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Figure 2 | BMC Plant Biology

Figure 2

From: Adaptive expansion of the maize maternally expressed gene (Meg) family involves changes in expression patterns and protein secondary structures of its members

Figure 2

Phylogenetic analyses of maize Meg genes identifies adaptative amino acid substitutions. (A) We reconstructed maximum likelihood phylogenies from protein and corresponding DNA sequence data. SH-like aLRT support [28] at key nodes is shown for protein sequence data with and without Gblocks [29] processing to remove unreliable alignment positions (top row) and DNA alignments with and without Gblocks processing (bottom row). Nodes having <0.8 SH-like aLRT support in any analysis are collapsed, and the tree is rooted using gene-species tree reconciliation to minimize duplication/loss events. A blue star indicates significant support for adaptative substitutions in that specific branch (p < 0.05 after correcting for multiple tests), inferred using codon-based analysis (see Methods). (B) We plot amino-acid substitutions inferred as adaptive by branch-sites analysis (Zhang et al) [30] along the alignment of Meg protein sequences (green arrows). Biochemical properties of amino acids are marked as pink for hydrophilic polar, green for hydrophilic polar uncharged, red for hydrophilic polar basic, and blue for hydrophobic nonpolar amino acids. Conserved cysteine residues are highlighted in orange.

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