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

Abstract

Interactions between extrinsic factors, such as disruptive selection, and intrinsic factors, such as genetic incompatibilities among loci, can contribute to 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 history of divergence with continuous gene flow between these species. We found an abundance of advanced generation hybrids and a lack of loci exhibiting large allele frequency differences 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. Our results are consistent with extrinsic factors, such as climate, being an important isolating mechanism for these species. A buildup of intrinsic incompatibilities and of co-adapted gene complexes is also apparent in our results, 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 creating and enforcing species boundaries. Overall, we 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.

Limber pine (Pinus flexilis James) genetic map constructed by exome‐seq provides insight into the evolution of disease resistance and a genomic resource for genomics‐based breeding

“…For breeding and conservation programs, it is very important to know whether the MGRs found within the species among distant geographical sites are the same locus. Limber pine is closely related to southwestern white pine, and hybridization has taken place in at least some areas where these species overlap (Menon et al ., ). MGR has been previously documented in southwestern white pine in the US portion of the species range (Kinloch and Dupper, ; Sniezko et al ., ).…”

Genotyping‐by‐sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen (Populus tremuloides)

“…We chose to estimate tree graph relationships of P. tremuloides genetic clusters, in a model that adds migration edges between lineages on the tree. However, a phylogeography study of quaking aspen such as that suggested above, based on expanded sampling, would be better positioned for making statistical phylogeographical inferences of the best‐fit model describing the timing and demographic changes associated with divergences of P. tremuloides genetic clusters inferred herein (e.g., Gutenkunst et al, 2009; Robinson et al, 2014; Boehm et al, 2015; Menon et al, 2018). Such a study would also be able to improve on our study by testing and refining our inferences about the timing and magnitude of admixture between P. tremuloides clusters 2 and 3.…”

Combining mitochondrial and nuclear genome analyses to dissect the effects of colonization, environment, and geography on population structure in Pinus tabuliformis

“…Restriction‐site‐associated DNA sequencing (e.g., genotyping‐by‐sequencing, GBS) is an effective approach for generating genetic data over thousands of loci and is increasingly being used to obtain population genomic perspective in non‐model forest trees (Parchman, Jahner, Uckele, Galland, & Eckert, ). However, to date, only a few investigations have explored GBS for dissecting the organization of genetic variation across landscapes in conifers (Johnson, Gaddis, Cairns, Konganti, & Krutovsky, ; Menon et al., ), probably due to difficulties in optimizing the technique in complex conifer genome analysis.…”