Computational protocol: Rapid diversification of homothorax expression patterns after gene duplication in spiders

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Protocol publication

[…] For the phylogenetic analysis of hth we searched for larger/complete open reading frames in the transcriptomes of Ph. phalangioides (unpublished data) and P. tepidariorum [] using D. melanogaster and C. salei hth homologs as search queries. With the same query sequences we also searched in the published genome resource of the scorpion Mesobuthus martensii (M. martensii) [], which resulted in three fragments with similarity to hth, named MMa38611, MMa00258, and MMa39038 (note that MMa00258 is very short and thus might be an incompletely assembled fragment). For the protein and nucleotide alignments of the hth orthologs we used previously published hth-related sequences from various metazoan species plus all hth sequences identified in the transcriptomes of P. tepidariorum and Ph. phalangioides and the genome of M. martensii (see list of species and accession numbers in Additional file ).Sequences were aligned with Clustal Omega [] using default settings (the alignments are available in Nexus format in Additional file and Additional file ). Phylogenetic trees were calculated using the parallel version of MRBAYES (version 3.2.5) []. For the protein alignment, after testing mixed amino acid substitution models the Jones model was chosen to generate topological convergence using Metropolis coupling for 179,000 generations after reaching an average standard deviation of split frequencies below 0.01. A total number of 718 trees were written in 2 files (each file contained 359 trees of which 270 were sampled). In the nucleotide sequence analysis (using Metropolis coupling and the 4by4 nucleotide substitution model) an average standard deviation of split frequencies of 0.023742 was reached after 9 million generations. A total of 36,002 trees were written in 2 files (18,001 trees per file of which 13,501 were sampled). The 50% majority rule consensus trees shown in Fig. and Additional file were visualized with Geneious (version 9.1.3) [].Fig. 1 […]

Pipeline specifications

Software tools Clustal Omega, MrBayes, Geneious
Application Phylogenetics
Organisms Parasteatoda tepidariorum, Pholcus phalangioides