Computational protocol: An Extensive Field Survey Combined with a Phylogenetic Analysis Reveals Rapid and Widespread Invasion of Two Alien Whiteflies in China

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Protocol publication

[…] The 48 sequences obtained from the above analysis were supplemented with a further 131 sequences from GenBank. The sequences were aligned using ClustalX (ver. 1.81; ) and then checked for duplicates, gaps, ambiguous bases, pseudogenes and sequences which were shorter than the required 610 bases starting with 5′GCTATAATAACT. The final dataset contained 88 sequences plus a further 9 outgroup sequences from the species B. afer, B. berbericola, B. subdecipiens, B. tuberculata, B. atriplex, B. emiliae and an undescribed species of Bemisia closely related to B. atriplex from the host plant Rhagodia parabolica. Dinsdale et al. showed that members of the B. tabaci species complex could be readily assigned to species by comparison against consensus sequences. They determined that an unknown sequence was a match for a consensus sequence if it diverged by <3.5%; if an unknown sequence diverged by >3.5% from any of the 24 consensus sequences then this was likely to be a new putative species. Some individuals from our samples diverged from all known consensus sequences by >3.5% so a Bayesian phylogenetic analysis following the method used in Dinsdale et al. was undertaken using the MrBayes (ver 3.1; ). We partitioned the data using a codon-partition model in which each codon position was allowed its own parameter estimates. The best-fit model of evolution was determined by the Likelihood Ratio Test using Modeltest 3.6 . All partitions were allowed a GTR + invariants + gamma model and analyses were run for 10 million generations by using eight chains and sampling every 1,000 generations. The burn-in period (n = 260) was determined by comparing graphical output from the SUMP command and checking that the harmonic means of the separate runs had converged to within two units. Dinsdale et al. showed that the members of the B. tabaci complex from Asia formed an extremely well defined monophyletic group. As we were interested only in the relationships between Asian members of the complex, we did not include non-Asian members of the complex. The subsequent consensus tree was visualised using Treeview (Page RDM 2001) and putative species names are those from in Dinsdale et al. except where a new putative species has been identified. […]

Pipeline specifications

Software tools Clustal W, MrBayes, ModelTest-NG, TreeViewX
Application Phylogenetics
Organisms Bemisia tabaci