Table 2 . Genomic changes in allopolyploid wheat thought to promote and facilitate speciation (adapted from Feldman et al. 2012).

Structural	Functional
1. Revolutionary changes occur during or soon after allopolyploidization, lead to diploidization and are often reproducible
Genetic • Elimination of low-copy DNA sequences • Elimination, reduction or amplification of high-copy sequences • Intergenomic invasion of DNA sequences • Elimination of rRNA and 5S RNA genes	Genetic • Gene loss/loss of function • Rewiring of gene expression through novel intergenomic interactions • Novel dosage responses (positive, negative, dosage compensation) • Gene suppression or activation • Transcriptional activation of transposons that may affect nearby genes • New transposon insertion/excision
Epigenetic • Chromatin remodeling • Chromatin modification • Heterochromatinization • DNA methylation • Small RNA activation or repression	Epigenetic • Gene silencing or activation through changes in methylation or small RNAs or through chromatin modifications • Transposon silencing or activation through demethylation or changes in small RNAs or through chromatin modifications
2. Evolutionary changes facilitated by allopolyploidy in wheat occur during the evolution of the species by promoting species biodiversity (current knowledge is limited to the genetic rather than epigenetic changes)
• Chromosomal re-patterning (intra- and intergenomic translocations) • Introgression of chromosomal segments from alien genomes and production of recombinant genomes • Intergenomic transposons invasion	• Subfunctionalizations • Neofunctionalizations • New dosage effects through copy number variation • New allelic variations