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

Resolving the phylogenies of genera with a history of hybridisation and polyploidisation is difficult. Using genome-wide markers may help resolve the effects of introgressive hybridisation at the diploid level. In the case of polyploid hybrids, identifying and phasing the different parental homeologs is a huge challenge, especially in cases where more than two parental species have been involved. Betula (birches) is such a genus: its phylogeny has not been fully resolved and the parentage of many of its polyploids, which range from tetraploid to decaploid, remains unknown. Here, we seek to resolve these issues using genome-wide assembled restriction site associated DNA (RAD) contigs with an average length of 675 bp from 27 diploid and 31 polyploid Betula species or subspecies. We used 50,870 loci to reconstruct the evolutionary relationships among diploid Betula species using both supermatrix and species tree methods. Our results show that the genus Betula was separated into two clades: (1) species with no or very narrow seed wings and (2) species with obvious or wide seed wings. Clade 1 contains some Betula species with narrow geographic distributions whereas Clade 2 contains some Betula species with very wide geographic distributions and important ecological and economic values. We made a reference containing over 88,000 homologous contigs from the 20 diploid Betula species, and mapped trimmed reads from each polyploid species to this reference. For all polyploid species, the rate of read-mapping to particular diploid species allowed us to tentatively identify at least one putative diploid progenitor. In cases where two or more parents could be identified, we used the read mapping data to sort the polyploid reads into different putative sub-genomes and used the extracted contigs, along with the diploids sequences, to build new phylogenies. This approach yielded a phylogenetic hypothesis for the genus Betula that includes the complex reticulate origins of the majority of its polyploid taxa.