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Research: Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches
- Fan Han,
- Sangeet Lamichhaney,
- B. Rosemary Grant,
- Peter R. Grant,
- Leif Andersson,
- and Matthew T. Webster
Genome Res. June 2017 27: 1004-1015; Published in Advance April 25, 2017, doi:10.1101/gr.212522.116
...between species in such regions but is homogenized by gene flow in the rest of the . Under this speciation-with-gene-flow model, genomic islands are resistant to gene flow and can expand due to divergence hitchhiking. Both absolute and relative measures of divergence are predicted to be elevated...
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Research: Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato
- Nicola J. Nadeau,
- Mayté Ruiz,
- Patricio Salazar,
- Brian Counterman,
- Jose Alejandro Medina,
- Humberto Ortiz-Zuazaga,
- Anna Morrison,
- W. Owen McMillan,
- Chris D. Jiggins,
- and Riccardo Papa
Genome Res. August 2014 24: 1316-1333; Published in Advance May 13, 2014, doi:10.1101/gr.169292.113
...between subspecies of Heliconius butterflies can be very narrow and are maintained by strong selection acting on color pattern. The comimetic species, H. erato and H. melpomene, have parallel hybrid zones in which both species undergo a change from one color pattern form to another. We use restriction...
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Research: Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers
- Reto Burri,
- Alexander Nater,
- Takeshi Kawakami,
- Carina F. Mugal,
- Pall I. Olason,
- Linnea Smeds,
- Alexander Suh,
- Ludovic Dutoit,
- Stanislav Bureš,
- Laszlo Z. Garamszegi,
- Silje Hogner,
- Juan Moreno,
- Anna Qvarnström,
- Milan Ružić,
- Stein-Are Sæther,
- Glenn-Peter Sætre,
- Janos Török,
- and Hans Ellegren
Genome Res. November 2015 25: 1656-1665; Published in Advance September 9, 2015, doi:10.1101/gr.196485.115
...selection, divergent selection contributes to the evolution of reduced diversity and increased differentiation in a fraction of regions with low recombination. Discussion Genome-wide variation in gene flow and the effects of linked selection represent two mutually nonexclusive processes that can Figure 3...
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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
...have considerable effects on the recombination landscape. There was no association between the inferred recombination rate and base composition, supporting a limited influence of GC-biased gene conversion in butterflies. We found significant but variable associations between the recombination rate...
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Research: Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)
- Gang Li,
- Brian W. Davis,
- Eduardo Eizirik,
- and William J. Murphy
Genome Res. January 2016 26: 1-11; Published in Advance October 30, 2015, doi:10.1101/gr.186668.114
...highlight the mosaic origin of modern felid s and the influence of sex chromosomes and sex-biased dispersal in post-speciation gene flow. A complete resolution of the tree of life will require comprehensive genomic sampling of biparental and sex-limited genetic variation to identify and control...
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Research: Inference of selective forces on house mouse genomes during secondary contact in East Asia
- Kazumichi Fujiwara,
- Shunpei Kubo,
- Toshinori Endo,
- Toyoyuki Takada,
- Toshihiko Shiroishi,
- Hitoshi Suzuki,
- and Naoki Osada
Genome Res. March 2024 34: 366-375; Published in Advance March 20, 2024, doi:10.1101/gr.278828.123
...isolation between subspecies, genetic studies have revealed a nonnegligible amount of gene flow, as well as occasional identification of hybrid genotypes (Orth et al. 1998; Ďureje et al. 2012; Fujiwara et al. 2022a). Studying the genetic differentiation and hybridization patterns in M. musculus thus...
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Mini-Review: Toward telomere-to-telomere cat genomes for precision medicine and conservation biology
- William J. Murphy and
- Andrew J. Harris
Genome Res. May 2024 34: 655-664; Published in Advance June 7, 2024, doi:10.1101/gr.278546.123
...that bouts of interspecific gene flow commonly occur following speciation despite the establishment of reproductive barriers that maintain species-level distinctiveness (Mallet et al. 2016; Edelman and Mallet 2021). The selective persistence of introgressed alleles has evolved from the adaptive benefit...
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Method: Variational inference using approximate likelihood under the coalescent with recombination
- Xinhao Liu,
- Huw A. Ogilvie,
- and Luay Nakhleh
Genome Res. November 2021 31: 2107-2119; Published in Advance August 23, 2021, doi:10.1101/gr.273631.120
...VICAR to analyze the demographic history of three Heliconius butterfly species. Previous methods to construct the evolutionary history of the Heliconius butterflies include a -wide maximum likelihood tree constructed on the whole- alignment (Zhang et al. 2016) or reticulate phylogenetic networks...

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