Gene phylogenies based on Maximum_likelihood

Phylogenetic analyses of 146 orthogroups comprising genes that function in nitrogen-fixing root nodulation in legumes (Legume symbiosis genes), and 415 orthogroups comprising Parasponia genes that are expressed higher in nodules than in roots (Nodule enhanced genes). Amino acid sequence alignments were generated using MAFFT version 7.017. Analyses were performed using RAxML version 8.2.11 setting gamma-distributed rate variation, estimating optimal models of amino acid sequence evolution (PROTGAMMAAUTO), and running 100 fast bootstrap replicates to assess clade support.