article published yes Daria Shipilina author 428A94B0-F248-11E8-B48F-1D18A9856A870000-0002-1145-9226 Arka Pal author 6AAB2240-CA9A-11E9-9C1A-D9D1E56974250000-0002-4530-8469 Sean Stankowski author 43161670-5719-11EA-8025-FABC3DDC885E Yingguang Frank Chan author Nicholas H Barton author 4880FE40-F248-11E8-B48F-1D18A9856A870000-0002-8548-5240 NiBa department Snapdragon Speciation project Formal methods for the design and analysis of complex systems project Understanding the evolution of continuous genomes project 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. https://research-explorer.ista.ac.at/download/12159/14062/2023_MolecularEcology_Shipilina.pdf application/pdfno Wiley2023 eng GeneticsEcologyEvolutionBehavior and Systematics 0962-1083 1365-294X 36433653 00090076200000110.1111/mec.16793 3261441-1457 https://research-explorer.ista.ac.at/record/20694 Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.” <i>Molecular Ecology</i>, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:<a href="https://doi.org/10.1111/mec.16793">10.1111/mec.16793</a>. D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology 32 (2023) 1441–1457. Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457. Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., &#38; Barton, N. H. (2023). On the origin and structure of haplotype blocks. <i>Molecular Ecology</i>. Wiley. <a href="https://doi.org/10.1111/mec.16793">https://doi.org/10.1111/mec.16793</a> Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” <i>Molecular Ecology</i>. Wiley, 2023. <a href="https://doi.org/10.1111/mec.16793">https://doi.org/10.1111/mec.16793</a>. Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure of haplotype blocks. <i>Molecular Ecology</i>. 2023;32(6):1441-1457. doi:<a href="https://doi.org/10.1111/mec.16793">10.1111/mec.16793</a> D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the origin and structure of haplotype blocks,” <i>Molecular Ecology</i>, vol. 32, no. 6. Wiley, pp. 1441–1457, 2023. 121592023-01-12T12:09:17Z2026-10-05T22:30:40Z