Supplementary Data for Kogay and Zhaxybayeva (2023)

GTA head-tail cluster genes:GTA_aln.zip: Multiple sequence alignments of 14 GTA head-tail cluster genes selected to represent 293 OTUs. The alignments are in FASTA format. GTA_uncstr_trees.zip: Phylogenetic trees of 14 GTA head-tail cluster genes reconstructed under unconstrained topological search. The trees are in Newick format. GTA_cstr_trees.zip: Phylogenetic trees of 11 reference GTA genes, whose topology was constrained to match the reference phylogenomic tree. The trees are in Newick format. Reference phylogenomic dataset:reference_tree.zip: Concatenated alignment of 84 phylogenetic marker genes found in 293 alphaproteobacterial genomes, in FASTA format (reference_tree_alignment.fasta). Reference phylogenomic tree reconstructed from the alignment, in Newick format (reference_tree_rooted.treefile). 1,470 alphaproteobacterial gene families:OG_seq.zip: Amino acid sequences of 1,470 gene families that are found in at least 50% of analyzed alphaproteobacterial genomes. The sequences are in FASTA format. OG_cstr_trees.zip: Phylogenetic trees of 1,470 gene families, whose topology was constrained to match the reference phylogenomic tree. The trees are in Newick format. Evolutionary Rate Covariation analyses:ERC_results_all.txt.zip: Covariation of evolutionary rates for all pairwise gene comparisons of 11 reference GTA genes and 1,470 gene families. Networks for Phaeobacter inhibens, Caulobacter crescentus and Dinoroseobacter shibae:networks.zip: co-evolutionary networks and their subnetworks of nodes with unambiguous GOG assignment, protein-protein interaction networks, fitness networks, and assignments of COG functional categories to nodes. Networks are in the “edge list” format.