Biased gene retention in the face of massive nuclear introgression obscures species relationships

Phylogenomic analyses are recovering previously hidden histories of hybridization, revealing the genomic consequences of these events on the architecture of extant genomes. We exploit a suite of genomic resources to show that introgressive hybridization occurred between close relatives of Arabidopsis, impacting our understanding of species relationships in the group. The composition of introgressed and retained genes indicates that selection against incompatible cytonuclear and nuclear-nuclear interactions likely acted during introgression, while neutral processes also contributed to genome composition through the retention of ancient haplotype blocks. We also developed a divergence-based test to distinguish donor from recipient lineages without the requirement of additional taxon-sampling. Finally, to our great surprise, we find that cytonuclear discordance appears to have arisen via extensive nuclear, rather than cytoplasmic, introgression, meaning that most of the genome was displaced during introgression, while only a small proportion of native alleles were retained.

INTROGRESSIVE HYBRIDIZATION BETWEEN RHODODENDRON KIUSIANUM AND R. KAEMPFERI (ERICACEAE) IN KYUSHU, JAPAN BASED ON CHLOROPLAST DNA MARKERS

Wild evergreen azalea populations of Rhododendron kiusianum and R. kaempferi (Ericaceae) were analysed using a chloroplast DNA (cpDNA) PCR-RFLP marker that was used to detect introgressive hybridization in our previous study of the Kirishima Mts populations.The populations of the intermediate region in the Unzen Mts, which show phenotypic variation, were demonstrated to result from interspecific hybridization between Rhododendron kiusianum and R. kaempferi, possessing cpDNA from either R. kiusianum (1030/420 bp) or R. kaempferi (950/420/80 bp).Most individuals of Rhododendron kiusianum in the Kujyu Mts, the Aso Mts and the surrounding mountains exhibited the PCR-RFLP pattern of R. kaempferi. These results from the Kujyu Mts and the Aso Mts indicate that natural hybridization and cytoplasmic introgression from Rhododendron kaempferi to R. kiusianum have occurred in the relatively distant past. In the case of Mt Yufudake and Mt Haneyama, the Rhododendron kiusianum population retains the effects of natural hybridization with R. kaempferi in the cpDNA as well as in the variation in flower characteristics.All individuals of Rhododendron kiusianum on Mt Onogaradake in the Takakuma Mts exhibit R. kiusianum cpDNA (1030/420 bp), in spite of variation in flower colour.