Data from: The genomic consequences of adaptive divergence and reproductive isolation between species of manakins

The processes of adaptation and speciation are expected to shape genomic
variation within and between diverging species. Here we analyze genomic
heterogeneity of genetic differentiation and introgression in a hybrid
zone between two bird species (Manacus candei and M. vitellinus) using 59
100 SNPs, a whole genome assembly, and Bayesian models. Measures of
genetic differentiation (inline image) and introgression (genomic cline
center [α] and rate [β]) were highly heterogeneous among loci. We
identified thousands of loci with elevated parameter estimates, some of
which are likely to be associated with variation in fitness in Manacus
populations. To analyze the genomic organization of differentiation and
introgression, we mapped SNPs onto a draft assembly of the M. vitellinus
genome. Estimates of inline image, α, and β were autocorrelated at very
short physical distances (< 100 bp), but much less so beyond this.
In addition, average statistical associations (linkage disequilibrium)
between SNPs were generally low and were not higher in admixed populations
than in populations of the parental species. Although they did not occur
with a constant probability across the genome, loci with elevated inline
image, α, and β were not strongly co-localized in the genome. Contrary to
verbal models that predict clustering of loci involved in adaptation and
isolation in discrete genomic regions, these results are consistent with
the hypothesis that genetic regions involved in adaptive divergence and
reproductive isolation are scattered throughout the genome. We also found
that many loci were characterized by both exceptional genetic
differentiation and introgression, consistent with the hypothesis that
loci involved in isolation are also often characterized by a history of
divergent selection. However, the concordance between isolation and
differentiation was only partial, indicating a complex architecture and
history of loci involved in isolation.