Abstract
BackgroundLodgepole pine (Pinus contorta) and interior spruce (Picea glauca, Picea engelmannii, and their hybrids) are distantly related conifer species. Previous studies identified 47 genes containing variants associated with environmental variables in both species, providing evidence of convergent local adaptation. However, if the intensity of purifying selection varies with the environment, clines in nucleotide diversity could evolve through linked (background) selection that would yield allele frequency-environment signatures resembling local adaptation. If similar geographic patterns in the strength of purifying selection occur in these species, this could result in the convergent signatures of local adaptation, especially if the landscape of recombination is conserved. In the present study, we investigated whether spatially/environmentally varying purifying selection could give rise to the convergent signatures of local adaptation that had previously reported.ResultsWe analyzed 86 lodgepole pine and 50 interior spruce natural populations spanning heterogeneous environments in western Canada where previous analyses had found signatures of convergent local adaptation. We estimated nucleotide diversity and Tajima’s D for each gene within each population and calculated the strength of correlations between nucleotide diversity and environmental variables. Overall, these estimates in the genes with previously identified convergent local adaptation signatures had no similar pattern between pine and spruce. Clines in nucleotide diversity along environmental variables were found for interior spruce, but not for lodgepole pine. In spruce, genes with convergent adaption signatures showed a higher strength of correlations than genes without convergent adaption signatures, but there was no such disparity in pine, which suggests the pattern in spruce may have arisen due to a combination of selection and hybridization.ConclusionsThe results rule out purifying/background selection as a driver of convergent local adaption signatures in lodgepole pine and interior spruce.
Highlights
Lodgepole pine (Pinus contorta) and interior spruce (Picea glauca, Picea engelmannii, and their hybrids) are distantly related conifer species
The similar genome organization between pine and spruce [14] would increase the likelihood that similar signatures of spatially or environmentally varying background selection could be found in both species, and such patterns could have been mistakenly interpreted as convergent local adaptation by Yeaman, Hodgins et al [2]
Genes with convergent adaption signatures showed a higher strength of correlations between environmental variables and nucleotide diversity than genes without signatures of convergent adaption, but there was no such disparity in pine (Fig. 5, Table 1, Additional file 1: Figures S4 & S5)
Summary
Lodgepole pine (Pinus contorta) and interior spruce (Picea glauca, Picea engelmannii, and their hybrids) are distantly related conifer species. Lodgepole pine (Pinus contorta) and interior spruce (Picea glauca, Picea engelmannii, and their hybrids) are among the most economically and ecologically valuable forest tree species in western Canada, inhabiting similar environmental gradients across boreal and montane environments. These two species diverged 140–190 million years ago [1]. (purifying and background selection) varies spatially with environment, clines in nucleotide diversity could evolve that would yield allele frequency-environment signatures resembling local adaptation [6,7,8]. Other studies have reported highly similar patterns of nucleotide diversity at the genome scale between distantly related species, along with broad correlations with recombination rate [13, 15], so this provides a plausible alternative explanation for the signatures of convergence observed in these conifers
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