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223 results for “adaptive selection”
Data from: Scans for signatures of selection in Russian cattle breed genomes reveal new candidate genes for environmental adaptation and acclimation
Domestication and selective breeding has resulted in over 1000 extant cattle breeds. Many of these breeds do not excel in important traits but are adapted to local environments. These adaptations are a valuable source of genetic material for efforts to improve commercial breeds. As a step toward this goal we identified candidate regions to be under selection in genomes of nine Russian native cattle breeds adapted to survive in harsh climates. After comparing our data to other breeds of European and Asian origins we found known and novel candidate genes that could potentially be related to domestication, economically important traits and environmental adaptations in cattle. The Russian cattle breed genomes contained regions under putative selection with genes that may be related to adaptations to harsh environments (e.g., AQP5, RAD50, and RETREG1). We found genomic signatures of selective sweeps near key genes related to economically important traits, such as the milk production (e.g., DGAT1, ABCG2), growth (e.g., XKR4), and reproduction (e.g., CSF2). Our data point to candidate genes which should be included in future studies attempting to identify genes to improve the extant breeds and facilitate generation of commercial breeds that fit better into the environments of Russia and other countries with similar climates.
Data from: The prediction of adaptive evolution: empirical application of the secondary theorem of selection and comparison to the breeder's equation
Adaptive evolution occurs when fitness covaries with genetic merit for a trait (or traits). The breeder's equation (BE), in both its univariate and multivariate forms, allows us to predict this process by combining estimates of selection on phenotype with estimates of genetic (co)variation. However, predictions are only valid if all factors causal for trait-fitness covariance are measured. While this requirement will rarely (if ever) be met in practice, it can be avoided by applying Robertson's secondary theorem of selection (STS). The STS predicts evolution by directly estimating the genetic basis of trait-fitness covariation with out any explicit model of selection. Here we apply the BE and STS to four morphological traits measured in Soay sheep (Ovis aries) from St. Kilda. Despite apparently positive selection on heritable size traits, sheep are not getting larger. However, while the BE predicts increasing size the STS does not, a discrepancy that suggests unmeasured factors are upwardly biasing our estimates of selection on phenotype. We suggest this is likely to be a general issue, and that wider application of the STS could offer at least a partial resolution to the common discrepancy between naive expectations and observed trait dynamics in natural populations.
Adaptation to a bacterial pathogen in Drosophila melanogaster is not aided by sexual selection
<p>Theory predicts that sexual selection should aid adaptation to novel environments, but empirical support for this idea is limited. Pathogens are a major driver of host evolution and, unlike abiotic selection pressures, undergo epidemiological and co-evolutionary cycles with the host involving adaptation and counteradaptation. Because of this, populations harbor ample genetic variation underlying immunity and the opportunity for sexual selection based on condition-dependent "good genes" is expected to be large. In this study, we evolved populations of <em>Drosophila melanogaster</em> in a 2-way factorial design manipulating sexual selection and pathogen presence, using a gram-negative insect pathogen <em>Pseudomonas entomophila</em>, for 14 generations. We then examined how the presence of sexual selection and the pathogen, as well as any potential interaction, affected the evolution of pathogen resistance. We found increased resistance to <em>P. entomophila</em> in populations that evolved under pathogen pressure, driven primarily by increased female survival after infection despite selection for resistance acting only on males over the course of experimental evolution. This result suggests that the genetic basis of resistance is in part shared between the sexes. We did not find any evidence of sexual selection aiding adaptation to pathogen, however, a finding contrary to the predictions of "good genes" theory. Our results therefore provide no support for a role for sexual selection in the evolution of immunity in this experimental system.</p>
Introgression, admixture and selection facilitate genetic adaptation to high-altitude environments in Chinese cattle
<p>Domestication and subsequent selection of cattle to form breeds and biological types that can adapt to different environments partitioned ancestral genetic diversity into distinct modern lineages. Genome-wide selection particularly for adaptation to extreme environments left detectable signatures genome-wide. We used high-density genotype data for 42 cattle breeds and identified the influence of <em>Bos grunniens</em> and <em>Bos javanicus</em> on the formation of Chinese indicine breeds that led to their divergence from India-origin Zebu. We also found evidence for introgression, admixture, and migration in most of the Chinese breeds. Selection signature analyses between high-altitude (>1800m) and low-altitude adapted breeds (<1500m) revealed candidate genes (<em>ACSS2</em>, <em>ALDOC,</em> <em>EPAS1</em>,<em> EGLN1, NUCB2</em>) and pathways that are putatively involved in hypoxia adaptation. Immunohistochemical, real-time PCR and CRISPR/cas9 <em>ACSS2</em>-knockout analyses suggests that the up-regulation of <em>ACSS2</em> expression in the liver promotes the metabolic adaptation of cells to hypoxia via the hypoxia-inducible factor pathway. High altitude adaptation involved the introgression of alleles from high-altitude adapted Yaks into Chinese <em>B. t. taurus </em>prior to their formation into recognized breeds and followed by selection. In addition to selection, adaptation to high altitude environments has been facilitated by admixture and introgression with locally adapted cattle populations.</p>
Both selection and drift drive the spatial pattern of adaptive genetic variation in a wild mammal
<p><span>The major histocompatibility complex (MHC) has been intensively studied to test for the relative effects of different evolutionary forces in recent decades. Pathogen-mediated balancing selection is generally thought to explain the high polymorphism observed in MHC genes, but it is still unclear to what extent MHC diversity is shaped by selection relative to neutral drift. In this study, we genotyped MHC class II DRB genes and 15 neutral microsatellite loci across 26 geographic populations of European badgers (<em>Meles meles</em>) covering most of their geographic range. By comparing the variation of microsatellites and the diversity of MHC at different levels, we demonstrate that both balancing selection and drift have shaped the evolution of MHC genes. When only MHC allelic identity was investigated, the spatial pattern of MHC variation was similar to that of microsatellites. By contrast, when functional aspects of the MHC diversity (e.g. immunological supertypes) were considered, balancing selection appears to decrease genetic structuring across populations. Our comprehensive sampling and analytical approach enable us to conclude that the likely mechanisms of selection are heterozygote advantage and/or rare-allele advantage. This study is a clear demonstration of how both balancing selection and genetic drift simultaneously affect the evolution of MHC genes in a widely-distributed wild mammal.</span></p>
Data from: Effects of gene action, marker density, and time since selection on the performance of landscape genomic scans of local adaptation
Genomic "scans" to identify loci that contribute to local adaptation are becoming increasingly common. Many methods used for such studies have assumed that local adaptation is created by loci experiencing antagonistic pleiotropy and that the selected locus itself is assayed, and few consider how signals of selection change through time. However, most empirical data sets have marker density too low to assume that a selected locus itself is assayed, researchers seldom know when selection was first imposed, and many locally adapted loci likely experience not antagonistic pleiotropy but conditional neutrality. We simulated data to evaluate how these factors affect the performance of tests for genotype-environment association. We found that three types of regression-based analyses (linear models, mixed linear models, and latent factor mixed models) and an implementation of BayEnv all performed well, with high rates of true positives and low rates of false positives, when the selected locus experienced antagonistic pleiotropy, and when the selected locus was assayed directly. However, all tests had reduced power to detect loci experiencing conditional neutrality, and the probability of detecting associations was sharply reduced when physically linked rather than causative loci were sampled. Antagonistic pleiotropy also maintained detectable genotype-environment associations much longer than conditional neutrality. Our analyses suggest that if local adaptation is often driven by loci experiencing conditional neutrality, genome-scan methods will have limited capacity to find loci responsible for local adaptation.
Data from: Selection from parasites favors immunogenetic diversity but not divergence among locally adapted host populations
The unprecedented polymorphism in the major histocompatibility complex (MHC) genes is thought to be maintained by balancing selection from parasites. However, do parasites also drive divergence at MHC loci between host populations, or do the effects of balancing selection maintain similarities among populations? We examined MHC variation in populations of the livebearing fish Poecilia mexicana and characterized their parasite communities. Poecilia mexicana populations in the Cueva del Azufre system are locally adapted to darkness and the presence of toxic hydrogen sulfide, and represent highly divergent ecotypes or incipient species. Parasite communities differed significantly across populations, and populations with higher parasite loads had higher levels of diversity at class II MHC genes. However, despite different parasite communities, marked divergence in adaptive traits and in neutral genetic markers, we found MHC alleles to be remarkably similar among host populations. Our findings indicate that balancing selection from parasites maintains immunogenetic diversity of hosts, but this process does not promote MHC divergence in this system. On the contrary, we suggest that balancing selection on immunogenetic loci may outweigh divergent selection causing divergence, thereby hindering host divergence and speciation. Our findings support the hypothesis that balancing selection maintains MHC similarities among lineages during and after speciation (trans-species evolution).
Selection in space and time: individual tree growth is adapted to tropical forest gap dynamics
<p>In the present study, we assessed genotypic diversity within closely-related sympatric tree species belonging to the widespread tropical tree species complex <em>Symphonia globulifera</em>. We addressed the fine-scale spatial and temporal genetic adaptations of individuals through differential growth strategies in response to forest gap dynamics. We finally compared the breadth of successional niches encountered by <em>Symphonia</em> species to other locally abundant species. Combining tree diameter censuses, indirect measures of light environment of the recent past and present, and single nucleotide polymorphisms (SNPs), we used population genomics, environmental association analyses, genome wide association and growth modelling to address the following questions:</p> <ul> <li>Are individual genotypes structured by the mosaic of light and competition environments resulting from forest gap dynamics?</li> <li>Is the growth of individuals determined by genotypes?</li> <li>Is there an association between genotypic adaptations to gap dynamics and to growth?</li> <li>How are genotypic adaptations to gap dynamics and to growth structured in time, i.e., across life stages?</li> <li>Are breadths of successional niches for <em>Symphonia</em> species wider than those of other locally abundant species?</li> </ul> <p>Find the analyses here : https://sylvainschmitt.github.io/GOING/introduction.html</p>
Local adaptation through countergradient selection in northern populations of Skeletonema marinoi
<p><span>Marine microorganisms have the potential to disperse widely with few obvious barriers to gene flow. However, among microalgae, several studies have demonstrated that species can be highly genetically structured with limited gene flow among populations, despite hydrographic connectivity. Ecological differentiation and local adaptation have been suggested as drivers of such population structure. Here we tested whether multiple strains from two genetically distinct Baltic Sea populations of the diatom <em>Skeletonema</em> <em>marinoi</em> showed evidence of local adaptation to their local environments; the estuarine Bothnian Sea and the marine Kattegat Sea. We performed reciprocal transplants of multiple strains between culture media based on water from the respective environments, and we also allowed competition between strains of estuarine and marine origin in both salinities. When grown alone, both marine and estuarine strains performed best in the high salinity environment, and estuarine strains always grew faster than marine strains. This result suggests local adaptation through countergradient selection, i.e. genetic effects counteract environmental effects. However, higher growth rate of the estuarine strains appears to have a cost in the marine environment and when strains were allowed to compete, marine strains performed better than estuarine strains in the marine environment. Thus, other traits are likely to also affect fitness. We provide evidence that tolerance to pH could be involved, and that estuarine strains which are adapted to a more fluctuating pH continue growing at higher pH than marine strains. </span></p>
Data for: Consequences of adaptation to larval crowding on sexual and fecundity selection in Drosophila melanogaster
<p><span>Sexual selection is a major force influencing the evolution of sexually reproducing species. Environmental factors such as larval density can manipulate adult condition and influence the direction and strength of sexual selection. While most studies on the influence of larval crowding on sexual selection are either correlational or single-generation manipulations, it is unclear how evolution under chronic larval crowding affects sexual selection. To answer this, we measured the strength of sexual selection of male and female <em>Drosophila</em> <em>melanogaster</em> that had evolved under chronic larval crowding for over 250 generations in the laboratory, along with their controls which had never experienced crowding, in a common garden high-density environment</span><span>. We measured selection coefficients on male mating success and sex-specific reproductive success, as separate estimates allowed dissection of sex-specific effects. We show that experimental evolution under chronic larval crowding decreases the strength of sexual and fecundity selection in males, but not in females, relative to populations experiencing crowding for the first time. The effect of larval crowding in reducing reproductive success is almost twice that in females than in males. Our study highlights the importance of studying how evolution in a novel, stressful environment can shape adult fitness in organisms. </span></p>
Supplemental data of the comment on "Sexual selection promotes giraffoid head-neck evolution and ecological adaptation"
<p>This dataset is the supplemental data of the comment paper on "Sexual selection promotes giraffoid head-neck evolution and ecological adaptation" (Hou et al., 2023, Science 379, eadd9559). 333 codings are rescored and the statements of 10 characters are modified, with notes and explanations in the Microsoft Excel file. </p>
Assessing the Efficacy and Safety of Selective Metabolically Adaptive Radiation Dose Escalation in Locally Advanced Non-Small Cell Lung Cancer Receiving Definitive Chemoradiotherapy
ClinicalTrials.gov study NCT02788461. IPD Sharing: NO. Countries: 1. Publications: 1.
Prospective Validation of 3D Dose Metrics as Selection Criteria for Adaptive Radiotherapy in Breast Cancer Patients
ClinicalTrials.gov study NCT03385031. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Adaptive Radiotherapy Using Plan Selection for Bladder Cancer
ClinicalTrials.gov study NCT01762527. IPD Sharing: Not stated. Countries: 1. Publications: 4.
Data from: Genomic response to selection for predatory behavior in a mammalian model of adaptive radiation
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Data from: Body size evolution on islands: are adult size variations in tiger snakes a non-adaptive consequence of selection on birth size?
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Introgression, admixture and selection facilitate genetic adaptation to high-altitude environments in Chinese cattle
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Data from: Control of adaptive action selection by secondary motor cortex during flexible visual categorization
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Data from: Energetic benefits and adaptations in mammalian limbs: scale effects and selective pressures
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Data from: Signatures of selection for environmental adaptation and zebu x taurine hybrid fitness in East African Shorthorn Zebu
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