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305 results for “divergent adaptation”
Data from: Temperature-dependent gene regulatory divergence underlies local adaptation with gene flow in the Atlantic silverside
<p>Gene regulatory divergence is thought to play an important role in adaptation, yet its extent and underlying mechanisms remain largely elusive for local adaptation with gene flow. Local adaptation is widespread in marine species despite generally high connectivity and is often associated with tightly linked genomic architectures, such as chromosomal inversions. To investigate gene regulatory evolution under gene flow and the role of inversions associated with local adaptation to a steep thermal gradient, we generated RNA-seq data from Atlantic silversides (<em>Menidia menidia</em>) from two locally adapted populations and their F1 hybrids, reared under two temperatures. We found substantial divergence in gene expression and thermal plasticity between populations, with up to 31% of genes being differentially expressed. Reduced thermal plasticity, temperature-dependent gene misexpression and the disruption of co-expression networks in hybrids point towards a role of regulatory incompatibilities in local adaptation, particularly under colder temperatures. Chromosomal inversions show an accumulation of regulatory incompatibilities but are not consistently enriched for differentially expressed genes. Together, these results suggest that gene regulation can diverge substantially among populations despite gene flow, partly due to the accumulation of temperature-dependent regulatory incompatibilities within inversions.</p>
Genetic divergence and local adaptation of Liriodendron driven by heterogeneous environments
<p><span>Ecological adaptive differentiation alters both the species diversity and intraspecific genetic diversity in forests, thus affecting the stability of forest ecosystems. Therefore, knowledge of the genetic underpinnings of the ecological adaptive differentiation of forest species is critical for effective species conservation. In this study, single-nucleotide polymorphisms (SNPs) from population transcriptomes were used to investigate the spatial distribution of genetic variation in <i>Liriodendron</i> to assess whether environmental variables can explain genetic divergence. We examined the contributions of environmental variables to population divergence and explored the genetic underpinnings of local adaptation using a landscape genomic approach. Niche models and statistical analyses showed significant niche divergence between <i>L. chinense</i> and <i>L. tulipifera</i>, suggesting that ecological adaptation may play a crucial role in driving interspecific divergence. We detected a new fine-scale genetic structure in <i>L. chinense</i>, and divergence of the six groups occurred during the late Pliocene to early Pleistocene. Redundancy analysis (RDA) revealed significant associations between genetic variation and multiple environmental variables. Environmental association analyses identified 67 environmental association loci (EALs; nonsynonymous SNPs) that underwent interspecific or intraspecific differentiation, 28 of which were associated with adaptive genes. These 28 candidate adaptive loci provide substantial evidence for local adaptation in <i>Liriodendron</i>. Our findings reveal ecological adaptive divergence pattern between <i>Liriodendron</i> species and provide novel insight into the role of heterogeneous environments in shaping genetic structure and driving local adaptation among populations, informing future <i>L. chinense</i> conservation efforts. </span></p>
Phenotype and QTL mapping data from: Genetic trade-offs underlie divergent life history strategies for local adaptation in white clover
<p>Local adaptation is common in plants, yet characterization of its underlying genetic basis is rare in herbaceous perennials. Moreover, while many plant species exhibit intraspecific chemical defense polymorphisms, their importance for local adaptation remains poorly understood. We examined the genetic architecture of local adaptation in a perennial, obligately-outcrossing herbaceous legume, white clover (<i>Trifolium repens</i>). This widespread species displays a well-studied chemical defense polymorphism for cyanogenesis (HCN release following tissue damage) and has evolved climate-associated cyanogenesis clines throughout its range. Two biparental F<sub>2</sub> mapping populations, derived from three parents collected in environments spanning the U.S. latitudinal species range (Duluth, MN, St. Louis, MO and Gainesville, FL), were grown in triplicate for two years in reciprocal common garden experiments in the parental environments (6,012 total plants). Vegetative growth and reproductive fitness traits displayed trade-offs across reciprocal environments, indicating local adaptation. Genetic mapping of fitness traits revealed a genetic architecture characterized by allelic trade-offs between environments, with 100% and 80% of fitness QTL in the two mapping populations showing significant QTL X E interactions, consistent with antagonistic pleiotropy. Across the genome there were three hotspots of QTL co-localization. Unexpectedly, we found little evidence that the cyanogenesis polymorphism contributes to local adaptation. Instead, divergent life history strategies in reciprocal environments were major fitness determinants: selection favored early investment in flowering at the cost of multi-year survival in the southernmost site vs. delayed flowering and multi-year persistence in the northern environments. Our findings demonstrate that multi-locus genetic tradeoffs contribute to contrasting life history characteristics that allow for local adaptation in this outcrossing herbaceous perennial.</p>
Adaptive divergence generates distinct plastic responses in two closely related Senecio species
<p><span>The evolution of plastic responses to external cues allows species to maintain fitness in response to the environmental variation they regularly experience. However, it remains unclear how plasticity evolves during adaptation. To test whether distinct patterns of plasticity are associated with adaptive divergence, we quantified plasticity for two closely related but ecologically divergent Sicilian daisy species (<i>Senecio, </i>Asteraceae). We sampled c.40 representative genotypes of each species from their native range on Mt Etna and then reciprocally transplanted multiple clones of each genotype into four field sites along an elevational gradient that included the native elevational range of each species, and two intermediate elevations. At each elevation we quantified survival and measured leaf traits that included investment (specific leaf area), morphology, chlorophyll fluorescence, pigment content and gene expression. Traits and differentially expressed genes that changed with elevation in one species often showed little change in the other species, or changed in the opposite direction. As evidence of adaptive divergence, both species performed better at their native site and better than the species from the other habitat. Adaptive divergence is therefore associated with the evolution of distinct plastic responses to environmental variation, despite these two species sharing a recent common ancestor.</span></p>
Divergence in Heliconius flight behaviour is associated with local adaptation to different forest structures
<p>Micro-habitat choice plays a major role in shaping local patterns of biodiversity. In butterflies, stratification in flight height has an important role in maintaining community diversity. The speciation in <em>Heliconius</em> butterflies is often associated with strong assortative mating, but ecological isolation and local adaptation is also considered essential. Despite its presumed importance, the role of behavioural shifts in early stages of speciation in response to differences in habitat structure is yet to be established. Here, we investigated variation in flight height behaviour in two closely related species, <em>H. erato cyrbia</em> and <em>H. himera</em>, which produce viable hybrids but are isolated across an environmental gradient, spanning lowland wet forest to high altitude scrub forest. We show that the two species fly at different heights in the wild, and demonstrate that this can be explained by differences in the vertical distribution of plant resources. We subsequently explored whether this divergence in flight height has a genetic component using common garden experiments. In both the wild and captivity, <em>H. himera</em> choose to fly lower and feed at lower positions, mirroring differences in resource availability in the wild. We suggest that this shift in foraging behaviour may reflect local adaptation to divergent forest structures highlighting the role of behaviour during early stages of speciation.</p>
Genomic divergence, local adaptation, and complex demographic history may inform management of a popular sportfish species complex
<p>We investigated genomic divergence, interspecific and intraspecific diversity and population structure, local directional selection, and complex demographic history in a popular freshwater species complex in the Central Interior Highlands, North America. Specifically, we assessed differentiation between the Neosho Bass (<em>Micropterus velox</em>) and Smallmouth Bass (<em>M. dolomieu</em>) where their ranges are parapatric in this ecoregion. We scanned the genome for signatures of local direction and mapped divergence at selected SNPs at the population level. Additionally, we identified stream populations with extensive admixture, and we used a model-testing framework to investigate complex demographic histories between the two species.</p> <p>Raw ddRADseq .fastq sequence files, along with intermediate processing files, finalized VCF files, a data summary report, and other data information, are given in the "smb_ddRAD_rawdata.tar file. Metadata, including sample_id, species designation, and stream population, are given in the "metadata.xlsx" file.</p>
Data and supplementary materials from: Large genetic divergence underpins cryptic local adaptation across ecological and evolutionary gradients
<p><span>Environmentally covarying local adaptation is a form of cryptic local adaptation in which the covariance of the genetic and environmental effects on a phenotype obscures the divergence between locally adapted genotypes. Here, we systematically document the magnitude and drivers of the genetic effect (V<sub>G</sub>) for two forms of environmentally covarying local adaptation: counter- and cogradient variation. Using a hierarchical Bayesian meta-analysis, we calculated the overall effect size of V<sub>G</sub> as 1.05 and 2.13 for populations exhibiting countergradient or cogradient variation, respectively. These results indicate that the genetic contribution to phenotypic variation represents a 1.05 to 2.13 standard deviation change in trait value between the most disparate populations depending on if populations are expressing counter- or cogradient variation. We also found that while there was substantial variance among abiotic and biotic covariates, the covariates with the largest mean effects were temperature (2.41) and gamete size (2.81). Our results demonstrate the pervasiveness and large genetic effects underlying environmentally covarying local adaptation in wild populations and highlights the importance of accounting for these effects in future studies.</span></p>
High-density genomic data reveal fine-scale population structure and pronounced islands of adaptive divergence in lake whitefish (Coregonus clupeaformis) from Lake Michigan
<p>Understanding patterns of genetic structure and adaptive variation in natural populations is crucial for informing conservation and management. Past genetic research using 11 microsatellite loci identified six genetic stocks of lake whitefish (<em>Coregonus clupeaformis</em>) within Lake Michigan, USA. However, ambiguity in genetic stock assignments suggested those neutral microsatellite markers did not provide adequate power for delineating lake whitefish stocks in this system, prompting calls for a genomics approach to investigate stock structure. Here, we generated a dense genomic dataset to characterize population structure and investigate patterns of neutral and adaptive genetic diversity among lake whitefish populations in Lake Michigan. Using Rapture sequencing, we genotyped 829 individuals collected from 17 baseline populations at 197,588 SNP markers after quality filtering. Although the overall pattern of genetic structure was similar to the previous microsatellite study, our genomic data provided several novel insights. Our results indicated a large genetic break between the northwestern and eastern sides of Lake Michigan, and we found a much greater level of population structure on the eastern side compared to the northwestern side. Collectively, we observed five genomic islands of adaptive divergence on five different chromosomes. Each island displayed a different pattern of population structure, suggesting that combinations of genotypes at these adaptive regions are facilitating local adaptation to spatially heterogenous selection pressures. Additionally, we identified a large linkage disequilibrium block of ~8.5 Mb on chromosome 20 that is suggestive of a putative inversion but with a low frequency of the minor haplotype. Our study provides a comprehensive assessment of population structure and adaptive variation that can help inform management of Lake Michigan's lake whitefish fishery and highlights the utility of incorporating adaptive loci into fisheries management. </p>
Dimensionality and modularity of adaptive variation: Divergence in threespine stickleback from diverse environments
<p>Populations are subjected to diverse environmental conditions that affect fitness and induce evolutionary or plastic responses, resulting in phenotypic divergence among populations. Some authors contend such divergence is concentrated along a single major axis of trait covariance, even if that axis does not lead populations directly toward fitness optimum. Other authors argue that divergence can occur readily along many phenotype axes at the same time. We use populations of threespine stickleback (<em>Gasterosteus aculeatus</em>) from 14 lakes with contrasting ecological conditions to find some resolution along the continuum between these two extremes. Unlike many previous studies, we included several functional suites of traits (defensive, swimming, trophic) potentially subject to different sources of selection. We find that populations exhibit dimensionality of divergence that is high enough to preclude a history of constraint along a single axis – both for divergence in multivariate mean trait values and for the structure of trait covariances. Dimensionality varied among trait suites and were strongly influenced by the inclusion of specific traits, and integration of trait suites varied between populations. We leverage this variation into new insights about the process of divergence and suggest that similar analyses could increase understanding of other adaptive radiations. </p>
Genomic signatures of rapid adaptive divergence in a tropical montane species
<p>This dataset contains data from a study described in the paper: Ericson, P.G.P., Irestedt, M., She, H., and Qu, Y. (2021) "Genomic signatures of rapid adaptive divergence in a tropical montane species". <em>Biology Letters</em> (in print).</p> <p>The study investigates allopatric divergence and selection in Archbold's Bowerbird (<i>Amblyornis papuensis</i>), an iconic bird living in a tropical mountain region in New Guinea, using a novel chromosome-level genome and population genomic comparisons.</p> <p>Our results show that the two populations inhabiting the eastern and western Central Range became isolated ca 11,800 years ago, probably because the suitable habitats for this cold-tolerating bird decreased when the climate got warmer. Our genomic scans detect that genes in highly divergent genomic regions are over-represented in developmental processes, which is likely associated with the observed differences in body size between the populations. Overall, our results suggest that environmental differences between eastern and western Central Range likely drive adaptive divergence between them.</p>
Data from: Genomic differentiation during speciation-with-gene-flow: comparing geographic and host-related variation in divergent life history adaptation in Rhagoletis pomonella
A major goal of evolutionary biology is to understand how variation within populations gets partitioned into differences between reproductively isolated species. Here, we examine the degree to which diapause life history timing, a critical adaptation promoting population divergence, explains geographic and host-related genetic variation in ancestral hawthorn and recently derived apple-infesting races of Rhagoletis pomonella. Our strategy involved combining experiments on two different aspects of diapause (initial diapause intensity and adult eclosion time) with a geographic survey of genomic variation across four sites where apple and hawthorn flies co-occur from north to south in the Midwestern USA. The results demonstrated that the majority of the genome showing significant geographic and host-related variation can be accounted for by initial diapause intensity and eclosion time. Local genomic differences between sympatric apple and hawthorn flies were subsumed within broader geographic clines; allele frequency differences within the races across the Midwest were 2 to 3-fold greater than those between the races in sympatry. As a result, sympatric apple and hawthorn populations displayed more limited genomic clustering compared to geographic populations within the races. The findings suggest that with reduced gene flow and increased selection on diapause equivalent to that seen between geographic sites, the host races may be recognized as different genotypic entities in sympatry, and perhaps species, a hypothesis requiring future genomic analysis of related sibling species to R. pomonella to test. Our findings concerning the way selection and geography interplay could be of broad significance for many cases of earlier stages of divergence-with-gene flow, including (1) where only modest increases in geographic isolation and the strength of selection may greatly impact genetic coupling and (2) the dynamics of how spatial and temporal standing variation is extracted by selection to generate differences between new and discrete units of biodiversity.
Evolutionary divergence of potential drought adaptations between two subspecies of an annual plant: Are trait combinations facilitated, independent, or constrained?
<p><b><span>Premise</span></b><span>: Whether drought-adaptation mechanisms tend to evolve together, evolve independently, and/or evolve constrained by genetic architecture is incompletely resolved, particularly for water relations traits besides gas exchange. We addressed this issue in two subspecies of </span><i>Clarkia xantiana</i><span> (Onagraceae), California winter annuals that separated approximately 65,000 years ago and are adapted, partly by differences in flowering time, to native ranges differing in precipitation.</span></p> <p><b><span>Methods: </span></b><span>In these subspecies and in recombinant inbred lines (RILs) from a cross between them we scored traits related to drought adaptation (timing of seed germination and of flowering; succulence; pressure-volume curve parameters) in common environments.</span></p> <p><b><span>Results: </span></b><span>The subspecies native to more arid environments (<i>parviflora</i>) exhibited slower seed germination in saturated conditions, earlier flowering, and greater succulence, likely indicating superior drought avoidance, drought escape, and dehydration resistance via water storage, respectively. The other subspecies (<i>xantiana</i>) had lower osmotic potential at full turgor and lower water potential at turgor loss, implying superior dehydration tolerance. Genetic correlations among RILs suggest facilitated evolution of some trait combinations and independence of others. Where genetic correlations exist, subspecies differences fell along them, with the exception of differences in succulence and turgor loss point. In that case, subspecies difference overcame genetic correlations, possibly reflecting strong selection and/or antagonistic genetic correlations with other traits. </span></p> <p><b><span>Conclusions:</span></b><span> <i>Clarkia xantiana </i>subspecies' differ in multiple mechanisms of drought adaptation. Genetic architecture generally does not seem to have constrained the evolution of these mechanisms, and it may have facilitated the evolution of some of trait combinations. </span></p>
Data from: Genome-wide analysis reveals associations between climate and regional patterns of adaptive divergence and dispersal in American pikas
<p>Understanding the role of adaptation in species responses to climate change is important for evaluating the evolutionary potential of populations and informing conservation efforts. Population genomics provides a useful approach for identifying putative signatures of selection and the underlying environmental factors or biological processes that may be involved. Here, we employed a population genomic approach within a space-for-time study design to investigate the genetic basis of local adaptation and reconstruct patterns of movement across rapidly changing environments in a thermally-sensitive mammal, the American pika (<i>Ochotona princeps</i>). Using genotypic data at 49,074 single nucleotide polymorphisms (SNPs), we analyzed patterns of genome-wide diversity, structure, and migration along three independent elevational transects located at the northern extent (Tweedsmuir South Provincial Park, British Columbia, Canada) and core (North Cascades National Park, Washington, USA) of the Cascades lineage. We identified 899 robust outlier SNPs within- and among-transects. Of those annotated to genes with known function, many were linked with cellular processes related to climate stress including ATP-binding, ATP citrate synthase activity, ATPase activity, hormone activity, metal ion-binding, and protein-binding. Moreover, we detected evidence for contrasting patterns of directional migration along transects across geographic regions that suggest an increased propensity for American pikas to disperse among lower elevation populations at higher latitudes where environments are generally cooler. Ultimately, our data indicate that fine-scale demographic patterns and adaptive processes may vary among populations of American pikas, providing an important context for evaluating biotic responses to climate change in this species and other alpine-adapted mammals.</p>
Divergent response and adaptation of specific leaf area to environmental change at different spatio-temporal scales jointly improve plant survival
<p><span>Specific leaf area (SLA) is one of the most important plant functional traits. </span><span>It </span><span>integrates multiple functions and reflects strategies of plants to obtain resources. </span><span>How plants employ different strategies (e.g., through SLA) to respond to dynamic environmental conditions remains poorly understood.This study aimed to </span><span>explore the s</span><span>patial variation in SLA and divergent adaptation of plants by changing SLA </span><span>through the lens of biogeographic patterns, evolutionary history, and short-term responses. SLA data for 5424 plant species from 76 natural communities in China were systematically measured and integrated with meta-analysis of field experiments (i.e., global warming, drought, and nitrogen addition). The mean value of SLA across all species was 21.8 m2 kg–1, ranging from 0.9 to 110.2 m2 kg–1. SLA differed among different ecosystems, temperature zones, vegetation types, and functional groups. Phylogeny had a weak effect on SLA, but plant species evolved toward higher SLA. Furthermore, plants responded nonlinearly to environmental change by changing SLA. Unexpectedly, radiation was one of the main factors determining the spatial variation in SLA on a large scale. Conversely, short-term manipulative experiments showed that SLA increased with increased resource availability and tended to stabilize with treatment duration. However, different species exhibited varying response patterns. Overall, long-term adaptation of plants to environmental gradients and its short-term response to resource pulses through variation in SLA jointly improve plant adaptability to a changing environment. Overall SLA-environment relationships should be emphasized as a multidimensional strategy for elucidating environmental change in future research. </span></p>
The genetic basis of plumage coloration and elevation adaptation in a clade of recently diverged alpine and arctic songbirds
<p>Trait genetic architecture plays an important role in the probability that variation in that trait leads to divergence and speciation. In some cases, speciation may be driven by the generation of novel phenotypes through the recombination of genes associated with traits that are important for local adaptation or sexual selection. Here, we investigate the genetic basis of three plumage color traits, and one ecological trait, breeding elevation, in a recent avian radiation, the North American rosy-finches (<em>Leucosticte</em> spp.). We identify unique genomic regions associated with each trait and highlight 11 candidate genes. Among these are well-characterized melanogenesis genes, including Mitf and Tyrp1, and previously reported hypoxia-related genes including Egln1. Additionally, we use mitochondrial data to date the divergence of rosy-finch clades which appear to have diverged within the past 250 ky. Given the low levels of genome-wide differentiation among rosy-finch taxa, and evidence for extensive introgression in North America, plumage coloration and adaptation to high elevations have likely played large roles in generating the observed patterns of lineage divergence. The relative independence of these candidate regions across the genome suggests that recombination might have led to multiple phenotypes, and subsequent rosy-finch speciation, over short periods of time.</p>
Data from: Components of local adaptation and divergence in pollination efficacy in a coevolving species interaction
<p>Selection leading to adaptation to interactions may generate rapid evolutionary feedbacks and drive diversification of species interactions. The challenge is to understand how the many traits of interacting species combine to shape local adaptation in ways directly or indirectly resulting in diversification. We used the well-studied interactions between <em>Lithophragma</em> plants (Saxifragaceae) and <em>Greya</em> moths (Prodoxidae) to evaluate how plants and moths together contribute to local divergence in pollination efficacy. Specifically, we studied <em>L. bolanderi</em> and its two specialized <em>Greya</em> moth pollinators in two contrasting environments in the Sierra Nevada, California. Both moths pollinate <em>L. bolanderi</em> during nectaring, and one of them – <em>G. politella</em> – also while ovipositing through the floral corolla into the ovary. Firstly, field surveys of floral visitors and the presence of <em>G. politella</em> eggs and larvae in developing capsules showed that one population is visited only by <em>G. politella</em> and few other pollinators, whereas the other is visited by both <em>Greya</em> species and other pollinators. Secondly, <em>L. bolanderi</em> in these two natural populations differed in several floral traits putatively important for pollination efficacy. Thirdly, laboratory experiments with greenhouse-grown plants and field-collected moths showed that <em>L. bolanderi</em> is more efficiently pollinated by local compared to non-local nectaring moths of both species. Pollination efficacy of ovipositing <em>G. politella</em> was also higher for local moths for the <em>L. bolanderi</em> population that relies more heavily on this species in nature. Finally, time-lapse photography in the laboratory showed that <em>G. politella</em> from different populations differ in oviposition behavior, suggesting the potential for local adaptation also among <em>Greya</em> populations. Collectively, our results are a rare example of components of local adaptation contributing to divergence in pollination efficiency in a coevolving interaction and, thus, provide insights into how geographic mosaics of coevolution may lead to coevolutionary diversification in species interactions.</p>
Data from: A comparative test for divergent adaptation: inferring speciation drivers from functional trait divergence
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Data from: Adaptive landscape genetics and malaria across divergent island bird populations
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Natural toxic impact and thyroid signaling interplay orchestrates riverine adaptive divergence of salmonid fish
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Genomic signatures of rapid adaptive divergence in a tropical montane species
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