loading page

On the origin and structure of haplotype blocks
  • +2
  • Daria Shipilina,
  • Arka Pal,
  • Sean Stankowski,
  • Yingguang Frank Chan,
  • Nick Barton
Daria Shipilina
Uppsala University

Corresponding Author:[email protected]

Author Profile
Arka Pal
IST Austria
Author Profile
Sean Stankowski
IST Austria
Author Profile
Yingguang Frank Chan
Friedrich Miescher Laboratory of the Max Planck Society
Author Profile
Nick Barton
IST Austria
Author Profile


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, which is missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure as full ARG, or as a sequence of trees. While some of these new methods are computationally efficient, they still lack features to aid exploration of the haplotype blocks, as we define them, thus calling for the development of new methods. 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