ArticlePloS one2012
LDx: estimation of linkage disequilibrium from high-throughput pooled resequencing data.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers, 1 of them a synthesis that pooled it.
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Who cites it
53 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Early life-stage thermal resilience is determined by climate-linked regulatory variation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Beneficial reversal of dominance maintains a large-effect resistance polymorphism under fluctuating insecticide selection.Nature ecology & evolution · 2025Article
- Pervasive sex-dependent effects in the genetic architecture of starvation resistance inScience advances · 2025Article
- Footprints of Worldwide Adaptation in Structured Populations of Drosophila melanogaster Through the Expanded DEST 2.0 Genomic Resource.Molecular biology and evolution · 2025Article
- Natural variation in phospholipase IPLA2-VIA contributes to starvation sensitivity inbioRxiv : the preprint server for biology · 2025Article
- Limited Migration From Physiological Refugia Constrains the Rescue of Native Gastropods Facing an Invasive Predator.Evolutionary applications · 2024Article
- Adaptation to seasonal reproduction and environment-associated factors drive temporal and spatial differentiation in northwest Atlantic herring despite gene flow.Evolutionary applications · 2024Article
- Elevated HIV Viral Load is Associated with Higher Recombination Rate In Vivo.Molecular biology and evolution · 2024Article
- Elevated HIV viral load is associated with higher recombination ratebioRxiv : the preprint server for biology · 2023Article
- The genomic basis and environmental correlates of local adaptation in the Atlantic horse mackerel (Evolutionary applications · 2023Article
- Article
- Genetic Drift Shapes the Evolution of a Highly Dynamic Metapopulation.Molecular biology and evolution · 2022Article
- Experimental evolution reveals the synergistic genomic mechanisms of adaptation to ocean warming and acidification in a marine copepod.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Genome-wide signatures of synergistic epistasis during parallel adaptation in a Baltic Sea copepod.Nature communications · 2022Article
- Whole genome resequencing reveals signatures of rapid selection in a virus-affected commercial fishery.Molecular ecology · 2022Article
- Genetic Variation in Reproductive Investment Across an Ephemerality Gradient in Daphnia pulex.Molecular biology and evolution · 2022Article
- Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource.Molecular biology and evolution · 2021Article
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3 authors.
Funding
Abstract
High-throughput pooled resequencing offers significant potential for whole genome population sequencing. However, its main drawback is the loss of haplotype information. In order to regain some of this information, we present LDx, a computational tool for estimating linkage disequilibrium (LD) from pooled resequencing data. LDx uses an approximate maximum likelihood approach to estimate LD (r(2)) between pairs of SNPs that can be observed within and among single reads. LDx also reports r(2) estimates derived solely from observed genotype counts. We demonstrate that the LDx estimates are highly correlated with r(2) estimated from individually resequenced strains. We discuss the performance of LDx using more stringent quality conditions and infer via simulation the degree to which performance can improve based on read depth. Finally we demonstrate two possible uses of LDx with real and simulated pooled resequencing data. First, we use LDx to infer genomewide patterns of decay of LD with physical distance in D. melanogaster population resequencing data. Second, we demonstrate that r(2) estimates from LDx are capable of distinguishing alternative demographic models representing plausible demographic histories of D. melanogaster.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.