Post‐hybridization introgression and natural selection promoted genomic divergence of Aegilops speltoides and the four S*‐genome diploid species

Abstract

SUMMARYUnderstanding how different driving forces have promoted biological divergence and speciation is one of the central issues in evolutionary biology. The Triticum/Aegilops species complex contains 13 diploid species belonging to the A‐, B‐ and D‐lineages and offers an ideal system to address the evolutionary dynamics of lineage fusion and splitting. Here, we sequenced the whole genomes of one S‐genome species (Aegilops speltoides) of the B‐lineage and four S*‐genome diploid species (Aegilops bicornis, Aegilops longissima, Aegilops sharonensis and Aegilops searsii) of the D‐lineage at the population level. We performed detailed comparisons of the five species and with the other four representative A‐, B‐ and D‐lineage species. Our estimates identified frequent genetic introgressions from A‐ and B‐lineages to the D‐lineage species. A remarkable observation is the contrasting distributions of putative introgressed loci by the A‐ and B‐lineages along all the seven chromosomes to the extant D‐lineage species. These genetic introgressions resulted in high levels of genetic divergence at centromeric regions between Ae. speltoides (B‐lineage) and the other four S*‐genome diploid species (D‐lineage), while natural selection is a potential contributor to divergence among the four S*‐genome species at telomeric regions. Our study provides a genome‐wide view on how genetic introgression and natural selection acted together yet chromosome‐regionally divided to promote genomic divergence among the five S‐ and S*‐genome diploid species, which provides new and nuanced insights into the evolutionary history of the Triticum/Aegilops species complex.