Influence of environmental conditions at spawning sites and migration routes on adaptive variation and population connectivity in Chinook salmon

Many species that undergo long breeding migrations, such as anadromous fishes, face highly heterogeneous environments along their migration corridors and at their spawning sites. These environmental challenges encountered at different life stages may act as strong selective pressures and drive local adaptation. However, the relative influence of environmental conditions along the migration corridor compared with the conditions at spawning sites on driving selection is still unknown. In this study, we performed genome–environment associations (GEA) to understand the relationship between landscape and environmental conditions driving selection in seven populations of the anadromous Chinook salmon (Oncorhynchus tshawytscha)—a species of important economic, social, cultural, and ecological value—in the Columbia River basin. We extracted environmental variables for the shared migration corridors and at distinct spawning sites for each population, and used a Pool‐seq approach to perform whole genome resequencing. Bayesian and univariate GEA tests with migration‐specific and spawning site‐specific environmental variables indicated many more candidate SNPs associated with environmental conditions at the migration corridor compared with spawning sites. Specifically, temperature, precipitation, terrain roughness, and elevation variables of the migration corridor were the most significant drivers of environmental selection. Additional analyses of neutral loci revealed two distinct clusters representing populations from different geographic regions of the drainage that also exhibit differences in adult migration timing (summer vs. fall). Tests for genomic regions under selection revealed a strong peak on chromosome 28, corresponding to the GREB1L/ROCK1 region that has been identified previously in salmonids as a region associated with adult migration timing. Our results show that environmental variation experienced throughout migration corridors imposed a greater selective pressure on Chinook salmon than environmental conditions at spawning sites.     

Forest tree species adaptation to climate across biomes: Building on the legacy of ecological genetics to anticipate responses to climate change

Intraspecific variation plays a critical role in extant and future forest responses to climate change. Forest tree species with wide climatic niches rely on the intraspecific variation resulting from genetic adaptation and phenotypic plasticity to accommodate spatial and temporal climate variability. A centuries-old legacy of forest ecological genetics and provenance trials has provided a strong foundation upon which to continue building on this knowledge, which is critical to maintain climate-adapted forests. Our overall objective is to understand forest trees intraspecific responses to climate across species and biomes, while our specific objectives are to describe ecological genetics models used to build our foundational knowledge, summarize modeling approaches that have expanded the traditional toolset, and extensively review the literature from 1994 to 2021 to highlight the main contributions of this legacy and the new analyzes of provenance trials. We reviewed 103 studies comprising at least three common gardens, which covered 58 forest tree species, 28 of them with range-wide studies. Although studies using provenance trial data cover mostly commercially important forest tree species from temperate and boreal biomes, this synthesis provides a global overview of forest tree species adaptation to climate. We found that evidence for genetic adaptation to local climate is commonly present in the species studied (79%), being more common in conifers (87.5%) than in broadleaf species (67%). In 57% of the species, clines in fitness-related traits were associated with temperature variables, in 14% of the species with precipitation, and in 25% of the species with both. Evidence of adaptation lags was found in 50% of the species with range-wide studies. We conclude that ecological genetics models and analysis of provenance trial data provide excellent insights on intraspecific genetic variation, whereas the role and limits of phenotypic plasticity, which will likely determine the fate of extant forests, is vastly understudied.     

Evidence of genomic adaptation to climate in Eucalyptus microcarpa: Implications for adaptive potential to projected climate change

Understanding whether populations can adapt in situ or whether interventions are required is of key importance for biodiversity management under climate change. Landscape genomics is becoming an increasingly important and powerful tool for rapid assessments of climate adaptation, especially in long‐lived species such as trees. We investigated climate adaptation in Eucalyptus microcarpa using the DArTseq genomic approach. A combination of F_ST outlier and environmental association analyses were performed using >4200 genomewide single nucleotide polymorphisms (SNPs) from 26 populations spanning climate gradients in southeastern Australia. Eighty‐one SNPs were identified as putatively adaptive, based on significance in F_ST outlier tests and significant associations with one or more climate variables related to temperature (70/81), aridity (37/81) or precipitation (35/81). Adaptive SNPs were located on all 11 chromosomes, with no particular region associated with individual climate variables. Climate adaptation appeared to be characterized by subtle shifts in allele frequencies, with no consistent fixed differences identified. Based on these associations, we predict adaptation under projected changes in climate will include a suite of shifts in allele frequencies. Whether this can occur sufficiently rapidly through natural selection within populations, or would benefit from assisted gene migration, requires further evaluation. In some populations, the absence or predicted increases to near fixation of particular adaptive alleles hint at potential limits to adaptive capacity. Together, these results reinforce the importance of standing genetic variation at the geographic level for maintaining species’ evolutionary potential.     

Finding common ground: Toward comparable indicators of adaptive capacity of tree species to a changing climate

Adaptive capacity, one of the three determinants of vulnerability to climate change, is defined as the capacity of species to persist in their current location by coping with novel environmental conditions through acclimation and/or evolution. Although studies have identified indicators of adaptive capacity, few have assessed this capacity in a quantitative way that is comparable across tree species. Yet, such multispecies assessments are needed by forest management and conservation programs to refine vulnerability assessments and to guide the choice of adaptation measures. In this paper, we propose a framework to quantitatively evaluate five key components of tree adaptive capacity to climate change: individual adaptation through phenotypic plasticity, population phenotypic diversity as influenced by genetic diversity, genetic exchange within populations, genetic exchange between populations, and genetic exchange between species. For each component, we define the main mechanisms that underlie adaptive capacity and present associated metrics that can be used as indices. To illustrate the use of this framework, we evaluate the relative adaptive capacity of 26 northeastern North American tree species using values reported in the literature. Our results show adaptive capacity to be highly variable among species and between components of adaptive capacity, such that no one species ranks consistently across all components. On average, the conifer Picea glauca and the broadleaves Acer rubrum and A. saccharinum show the greatest adaptive capacity among the 26 species we documented, whereas the conifers Picea rubens and Thuja occidentalis, and the broadleaf Ostrya virginiana possess the lowest. We discuss limitations that arise when comparing adaptive capacity among species, including poor data availability and comparability issues in metrics derived from different methods or studies. The breadth of data required for such an assessment exemplifies the multidisciplinary nature of adaptive capacity and the necessity of continued cross‐collaboration to better anticipate the impacts of a changing climate.     

Adaptation genomics: next generation sequencing reveals a shared haplotype for rapid early development in geographically and genetically distant populations of rainbow trout

Local adaptation occurs when a population evolves a phenotype that confers a selective advantage in its local environment, but which may not be advantageous in other habitats. Restricted gene flow and strong selection pressures are prerequisites for local adaptation. Fishes in the family Salmonidae are predicted to provide numerous examples of local adaptation because of the high fidelity of returning to spawn in their natal streams, which results in highly structured populations, and the wide diversity of environments that salmonids have colonized. These conditions are ideally suited for producing a set of specialist phenotypes, whose fitness is maximized for one specific habitat, rather than a generalist phenotype similarly viable in several environments. Understanding patterns and processes leading to local adaptations has long been a goal of evolutionary biology, but it is only recently that identifying the molecular basis for local adaptation has become feasible because of advances in genomic technologies. The study of shared adaptive phenotypes in populations that are both geographically distant and genetically distinct should reveal some of the fundamental molecular mechanisms associated with local adaptation. In this issue of Molecular Ecology, Miller et al. (2012) make a significant contribution to the development of adaptation genomics. This study suggests that salmonids use standing genetic variation to select beneficial alleles for local adaptations rather than de novo mutations in the same gene or alternative physiological pathways. Identifying the genetic basis for local adaptation has major implications for the management, conservation and potential restoration of salmonid populations.     

Insights into the neutral and adaptive processes shaping the spatial distribution of genomic variation in the economically important Moroccan locust (Dociostaurus maroccanus)

Understanding the processes that shape neutral and adaptive genomic variation is a fundamental step to determine the demographic and evolutionary dynamics of pest species. Here, we use genomic data obtained via restriction site‐associated DNA sequencing to investigate the genetic structure of Moroccan locust (Dociostaurus maroccanus) populations from the westernmost portion of the species distribution (Iberian Peninsula and Canary Islands), infer demographic trends, and determine the role of neutral versus selective processes in shaping spatial patterns of genomic variation in this pest species of great economic importance. Our analyses showed that Iberian populations are characterized by high gene flow, whereas the highly isolated Canarian populations have experienced strong genetic drift and loss of genetic diversity. Historical demographic reconstructions revealed that all populations have passed through a substantial genetic bottleneck around the last glacial maximum (~21 ka BP) followed by a sharp demographic expansion at the onset of the Holocene, indicating increased effective population sizes during warm periods as expected from the thermophilic nature of the species. Genome scans and environmental association analyses identified several loci putatively under selection, suggesting that local adaptation processes in certain populations might not be impeded by widespread gene flow. Finally, all analyses showed few differences between outbreak and nonoutbreak populations. Integrated pest management practices should consider high population connectivity and the potential importance of local adaptation processes on population persistence.     

Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation

Adaptive genetic variation has been thought to originate primarily from either new mutation or standing variation. Another potential source of adaptive variation is adaptive variants from other (donor) species that are introgressed into the (recipient) species, termed adaptive introgression. Here, the various attributes of these three potential sources of adaptive variation are compared. For example, the rate of adaptive change is generally thought to be faster from standing variation, slower from mutation and potentially intermediate from adaptive introgression. Additionally, the higher initial frequency of adaptive variation from standing variation and lower initial frequency from mutation might result in a higher probability of fixation of the adaptive variants for standing variation. Adaptive variation from introgression might have higher initial frequency than new adaptive mutations but lower than that from standing variation, again making the impact of adaptive introgression variation potentially intermediate. Adaptive introgressive variants might have multiple changes within a gene and affect multiple loci, an advantage also potentially found for adaptive standing variation but not for new adaptive mutants. The processes that might produce a common variant in two taxa, convergence, trans‐species polymorphism from incomplete lineage sorting or from balancing selection and adaptive introgression, are also compared. Finally, potential examples of adaptive introgression in animals, including balancing selection for multiple alleles for major histocompatibility complex (MHC), S and csd genes, pesticide resistance in mice, black colour in wolves and white colour in coyotes, Neanderthal or Denisovan ancestry in humans, mimicry genes in Heliconius butterflies, beak traits in Darwin's finches, yellow skin in chickens and non‐native ancestry in an endangered native salamander, are examined.     

Regional differences in the abiotic environment contribute to genomic divergence within a wild tomato species

The wild currant tomato Solanum pimpinellifolium inhabits a wide range of abiotic habitats across its native range of Ecuador and Peru. Although it has served as a key genetic resource for the improvement of domestic cultivars, little is known about the genetic basis of traits underlying local adaptation in this species, nor what abiotic variables are most important for driving differentiation. Here we use redundancy analysis (RDA) and other multivariate statistical methods (structural equation modelling [SEM] and generalized dissimilarity modelling [GDM]) to quantify the relationship of genomic variation (6,830 single nucleotide polymorphisms [SNPs]) with climate and geography, among 140 wild accessions. RDA, SEM and GDM each identified environment as explaining more genomic variation than geography, suggesting that local adaptation to heterogeneous abiotic habitats may be an important source of genetic diversity in this species. Environmental factors describing temporal variation in precipitation and evaporative demand explained the most SNP variation among accessions, indicating that these forces may represent key selective agents. Lastly, by studying how SNP–environment associations vary throughout the genome (44,064 SNPs), we mapped the location and investigated the functions of loci putatively contributing to climatic adaptations. Together, our findings indicate an important role for selection imposed by the abiotic environment in driving genomic differentiation between populations.     

Landscape genomics reveals genetic evidence of local adaptation in a widespread tree,the Chinese wingnut (Pterocarya stenoptera)

Understanding the genetic basis underpinning local adaptation is one of the fundamental issues in ecological and evolutionary biology. In this study, we investigated the genomic basis underlying local adaptation of the Chinese wingnut (Pterocarya stenoptera C. DC). Our population genomic analyses revealed nine spatial genetic clusters across the current distribution range of this species. Based on the assessment of genetic–environment association, we found that adaptive divergence of the P. stenoptera populations were mainly shaped by solar radiation during fruit development, temperature seasonality, annual temperature, precipitation, and air humidity. In particular, our genome-wide scanning identified a total of 801 candidate single nucleotide polymorphisms (SNPs) that are highly correlated with diverse environmental factors. Further functional annotation of the SNPs identified some candidate genes that are involved into temperature, water, and light adaptation. Taken together, our results suggest that natural selection during local adaptation has contributed to the success of survival to diverse heterogenous environmental conditions. Our study provides important insights into the fundamental knowledge of the genetic basis underlying the local adaptation of non-model species.     

Contrasting patterns of local adaptation along climatic gradients between a sympatric parasitic and autotrophic tree species

Sympatric tree species are subject to similar climatic drivers, posing a question as to whether they display comparable adaptive responses. However, no study has explicitly examined local adaptation of co‐occurring parasitic and autotrophic plant species to the abiotic environment. Here we test the hypotheses that a generalist parasitic tree would display a weaker signal of selection and that genomic variation would associate with fewer climatic variables (particularly precipitation) but have similar spatial patterns to a sympatric autotrophic tree species. To test these hypotheses, we collected samples from 17 sites across the range of two tree species, the hemiparasite Nuytsia floribunda (n = 264) and sympatric autotroph Melaleuca rhaphiophylla (n = 272). We obtained 5,531 high‐quality genome‐wide single nucleotide polymorphisms (SNPs) for M. rhaphiophylla and 6,727 SNPs for N. floribunda using DArTseq genome scan technology. Population differentiation and environmental association approaches were used to identify signals of selection. Generalized dissimilarly modelling was used to detect climatic and spatial patterns of local adaptation across climatic gradients. Overall, 322 SNPs were identified as putatively adaptive for the autotroph, while only 57 SNPs were identified for the parasitic species. We found genomic variation to associate with different sets of bioclimatic variables for each species, with precipitation relatively less important for the parasite. Spatial patterns of predicted adaptive variability were different and indicate that co‐occurring species with disparate life history traits may not respond equally to selective pressures (i.e., temperature and precipitation). Together, these findings provide insight into local adaptation of sympatric parasitic and autotrophic tree species to abiotic environments.     

Lack of adaptation from standing genetic variation despite the presence of putatively adaptive alleles in introduced sweet vernal grass (Anthoxanthum odoratum)

Population genetic theory predicts that the availability of appropriate standing genetic variation should facilitate rapid evolution when species are introduced to new environments. However, few tests of rapid evolution have been paired with empirical surveys for the presence of previously identified adaptive genetic variants in natural populations. In this study, we examined local adaptation to soil Al toxicity in the introduced range of sweet vernal grass (Anthoxanthum odoratum), and we genotyped populations for the presence of Al tolerance alleles previously identified at the long‐term ecological Park Grass Experiment (PGE, Harpenden, UK) in the species native range. We found that markers associated with Al tolerance at the PGE were present at appreciable frequency in introduced populations. Despite this, there was no strong evidence of local adaptation to soil Al toxicity among populations. Populations demonstrated significantly different intrinsic root growth rates in the absence of Al. This suggests that selection on correlated root growth traits may constrain the ability of populations to evolve significantly different root growth responses to Al. Our results demonstrate that genotype–phenotype associations may differ substantially between the native and introduced parts of a species range and that adaptive alleles from a native species range may not necessarily promote phenotypic differentiation in the introduced range.     

Combining genotype,phenotype, and environmental data to delineate site‐adjusted provenance strategies for ecological restoration

Despite the importance of climate‐adjusted provenancing to mitigate the effects of environmental change, climatic considerations alone are insufficient when restoring highly degraded sites. Here we propose a comprehensive landscape genomic approach to assist the restoration of moderately disturbed and highly degraded sites. To illustrate it we employ genomic data sets comprising thousands of single nucleotide polymorphisms from two plant species suitable for the restoration of iron‐rich Amazonian Savannas. We first use a subset of neutral loci to assess genetic structure and determine the genetic neighbourhood size. We then identify genotype‐phenotype‐environment associations, map adaptive genetic variation, and predict adaptive genotypes for restoration sites. Whereas local provenances were found optimal to restore a moderately disturbed site, a mixture of genotypes seemed the most promising strategy to recover a highly degraded mining site. We discuss how our results can help define site‐adjusted provenancing strategies, and argue that our methods can be more broadly applied to assist other restoration initiatives.     

Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity

Adaptive differences across species’ ranges can have important implications for population persistence and conservation management decisions. Despite advances in genomic technologies, detecting adaptive variation in natural populations remains challenging. Key challenges in gene–environment association studies involve distinguishing the effects of drift from those of selection and identifying subtle signatures of polygenic adaptation. We used paired‐end restriction site‐associated DNA sequencing data (6,605 biallelic single nucleotide polymorphisms; SNPs) to examine population structure and test for signatures of adaptation across the geographic range of an iconic Australian endemic freshwater fish species, the Murray cod Maccullochella peelii. Two univariate gene–association methods identified 61 genomic regions associated with climate variation. We also tested for subtle signatures of polygenic adaptation using a multivariate method (redundancy analysis; RDA). The RDA analysis suggested that climate (temperature‐ and precipitation‐related variables) and geography had similar magnitudes of effect in shaping the distribution of SNP genotypes across the sampled range of Murray cod. Although there was poor agreement among the candidate SNPs identified by the univariate methods, the top 5% of SNPs contributing to significant RDA axes included 67% of the SNPs identified by univariate methods. We discuss the potential implications of our findings for the management of Murray cod and other species generally, particularly in relation to informing conservation actions such as translocations to improve evolutionary resilience of natural populations. Our results highlight the value of using a combination of different approaches, including polygenic methods, when testing for signatures of adaptation in landscape genomic studies.     

A heuristic model on the role of plasticity in adaptive evolution: plasticity increases adaptation,population viability and genetic variation

An ongoing new synthesis in evolutionary theory is expanding our view of the sources of heritable variation beyond point mutations of fixed phenotypic effects to include environmentally sensitive changes in gene regulation. This expansion of the paradigm is necessary given ample evidence for a heritable ability to alter gene expression in response to environmental cues. In consequence, single genotypes are often capable of adaptively expressing different phenotypes in different environments, i.e. are adaptively plastic. We present an individual-based heuristic model to compare the adaptive dynamics of populations composed of plastic or non-plastic genotypes under a wide range of scenarios where we modify environmental variation, mutation rate and costs of plasticity. The model shows that adaptive plasticity contributes to the maintenance of genetic variation within populations, reduces bottlenecks when facing rapid environmental changes and confers an overall faster rate of adaptation. In fluctuating environments, plasticity is favoured by selection and maintained in the population. However, if the environment stabilizes and costs of plasticity are high, plasticity is reduced by selection, leading to genetic assimilation, which could result in species diversification. More broadly, our model shows that adaptive plasticity is a common consequence of selection under environmental heterogeneity, and hence a potentially common phenomenon in nature. Thus, taking adaptive plasticity into account substantially extends our view of adaptive evolution.     

Evolution in heterogeneous environments and the potential of maintenance of genetic variation in traits of adaptive significance

The maintenance of genetic variation in traits of adaptive significance has been a major dilemma of evolutionary biology. Considering the pattern of increased genetic variation associated with environmental clines and heterogeneous environments, selection in heterogeneous environments has been proposed to facilitate the maintenance of genetic variation. Some models examining whether genetic variation can be maintained, in heterogeneous environments are reviewed. Genetic mechanisms that constrain evolution in quantitative genetic traits indicate that genetic variation can be maintained but when is not clear. Furthermore, no comprehensive models have been developed, likely due to the genetic and environmental complexity of this issue. Therefore, I have suggested two empirical approaches to provide insight for future theoretical and empirical research. Traditional path analysis has been a very powerful approach for understanding phenotypic selection. However, it requires substantial information on the biology of the study system to construct a causal model and alternatives. Exploratory path analysis is a data driven approach that uses the statistical relationships in the data to construct a set of models. For example, it can be used for understanding phenotypic selection in different environments, where there is no prior information to develop path models in the different environments. Data from Brassica rapa grown in different nutrients indicated that selection changed in the different environments. Experimental evolutionary studies will provide direct tests as to when genetic variation is maintained.     

Genomic Architecture of Rapid Parallel Adaptation to Fresh Water in a Wild Fish

Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. However, the genetic architecture underlying these adaptive changes is still poorly understood. Using population genomic approaches, we investigated the genomic architecture that underlies rapid parallel adaptation of Coilia nasus to fresh water by comparing four freshwater-resident populations with their ancestral anadromous population. Linkage disequilibrium network analysis and population genetic analyses revealed two putative large chromosome inversions on LG6 and LG22, which were enriched for outlier loci and exhibited parallel association with freshwater adaptation. Drastic frequency shifts and elevated genetic differentiation were observed for the two chromosome inversions among populations, suggesting that both inversions would undergo divergent selection between anadromous and resident ecotypes. Enrichment analysis of genes within chromosome inversions showed significant enrichment of genes involved in metabolic process, immunoregulation, growth, maturation, osmoregulation, and so forth, which probably underlay differences in morphology, physiology and behavior between the anadromous and freshwater-resident forms. The availability of beneficial standing genetic variation, large optimum shift between marine and freshwater habitats, and high efficiency of selection with large population size could lead to the observed rapid parallel adaptive genomic change. We propose that chromosomal inversions might have played an important role during the evolution of rapid parallel ecological divergence in the face of environmental heterogeneity in C. nasus. Our study provides insights into the genomic basis of rapid adaptation of complex traits in novel habitats and highlights the importance of structural genomic variants in analyses of ecological adaptation.     

Adaptive phenotypic and genomic divergence in the common chaffinch (Fringilla coelebs) following niche expansion within a small oceanic island

According to models of ecological speciation, adaptation to adjacent, contrasting habitat types can lead to population divergence given strong enough environment-driven selection to counteract the homogenizing effect of gene flow. We tested this hypothesis in the common chaffinch (Fringilla coelebs) on the small island of La Palma, Canary Islands, where it occupies two markedly different habitats. Isotopic (δ¹³C, δ¹⁵N) analysis of feathers indicated that birds in the two habitats differed in ecosystem and/or diet, and analysis of phenotypic traits revealed significant differences in morphology and plumage colouration that are consistent with ecomorphological and ecogeographical predictions respectively. A genome-wide survey of single-nucleotide polymorphism revealed marked neutral structure that was consistent with geography and isolation by distance, suggesting low dispersal. In contrast, loci putatively under selection identified through genome-wide association and genotype-environment association analyses, revealed a marked adaptive divergence between birds in both habitats. Loci associated with phenotypic and environmental differences among habitats were distributed across the genome, as expected for polygenic traits involved in local adaptation. Our results suggest a strong role for habitat-driven local adaptation in population divergence in the chaffinches of La Palma, a process that appears to be facilitated by a strong reduction in effective dispersal distances despite the birds' high dispersal capacity.     

The search for loci under selection: trends,biases and progress

Detecting genetic variants under selection using F_ST outlier analysis (OA) and environmental association analyses (EAAs) are popular approaches that provide insight into the genetic basis of local adaptation. Despite the frequent use of OA and EAA approaches and their increasing attractiveness for detecting signatures of selection, their application to field‐based empirical data have not been synthesized. Here, we review 66 empirical studies that use Single Nucleotide Polymorphisms (SNPs) in OA and EAA. We report trends and biases across biological systems, sequencing methods, approaches, parameters, environmental variables and their influence on detecting signatures of selection. We found striking variability in both the use and reporting of environmental data and statistical parameters. For example, linkage disequilibrium among SNPs and numbers of unique SNP associations identified with EAA were rarely reported. The proportion of putatively adaptive SNPs detected varied widely among studies, and decreased with the number of SNPs analysed. We found that genomic sampling effort had a greater impact than biological sampling effort on the proportion of identified SNPs under selection. OA identified a higher proportion of outliers when more individuals were sampled, but this was not the case for EAA. To facilitate repeatability, interpretation and synthesis of studies detecting selection, we recommend that future studies consistently report geographical coordinates, environmental data, model parameters, linkage disequilibrium, and measures of genetic structure. Identifying standards for how OA and EAA studies are designed and reported will aid future transparency and comparability of SNP‐based selection studies and help to progress landscape and evolutionary genomics.     

Utility of closely related taxa for genetic studies of adaptive variation and speciation: Current state and perspectives in plants with focus on forest tree species

Studies of adaptation and speciation have greatly benefited from rapid progress of DNA sequencing and genotyping technologies. Comparative genomics of closely related taxa has great potential to advance evolutionary research on genetic architecture of adaptive traits and reproductive isolation. Such studies that utilized closely related plant species and ecotypes have already provided some important insights into genomic regions and/or genes that are potentially involved in local adaptation and speciation. The choice of an appropriate species model for such research is crucial. The paper discusses current approaches used to reveal the patterns of intra‐ and interspecific divergence due to natural selection. Its outcomes in herbaceous plants and forest trees are briefly summarized and compared to reveal general regularities concerning evolutionary processes. We then highlight the importance of multispecies studies and discuss the utility of several related pine taxa as fine candidates for evolutionary inferences. Genetically similar but ecologically and phenotypically diverged taxa seem a promising study system to search for genomic patterns of speciation and adaptive variation.