Interior Spruce Research Articles

Growth responses to thinning from below in uneven-aged interior Douglas-fir dominated stands

We assessed the impacts of three approaches to thinning from below with varying spatial patterns on several stand and individual tree variables for interior Douglas-fir ( Pseudotsuga menziesii var. glauca (Beissn.) Franco), interior spruce ( Picea glauca (Moench) Voss × Picea engelmannii Engelm.), and lodgepole pine ( Pinus contorta Dougl. Ex Loud. var. latifolia Englem.) in central British Columbia, Canada. The three thinning treatments were two experimental “clumped” treatments (3 m Clumped and 5 m Clumped) and the Standard (more uniform spacing) thinning treatment that was employed operationally at that time. We used long-term data from 24 plots measured five times over 21 years. Thinning increased stand basal area increment, with the plots that received the 5 m Clumped treatment having significantly higher periodic annual relative basal area increment than the unthinned Control plots. The responses for the two clumped treatments were not any lower than the Standard. The 3 m Clumped treatment was best if one is concerned about fast recovery of the growing space; however, the 5 m Clumped spacing treatment may be preferable if higher individual tree vigour is needed for resistance and resilience to fire, insects, and disease.

Optimization and validation of universal response functions for interior spruce (Picea glauca, Picea engelmannii, and their hybrids)

Ecological models, including various forms of population transfer and response functions, have been widely employed to predict the performance of forest trees under future climate conditions. However, the accuracy of model predictions remains a challenge due to the lack of systematic model optimization and validation processes. In this study, we explored a series of candidate universal response functions (URFs) based on comprehensive provenance trials for interior spruce, a tree hybrid complex of great ecological and economic importance in British Columbia. We first developed URFs with various numbers of climate variables and their combinations, then evaluated and validated these models with conventional statistical methods. Although these models showed high predictive power and performed well in statistical validation, the map visualizations of these models varied substantially. Therefore, we further conducted a pixel-wise spatial validation based on site productivity data to identify the model with the best performance. Finally, we analyzed the impact of climate change on interior spruce based on the final model. Our results revealed that: 1) a minimum number of independent climate variables is required to generate a reliable and informative ecological model; 2) spatial validation is critical to ensure the credibility of ecological models; 3) among-population variation resulting from local adaptation is relatively weak, indicating a potential for modest productivity gains from selecting well-adapted populations for stand establishment; and 4) most of the current interior spruce habitat is projected to be vulnerable to anthropogenic climate change, largely due to temperature rise, with a major upslope shift predicted.

Picturing local adaptation: Spectral and structural traits from drone remote sensing reveal clinal responses to climate transfer in common-garden trials of interior spruce (Picea engelmannii × glauca).

Common-garden trials of forest trees provide phenotype data used to assess growth and local adaptation; this information is foundational to tree breeding programs, genecology, and gene conservation. As jurisdictions consider assisted migration strategies to match populations to suitable climates, in situ progeny and provenance trials provide experimental evidence of adaptive responses to climate change. We used drone technology, multispectral imaging, and digital aerial photogrammetry to quantify spectral traits related to stress, photosynthesis, and carotenoids, and structural traits describing crown height, size, and complexity at six climatically disparate common-garden trials of interior spruce (Picea engelmannii × glauca) in western Canada. Through principal component analysis, we identified key components of climate related to temperature, moisture, and elevational gradients. Phenotypic clines in remotely sensed traits were analyzed as trait correlations with provenance climate transfer distances along principal components (PCs). We used traits showing clinal variation to model best linear unbiased predictions for tree height (R2 = .98-.99, root mean square error [RMSE] = 0.06-0.10 m) and diameter at breast height (DBH, R2 = .71-.97, RMSE = 2.57-3.80 mm) and generated multivariate climate transfer functions with the model predictions. Significant (p < .05) clines were present for spectral traits at all sites along all PCs. Spectral traits showed stronger clinal variation than structural traits along temperature and elevational gradients and along moisture gradients at wet, coastal sites, but not at dry, interior sites. Spectral traits may capture patterns of local adaptation to temperature and montane growing seasons which are distinct from moisture-limited patterns in stem growth. This work demonstrates that multispectral indices improve the assessment of local adaptation and that spectral and structural traits from drone remote sensing produce reliable proxies for ground-measured height and DBH. This phenotyping framework contributes to the analysis of common-garden trials towards a mechanistic understanding of local adaptation to climate.

Building resiliency in conifer forests: Interior spruce crosses among weevil resistant and susceptible parents produce hybrids appropriate for multi-trait selection.

Tree planting programs now need to consider climate change increasingly, therefore, the resistance to pests plays an essential role in enabling tree adaptation to new ranges through tree population movement. The weevil Pissodes strobi (Peck) is a major pest of spruces and substantially reduces lumber quality. We revisited a large Interior spruce provenance/progeny trial (2,964 genotypes, 42 families) of varying susceptibility, established in British Columbia. We employed multivariate mixed linear models to estimate covariances between, and genetic control of, juvenile height growth and resistance traits. We performed linear regressions and ordinal logistic regressions to test for impact of parental origin on growth and susceptibility to the pest, respectively. A significant environmental component affected the correlations between resistance and height, with outcomes dependent on families. Parents sourced from above 950 m a.s.l. elevation negatively influenced host resistance to attacks, probably due to higher P. engelmannii proportion. For the genetic contribution of parents sourced from above 1,200 m a.s.l., however, we found less attack severity, probably due to a marked mismatch in phenologies. This clearly highlights that interspecific hybrid status might be a good predictor for weevil attacks and delineates the boundaries of successful spruce population movement. Families resulting from crossing susceptible parents generally showed fast-growing trees were the most affected by weevil attacks. Such results indicate that interspecific 'hybrids' with a higher P. glauca ancestry might be genetically better equipped with an optimized resource allocation between defence and growth and might provide the solution for concurrent improvement in resistance against weevil attacks, whilst maintaining tree productivity.

Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes.

Spruces (Picea spp.) are coniferous trees widespread in boreal and mountainous forests of the northern hemisphere, with large economic significance and enormous contributions to global carbon sequestration. Spruces harbor very large genomes with high repetitiveness, hampering their comparative analysis. Here, we present and compare the genomes of four different North American spruces: the genome assemblies for Engelmann spruce (Picea engelmannii) and Sitka spruce (Picea sitchensis) together with improved and more contiguous genome assemblies for white spruce (Picea glauca) and for a naturally occurring introgress of these three species known as interior spruce (P. engelmannii × glauca × sitchensis). The genomes were structurally similar, and a large part of scaffolds could be anchored to a genetic map. The composition of the interior spruce genome indicated asymmetric contributions from the three ancestral genomes. Phylogenetic analysis of the nuclear and organelle genomes revealed a topology indicative of ancient reticulation. Different patterns of expansion of gene families among genomes were observed and related with presumed diversifying ecological adaptations. We identified rapidly evolving genes that harbored high rates of non-synonymous polymorphisms relative to synonymous ones, indicative of positive selection and its hitchhiking effects. These gene sets were mostly distinct between the genomes of ecologically contrasted species, and signatures of convergent balancing selection were detected. Stress and stimulus response was identified as the most frequent function assigned to expanding gene families and rapidly evolving genes. These two aspects of genomic evolution were complementary in their contribution to divergent evolution of presumed adaptive nature. These more contiguous spruce giga-genome sequences should strengthen our understanding of conifer genome structure and evolution, as their comparison offers clues into the genetic basis of adaptation and ecology of conifers at the genomic level. They will also provide tools to better monitor natural genetic diversity and improve the management of conifer forests. The genomes of four closely related North American spruces indicate that their high similarity at the morphological level is paralleled by the high conservation of their physical genome structure. Yet, the evidence of divergent evolution is apparent in their rapidly evolving genomes, supported by differential expansion of key gene families and large sets of genes under positive selection, largely in relation to stimulus and environmental stress response.

Climate data for field trials: onsite micro stations versus ClimateNA

Ecological studies in diverse environmental fields require accurate climate data for point locations that are often distant from reliable public weather stations. “Onsite” micro weather stations can be established directly at research locations, but purchase, establishment, and maintenance costs and data gaps can limit their feasibility. Alternatively, climate data for point locations can be predicted from ClimateNA, a publicly available software package, but the prediction accuracy in remote and mountainous locations is uncertain. We compared ClimateNA predictions with observations from onsite weather stations located at 11 interior spruce provenance trials in British Columbia, Canada. We found that ClimateNA predictions were highly accurate for temperature variables but moderate for precipitation variables when compared with onsite weather data. Growth response functions developed with the two data sources showed similar shapes for temperature variables. Our results suggest that (1) temperature variables can be accurately predicted at remote and mountainous locations using ClimateNA; (2) precipitation variables are more accurately predicted with ClimateNA than with onsite weather stations, which are considerably affected by random factors; and (3) response functions provide an effective, independent tool to assess alternative sources of climate data. Our results recommend the use of ClimateNA over onsite weather stations, except where highly accurate precipitation data are required, in which case, high-quality onsite weather stations must be established and carefully maintained.

Lodgepole pine and interior spruce radial growth response to climate and topography in the Canadian Rocky Mountains, Alberta

Climate change may have spatially variable impacts on growth of trees in topographically diverse environments, making generalizing across broad spatial and temporal extents inappropriate. Therefore, topography must be considered when analyzing growth response to climate. We address these topo-climatic relationships in the Canadian Rocky Mountains, focusing on lodgepole pine (Pinus contorta Douglas ex Louden) and interior spruce (Picea glauca (Moench) Voss × Picea engelmannii hybrid Parry) growth response to climate, Palmer drought severity index (PDSI), aspect, and slope angle. Climate variables correlate with older lodgepole pine growth on south- and west-facing slopes, including previous August temperature, winter and spring precipitation, and previous late-summer and current spring PDSI, but younger lodgepole pine were generally less sensitive to climate. Climate variables correlate with interior spruce growth on all slope aspects, with winter temperature and PDSI important for young and old individuals. Numerous monthly growth–climate correlations are not temporally stable, with shifts over the past century, and response differs by slope aspect and angle. Both species are likely to be negatively affected by moisture stress in the future in some, but not all, topographic environments. Results suggest species-specific and site-specific spatiotemporally diverse climate–growth responses, indicating that climate change is likely to have spatially variable impacts on radial growth response in mountainous environments.

Assisted migration poleward rather than upward in elevation minimizes frost risks in plantations

When assisted migration is used to address climate change, tree seedlings may have to be moved to substantially colder environments in anticipation of climate warming over their life span. Here, we evaluate frost risks for four economically important forest tree species of western Canada, Douglas-fir (Pseudotsuga menziesii), lodgepole pine (Pinus contorta), interior spruce (Picea glauca, P. engelmannii, and their hybrids), and western larch (Larix occidentalis), when moved to adjacent northern and higher elevation seed zones that are cooler by approximately 2 °C. Changes to risks of damaging frosts among seed zones are evaluated during two 30-day periods, after dormancy release in spring and before onset of dormancy in fall, assuming a temperature-dominated day of bud break and a critical photoperiod-controlled onset of dormancy in fall. Based on daily interpolated climate data between 1980 and 2019, we find that late spring and early fall frost risks do not change significantly for transfers toward the north (<1 percentage point in most cases). In contrast, moving planting stock toward higher elevation generally leads to a substantial increase in exposure to unseasonal frosts (late spring frosts: 0.5% to 9.4%, early fall frosts: 0.8% to 17.1%). We conclude that transfers toward the north are preferable to transfers up in elevation in reforestation of these tree species in western Canada.

Linkage disequilibrium vs. pedigree: Genomic selection prediction accuracy in conifer species.

BackgroundThe presupposition of genomic selection (GS) is that predictive accuracies should be based on population-wide linkage disequilibrium (LD). However, in species with large, highly complex genomes the limitation of marker density may preclude the ability to resolve LD accurately enough for GS. Here we investigate such an effect in two conifer species with ~ 20 Gbp genomes, Douglas-fir (Pseudotsuga menziesii Mirb. (Franco)) and Interior spruce (Picea glauca (Moench) Voss x Picea engelmannii Parry ex Engelm.). Random sampling of markers was performed to obtain SNP sets with totals in the range of 200–50,000, this was replicated 10 times. Ridge Regression Best Linear Unbiased Predictor (RR-BLUP) was deployed as the GS method to test these SNP sets, and 10-fold cross-validation was performed on 1,321 Douglas-fir trees, representing 37 full-sib F1 families and on 1,126 Interior spruce trees, representing 25 open-pollinated (half-sib) families. Both trials are located on 3 sites in British Columbia, Canada.ResultsAs marker number increased, so did GS predictive accuracy for both conifer species. However, a plateau in the gain of accuracy became apparent around 10,000–15,000 markers for both Douglas-fir and Interior spruce. Despite random marker selection, little variation in predictive accuracy was observed across replications. On average, Douglas-fir prediction accuracies were higher than those of Interior spruce, reflecting the difference between full- and half-sib families for Douglas-fir and Interior spruce populations, respectively, as well as their respective effective population size.ConclusionsAlthough possibly advantageous within an advanced breeding population, reducing marker density cannot be recommended for carrying out GS in conifers. Significant LD between markers and putative causal variants was not detected using 50,000 SNPS, and GS was enabled only through the tracking of relatedness in the populations studied. Dramatically increasing marker density would enable said markers to better track LD with causal variants in these large, genetically diverse genomes; as well as providing a model that could be used across populations, breeding programs, and traits.

Assessing Differences in Competitive Effects Among Tree Species in Central British Columbia, Canada

Research Highlights: We investigated the competitive interactions among three tree species (interior Douglas-fir (Pseudotsuga menziesii var. glauca (Beissn.) Franco), interior spruce (Picea glauca [Moench] Voss × Picea engelmannii Engelm.), and lodgepole pine (Pinus contorta Dougl. Ex Loud. var. latifolia Englem.)) in multi-aged stands in central British Columbia, Canada. Background and Objectives: Understanding competitive interactions among tree species in mixed-species stands is fundamental to supporting silvicultural decision-making in such stands. Using the periodic annual basal area increment for single trees as our dependent variable, we investigated whether neighboring trees competed with subject trees independently of species identity. We also examined the differences in single-tree basal area growth among the three conifer species over time under different levels of competition. Materials and Methods: We developed several spatially explicit, single-tree basal area growth models for interior Douglas-fir, interior spruce, and lodgepole pine using data from 16 plots in two blocks of a long-term study (five measurements over a 21-year period) on the response to pre-commercial thinning. We compared these equations to assess whether intraspecific or interspecific competition predominated. We also examined the differences in basal area growth among the three conifer species over time under different levels of competition. Results: We found asymmetrical relationships between the conifer trees and their neighbors for all species, indicating that the main driver limiting growth in these stands is aboveground competition for light. There was evidence of higher intraspecific competition for small (&lt;10.0 cm DBH) interior Douglas-fir in one block. However, there was no general pattern among larger subject trees with respect to the identity of neighborhood competitive effects and the equivalence of neighbors. We observed a higher level of basal area growth over time for interior Douglas-fir than for lodgepole pine and interior spruce, irrespective of the competition intensity and, not surprisingly, the growth rate declined with increasing competition levels for the three species. Conclusions: Our results provide an understanding of how interior Douglas-fir stands will develop over time and information on species interactions that could help forest managers explore different silvicultural options and their effects on individual tree growth in these complex stands.

Purifying selection does not drive signatures of convergent local adaptation of lodgepole pine and interior spruce

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.

Partial correlation analysis of transcriptomes helps detangle the growth and defense network in spruce

In plants, there can be a trade-off between resource allocations to growth vs defense. Here, we use partial correlation analysis of gene expression to make inferences about the nature of this interaction. We studied segregating progenies of Interior spruce subject to weevil attack. In a controlled experiment, we measured pre-attack plant growth and post-attack damage with several morphological measures, and profiled transcriptomes of 188 progeny. We used partial correlations of individual transcripts (expressed sequence tags, ESTs) with pairs of growth/defense traits to identify important nodes and edges in the inferred underlying gene network, for example, those pairs of growth/defense traits with high mutual correlation with a single EST transcript. We give a method to identify such ESTs. A terpenoid ABC transporter gene showed strongest correlations (P=0.019); its transcript represented a hub within the compact 166-member gene-gene interaction network (P=0.004) of the negative genetic correlations between growth and subsequent pest attack. A small 21-member interaction network (P=0.004) represented the uncovered positive correlations. Our study demonstrates partial correlation analysis identifies important gene networks underlying growth and susceptibility to the weevil in spruce. In particular, we found transcripts that strongly modify the trade-off between growth and defense, and allow identification of networks more central to the trade-off.

Multienvironment genomic variance decomposition analysis of open-pollinated Interior spruce (Picea glauca x engelmannii)

The advantages of open-pollinated (OP) family testing over controlled crossing (i.e., structured pedigree) are the potential to screen and rank a large number of parents and offspring with minimal cost and efforts; however, the method produces inflated genetic parameters as the actual sibling relatedness within OP families rarely meets the half-sib relatedness assumption. Here, we demonstrate the unsurpassed utility of OP testing after shifting the analytical mode from pedigree- (ABLUP) to genomic-based (GBLUP) relationship using phenotypic tree height (HT) and wood density (WD) and genotypic (30k SNPs) data for 1126 38-year-old Interior spruce (Picea glauca (Moench) Voss x P. engelmannii Parry ex Engelm.) trees, representing 25 OP families, growing on three sites in Interior British Columbia, Canada. The use of the genomic realized relationship permitted genetic variance decomposition to additive, dominance, and epistatic genetic variances, and their interactions with the environment, producing more accurate narrow-sense heritability and breeding value estimates as compared to the pedigree-based counterpart. The impact of retaining (random folding) vs. removing (family folding) genetic similarity between the training and validation populations on the predictive accuracy of genomic selection was illustrated and highlighted the former caveats and latter advantages. Moreover, GBLUP models allowed breeding value prediction for individuals from families that were not included in the developed models, which was not possible with the ABLUP. Response to selection differences between the ABLUP and GBLUP models indicated the presence of systematic genetic gain overestimation of 35 and 63% for HT and WD, respectively, mainly caused by the inflated estimates of additive genetic variance and individuals’ breeding values given by the ABLUP models. Extending the OP genomic-based models from single to multisite made the analysis applicable to existing OP testing programs.

Bioinformatically predicted deleterious mutations reveal complementation in the interior spruce hybrid complex

BackgroundMutation load is expected to be reduced in hybrids via complementation of deleterious alleles. While local adaptation of hybrids confounds phenotypic tests for reduced mutation load, it may be possible to assess variation in load by analyzing the distribution of putatively deleterious alleles. Here, we use this approach in the interior spruce (Picea glauca x P. engelmannii) hybrid complex, a group likely to suffer from high mutation load and in which hybrids exhibit local adaptation to intermediate conditions. We used PROVEAN to bioinformatically predict whether non-synonymous alleles are deleterious, based on conservation of the position and abnormality of the amino acid change.ResultsAs expected, we found that predicted deleterious alleles were at lower average allele frequencies than alleles not predicted to be deleterious. We were unable to detect a phenotypic effect on juvenile growth rate of the many rare alleles predicted to be deleterious. Both the proportion of alleles predicted to be deleterious and the proportion of loci homozygous for predicted deleterious alleles were higher in P. engelmannii (Engelmann spruce) than in P. glauca (white spruce), due to higher diversity and frequencies of rare alleles in Engelmann. Relative to parental species, the proportion of alleles predicted to be deleterious was intermediate in hybrids, and the proportion of loci homozygous for predicted deleterious alleles was lowest.ConclusionGiven that most deleterious alleles are recessive, this suggests that mutation load is reduced in hybrids due to complementation of deleterious alleles. This effect may enhance the fitness of hybrids.

Growth gains from selective breeding in a spruce hybrid zone do not compromise local adaptation to climate

Hybrid zones contain extensive standing genetic variation that facilitates rapid responses to selection. The Picea glauca × Picea engelmannii hybrid zone in western Canada is the focus of tree breeding programs that annually produce ~90 million reforestation seedlings. Understanding the direct and indirect effects of selective breeding on adaptive variation is necessary to implement assisted gene flow (AGF) polices in Alberta and British Columbia that match these seedlings with future climates. We decomposed relationships among hybrid ancestry, adaptive traits, and climate to understand the implications of selective breeding for climate adaptations and AGF strategies. The effects of selection on associations among hybrid index estimated from ~6,500 SNPs, adaptive traits, and provenance climates were assessed for ~2,400 common garden seedlings. Hybrid index differences between natural and selected seedlings within breeding zones were small in Alberta (average +2%), but larger and more variable in BC (average −7%, range −24% to +1%), slightly favoring P. glauca ancestry. The average height growth gain of selected seedlings over natural seedlings within breeding zones was 36% (range 12%–86%). Clines in growth with temperature‐related variables were strong, but differed little between selected and natural populations. Seedling hybrid index and growth trait associations with evapotranspiration‐related climate variables were stronger in selected than in natural seedlings, indicating possible preadaptation to drier future climates. Associations among cold hardiness, hybrid ancestry, and cold‐related climate variables dominated signals of local adaptation and were preserved in breeding populations. Strong hybrid ancestry–phenotype–climate associations suggest that AGF will be necessary to match interior spruce breeding populations with shifting future climates. The absence of antagonistic selection responses among traits and maintenance of cold adaptation in selected seedlings suggests breeding populations can be safely redeployed using AGF prescriptions similar to those of natural populations.

CNVs into the wild: screening the genomes of conifer trees (Picea spp.) reveals fewer gene copy number variations in hybrids and links to adaptation

BackgroundCopy number variations (CNVs) have been linked to different phenotypes in human, including many diseases. A genome-scale understanding of CNVs is available in a few plants but none are wild species, leaving a knowledge gap regarding their genome biology and evolutionary role. We developed a reliable CNV detection method for species lacking contiguous reference genome. We selected multiple probes within 14,078 gene sequences and developed comparative genome hybridization on arrays. Gene CNVs were assessed in three full-sib families from species with 20 Gb genomes, i.e., white and black spruce, and interior spruce - a natural hybrid.ResultsWe discovered hundreds of gene CNVs in each species, 3612 in total, which were enriched in functions related to stress and defense responses and narrow expression profiles, indicating a potential role in adaptation. The number of shared CNVs was in accordance with the degree of relatedness between individuals and species. The genetically mapped subset of these genes showed a wide distribution across the genome, implying numerous structural variations. The hybrid family presented significantly fewer CNVs, suggesting that the admixture of two species within one genome reduces the occurrence of CNVs.ConclusionsThe approach we developed is of particular interest in non-model species lacking a reference genome. Our findings point to a role for CNVs in adaptation. Their reduced abundance in the hybrid may limit genetic variability and evolvability of hybrids. We propose that CNVs make a qualitatively distinct contribution to adaptation which could be important for short term change.

Genetic convergence to the extreme

Convergent Evolution Species in the same habitat may be only distantly related but yet share the need to adapt to environmental extremes. Yeaman et al. examined the underlying genetics of local environmental adaptation in lodgepole pine and interior spruce, which diverged over 140 million years ago (see the Perspective by Hancock). A suite of duplicated genes, which exhibited the hallmark of selection, were associated with cold tolerance in both species. Adaptations to climate may therefore be genetically constrained, even among distantly related species. Science , this issue p. [1431][1]; see also p. [1362][2] [1]: /lookup/doi/10.1126/science.aaf7812 [2]: /lookup/doi/10.1126/science.aai8284

Convergent local adaptation to climate in distantly related conifers.

When confronted with an adaptive challenge, such as extreme temperature, closely related species frequently evolve similar phenotypes using the same genes. Although such repeated evolution is thought to be less likely in highly polygenic traits and distantly related species, this has not been tested at the genome scale. We performed a population genomic study of convergent local adaptation among two distantly related species, lodgepole pine and interior spruce. We identified a suite of 47 genes, enriched for duplicated genes, with variants associated with spatial variation in temperature or cold hardiness in both species, providing evidence of convergent local adaptation despite 140 million years of separate evolution. These results show that adaptation to climate can be genetically constrained, with certain key genes playing nonredundant roles.

Exome capture from the spruce and pine giga-genomes.

Sequence capture is a flexible tool for generating reduced representation libraries, particularly in species with massive genomes. We used an exome capture approach to sequence the gene space of two of the dominant species in Canadian boreal and montane forests - interior spruce (Picea glauca x engelmanii) and lodgepole pine (Pinus contorta). Transcriptome data generated with RNA-seq were coupled with draft genome sequences to design baits corresponding to 26824 genes from pine and 28649 genes from spruce. A total of 579 samples for spruce and 631 samples for pine were included, as well as two pine congeners and six spruce congeners. More than 50% of targeted regions were sequenced at >10× depth in each species, while ~12% captured near-target regions within 500bp of a bait position were sequenced to a depth >10×. Much of our read data arose from off-target regions, which was likely due to the fragmented and incomplete nature of the draft genome assemblies. Capture in general was successful for the related species, suggesting that baits designed for a single species are likely to successfully capture sequences from congeners. From these data, we called approximately 10 million SNPs and INDELs in each species from coding regions, introns, untranslated and flanking regions, as well as from the intergenic space. Our study demonstrates the utility of sequence capture for resequencing in complex conifer genomes, suggests guidelines for improving capture efficiency and provides a rich resource of genetic variants for studies of selection and local adaptation in these species.

Expression Divergence Is Correlated with Sequence Evolution but Not Positive Selection in Conifers.

The evolutionary and genomic determinants of sequence evolution in conifers are poorly understood, and previous studies have found only limited evidence for positive selection. Using RNAseq data, we compared gene expression profiles to patterns of divergence and polymorphism in 44 seedlings of lodgepole pine (Pinus contorta) and 39 seedlings of interior spruce (Picea glauca × engelmannii) to elucidate the evolutionary forces that shape their genomes and their plastic responses to abiotic stress. We found that rapidly diverging genes tend to have greater expression divergence, lower expression levels, reduced levels of synonymous site diversity, and longer proteins than slowly diverging genes. Similar patterns were identified for the untranslated regions, but with some exceptions. We found evidence that genes with low expression levels had a larger fraction of nearly neutral sites, suggesting a primary role for negative selection in determining the association between evolutionary rate and expression level. There was limited evidence for differences in the rate of positive selection among genes with divergent versus conserved expression profiles and some evidence supporting relaxed selection in genes diverging in expression between the species. Finally, we identified a small number of genes that showed evidence of site-specific positive selection using divergence data alone. However, estimates of the proportion of sites fixed by positive selection (α) were in the range of other plant species with large effective population sizes suggesting relatively high rates of adaptive divergence among conifers.