Evolution of the correlated genomic variation landscape across a divergence continuum in the genus Castanopsis

The heterogeneous landscape of genomic variation has been well documented
in population genomic studies. However, disentangling the
intricate interplay of evolutionary forces influencing the genetic
variation landscape over time remains challenging. In this study,
we assembled a chromosome-level genome for Castanopsis eyrei and
sequenced the whole genomes of 276 individuals from 12
Castanopsis species, spanning a broad divergence
continuum. We found highly correlated genomic variation
landscapes across these species. Furthermore, variations in genetic
diversity and differentiation along the genome were strongly associated
with recombination rates and gene density. These results suggest that
long-term linked selection and conserved genomic features have contributed
to the formation of a common genomic variation landscape. By
examining how correlations between population summary statistics change
throughout the species divergence continuum, we determined that background
selection alone does not fully explain the observed patterns of genomic
variation; the effects of recurrent selective sweeps must be
considered. We further revealed that extensive gene flow has
significantly influenced patterns of genomic variation in Castanopsis
species. The estimated admixture proportion correlated positively with
recombination rate and negatively with gene density, supporting a scenario
of selection against gene flow. Additionally, putative introgression
regions exhibited strong signals of positive selection, an enrichment of
functional genes, and reduced genetic burdens, indicating that adaptive
introgression has played a role in shaping the genomes of hybridizing
species. This study provides insights into how different evolutionary
forces have interacted in driving the evolution of the genomic variation
landscape.