Computational protocol: Extreme Food-Plant Specialisation in Megabombus Bumblebees as a Product of Long Tongues Combined with Short Nesting Seasons

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Protocol publication

[…] ClustalX2 (version 2.0) was used for multiple alignment of sequences [] and Collapse (version 1.2) was used to identify unique haplotypes. The best nucleotide substitution model according to jModeltest (version 2.1.3, accessed 2014) Akaike Information Criterion (AIC) [] was GTR+I+G. Species from the subgenera Subterranneobombus and Thracobombus were used as out-groups, according to the estimate of phylogeny for Bombus by Cameron et al. []. Phylogeny was estimated with BEAST (www.beast.bio.ed.ac.uk, accessed 2014) [], using a speciation model of a constant-size coalescent process, consistent with the null hypothesis that there is a single species. The clock model was set to lognormal relaxed clock (uncorrelated), and chain length was set to 500 million generations with a sampling frequency of one in 50,000. The consensus tree was built by TreeAnnotator (version 1.7.5, accessed 2014) with a burn-in of 1000 samples. [...] No fossils of species from this subgenus are available for dating the tree. The only available estimate is from a molecular study []. For the species discovered with the GMYC models, we built a tree as the best estimate of species’ phylogeny using a birth-death model for the speciation process. Events in this tree were dated with Figtree (version 1.4.2) calibrated with the molecular estimate []. […]

Pipeline specifications

Software tools Clustal W, jModelTest, BEAST, FigTree
Application Phylogenetics