@article{20190,
  abstract     = {A major goal of speciation research is identifying loci that underpin barriers to gene flow. Population genomics takes a ‘bottom-up’ approach, scanning the genome for molecular signatures of processes that drive or maintain divergence. However, interpreting the ‘genomic landscape’ of speciation is complicated, because genome scans conflate multiple processes, most of which are not informative about gene flow. However, studying replicated population contrasts, including multiple incidences of secondary contact, can strengthen inferences. In this paper, we use linked-read sequencing (haplotagging), FST scans and genealogical methods to characterise the genomic landscape associated with replicate hybrid zone formation. We studied two flower colour varieties of the common snapdragon, Antirrhinum majus subspecies majus, that form secondary hybrid zones in multiple independent valleys in the Pyrenees. Consistent with past work, we found very low differentiation at one well-studied zone (Planoles). However, at a second zone (Avellanet), we found stronger differentiation and greater heterogeneity, which we argue is due to differences in the amount of introgression following secondary contact. Topology weighting of genealogical trees identified loci where haplotype diversity was associated with the two snapdragon varieties. Two of the strongest associations were at previously identified flower colour loci: Flavia, that affects yellow pigmentation, and Rosea/Eluta, two linked loci that affect magenta pigmentation. Preliminary analysis of coalescence times provides additional evidence for selective sweeps at these loci and barriers to gene flow. Our study highlights the impact of demographic history on the differentiation landscape, emphasising the need to distinguish between historical divergence and recent introgression.},
  author       = {Pal, Arka and Shipilina, Daria and Le Moan, Alan and Mcnairn, Adrian J. and Grenier, Jennifer K. and Kucka, Marek and Coop, Graham and Chan, Yingguang Frank and Barton, Nicholas H and Field, David and Stankowski, Sean},
  issn         = {1365-294X},
  journal      = {Molecular Ecology},
  number       = {22},
  publisher    = {Wiley},
  title        = {{Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum}},
  doi          = {10.1111/mec.70067},
  volume       = {34},
  year         = {2025},
}

@article{14796,
  abstract     = {Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer–specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer–specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step.},
  author       = {Stankowski, Sean and Zagrodzka, Zuzanna B. and Garlovsky, Martin D. and Pal, Arka and Shipilina, Daria and Garcia Castillo, Diego Fernando and Lifchitz, Hila and Le Moan, Alan and Leder, Erica and Reeve, James and Johannesson, Kerstin and Westram, Anja M and Butlin, Roger K.},
  issn         = {1095-9203},
  journal      = {Science},
  number       = {6678},
  pages        = {114--119},
  publisher    = {American Association for the Advancement of Science},
  title        = {{The genetic basis of a recent transition to live-bearing in marine snails}},
  doi          = {10.1126/science.adi2982},
  volume       = {383},
  year         = {2024},
}

@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},
}