Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles

Abstract

AbstractIntrogression allows polyploid species to acquire new genomic content from diploid progenitors or from other unrelated diploid or polyploid lineages, contributing to genetic diversity and facilitating adaptive allele discovery. In some cases, high levels of introgression elicit the replacement of large numbers of alleles inherited from the polyploid’s ancestral species, profoundly reshaping the polyploid’s genomic composition. In such complex polyploids it is often difficult to determine which taxa were the progenitor species and which taxa provided additional introgressive blocks through subsequent hybridization. Here, we use population-level genomic data to reconstruct the phylogenetic history ofBetula pubescens(downy birch), a tetraploid species often assumed to be of allopolyploid origin and which is known to hybridize with at least four other birch species. This was achieved by modeling of polyploidization and introgression events under the multispecies coalescent and then using an approximate Bayesian computation (ABC) rejection algorithm to evaluate and compare competing polyploidization models. We provide evidence thatB. pubescensis the outcome of an autoploid genome doubling event in the common ancestor ofB. pendulaand its extant sister species,B. platyphylla, that took place approximately 178,000-188,000 generations ago. Extensive hybridization withB. pendula,B. nana, andB. humilisfollowed in the aftermath of autopolyploidization, with the relative contribution of each of these species to theB. pubescensgenome varying markedly across the species’ range. Functional analysis ofB. pubescensloci containing alleles introgressed fromB. nanaidentified multiple genes involved in climate adaptation, while loci containing alleles derived fromB. humilisrevealed several genes involved in the regulation of meiotic stability and pollen viability in plant species.