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A map of climate change-driven natural selection in Arabidopsis thaliana

https://doi.org/10.1101/321133
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Overview of Admixture Mapping
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1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana
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Random Forests
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Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines
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Climate change and evolutionary adaptation
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The genomic basis of adaptive evolution in threespine sticklebacks
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On the post-glacial spread of human commensal Arabidopsis thaliana
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Middle-Eastern plant communities tolerate 9 years of drought in a multi-site climate manipulation experiment
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Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel
inferredcites →https://doi.org/10.1038/ng.2678openalex-snapshot
Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden
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A unified mixed-model method for association mapping that accounts for multiple levels of relatedness
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Anthropogenic warming exacerbates European soil moisture droughts
inferredcites →https://doi.org/10.1038/s41559-017-0423-0openalex-snapshot
Genomic basis and evolutionary potential for extreme drought adaptation in Arabidopsis thaliana
inferredcites →https://doi.org/10.1038/s41559-017-0434-xopenalex-snapshot
Genotypic variability enhances the reproducibility of an ecological study
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TerraClimate, a high-resolution global dataset of monthly climate and climatic water balance from 1958–2015
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Drought stress and carbon uptake in an Amazon forest measured with spaceborne imaging spectroscopy
inferredcites →https://doi.org/10.1073/pnas.1421416112openalex-snapshot
Coselected genes determine adaptive variation in herbivore resistance throughout the native range of Arabidopsis thaliana
inferredcites →https://doi.org/10.1073/pnas.1702994114openalex-snapshot
Seasonally fluctuating selection can maintain polymorphism at many loci via segregation lift
inferredcites →https://doi.org/10.1073/pnas.1709141115openalex-snapshot
Adaptive diversification of growth allometry in the plant Arabidopsis thaliana
inferredcites →https://doi.org/10.1073/pnas.1719998115openalex-snapshot
Combining population genomics and fitness QTLs to identify the genetics of local adaptation in Arabidopsis thaliana
inferredcites →https://doi.org/10.1086/281699openalex-snapshot
Aridity as a Stimulus to Plant Evolution
inferredcites →https://doi.org/10.1086/281792openalex-snapshot
Genetic Equilibrium When More Than One Ecological Niche is Available
inferredcites →https://doi.org/10.1086/319193openalex-snapshot
The Strength of Phenotypic Selection in Natural Populations
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PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
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A Quantitative Survey of Local Adaptation and Fitness Trade‐Offs
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The variant call format and VCFtools
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S weep F inder 2: increased sensitivity, robustness and flexibility
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General Models of Multilocus Evolution
inferredcites →https://doi.org/10.1093/nar/gkw986openalex-snapshot
AraPheno: a public database for Arabidopsis thaliana phenotypes
inferredcites →https://doi.org/10.1098/rsbl.2014.0871openalex-snapshot
Mutation accumulation and the formation of range limits
inferredcites →https://doi.org/10.1098/rspb.2016.2104openalex-snapshot
Rates of change in climatic niches in plant and animal populations are much slower than projected climate change
inferredcites →https://doi.org/10.1101/186767openalex-snapshot
A rainfall-manipulation experiment with 517 Arabidopsis thaliana accessions
inferredcites →https://doi.org/10.1101/208512openalex-snapshot
Image-based methods for phenotyping growth dynamics and fitness components in Arabidopsis thaliana
inferredcites →https://doi.org/10.1101/337543openalex-snapshot
Broad geographic sampling reveals predictable, pervasive, and strong seasonal adaptation in Drosophila
inferredcites →https://doi.org/10.1101/gr.4252305openalex-snapshot
Genomic scans for selective sweeps using SNP data
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Coherent synthesis of genomic associations with phenotypes and home environments
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Identifying targets and agents of selection: innovative methods to evaluate the processes that contribute to local adaptation
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The spatial patterns of directional phenotypic selection
inferredcites →https://doi.org/10.1111/ele.12238openalex-snapshot
Experimental evidence for ecological selection on genome variation in the wild
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Ecological genomics meets community‐level modelling of biodiversity: mapping the genomic landscape of current and future environmental adaptation
inferredcites →https://doi.org/10.1111/ele.12604openalex-snapshot
A synthesis of transplant experiments and ecological niche models suggests that range limits are often niche limits
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Time to get moving: assisted gene flow of forest trees
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STRONG SELECTION GENOME-WIDE ENHANCES FITNESS TRADE-OFFS ACROSS ENVIRONMENTS AND EPISODES OF SELECTION
inferredcites →https://doi.org/10.1111/evo.13508openalex-snapshot
Spatio-temporal variation in fitness responses to contrasting environments inArabidopsis thaliana
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05522.xopenalex-snapshot
Genetic trade‐offs and conditional neutrality contribute to local adaptation
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05709.xopenalex-snapshot
Characterizing genomic variation of Arabidopsis thaliana : the roles of geography and climate
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It’s about time: the temporal dynamics of phenotypic selection in the wild
inferredcites →https://doi.org/10.1111/j.1467-9868.2005.00503.xopenalex-snapshot
Regularization and Variable Selection Via the Elastic Net
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THE GENETIC BASIS OF EVOLUTIONARY CHANGE
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PLEIOTROPY CAUSES LONG‐TERM GENETIC CONSTRAINTS ON LIFE‐HISTORY EVOLUTION INBRASSICA RAPA
inferredcites →https://doi.org/10.1111/mec.13559openalex-snapshot
The genetic consequences of selection in natural populations
inferredcites →https://doi.org/10.1111/mec.13867openalex-snapshot
Multilocus approaches for the measurement of selection on correlated genetic loci
inferredcites →https://doi.org/10.1126/science.1209244openalex-snapshot
Adaptation to Climate Across the Arabidopsis thaliana Genome
inferredcites →https://doi.org/10.1126/science.1209271openalex-snapshot
A Map of Local Adaptation in Arabidopsis thaliana
inferredcites →https://doi.org/10.1126/science.aaa4984openalex-snapshot
Accelerating extinction risk from climate change
inferredcites →https://doi.org/10.1126/science.aan4380openalex-snapshot
Genomic signals of selection predict climate-driven population declines in a migratory bird
inferredcites →https://doi.org/10.1126/science.aap9125openalex-snapshot
Natural selection and the predictability of evolution in Timema stick insects
inferredcites →https://doi.org/10.1126/science.aar3646openalex-snapshot
The projected effect on insects, vertebrates, and plants of limiting global warming to 1.5°C rather than 2°C
inferredcites →https://doi.org/10.1146/annurev-ecolsys-110512-135920openalex-snapshot
Genetic Draft, Selective Interference, and Population Genetics of Rapid Adaptation
inferredcites →https://doi.org/10.1177/154405910408300516openalex-snapshot
Indian Hedgehog: A Mechanotransduction Mediator in Condylar Cartilage
inferredcites →https://doi.org/10.1371/journal.pbio.1001388openalex-snapshot
Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?
inferredcites →https://doi.org/10.1371/journal.pgen.1000843openalex-snapshot
The Scale of Population Structure in Arabidopsis thaliana
inferredcites →https://doi.org/10.1371/journal.pgen.1003264openalex-snapshot
Polygenic Modeling with Bayesian Sparse Linear Mixed Models
inferredcites →https://doi.org/10.1371/journal.pgen.1004412openalex-snapshot
A Population Genetic Signal of Polygenic Adaptation
inferredcites →https://doi.org/10.1371/journal.pgen.1004551openalex-snapshot
The Population Genetics of Evolutionary Rescue
inferredcites →https://doi.org/10.1371/journal.pone.0004010openalex-snapshot
A Meta-Analysis of Local Adaptation in Plants
inferredcites →https://doi.org/10.1371/journal.pone.0087836openalex-snapshot
Deciphering the Adjustment between Environment and Life History in Annuals: Lessons from a Geographically-Explicit Approach in Arabidopsis thaliana
inferredcites →https://doi.org/10.1534/genetics.104.117275openalex-snapshot
Detecting Selection in Population Trees: The Lewontin and Krakauer Test Extended
inferredcites →https://doi.org/10.1534/genetics.110.114819openalex-snapshot
Using Environmental Correlations to Identify Loci Underlying Local Adaptation
inferredcites →https://doi.org/10.1534/genetics.111.134288openalex-snapshot
The Effects of Deleterious Mutations on Evolution at Linked Sites
inferredcites →https://doi.org/10.1534/genetics.116.196972openalex-snapshot
Rapid Adaptation of a Polygenic Trait After a Sudden Environmental Shift
inferredcites →https://doi.org/10.1534/genetics.118.300786openalex-snapshot
Tread Lightly Interpreting Polygenic Tests of Selection
inferredcites →https://doi.org/10.1534/genetics.166.1.449openalex-snapshot
The Dominance of the Herbicide Resistance Cost in Several Arabidopsis thaliana Mutant Lines
inferredcites →https://doi.org/10.18637/jss.v028.i05openalex-snapshot
Building Predictive Models in R Using the caret Package
inferredcites →https://doi.org/10.18637/jss.v028.i08openalex-snapshot
Implementing a Class of Permutation Tests: The coin Package
inferredcites →https://doi.org/10.18637/jss.v033.i02openalex-snapshot
MCMC Methods for Multi-Response Generalized Linear Mixed Models: The MCMCglmm R Package
inferredcites →https://doi.org/10.3169/itej.72.736openalex-snapshot
OpenCV: Open Source Computer Vision Library
inferredcites →https://doi.org/10.3835/plantgenome2011.08.0024openalex-snapshot
Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP
inferredcites →https://doi.org/10.4161/fly.19695openalex-snapshot
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff
inferredcites →https://doi.org/10.5334/jors.acopenalex-snapshot
Mahotas: Open source software for scriptable computer vision

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/ece3.8103openalex-snapshot
Phylogeography of a widely distributed plant species reveals cryptic genetic lineages with parallel phenotypic responses to warming and drought conditions
inferred← citeshttps://doi.org/10.1086/720619openalex-snapshot
Combining Climatic and Genomic Data Improves Range-Wide Tree Height Growth Prediction in a Forest Tree
inferred← citeshttps://doi.org/10.1101/186767openalex-snapshot
A rainfall-manipulation experiment with 517 Arabidopsis thaliana accessions
inferred← citeshttps://doi.org/10.1101/2020.07.14.194407openalex-snapshot
Non-additive polygenic models improve predictions of fitness traits in three eukaryote model species
inferred← citeshttps://doi.org/10.1111/mec.16367openalex-snapshot
Polygenic adaptation and negative selection across traits, years and environments in a long‐lived plant species (Pinus pinaster Ait., Pinaceae)
inferred← citeshttps://doi.org/10.1111/nph.16593openalex-snapshot
Competition × drought interactions change phenotypic plasticity and the direction of selection on Arabidopsis traits
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Understanding the origin and predicting adaptive genetic variation at large scale in the genomic era : a case study in maritime pine
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