Molecular Evidence for Functional Divergence and Decay of a Transcription Factor Derived from Whole - Genome Duplication in Arabidopsis thaliana . Functional divergence between duplicate transcription factors ( TFs ) has been linked to critical events in the evolution of land plants and can result from changes in patterns of expression , binding site divergence , and / or interactions with other proteins . Although plant TFs tend to be retained post polyploidization , many are lost within tens to hundreds of million years . Thus , it can be hypothesized that some TFs in plant genomes are in the process of becoming pseudogenes . Here , we use a pair of salt tolerance - conferring transcription factors , DWARF AND DELAYED FLOWERING1 ( DDF1 ) and DDF2 , that duplicated through paleopolyploidy 50 to 65 million years ago , as examples to illustrate potential mechanisms leading to duplicate retention and loss . We found that the expression patterns of Arabidopsis thaliana ( At ) DDF1 and AtDDF2 have diverged in a highly asymmetric manner , and AtDDF2 has lost most inferred ancestral stress responses . Consistent with promoter disablement , the AtDDF2 promoter has fewer predicted cis - elements and a methylated repetitive element . Through comparisons of AtDDF1 , AtDDF2 , and their Arabidopsis lyrata orthologs , we identified significant differences in binding affinities and binding site preference . In particular , an AtDDF2 - specific substitution within the DNA - binding domain significantly reduces binding affinity . Cross - species analyses indicate that both AtDDF1 and AtDDF2 are under selective constraint , but among A. thaliana accessions , AtDDF2 has a higher level of nonsynonymous nucleotide diversity compared with AtDDF1 . This may be the result of selection in different environments or may point toward the possibility of ongoing functional decay despite retention for millions of years after gene duplication . © 2015 American Society of Plant Biologists . All Rights Reserved .