Computational protocol: Phylogenetic Insights into Chinese Rubus (Rosaceae) from Multiple Chloroplast and Nuclear DNAs

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[…] Sequences of the six examined regions were edited and assembled using CLC Genomics Workbench (v7.5, CLC bio, Qiagen, Boston, MA). After manually editing, final datasets were aligned separately with Muscle (Edgar, ), and adjusted in the Molecular Evolutionary Genetics Analysis software (MEGA6) (Tamura et al., ) with gaps treated as missing data.Before tree reconstruction, we performed partition homogeneity test (PHT) in PAUP v4.0 b10 (1000 replicates, invariable sites excluded) for the plastic and nuclear datasets (Swofford, ). According to the obtained PHT results, we applied partitioned phylogeny analyses by using maximum likelihood (ML) and bayesian inference (BI) methods for the combined cpDNA or nDNA datasets, with assignment that each partition had its own evolutionary rate. DNA substitution models were selected out from JModelTest v2.1.1 (Darriba et al., ) according to Akaike Information Criterion (AIC) (Akaike, ) for each gene.We inferred the ML trees using the edge-linked partitioned phylogeny in IQ-TREE v1.4.2, which could implemented individual assigned substitution models for each partition (Nguyen et al., ; Chernomor et al., ). One thousand regular bootstrap replicates were performed to obtain confidence values for the branches. The values were considered to be low when strictly inferior to 65%, moderate between 65 and 80% and strong when superior to 80%. BI analyses were performed using MrBayes v3.2.1 with partitioned genes (Ronquist et al., ). The Markov chains Monte Carlo (MCMC) algorithm was run for 6,000,000 generations with one cold and three heated chains, starting with a random tree and sampling one tree every 1000 generations. The first 1,500,000 generations were treated as burn-in. An adequate burn-in value for each analysis was assessed using the software Tracer 1.5 (Rambaut and Drummond, ) and a 50% majority-rule consensus tree was then computed.Phylogenetic network was constructed for combined nuclear datasets using SplitTree v4.14.2 (Huson and Bryant, ). Network analysis was performed using the NeighborNet algorithm with Kimura 2-parameter (K2P) distance and Ordinary Least Square Method implemented. […]

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