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On the origin and structure of haplotype blocks
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  • Daria Shipilina,
  • Arka Pal,
  • Sean Stankowski,
  • Yingguang Frank Chan,
  • Nick Barton
Daria Shipilina
Uppsala University

Corresponding Author:[email protected]

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Arka Pal
IST Austria
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Sean Stankowski
IST Austria
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Yingguang Frank Chan
Friedrich Miescher Laboratory of the Max Planck Society
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Nick Barton
IST Austria
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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 relation between haplotype blocks and ancestral structure, emphasising 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 dataset. While the arrival of computationally efficient methods makes it possible to apply these concepts broadly, existing and new methods could include tools for the identification and 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.
13 Jan 2022Submitted to Molecular Ecology
17 Jan 2022Submission Checks Completed
17 Jan 2022Assigned to Editor
07 Feb 2022Reviewer(s) Assigned
15 Mar 2022Review(s) Completed, Editorial Evaluation Pending
04 Apr 2022Editorial Decision: Revise Minor
14 Jun 2022Review(s) Completed, Editorial Evaluation Pending
14 Jun 20221st Revision Received
01 Jul 2022Reviewer(s) Assigned
17 Oct 2022Editorial Decision: Revise Minor
16 Nov 2022Review(s) Completed, Editorial Evaluation Pending
16 Nov 20222nd Revision Received
18 Nov 2022Editorial Decision: Accept