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Research: Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths
- Fangyuan Yang,
- Li-Jun Cao,
- Petr Nguyen,
- Zhong-Zheng Ma,
- Jin-Cui Chen,
- Wei Song,
- and Shu-Jun Wei
Genome Res. January 2025 35: 66-77; Published in Advance January 6, 2025, doi:10.1101/gr.279569.124
.... The features of SA-fused chromosomes were explored in Tortricidae using transcriptomic and multiple genomic approaches. Then, we analyzed genomic divergence and adaptive evolution of the SA-fused chromosomes on using molecular evolution and population genetic analyses. Our results provide new insights into how...
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Research: Genome-wide evidence for speciation with gene flow in Heliconius butterflies
- Simon H. Martin,
- Kanchon K. Dasmahapatra,
- Nicola J. Nadeau,
- Camilo Salazar,
- James R. Walters,
- Fraser Simpson,
- Mark Blaxter,
- Andrea Manica,
- James Mallet,
- and Chris D. Jiggins
Genome Res. November 2013 23: 1817-1828; Published in Advance September 17, 2013, doi:10.1101/gr.159426.113
...is similar in sympatry and allopatry. The Peruvian pair has convergent wing patterns, and narrow tracts of the have here introgressed at both color pattern loci (The HeliconiusGenome Consortium 2012; Pardo-Diaz et al. 2012). Indeed, at both loci, there is a narrow trough of low FST between these populations...
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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
...Piedras, San Juan, Puerto Rico 00921; 8Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panama Hybrid zones can be valuable tools for studying evolution and identifying genomic regions responsible for adaptive divergence and underlying phenotypic variation. Hybrid zones...
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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
...species. Similar to Heliconius butterflies (Martin et al. 2013), already in the geographically most isolated populations within collared and pied flycatchers, regions corresponding to differentiation islands between species exhibited higher FST within species than the genomic background of low...
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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
...coalescent with recombination. (A) The evolutionary history of a sample of four extant individuals in two divergent populations from their MRCA (solid magenta circle). The recombination node (solid orange circle) results in an ancestral recombination graph (ARG), shown in B. (C) The genealogy of genomic...
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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
...encroachment, poaching, deforestation, and climate change are drastically reducing felid numbers. We have highlighted groups of species where further population genomic sampling will better define the architecture of admixture and genes underlying adaptive introgression and divergence. Differentiating between...
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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
...-related genetic variants, the molecular basis for mammalian pigmentation and patterning, and species-specific adaptations. Improved genomic surveillance of natural and captive populations across the cat family tree will increase our understanding of the genetic architecture of traits, population dynamics...

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