ArticleMolecular ecology2023
On the origin and structure of haplotype blocks.
Article in Molecular ecology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Genome-wide analyses of an avian herpesvirus identify 10 loci associated with tumorigenicity and vaccine escape.Science advances · 2026Article
- Beyond Data: Artificial intelligence, knowledge graphs, and the next revolution in wheat breeding.Plant communications · 2026Review
- SLAB: A Sweep Line Algorithm in PBWT for Finding Haplotype Block Cores.bioRxiv : the preprint server for biology · 2026Article
- ACE-Dependent Alzheimer's Disease: Blood ACE Phenotyping of the Most Prevalent and DamagingBiomedicines · 2026Article
- SNPs with High Linkage Disequilibrium Increase the Explained Genetic Variance and the Reliability of Genomic Predictions.Animals : an open access journal from MDPI · 2026Article
- A model-free method for genealogical inference without phasing and its application for topology weighting.Genetics · 2026Article
- The promise and challenge of spatial inference with the full ancestral recombination graph under Brownian motion.G3 (Bethesda, Md.) · 2025Article
- The Distribution and Dispersal of Large Haploblocks in a Superspecies.Molecular ecology · 2025Article
- Genealogical Analysis of Replicate Flower Colour Hybrid Zones in Antirrhinum.Molecular ecology · 2025Article
- The Shapes of Clines and Wavefronts.Molecular ecology · 2025Review
- Large Inversion Polymorphisms are Widespread in North American Songbirds.Genome biology and evolution · 2025Article
- The Length of Haplotype Blocks and Signals of Structural Variation in Reconstructed Genealogies.Molecular biology and evolution · 2025Article
- Leveraging Whole Genomes, Mitochondrial DNA and Haploblocks to Decipher Complex Demographic Histories: An Example From a Broadly Admixed Arctic Fish.Molecular ecology · 2025Article
- High-recombining genomic regions affect demography inference based on ancestral recombination graphs.Genetics · 2025Article
- Article
- A general and efficient representation of ancestral recombination graphs.bioRxiv : the preprint server for biology · 2024Article
- Exploring the role of underrepresented populations in polygenic risk scores for neurodegenerative disease risk prediction.Frontiers in neuroscience · 2024Article
- iHDSel software: The price equation and the population stability index to detect genomic patterns compatible with selective sweeps. An example with SARS-CoV-2.Biology methods & protocols · 2024Article
- The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics.PLoS genetics · 2024Review
- Article
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5 authors.
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Abstract
The term "haplotype block" is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a "hard" selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked-read sequencing technologies.
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