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A generalised approach to detect selected haplotype blocks in Evolve and Resequence experiments

https://doi.org/10.1101/691659
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What this work says

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

inferredcites →https://doi.org/10.1016/j.gde.2013.10.002openalex-snapshot
Promises and limitations of hitchhiking mapping
inferredcites →https://doi.org/10.1038/nature09352openalex-snapshot
Genome-wide analysis of a long-term evolution experiment with Drosophila
inferredcites →https://doi.org/10.1038/nrg3803openalex-snapshot
Sequencing pools of individuals — mining genome-wide polymorphism data without big funding
inferredcites →https://doi.org/10.1038/nrg3937openalex-snapshot
Elucidating the molecular architecture of adaptation via evolve and resequence experiments
inferredcites →https://doi.org/10.1093/bioinformatics/btr589openalex-snapshot
PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)
inferredcites →https://doi.org/10.1093/bioinformatics/btu670openalex-snapshot
Accurate estimation of haplotype frequency from pooled sequencing data and cost-effective identification of rare haplotype carriers by overlapping pool sequencing
inferredcites →https://doi.org/10.1093/biomet/10.4.507openalex-snapshot
FREQUENCY DISTRIBUTION OF THE VALUES OF THE CORRELATION COEFFIENTS IN SAMPLES FROM AN INDEFINITELY LARGE POPU;ATION
inferredcites →https://doi.org/10.1093/gbe/evz082openalex-snapshot
DNA Motifs Are Not General Predictors of Recombination in Two Drosophila Sister Species
inferredcites →https://doi.org/10.1093/molbev/mst016openalex-snapshot
Maximum Likelihood Estimation of Frequencies of Known Haplotypes from Pooled Sequence Data
inferredcites →https://doi.org/10.1093/molbev/mst111openalex-snapshot
Combining Genome-Wide Methods to Investigate the Genetic Complexity of Courtship Song Variation in Drosophila melanogaster
inferredcites →https://doi.org/10.1093/molbev/mst205openalex-snapshot
Massive Habitat-Specific Genomic Response in D. melanogaster Populations during Experimental Evolution in Hot and Cold Environments
inferredcites →https://doi.org/10.1093/molbev/mst221openalex-snapshot
A Guide for the Design of Evolve and Resequencing Studies
inferredcites →https://doi.org/10.1093/molbev/msu256openalex-snapshot
Standing Genetic Variation Drives Repeatable Experimental Evolution in Outcrossing Populations of Saccharomyces cerevisiae
inferredcites →https://doi.org/10.1093/molbev/msu320openalex-snapshot
Patterns of Linkage Disequilibrium and Long Range Hitchhiking in Evolving Experimental Drosophila melanogaster Populations
inferredcites →https://doi.org/10.1093/molbev/msv136openalex-snapshot
Whole-Genome Resequencing of Experimental Populations Reveals Polygenic Basis of Egg-Size Variation in Drosophila melanogaster
inferredcites →https://doi.org/10.1093/molbev/msw210openalex-snapshot
Reconstruction of Haplotype-Blocks Selected during Experimental Evolution
inferredcites →https://doi.org/10.1093/molbev/msx225openalex-snapshot
Quantifying Selection with Pool-Seq Time Series Data
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05673.xopenalex-snapshot
Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles
inferredcites →https://doi.org/10.1111/j.1558-5646.2012.01710.xopenalex-snapshot
GENOMIC BASIS OF AGING AND LIFE-HISTORY EVOLUTION IN DROSOPHILA MELANOGASTER
inferredcites →https://doi.org/10.1111/mec.12594openalex-snapshot
Inference of chromosomal inversion dynamics from P ool‐ S eq data in natural and laboratory populations of D rosophila melanogaster
inferredcites →https://doi.org/10.1111/mec.14992openalex-snapshot
Shifting the paradigm in Evolve and Resequence studies: From analysis of single nucleotide polymorphisms to selected haplotype blocks
inferredcites →https://doi.org/10.1126/science.1212986openalex-snapshot
The Molecular Diversity of Adaptive Convergence
inferredcites →https://doi.org/10.1186/s13059-017-1381-1openalex-snapshot
RNA virus interference via CRISPR/Cas13a system in plants
inferredcites →https://doi.org/10.1186/s13059-018-1503-4openalex-snapshot
A simple genetic basis of adaptation to a novel thermal environment results in complex metabolic rewiring in Drosophila
inferredcites →https://doi.org/10.1214/19-aoas1301openalex-snapshot
Modifying the Chi-square and the CMH test for population genetic inference: Adapting to overdispersion
inferredcites →https://doi.org/10.1371/journal.pbio.3000128openalex-snapshot
Genetic redundancy fuels polygenic adaptation in Drosophila
inferredcites →https://doi.org/10.1371/journal.pcbi.1006413openalex-snapshot
MimicrEE2: Genome-wide forward simulations of Evolve and Resequencing studies
inferredcites →https://doi.org/10.1371/journal.pcbi.1006581openalex-snapshot
Efficient pedigree recording for fast population genetics simulation
inferredcites →https://doi.org/10.1371/journal.pgen.1001336openalex-snapshot
Population-Based Resequencing of Experimentally Evolved Populations Reveals the Genetic Basis of Body Size Variation in Drosophila melanogaster
inferredcites →https://doi.org/10.1371/journal.pone.0015292openalex-snapshot
PoolHap: Inferring Haplotype Frequencies from Pooled Samples by Next Generation Sequencing
inferredcites →https://doi.org/10.1371/journal.pone.0016163openalex-snapshot
E2F1 Regulates Cellular Growth by mTORC1 Signaling
inferredcites →https://doi.org/10.1534/genetics.111.127530openalex-snapshot
Circumventing Heterozygosity: Sequencing the Amplified Genome of a Single HaploidDrosophila melanogasterEmbryo
inferredcites →https://doi.org/10.1534/genetics.113.155515openalex-snapshot
High-Resolution Mapping of Complex Traits with a Four-Parent Advanced Intercross Yeast Population
inferredcites →https://doi.org/10.1534/genetics.116.187104openalex-snapshot
Genomic Trajectories to Desiccation Resistance: Convergence and Divergence Among Replicate Selected Drosophila Lines
inferredcites →https://doi.org/10.1534/genetics.118.301429openalex-snapshot
Replicability of Introgression Under Linked, Polygenic Selection
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing

What points at this work

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

inferred← citeshttps://doi.org/10.1101/2020.06.25.170878openalex-snapshot
The adaptive architecture is shaped by population ancestry and not by selection regime
inferred← citeshttps://doi.org/10.1101/2020.07.09.191924openalex-snapshot
Multiple Haplotype Reconstruction from Allele Frequency Data
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