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215 results for “environmental adaptation”
Landscape genomics reveals genetic signals of environmental adaptation of African wild eggplant
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The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic
The Arctic is one of the most extreme terrestrial environments on the planet. Here we present the first complete genome assembly of a plant adapted to the high Arctic, Draba nivalis (Brassicaceae), an attractive model species for studying plant adaptation to the stresses imposed by this harsh environment. We used an iterative scaffolding strategy with data from short-reads, single-molecule long reads, proximity ligation data, and a genetic map to produce a 302 Mb assembly that is highly contiguous with 91.6% assembled into eight chromosomes (the base chromosome number). To identify candidate genes and gene families that may have facilitated adaptation to Arctic environmental stresses, we performed comparative genomic analyses with nine non-Arctic Brassicaceae species. We show that the D. nivalis genome contains expanded suites of genes associated with drought and cold stress (e.g. related to the maintenance of oxidation-reduction homeostasis, meiosis, and signaling pathways). The expansions of gene families associated with these functions appear to be driven in part by the activity of transposable elements. Tests of positive selection identify suites of candidate genes associated with meiosis and photoperiodism, as well as cold, drought, and oxidative stress responses. Our results reveal a multifaceted landscape of stress adaptation in the D. nivalis genome, offering avenues for the continued development of this species as an Arctic model plant.
Data from : Environmental predictability drives adaptive within- and transgenerational plasticity of heat tolerance across life stages and climatic regions
<p>Although environmental variability and predictability have been proposed as the underlying ecological context in which transgenerational plasticity (<i>TGP</i>) arises, the adaptive significance and interaction with within-generation plasticity (<i>WGP</i>) in such scenarios is still poorly understood. In order to investigate these questions, we considered the tolerance to upper thermal limits of larvae and adults of the desert endemic <i>Drosophila mojavensis </i>adapted to different climatic regions (Desert vs Mediterranean climate). Thermal plasticity was investigated by acclimating parents and offspring at 36°C (versus at 25°C). We then used historical temperature variation data from both regions to perform individual-based simulations by modeling expected components of adaptive plasticity in multiple life stages. Thermal response to ramping heat shocks was more pronounced in larvae, where acclimation treatments in parents and offspring increased their heat-shock performance, while heat knockdown in adults was only increased by offspring acclimation of adults. The relative contribution of <i>WGP</i> and <i>TGP</i> was greater for the population from the more thermally variable Sonoran Desert. Similarly, individual-based simulations of evolving maternal effects indicated that variation in tolerance to upper thermal limits across life stages and climates is expected from its adaptive significance in response to environmental predictability. Our approach offers a new perspective and interpretation of adaptive plasticity, demonstrating that environmental predictability can drive thermal responses across generations and life stages in a scenario with regional climate variability.</p>
Data from: Signatures of selection and environmental adaptation across the goat genome post-domestication
<p>Background: Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, approximately 600 goat breeds have developed worldwide; they differ considerably from one another in terms of phenotypic characteristics and are adapted to a wide range of climatic conditions. In this work, we analyzed the AdaptMap goat dataset, which is composed of data from more than 3000 animals collected worldwide and genotyped with the CaprineSNP50 BeadChip. These animals were partitioned into groups based on geographical area, production uses, available records on solid coat color and environmental variables including the sampling geographical coordinates, to investigate the role of natural and/or artificial selection in shaping the genome of goat breeds.</p> <p>Results: Several signatures of selection on different chromosomal regions were detected across the different breeds, sub-geographical clusters, phenotypic and climatic groups. These regions contain genes that are involved in important biological processes, such as milk-, meat- or fiber-related production, coat color, glucose pathway, oxidative stress response, size, and circadian clock differences. Our results confirm previous findings in other species on adaptation to extreme environments and human purposes and provide new genes that could explain some of the differences between goat breeds according to their geographical distribution and adaptation to different environments.</p> <p>Conclusions: These analyses of signatures of selection provide a comprehensive first picture of the global domestication process and adaptation of goat breeds and highlight possible genes that may have contributed to the differentiation of this species worldwide.</p>
Data from: Seascape genomics reveals adaptive divergence in a connected and commercially important mollusc, the greenlip abalone (Haliotis laevigata), along a longitudinal environmental gradient
Populations of broadcast spawning marine organisms often have large sizes and are exposed to reduced genetic drift. Under such scenarios, strong selection associated with spatial environmental heterogeneity is expected to drive localized adaptive divergence, even in the face of connectivity. We tested this hypothesis using a seascape genomics approach in the commercially important greenlip abalone (Haliotis laevigata). We assessed how its population structure has been influenced by environmental heterogeneity along a zonal coastal boundary in southern Australia linked by strong oceanographic connectivity. Our datasets include 9,109 filtered SNPs for 371 abalones from 13 localities and environmental mapping across ~800 km. Genotype-environment association analyses and outlier tests defined 8,786 putatively neutral and 323 candidate adaptive loci. From a neutral perspective, the species is better represented by a metapopulation with very low differentiation (global FST=0.0081) and weak isolation by distance following a stepping stone model. For the candidate adaptive loci, however, model-based and model-free approaches indicated five divergent population clusters. After controlling for spatial distance, the distribution of putatively adaptive variation was strongly correlated to selection linked to minimum sea surface temperature and oxygen concentration. Around 80 candidates were annotated to genes with functions related to high temperature and/or low oxygen tolerance, including genes that influence the resilience of abalone species found in other biogeographic regions. Our study includes a documented example about the uptake of genomic information in fisheries management and supports the hypothesis of adaptive divergence due to coastal environmental heterogeneity in a connected metapopulation of a broadcast spawner.
Data from: Evolution of mating behaviour between two populations adapting to common environmental conditions
Populations from the same species may be differentiated across contrasting environments, potentially affecting reproductive isolation among them. When such populations meet in a novel common environment, this isolation may be modified by biotic or abiotic factors. Curiously, the latter have been overlooked. We filled this gap by performing experimental evolution of three replicates of two populations of Drosophila subobscura adapting to a common laboratorial environment, and simulated encounters at three time points during this process. Previous studies showed that these populations were highly differentiated for several life-history traits and chromosomal inversions. First, we show initial differentiation for some mating traits, such as assortative mating and male mating rate, but not others (e.g., female mating latency). Mating frequency increased during experimental evolution in both sets of populations. The assortative mating found in one population remained constant throughout the adaptation process, while disassortative mating of the other population diminished across generations. Additionally, differences in male mating rate were sustained across generations. This study shows that mating behavior evolves rapidly in response to adaptation to a common abiotic environment, although with a complex pattern that does not correspond to the quick convergence seen for life-history traits.
Data from: Does genetic variation maintained by environmental heterogeneity facilitate adaptation to novel selection?
Environmental heterogeneity helps maintain genetic variation in fitness. Therefore, one might predict that populations living in heterogeneous environments have higher adaptive potential than populations living in homogeneous environments. Such a prediction could be useful in guiding conservation priorities without requiring detailed genetic studies. However, this prediction will be true only if the additional genetic variation maintained by environmental heterogeneity can be used to respond to novel selection. Here we examine the effect of environmental heterogeneity on future adaptability using replicated experimental Drosophila melanogaster populations that had previously evolved for ∼100 generations under one of four selective regimes: constant salt-enriched larvae medium, constant cadmium-enriched larvae medium, and two heterogeneous regimes that vary either temporally or spatially between the two media. Replicates of these experimental populations were subjected to a novel heat stress while being maintained in their original larval diet selection regimes. Adaptation to increased temperature was measured with respect to female productivity and male siring success after ∼20 generations. For female productivity, there was evidence of adaptation overall and heterogeneous populations had a larger adaptive response than homogeneous populations. There was less evidence of adaptation overall for male siring success and no support for faster adaptation in heterogeneous populations.
Data from: Detection of environmental and morphological adaptation despite high landscape genetic connectivity in a pest grasshopper (Phaulacridium vittatum)
Widespread species that exhibit both high gene flow and the capacity to occupy heterogeneous environments make excellent models for examining local selection processes along environmental gradients. Here we evaluate the influence of temperature and landscape variables on genetic connectivity and signatures of local adaptation in Phaulacridium vittatum, a widespread agricultural pest grasshopper, endemic to Australia. With sampling across a 900 km latitudinal gradient, we genotyped 185 P. vittatum from 19 sites at 11,408 single nucleotide polymorphisms (SNPs) using ddRAD sequencing. Despite high gene flow across sites (pairwise Fst = 0.0003-0.08), landscape genetic resistance modelling identified a positive non-linear effect of mean annual temperature on genetic connectivity. Urban areas and water bodies had a greater influence on genetic distance among sites than pasture, agricultural areas, and forest. Together, Fst outlier tests and Environmental Association Analysis (EAA) detected 242 unique SNPs under putative selection, with the highest numbers associated with latitude, mean annual temperature, and body size. A combination of landscape genetic connectivity analysis together with EAA identified mean annual temperature as a key driver of both neutral gene flow and environmental selection processes. Gene annotation of putatively adaptive SNPs matched with gene functions for olfaction, metabolic detoxification and ultra-violet light shielding. Our results imply that this widespread agricultural pest has the potential to spread and adapt under shifting temperature regimes and land cover change.
Data from: Microgeographic patterns of genetic divergence and adaptation across environmental gradients in Boechera stricta (Brassicaceae)
Abiotic and biotic conditions often vary continuously across the landscape, imposing divergent selection on local populations. We used a provenance trial approach to examine microgeographic variation in local adaptation in Boechera stricta (Brassicaceae), a perennial forb native to the Rocky Mountains. In montane ecosystems, environmental conditions change considerably over short spatial scales, such that neighboring populations can be subject to different selective pressures. Using accessions from southern (Colorado) and northern (Idaho) populations, we characterized spatial variation in genetic similarity via microsatellite markers. We then transplanted genotypes from multiple local populations into common gardens in both regions. Continuous variation in local adaptation emerged for several components of fitness. In Idaho, genotypes from warmer environments (low elevation or south facing sites) were poorly adapted to the north-facing garden. In high and low elevation Colorado gardens, susceptibility to insect herbivory increased with source elevation. In the high elevation Colorado garden, germination success peaked for genotypes that evolved at similar elevations as the garden, and declined for genotypes from higher and lower elevations. We also found evidence for local maladaptation in survival and fecundity components of fitness in the low elevation Colorado garden. This approach is a necessary first step in predicting how global change could affect evolutionary dynamics.
Data from: Parental environmental effects due to contrasting watering adapt competitive ability, but not drought tolerance, in offspring of a semi-arid annual Brassicaceae
1. Parental effects (PE) can be adaptive and improve offspring performance when parents and offspring experience similar environmental conditions. However, it is unknown whether adaptive PE exist also in habitats where such similarity is unlikely due to strong temporal variation. In particular, we do not know whether PE can adapt offspring to fluctuating levels of neighbour competition in such habitats. 2. Here, we tested for adaptive PE in terms of two key environmental factors in a semi-arid annual system, competition and drought. While rainfall was stochastic in the study site, the competitive environment was partly predictable: higher plant densities followed after favourable (rainy) years due to high seed production. We therefore expected PE to adapt the offspring's competitive ability to these (predictable) fluctuations in plant densities, rather than to adapt the offspring's drought tolerance to the (unpredictable) occurrence of intensified drought. 3. Parental plants of Biscutella didyma, an annual Brassicaceae, were raised under favourable watering and under drought conditions. Offspring performance was then tested under a full-factorial combination of two neighbour regimes and six watering levels in the glasshouse. 4. Offspring of parents grown under favourable conditions were stronger competitors. This was associated with a small shift in phenology but not with higher parental seed provisioning. Offspring from parents grown under drought showed no improved drought tolerance. Moreover, no PE were detectable when offspring were grown without neighbours. 5. Our results suggest a novel path of adaptive PE: higher competitive ability was induced in offspring that were more likely to experience high neighbour densities. Together with the lack of adaptive PE towards drought tolerance, this emphasizes that a correlation between parental and offspring environment is crucial for adaptive PE to evolve. Our results also call for the inclusion of competitive effects in future PE studies. 6. Synthesis. This study demonstrates the important role of adaptive PE for plant fitness (regarding competition) but also their limits (regarding drought) in temporally variable environments, based on the predictability of the respective environmental factor.
Data from: Adaptations between ecotypes and along environmental gradients in Panicum virgatum
Determining the patterns and mechanisms of natural selection in the wild is of fundamental importance to understanding the differentiation of populations and the evolution of new species. However, it is often unknown the extent to which adaptive genetic variation is distributed among ecotypes between distinct habitats versus along large-scale geographic environmental gradients, such as those that track latitude. Classic selection in the wild experiments in switchgrass, Panicum virgatum, tested for adaptation at both of these levels of natural variation. Here we review what these field experiments, as well as modern agronomic field trials, have taught us about natural variation and selection at both the ecotype and environmental gradient level in P. virgatum. With the recent genome sequencing efforts of P. virgatum, it is poised to become an excellent system for understanding the adaptation of grassland species across the eastern half of North America. The identification of genetic loci involved in different types of adaptations will help to understand the evolutionary mechanisms of diversification within P. virgatum and provide useful information for the breeding of high yielding cultivars for different ecoregions.
Data from: Maternal effects in a wild songbird are environmentally plastic but only marginally alter the rate of adaptation
Despite ample evidence for the presence of maternal effects (MEs) in a variety of traits and strong theoretical indications for their evolutionary consequences, empirical evidence to what extent MEs can influence evolutionary responses to selection remains ambiguous. We tested the degree to which MEs can alter the rate of adaptation of a key life-history trait, clutch size, using an individual-based model approach parameterized with experimental data from a long-term study of great tits (Parus major). We modeled two types of MEs: (i) an environmentally plastic ME, in which the relationship between maternal and offspring clutch size depended on the maternal environment via offspring condition, and (ii) a fixed ME, in which this relationship was constant. Although both types of ME affected the rate of adaptation following an abrupt environmental shift, the overall effects were small. We conclude that evolutionary consequences of MEs are modest at best in our study system, at least for the trait and the particular type of ME we considered here. A closer link between theoretical and empirical work on MEs would hence be useful to obtain accurate predictions about the evolutionary consequences of MEs more generally.
Data from: Evidence of local adaptation to fine- and coarse-grained environmental variability in Poa alpina in the Swiss Alps
In the alpine landscape, characterized by high spatiotemporal heterogeneity and barriers, divergent selection is likely to lead to local adaptation of plant populations either through adaptive genetic differentiation or through phenotypic plasticity. The relative importance of these processes has rarely been investigated in relation to the spatial scale of environmental heterogeneity. In this study, we used reciprocal transplantation experiments of populations across nearby and distant field sites to shed light on these complementary processes. We reciprocally transplanted populations of the widespread alpine grass, Poa alpina, within and across regions in the Swiss Alps. We inferred local adaptation at the metapopulation level by comparing fitness of plants transplanted to their site of origin and to nearby or distant novel sites. Additionally, we measured specific leaf area (SLA) and performed selection analyses to investigate directional selection on mean trait value at each field site and on the degree of plasticity of this trait to assess whether plastic responses were adaptive. In parallel, all populations were genotyped with microsatellite markers to assess neutral molecular differentiation. Molecular differentiation was high among populations within and among regions, indicating restricted gene flow among P. alpina populations. Reproductive biomass was highest in individuals grown in their region of origin, revealing local adaptation to coarse-grained environmental variability. Similarly, inflorescence height, associated with reproductive biomass, reflected adaptation to fine- and coarse-grained environmental variability. Furthermore, we found evidence that plasticity in SLA across coarse-grained habitats was correlated with plant fitness, suggesting that plasticity in this trait is adaptive. Synthesis. Our results revealed adaptive genetic differentiation between P. alpina populations in the Swiss Alps reflecting local adaptation. Furthermore, high phenotypic plasticity in SLA contributed to the maintenance of fitness homoeostasis across habitats. Hence, adaptive genetic differentiation and phenotypic plasticity play a complementary role for adaption of P. alpina to environmental heterogeneity in the Swiss Alps and both may be critical to mitigate local extinction risk under rapid climate change.
Data from: Adaptive genetic divergence along narrow environmental gradients in four stream insects
A central question linking ecology with evolutionary biology is how environmental heterogeneity can drive adaptive genetic divergence among populations. We examined adaptive divergence of four stream insects from six adjacent catchments in Japan by combining field measures of habitat and resource components with genome scans of non-neutral Amplified Fragment Length Polymorphism (AFLP) loci. Neutral genetic variation was used to measure gene flow and non-neutral genetic variation was used to test for adaptive divergence. We identified the environmental characteristics contributing to divergence by comparing genetic distances at non-neutral loci between sites with Euclidean distances for each of 15 environmental variables. Comparisons were made using partial Mantel tests to control for geographic distance. In all four species, we found strong evidence for non-neutral divergence along environmental gradients at between 6 and 21 loci per species. The relative contribution of these environmental variables to each species' ecological niche was quantified as the specialization index, S, based on ecological data. In each species, the variable most significantly correlated with genetic distance at non-neutral loci was the same variable along which each species was most narrowly distributed (i.e., highest S). These were gradients of elevation (two species), chlorophyll-a, and ammonia-nitrogen. This adaptive divergence occurred in the face of ongoing gene flow (Fst = 0.01–0.04), indicating that selection was strong enough to overcome homogenization at the landscape scale. Our results suggest that adaptive divergence is pronounced, occurs along different environmental gradients for different species, and may consistently occur along the narrowest components of species' niche.
Data from: Accounting for observation processes across multiple levels of uncertainty improves inference of species distributions and guides adaptive sampling of environmental DNA
Understanding factors that influence observation processes is critical for accurate assessment of underlying ecological processes. When indirect methods of detection, such as environmental DNA, are used to determine species presence, additional levels of uncertainty from observation processes need to be accounted for. We conducted a field trial to evaluate observation processes of a terrestrial invasive species (wild pigs- Sus scrofa) from DNA in water bodies. We used a multi-scale occupancy analysis to estimate different levels of observation processes (detection, p): the probability DNA is available per sample (θ), the probability of capturing DNA per extraction (γ), and the probability of amplification per qPCR run (δ). We selected four sites for each of three water body types and collected 10 samples per water body during two months (September and October 2016) in central Texas. Our methodology can be used to guide sampling adaptively to minimize costs while improving inference of species distributions. Using a removal sampling approach was more efficient than pooling samples, and was unbiased. Availability of DNA varied by month, was considerably higher when water pH was near neutral, and was higher in ephemeral streams relative to wildlife guzzlers and ponds. To achieve a cumulative detection probability greater than 90% (including availability, capture, and amplification), future studies should collect 20 water samples per site, conduct at least 2 extractions per sample, and conduct 5 qPCR replicates per extraction. Accounting for multiple levels of uncertainty of observation processes improved estimation of the ecological processes and provided guidance for future sampling designs.
Data from: Genetic architecture of adaptation to novel environmental conditions in a predominantly selfing allopolyploid plant
Genetic architecture of adaptation is traditionally studied in the context of local adaptation, viz. spatially varying conditions experienced by the species. However, human made changes in the natural environment pose a new context to this issue, i.e. adaptation to an environment that is new for the species. In this study, we used crossbreeding to analyze genetic architecture of adaptation to conditions not currently experienced by the species but with high probability of encounter in the near future due to the global climate change. We performed targeted inter-population crossing using genotypes from two core and two peripheral Triticum dicoccoides populations and grew up the parents and three generations of hybrids in a greenhouse under simulated desert conditions to analyze the genetic architecture of adaptation to these conditions and an effect of gene flow from plants having different origin. The observed in allopolyploid T. dicoccoides low importance of epistatic gene interactions and low probability of hybrid breakdown appear to be the result of permanent fixation of heterozygosity and lack of inter-genomic recombination in this species. At the same time, predominant but not complete selfing combined with an advantage of bivalent pairing of homologous chromosomes appear to maintain high genetic variability in T. dicoccoides, greatly enhancing its adaptive ability.
Data from: Environmental adaptation in Chinook salmon (Oncorhynchus tshawytscha) throughout their North American range
Landscape genomics is a rapidly growing field with recent advances in both genotyping efficiency and statistical analyses that provide insight towards local adaptation of populations under varying environmental and selective pressure. Chinook salmon (Oncorhynchus tshawytscha) are a broadly distributed Pacific salmon species, occupying a diversity of habitats throughout the northeastern Pacific with pronounced variation in environmental and climate features but little is understood regarding local adaptation in this species. We used a multivariate method, redundancy analysis (RDA), to identify polygenic correlations between 19 703 SNP loci and a suite of environmental variables in 46 collections of Chinook salmon (1956 total individuals) distributed throughout much of its North American range. Models in RDA were conducted on both rangewide and regional scales by hierarchical partitioning of the populations into three distinct genetic lineages. Our results indicate that between 5.8 and 21.8% of genomic variation can be accounted for by environmental features, and 566 putatively adaptive loci were identified as targets of environmental adaptation. The most influential drivers of adaptive divergence included precipitation in the driest quarter of the year (Rangewide and North Coastal Lineage, anova P = 0.002 and 0.01, respectively), precipitation in the wettest quarter of the year (Interior Columbia River Stream-Type Lineage, anova P = 0.03), variation in mean diurnal range in temperature (South Coastal Lineage, anova P = 0.005), and migration distance (Rangewide, anova P = 0.001). Our results indicate that environmental features are strong drivers of adaptive genomic divergence in this species, and provide a foundation to investigate how Chinook salmon might respond to global environmental change.
Data from: Parallel evolution and adaptation to environmental factors in a marine flatfish: implications for fisheries and aquaculture management of the turbot (Scophthalmus maximus)
Unraveling adaptive genetic variation represents, in addition to the estimate of population demographic parameters, a cornerstone for the management of aquatic natural living resources, which in turn, represent the raw material for breeding programs. The turbot (Scophthalmus maximus) is a marine flatfish of high commercial value living on the European continental shelf. While wild populations are declining, aquaculture is flourishing in Southern Europe. We evaluated the genetic structure of turbot throughout its natural distribution range (672 individuals; 20 populations) by analyzing allele frequency data from 755 Single Nucleotide Polymorphism discovered and genotyped by Double Digest RAD Sequencing. The species was structured into four main regions: Baltic Sea, Atlantic Ocean, Adriatic Sea and Black Sea, with subtle differentiation apparent at the distribution margins of the Atlantic region. Genetic diversity and effective population size estimates were highest in the Atlantic populations, the area of greatest occurrence, while turbot from other regions showed lower levels, reflecting geographical isolation and reduced abundance. Divergent selection was detected within and between the Atlantic Ocean and Baltic Sea regions, and also when comparing these two regions with the Black Sea. Evidence of parallel evolution was detected between the two low salinity regions, the Baltic and Black seas. Correlation between genetic and environmental variation indicated that temperature and salinity were probably the main environmental drivers of selection. Mining around the four genomic regions consistently inferred to be under selection identified candidate genes related to osmoregulation, growth and resistance to diseases. The new insights are useful for the management of turbot fisheries and aquaculture by providing the baseline for evaluating the consequences of turbot releases from restocking and farming.
Data from: Adaptive evolution and environmental durability jointly structure phylodynamic patterns in avian influenza viruses
Avian influenza viruses (AIVs) have been pivotal to the origination of human pandemic strains. Despite their scientific and public health significance, however, there remains much to be understood about the ecology and evolution of AIVs in wild birds, where major pools of genetic diversity are generated and maintained. Here, we present comparative phylodynamic analyses of human and AIVs in North America, demonstrating (i) significantly higher standing genetic diversity and (ii) phylogenetic trees with a weaker signature of immune escape in AIVs than in human viruses. To explain these differences, we performed statistical analyses to quantify the relative contribution of several potential explanations. We found that HA genetic diversity in avian viruses is determined by a combination of factors, predominantly subtype-specific differences in host immune selective pressure and the ecology of transmission (in particular, the durability of subtypes in aquatic environments). Extending this analysis using a computational model demonstrated that virus durability may lead to long-term, indirect chains of transmission that, when coupled with a short host lifespan, can generate and maintain the observed high levels of genetic diversity. Further evidence in support of this novel finding was found by demonstrating an association between subtype-specific environmental durability and predicted phylogenetic signatures: genetic diversity, variation in phylogenetic tree branch lengths, and tree height. The conclusion that environmental transmission plays an important role in the evolutionary biology of avian influenza viruses—a manifestation of the "storage effect"—highlights the potentially unpredictable impact of wildlife reservoirs for future human pandemics and the need for improved understanding of the natural ecology of these viruses.
Data from: Environmental adaptation contributes to gene polymorphism across the Arabidopsis thaliana genome
The level of within-species polymorphism differs greatly among genes in a genome. Many genomic studies have investigated the relationship between gene polymorphism and factors such as recombination rate or expression pattern. However, the polymorphism of a gene is affected not only by its physical properties or functional constraints, but also by natural selection on organisms in their environments. Specifically, if functionally divergent alleles enable adaptation to different environments, locus-specific polymorphism may be maintained by spatially heterogeneous natural selection. To test this hypothesis and estimate the extent to which environmental selection shapes the pattern of genome-wide polymorphism, we define the 'environmental relevance' of a gene as the proportion of genetic variation explained by environmental factors, after controlling for population structure. We found substantial effects of environmental relevance on patterns of polymorphism among genes. In addition, the correlation between environmental relevance and gene polymorphism is positive, consistent with the expectation that balancing selection among heterogeneous environments maintains genetic variation at ecologically important genes. Comparison of the gene ontology annotations shows that genes with high environmental relevance are enriched in unknown function categories. These results suggest an important role for environmental factors in shaping genome-wide patterns of polymorphism and indicate another direction of genomic study.
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