PHY_MLBS_tree_raxml

The maximum likelihood bootstrapping trees from "PHY_alignment.fas" (translated into amino acids), using RAxML (1000 replicates) under JTT + F model. Alphanumeric codes following species names are the four-letter 1KP transcriptome identifiers, Genbank accessions or both

NEO_ML_tree_garil

The maximum likelihood tree inferred from "NEO_alignment.fas", using Garli with genthreshfortopoterm set to 1,000,000 and 8 independent runs. We partitioned the data by codon position, and GTR+Γ+I, GTR+Γ+I, GTR+I models were applied to each codon position respectively. Alphanumeric codes following species names are the four-letter 1KP transcriptome identifiers, Genbank accessions or both

NEO_MLBS_tree_pos3_raxml

The maximum likelihood bootstrapping trees from "NEO_alignment.fas", using RAxML (1000 replicates; first and second codon excluded). Alphanumeric codes following species names are the four-letter 1KP transcriptome identifiers, Genbank accessions or both

NEO_BI_con_tree_MrBayes

The 50% majority consensus tree from MrBayes run (25% of the total generations were discarded as burn-in), based on "NEO_alignment.fas". The analysis was carried out with two independent MCMC runs, four chains each, and trees sampled every 1000 generations. We partitioned the data by codon position, and GTR+Γ+I, GTR+Γ+I, GTR+I models were applied to each codon position respectively. Substitution parameters were unlinked and the rate prior was set to vary among partitions. Alphanumeric codes following species names are the four-letter 1KP transcriptome identifiers, Genbank accessions or both

NEO_ML_tree_codonPhyML

The maximum likelihood tree inferred from "NEO_alignment.fas", using CodonPhyML. We used the GY model with four categories of non-synonymous/synonymous substitution rate ratios drawn from the discrete gamma distribution, and codon frequencies were estimated from the data under the F3X4 model. The tree topology search was done using the NNI approach, and branch support was estimated using the SH-like aLRT method. Alphanumeric codes following species names are the four-letter 1KP transcriptome identifiers, Genbank accessions or both

bluedevil_settings

The configuration file for BlueDevil.p

NEO_ML_tree_pos3_garli

The maximum likelihood tree inferred from "NEO_alignment.fas" (first and second codon excluded), using Garli with genthreshfortopoterm set to 1,000,000 and 8 independent runs. Alphanumeric codes following species names are the four-letter 1KP transcriptome identifiers, Genbank accessions or both

PHY_alignment

Alignment of plant phytochrome and neochrome, containing 139 sequences from 76 species. We only included the conserved domains (i.e., PAS, GAF, PHY, PAS repeats, HisKA and HATPase); the domain boundaries were identified by querying each scaffold against the NCBI Conserved Domain Database. Each domain was separately aligned (based on the amino acid sequences) using Muscle, and then concatenated. Alphanumeric codes following species names are the four-letter 1KP transcriptome identifiers, Genbank accessions or both

PHOT_alignment

Alignment of plant phototropin and neochrome, containing 163 sequences from 106 species. We only included the conserved domains (i.e., LOV1, LOV2 and STK); the domain boundaries were identified by querying each scaffold against the NCBI Conserved Domain Database. Each domain was separately aligned (based on the amino acid sequences) using Muscle, and then concatenated. Alphanumeric codes following species names are the four-letter 1KP transcriptome identifiers, Genbank accessions or both

NEO_MLBS_tree_pos12_raxml

The maximum likelihood bootstrapping trees from "NEO_alignment.fas", using RAxML (1000 replicates; third codon excluded). Alphanumeric codes following species names are the four-letter 1KP transcriptome identifiers, Genbank accessions or both