RT Journal Article SR Electronic T1 Parental legacy, demography, and introgression influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae) JF bioRxiv FD Cold Spring Harbor Laboratory SP 234096 DO 10.1101/234096 A1 Dmytro Kryvokhyzha A1 Adriana Salcedo A1 Mimmi C. Eriksson A1 Tianlin Duan A1 Nilesh Tawari A1 Jun Chen A1 Maria Guerrina A1 Julia M. Kreiner A1 Tyler V. Kent A1 Ulf Lagercrantz A1 John R. Stinchcombe A1 Sylvain Glémin A1 Stephen I. Wright A1 Martin Lascoux YR 2017 UL http://biorxiv.org/content/early/2017/12/13/234096.abstract AB Allopolyploidy is generally perceived as a major source of evolutionary novelties and as an instantaneous way to create isolation barriers. However, we do not have a clear understanding of how two subgenomes evolve and interact once they have fused in an allopolyploid species and how isolated they are from their relatives. Here, we address these questions by analyzing genomic and transcriptomic data of allotetraploid Capsella bursa-pastoris in three differentiated populations, Asia, Europe and the Middle East. We phased the two subgenomes, one descended from the outcrossing and highly diverse Capsella grandiflora (Cg) and the other one from the selfing and genetically depauperate Capsella orientalis (Co). For each subgenome, we assessed its relationship with the diploid relatives, temporal change of effective population size (Ne), signatures of positive and negative selection, and gene expression patterns. Introgression between C. bursa-pastoris and its diploid relatives was widespread and the two subgenomes were impacted differentially depending on geographic region. In all three regions, Ne of the two subgenomes decreased gradually and the Co subgenome accumulated more deleterious changes than Cg. Selective sweeps were more common on the Cg subgenome in Europe and the Middle East, and on the Co subgenome in Asia. In contrast, differences in expression were limited with the Cg subgenome slightly more expressed than Co in Europe and the Middle-East. In summary, after more than 100,000 generations of co-existence, the two subgenomes of C. bursa-pastoris still retained a strong signature of parental legacy and were differentially affected by introgression and selection.