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Ancient genomic variation underlies repeated ecological adaptation in young stickleback populations

https://doi.org/10.1101/167981
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What this work says

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

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The coalescent
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Adaptation from standing genetic variation
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Gene flow and the limits to natural selection
inferredcites →https://doi.org/10.1016/s0169-5347(02)02579-xopenalex-snapshot
Speciation in nature: the threespine stickleback model systems
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The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations
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On the genealogy of large populations
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Patterns of temporal change in single morphological characters of a Miocene stickleback fish
inferredcites →https://doi.org/10.1038/nature10944openalex-snapshot
The genomic basis of adaptive evolution in threespine sticklebacks
inferredcites →https://doi.org/10.1038/nature13301openalex-snapshot
Genetics of ecological divergence during speciation
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Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA
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The genomics of ecological vicariance in threespine stickleback fish
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The genetic theory of adaptation: a brief history
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Epistasis — the essential role of gene interactions in the structure and evolution of genetic systems
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Genome-wide genetic marker discovery and genotyping using next-generation sequencing
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Sequencing pools of individuals — mining genome-wide polymorphism data without big funding
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Contrasting effects of environment and genetics generate a continuum of parallel evolution
inferredcites →https://doi.org/10.1073/pnas.0308479101openalex-snapshot
Parallel genetic basis for repeated evolution of armor loss in Alaskan threespine stickleback populations
inferredcites →https://doi.org/10.1073/pnas.0408533102openalex-snapshot
Evolution and development of facial bone morphology in threespine sticklebacks
inferredcites →https://doi.org/10.1073/pnas.0901264106openalex-snapshot
Genetics and ecological speciation
inferredcites →https://doi.org/10.1073/pnas.1512020112openalex-snapshot
Evolution of stickleback in 50 years on earthquake-uplifted islands
inferredcites →https://doi.org/10.1073/pnas.1616755114openalex-snapshot
Population-genomic inference of the strength and timing of selection against gene flow
inferredcites →https://doi.org/10.1086/303204openalex-snapshot
Balanced Polymorphisms and the Evolution of Dominance
inferredcites →https://doi.org/10.1086/319501openalex-snapshot
A New Statistical Method for Haplotype Reconstruction from Population Data
inferredcites →https://doi.org/10.1086/428594openalex-snapshot
Accounting for Decay of Linkage Disequilibrium in Haplotype Inference and Missing-Data Imputation
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APE: Analyses of Phylogenetics and Evolution in R language
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btp696openalex-snapshot
pegas: an R package for population genetics with an integrated–modular approach
inferredcites →https://doi.org/10.1093/bioinformatics/bts184openalex-snapshot
ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R
inferredcites →https://doi.org/10.1093/genetics/105.2.437openalex-snapshot
EVOLUTIONARY RELATIONSHIP OF DNA SEQUENCES IN FINITE POPULATIONS
inferredcites →https://doi.org/10.1093/genetics/134.4.1289openalex-snapshot
The effect of deleterious mutations on neutral molecular variation.
inferredcites →https://doi.org/10.1093/molbev/mss075openalex-snapshot
Bayesian Phylogenetics with BEAUti and the BEAST 1.7
inferredcites →https://doi.org/10.1093/molbev/msu136openalex-snapshot
PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R
inferredcites →https://doi.org/10.1093/molbev/msx154openalex-snapshot
Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome
inferredcites →https://doi.org/10.1093/oso/9780198577287.003.0001openalex-snapshot
Introduction to the evolutionary biology of the threespine stickleback
inferredcites →https://doi.org/10.1093/oso/9780198577287.003.0009openalex-snapshot
Predators and Morphological Evolution in Threespine Stickleback
inferredcites →https://doi.org/10.1093/oso/9780198577287.003.0016openalex-snapshot
Evolutionary inference: the value of viewing evolution through stickleback-tinted glasses
inferredcites →https://doi.org/10.1098/rspb.2011.1552openalex-snapshot
Population genomics of parallel phenotypic evolution in stickleback across stream–lake ecological transitions
inferredcites →https://doi.org/10.1098/rspb.2015.1666openalex-snapshot
Introgressive hybridization facilitates adaptive divergence in a recent radiation of monkeyflowers
inferredcites →https://doi.org/10.1098/rstb.2011.0246openalex-snapshot
Coalescent patterns for chromosomal inversions in divergent populations
inferredcites →https://doi.org/10.1111/j.0014-3820.2002.tb01432.xopenalex-snapshot
ADAPTIVE DIVERGENCE AND THE BALANCE BETWEEN SELECTION AND GENE FLOW: LAKE AND STREAM STICKLEBACK IN THE MISTY SYSTEM
inferredcites →https://doi.org/10.1111/j.1365-294x.2010.04801.xopenalex-snapshot
Phylogeography of ninespine sticklebacks (Pungitius pungitius) in North America: glacial refugia and the origins of adaptive traits
inferredcites →https://doi.org/10.1111/j.1420-9101.2012.02496.xopenalex-snapshot
Plasticity and heritability of morphological variation within and between parapatric stickleback demes
inferredcites →https://doi.org/10.1111/j.1558-5646.2010.01195.xopenalex-snapshot
CRYPTIC GENETIC VARIATION AND BODY SIZE EVOLUTION IN THREESPINE STICKLEBACK
inferredcites →https://doi.org/10.1111/j.1558-5646.2012.01669.xopenalex-snapshot
EVIDENCE OF ADAPTATION FROM ANCESTRAL VARIATION IN YOUNG POPULATIONS OF BEACH MICE
inferredcites →https://doi.org/10.1111/mec.12089openalex-snapshot
The effect of RAD allele dropout on the estimation of genetic variation within and between populations
inferredcites →https://doi.org/10.1111/mec.12276openalex-snapshot
RAD seq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling
inferredcites →https://doi.org/10.1111/mec.12322openalex-snapshot
Recombination in the threespine stickleback genome—patterns and consequences
inferredcites →https://doi.org/10.1111/mec.12354openalex-snapshot
Stacks: an analysis tool set for population genomics
inferredcites →https://doi.org/10.1111/mec.12720openalex-snapshot
The genomic signature of parallel adaptation from shared genetic variation
inferredcites →https://doi.org/10.1111/mec.12796openalex-snapshot
Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow
inferredcites →https://doi.org/10.1111/mec.13478openalex-snapshot
Inferring the age of a fixed beneficial allele
inferredcites →https://doi.org/10.1111/mec.14226openalex-snapshot
Gene flow and selection interact to promote adaptive divergence in regions of low recombination
inferredcites →https://doi.org/10.1126/science.1070315openalex-snapshot
Unpredictable Evolution in a 30-Year Study of Darwin's Finches
inferredcites →https://doi.org/10.1126/science.1107239openalex-snapshot
Widespread Parallel Evolution in Sticklebacks by Repeated Fixation of Ectodysplasin Alleles
inferredcites →https://doi.org/10.1126/science.1159978openalex-snapshot
Natural Selection on a Major Armor Gene in Threespine Stickleback
inferredcites →https://doi.org/10.1126/science.1175826openalex-snapshot
On the Origin and Spread of an Adaptive Allele in Deer Mice
inferredcites →https://doi.org/10.1126/science.1258524openalex-snapshot
Extensive introgression in a malaria vector species complex revealed by phylogenomics
inferredcites →https://doi.org/10.1139/z86-339openalex-snapshot
Historical and ecological sources of variation among lake populations of threespine sticklebacks, Gasterosteus aculeatus, near Cook Inlet, Alaska
inferredcites →https://doi.org/10.1186/1471-2148-7-214openalex-snapshot
BEAST: Bayesian evolutionary analysis by sampling trees
inferredcites →https://doi.org/10.1371/journal.pbio.0020109openalex-snapshot
The Genetic Architecture of Parallel Armor Plate Reduction in Threespine Sticklebacks
inferredcites →https://doi.org/10.1371/journal.pbio.1001497openalex-snapshot
Indirect Evolution of Hybrid Lethality Due to Linkage with Selected Locus in Mimulus guttatus
inferredcites →https://doi.org/10.1371/journal.pbio.1002379openalex-snapshot
Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation
inferredcites →https://doi.org/10.1371/journal.pgen.1000862openalex-snapshot
Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags
inferredcites →https://doi.org/10.1371/journal.pgen.1003011openalex-snapshot
Distinguishing between Selective Sweeps from Standing Variation and from a De Novo Mutation
inferredcites →https://doi.org/10.1371/journal.pgen.1005397openalex-snapshot
Evidence for a Common Origin of Blacksmiths and Cultivators in the Ethiopian Ari within the Last 4500 Years: Lessons for Clustering-Based Inference
inferredcites →https://doi.org/10.1371/journal.pone.0003376openalex-snapshot
Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers
inferredcites →https://doi.org/10.1371/journal.pone.0003808openalex-snapshot
Whole Body Mechanics of Stealthy Walking in Cats
inferredcites →https://doi.org/10.1371/journal.pone.0037135openalex-snapshot
Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species
inferredcites →https://doi.org/10.1371/journal.pone.0042649openalex-snapshot
Estimates of Genetic Differentiation Measured by FST Do Not Necessarily Require Large Sample Sizes When Using Many SNP Markers
inferredcites →https://doi.org/10.1534/g3.111.000240openalex-snapshot
Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences
inferredcites →https://doi.org/10.1534/g3.115.017905openalex-snapshot
Genome Assembly Improvement and Mapping Convergently Evolved Skeletal Traits in Sticklebacks with Genotyping-by-Sequencing
inferredcites →https://doi.org/10.1534/genetics.105.047985openalex-snapshot
Chromosome Inversions, Local Adaptation and Speciation
inferredcites →https://doi.org/10.1534/genetics.114.162420openalex-snapshot
Modular Skeletal Evolution in Sticklebacks Is Controlled by Additive and Clustered Quantitative Trait Loci
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing
inferredcites →https://doi.org/10.7312/nei-92038openalex-snapshot
Molecular Evolutionary Genetics

What points at this work

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

inferred← citeshttps://doi.org/10.1002/evl3.169openalex-snapshot
The contribution of ancient admixture to reproductive isolation between European sea bass lineages
inferred← citeshttps://doi.org/10.1002/evl3.86openalex-snapshot
On the importance of time scales when studying adaptive evolution
inferred← citeshttps://doi.org/10.1093/biolinnean/blz106openalex-snapshot
Genetic divergence outpaces phenotypic evolution among threespine stickleback populations in old freshwater habitats
inferred← citeshttps://doi.org/10.1093/g3journal/jkab045openalex-snapshot
Complex pleiotropic genetic architecture of evolved heat stress and oxidative stress resistance in the nematode Caenorhabditis remanei
inferred← citeshttps://doi.org/10.1101/342352openalex-snapshot
Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers
inferred← citeshttps://doi.org/10.1111/1755-0998.12984openalex-snapshot
MobiSeq: De novo SNP discovery in model and non‐model species through sequencing the flanking region of transposable elements
inferred← citeshttps://doi.org/10.1534/g3.119.400564openalex-snapshot
A Few Stickleback Suffice for the Transport of Alleles to New Lakes
inferred← citeshttps://doi.org/10.1534/genetics.117.300610openalex-snapshot
Repeated Selection of Alternatively Adapted Haplotypes Creates Sweeping Genomic Remodeling in Stickleback
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