Resolving phylogeny and polyploid parentage using genus-wide genome-wide sequence data from birch trees

Abstract Numerous plant genera have a history including frequent hybridisation and polyploidisation, which often means that their phylogenies are not yet fully resolved. The genus Betula , which contains many ecologically important allopolyploid tree species, is a case in point. We generated genome-wide sequence data for 27 diploid and 31 polyploid Betula species or subspecies using restriction site associated DNA (RAD) sequences assembled into contigs with a mean length of 675 bp. We reconstructed the evolutionary relationships among diploid Betula species using both supermatrix and species tree methods. We identified progenitors of the polyploids according to the relative rates at which their reads mapped to contigs from different diploid species. We sorted the polyploid reads into different putative sub-genomes and used the extracted contigs, along with the diploid sequences, to build new phylogenies that included the polyploid sub-genomes. This approach yielded a highly evidenced phylogenetic hypothesis for the genus Betula , including the complex reticulate origins of the majority of its polyploid taxa. The genus was split into two well supported clades, which differ in their seed-wing morphology. We propose a new taxonomy for Betula , splitting it into two subgenera. We have resolved the parentage of many widespread and economically important polyploid tree species, opening the way for their population genomic study.