Data from: The role of hybridization during ecological divergence of southwestern white pine (Pinus strobiformis) and limber pine (P. flexilis)

Interactions between extrinsic factors, such as disruptive selection, and
intrinsic factors, such as genetic incompatibilities among loci, often
contribute towards the maintenance of species boundaries. The relative
roles of these factors in the establishment of reproductive isolation can
be examined using species pairs characterized by gene flow throughout
their divergence history. We investigated the process of speciation and
the maintenance of species boundaries between Pinus strobiformis and P.
flexilis. Utilizing ecological niche modeling, demographic modeling, and
genomic cline analyses, we illustrated a divergence history with
continuous gene flow. Our results supported an abundance of advanced
generation hybrids and a lack of loci exhibiting steep transition in
allele frequency across the hybrid zone. Additionally, we found evidence
for climate-associated variation in the hybrid index and niche divergence
between parental species and the hybrid zone. These results are consistent
with extrinsic factors, such as climate, being an important isolating
mechanism. A buildup of intrinsic incompatibilities and of co-adapted gene
complexes is also apparent, although these appear to be in the earliest
stages of development. This supports previous work in coniferous species
demonstrating the importance of extrinsic factors in facilitating
speciation. Overall, our findings lend support to the hypothesis that
varying strengths and directions of selection pressures across the long
lifespans of conifers, in combination with their life history strategies,
delay the evolution of strong intrinsic incompatibilities.