@article{12159,
  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.},
  author       = {Shipilina, Daria and Pal, Arka and Stankowski, Sean and Chan, Yingguang Frank and Barton, Nicholas H},
  issn         = {1365-294X},
  journal      = {Molecular Ecology},
  keywords     = {Genetics, Ecology, Evolution, Behavior and Systematics},
  number       = {6},
  pages        = {1441--1457},
  publisher    = {Wiley},
  title        = {{On the origin and structure of haplotype blocks}},
  doi          = {10.1111/mec.16793},
  volume       = {32},
  year         = {2023},
}

@inbook{14984,
  abstract     = {Hybrid zones are narrow geographic regions where different populations, races or interbreeding species meet and mate, producing mixed ‘hybrid’ offspring. They are relatively common and can be found in a diverse range of organisms and environments. The study of hybrid zones has played an important role in our understanding of the origin of species, with hybrid zones having been described as ‘natural laboratories’. This is because they allow us to study,in situ, the conditions and evolutionary forces that enable divergent taxa to remain distinct despite some ongoing gene exchange between them.},
  author       = {Stankowski, Sean and Shipilina, Daria and Westram, Anja M},
  booktitle    = {Encyclopedia of Life Sciences},
  isbn         = {9780470016176},
  publisher    = {Wiley},
  title        = {{Hybrid Zones}},
  doi          = {10.1002/9780470015902.a0029355},
  volume       = {2},
  year         = {2021},
}