geographical origin of Leucobryum boninense Sull. & Lesq. (Leucobryaceae, Musci) endemic to the Bonin Islands, Japan

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[…] We obtained rbcL sequence data of 14 samples belonging to 13 taxa and ITS sequence data of 21 samples belonging to 14 taxa of the genus Leucobryum from the DNA database. The obtained rbcL, rps4, 5′ trnK intron, matK, 3′ trnK intron, trnL-F, and ITS sequences were separately aligned using the program MUSCLE (Edgar ).We performed the Incongruence Length Difference (ILD) test (Farris et al. ) implemented in PAUP* version 4.0 beta (Swofford ) before phylogenetic reconstruction to confirm topological congruence between each DNA region. One hundred partition homogeneity replicates were implemented in the test using the heuristic search option with 100 random addition sequences. And then, we performed molecular phylogenetic analyses with combined all six chloroplast DNA plus one nuclear DNA sequences. When these analyses were carried out, identical sequences were pruned to include only one representative from each species. Therefore, a total of 35 operational taxonomic units, including outgroup, were used for the following analyses.Bayesian inference (BI) analysis was performed using MrBayes version 3.1.2 (Ronquist and Huelsenbeck ). The best-fitting model for nucleotide substitution was selected for the combined seven regions based on Akaike information criterion (Akaike ) implemented in MrModeltest 2.2 (Nylander ), and GTR +I + G model was chosen. The analysis was performed for 1,000,000 generations with four chains, with samples taken every 100 generations.Maximum likelihood (ML) analysis was conducted with PAUP* 4.0b10 using the best-fitting model GTR + I + G chosen by MrModeltest 2.2. A heuristic search algorithm was engaged with 100 random addition replicates and tree-bisection-reconnection (TBR) branch-swapping, and MulTrees on. The ML bootstrap value were computed in PAUP* 4.0b10 by running 1000 replicates with a full heuristic search using 100 random addition sequences, TBR branch-swapping, and MulTrees off (holding one tree at each step).Maximum parsimony (MP) analysis was performed using PAUP* 4.0b10. A heuristic search algorithm was engaged with 100 random addition replicates and TBR branch-swapping, and MulTrees on. Parsimony bootstrap values were calculated using PAUP* 4.0b10. The bootstrap analysis used 1,000 bootstrap replicates, the heuristic search algorithm, 100 random addition sequences, TBR branch-swapping, and MulTrees off (holding one tree at each step). […]

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