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1. Recombination-aware phylogenomics

   https://doi.org/10.1016/j.tree.2025.06.011  

   Burbrink, Frank T; DeBaun, Dylan; Foley, Nicole M; Murphy, William J (July 2025, Trends in Ecology & Evolution)
2. Recombination-aware phylogeographic inference using the structured coalescent with ancestral recombination

   https://doi.org/10.1371/journal.pcbi.1010422  

   Guo, Fangfang; Carbone, Ignazio; Rasmussen, David A. (August 2022, PLOS Computational Biology)

   Schiffels, Stephan (Ed.)

   Movement of individuals between populations or demes is often restricted, especially between geographically isolated populations. The structured coalescent provides an elegant theoretical framework for describing how movement between populations shapes the genealogical history of sampled individuals and thereby structures genetic variation within and between populations. However, in the presence of recombination an individual may inherit different regions of their genome from different parents, resulting in a mosaic of genealogical histories across the genome, which can be represented by an Ancestral Recombination Graph (ARG). In this case, different genomic regions may have different ancestral histories and so different histories of movement between populations. Recombination therefore poses an additional challenge to phylogeographic methods that aim to reconstruct the movement of individuals from genealogies, although also a potential benefit in that different loci may contain additional information about movement. Here, we introduce the Structured Coalescent with Ancestral Recombination (SCAR) model, which builds on recent approximations to the structured coalescent by incorporating recombination into the ancestry of sampled individuals. The SCAR model allows us to infer how the migration history of sampled individuals varies across the genome from ARGs, and improves estimation of key population genetic parameters such as population sizes, recombination rates and migration rates. Using the SCAR model, we explore the potential and limitations of phylogeographic inference using full ARGs. We then apply the SCAR to lineages of the recombining fungus Aspergillus flavus sampled across the United States to explore patterns of recombination and migration across the genome. 

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3. Was entropy conserved between BBN and recombination?

   https://doi.org/10.1103/PhysRevD.107.023525  

   Sobotka, Alexander C.; Erickcek, Adrienne L.; Smith, Tristan L. (January 2023, Physical Review D)
4. The coronavirus recombination pathway

   https://doi.org/10.1016/j.chom.2023.05.003  

   Wells, Heather L.; Bonavita, Cassandra M.; Navarrete-Macias, Isamara; Vilchez, Blake; Rasmussen, Angela L.; Anthony, Simon J. (June 2023, Cell Host & Microbe)
5. Surface-Radical Mobility Test by Self-Sorted Recombination: Symmetrical Product upon Recombination (SPR)

   https://doi.org/10.1021/acs.jpcb.1c01099  

   Belh, Sarah J.; Ghosh, Goutam; Greer, Alexander (April 2021, The Journal of Physical Chemistry B)

   null (Ed.)