Complex polyploids: Origins, genomic composition, and role of introgressed alleles

Introgression 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 polyploid, 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 of Betula 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 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 that B. pubescens is the outcome of an
autoploid genome doubling event in the common ancestor of B. pendula and
its extant sister species, B. platyphylla, that took place approximately
178,000-188,000 generations ago. Extensive hybridization with B. pendula,
B. nana, and B. humilis followed in the aftermath of autopolyploidization,
with the relative contribution of each of these species to the B.
pubescens genome varying markedly across the species' range.
Functional analysis of B. pubescens loci containing alleles introgressed
from B. nana identified multiple genes involved in climate adaptation,
while loci containing alleles derived from B. humilis revealed several
genes involved in the regulation of meiotic stability and pollen viability
in plant species.