Integrative analysis of plastome, single-copy nuclear gene Pgk1 and SLAF-seq data uncovers multiple-origin and introgression history in polyploid Agropyron cristatum

Elucidating the origins and mechanisms of polyploidization requires tracing the evolutionary history of polyploid species, particularly those with complex origins. <i>Agropyron cristatum</i>, traditionally regarded as an autopolyploid, exhibits characteristics indicative of a segmental allopolyploid. Here, we used phylogenetic analysis based on a low-copy nuclear gene (i.e., <i>Pgk1</i>), SLAF-seq, and plastome data from 20 diploid and 120 tetraploid <i>Agropyron</i> individuals to determine whether tetraploid <i>A. cristatum</i> arose from an allopolyploid or autopolyploid event. Phylogenetic analyses based on <i>Pgk1</i> and SLAF-seq data identified two distinct <i>A. cristatum</i> lineages that corresponded to the two main <i>Agropyron</i> habitats in Central Asia-Europe and East Asia-Qinghai-Tibet Plateau. These findings, taken together with molecular dating and gene flow analyses, suggest that the East Asian tetraploid <i>A. cristatum</i> originated via both autopolyploidy from <i>A. cristatum</i> and hybridization between diploid <i>A. cristatum</i> and <i>A. mongolicum</i>, with each diploid cytotype acting as a maternal donor. Furthermore, the Central Asia-Europe tetraploid <i>A. cristatum</i> originated solely via autopolyploidy of diploid <i>A. cristatum</i>. Our findings also indicate that rapid diversification of <i>Agropyron</i> was likely driven by climate oscillations, geographic isolation, introgressive hybridization, and chloroplast capture. These findings challenge simplistic views of autopolyploids and underscore substantial potential for achieving high levels of genetic and adaptive diversity through recurrent hybridization and reticulate evolution.