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Research: High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
- Yuan Lu,
- Edward Rice,
- Kang Du,
- Susanne Kneitz,
- Magali Naville,
- Corentin Dechaud,
- Jean-Nicolas Volff,
- Mikki Boswell,
- William Boswell,
- LaDeana Hillier,
- Chad Tomlinson,
- Kremitzki Milin,
- Ronald B. Walter,
- Manfred Schartl,
- and Wesley C. Warren
Genome Res. April 2023 33: 557-571; Published in Advance May 5, 2023, doi:10.1101/gr.277434.122
...High resolution s of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis Yuan Lu1,9, Edward Rice2,9, Kang Du1, Susanne Kneitz3, Magali Naville4, Corentin Dechaud4, Jean-Nicolas Volff4, Mikki Boswell1, William Boswell1, LaDeana Hillier5, Chad...
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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
...of the evolutionary process and the extent to which particular genes are re-used when evolving the same phenotypes (Papa et al. 2008a; Nadeau and Jiggins 2010). In this study, we use high-resolution scans to investigate patterns of divergence across two pairs of parallel hybrid zones in Peru and Ecuador. These occur...
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Research: Genomic architecture constrained placental mammal X Chromosome evolution
- Wesley A. Brashear,
- Kevin R. Bredemeyer,
- and William J. Murphy
Genome Res. August 2021 31: 1353-1365; Published in Advance July 22, 2021, doi:10.1101/gr.275274.121
...from an F1 domestic cat/Asian leopard cat hybrid and demonstrated the formation of the bipartite structure found in primate and rodent inactivated X Chromosomes. Conservation of gene order and recombination patterns is attributable to strong selective constraints on three-dimensional genomic...
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RESOURCE: Tracking the complex flow of chromosome rearrangements from the Hominoidea Ancestor to extant Hylobates and Nomascus Gibbons by high-resolution synteny mapping
- Doriana Misceo,
- Oronzo Capozzi,
- Roberta Roberto,
- Maria P. Dell’Oglio,
- Mariano Rocchi,
- Roscoe Stanyon,
- and Nicoletta Archidiacono
Genome Res. September 2008 18: 1530-1537; Published in Advance June 13, 2008, doi:10.1101/gr.078295.108
...revealed by parallel radiation hybrid mapping . Genome Res. 9 : 1223 – 1230 . ↵ Murphy, W.J. , Larkin, D.M. , Everts-van der Wind, A. , Bourque, G. , Tesler, G. , Auvil, L. , Beever, J.E. , Chowdhary, B.P. , Galibert, F. , Gatzke, L. , et al. ( 2005 ) Dynamics of mammalian chromosome evolution inferred...
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Research: Parallel evolution of transcriptome architecture during genome reorganization
- Sung Ho Yoon,
- David J. Reiss,
- J. Christopher Bare,
- Dan Tenenbaum,
- Min Pan,
- Joseph Slagel,
- Robert L. Moritz,
- Sujung Lim,
- Murray Hackett,
- Angeli Lal Menon,
- Michael W.W. Adams,
- Adam Barnebey,
- Steven M. Yannone,
- John A. Leigh,
- and Nitin S. Baliga
Genome Res. November 2011 21: 1892-1904; Published in Advance July 12, 2011, doi:10.1101/gr.122218.111
...Parallel evolution of transcriptome architecture during genome reorganization Sung Ho Yoon 1 , David J. Reiss 1 , J. Christopher Bare 1 , Dan Tenenbaum 1 , Min Pan 1 , Joseph Slagel 1 , Robert L. Moritz 1 , Sujung Lim...
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LETTER: Extensive Conservation of Sex Chromosome Organization Between Cat and Human Revealed by Parallel Radiation Hybrid Mapping
- William J. Murphy,
- Shan Sun,
- Zhang-Qun Chen,
- Jill Pecon-Slattery,
- and Stephen J. O'Brien
Genome Res. December 1, 1999 9: 1223-1230; doi:10.1101/gr.9.12.1223
....A. , Graves J.A.M. ( 1996 ) Comparative mapping identifies the fusion point of an ancient mammalian X-autosomal rearrangement. Genomics 35 : 66 – 70 . ↵ Yang Y.-P. , Womack J.E. ( 1998 ) Parallel radiation hybrid mapping: A powerful tool for high-resolution genomic comparison. Genome Res. 8 : 731 – 736...
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LETTER: A Radiation Hybrid Map of the Cat Genome: Implications for Comparative Mapping
- William J. Murphy,
- Shan Sun,
- Zhang-qun Chen,
- Naoya Yuhki,
- Deborah Hirschmann,
- Marilyn Menotti-Raymond,
- and Stephen J. O'Brien
Genome Res. May 1, 2000 10: 691-702; doi:10.1101/gr.10.5.691
.... 5 : 725 – 733 . ↵ Yang Y.P. , Womack J.E. ( 1998 ) Parallel radiation hybrid mapping: A powerful tool for high-resolution genomic comparison. Genome Res. 8 : 731 – 736 . ↵ Yogalingam G. , Litjens T. , Bielicki J. , Crawley A.C. , Muller V. , Anson D.S. , Hopwood J.J. ( 1996 ) Feline...
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Methods: Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements
- Josée Dostie,
- Todd A. Richmond,
- Ramy A. Arnaout,
- Rebecca R. Selzer,
- William L. Lee,
- Tracey A. Honan,
- Eric D. Rubio,
- Anton Krumm,
- Justin Lamb,
- Chad Nusbaum,
- Roland D. Green,
- and Job Dekker
Genome Res. October 2006 16: 1299-1309; Published in Advance September 5, 2006, doi:10.1101/gr.5571506
...Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements Josée Dostie 1 , Todd A. Richmond 2 , Ramy A. Arnaout 3 , 4 , 5 , Rebecca R. Selzer 2 , William L. Lee 3...
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REVIEW: Zooming in on the Human–Mouse Comparative Map: Genome Conservation Re-examined on a High-Resolution Scale
- Ethan A. Carver and
- Lisa Stubbs
Genome Res. December 1, 1997 7: 1123-1137; doi:10.1101/gr.7.12.1123
...human–mouse comparative maps are derived largely from alignment of mouse interspecific backcross (IB) maps with human genes localized by fluorescent in situ hybridization (FISH). Whereas high resolution IB maps permit gene order and spacing to be established with considerable accuracy, FISH mapping...
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Research: Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies
- Megan A. Supple,
- Heather M. Hines,
- Kanchon K. Dasmahapatra,
- James J. Lewis,
- Dahlia M. Nielsen,
- Christine Lavoie,
- David A. Ray,
- Camilo Salazar,
- W. Owen McMillan,
- and Brian A. Counterman
Genome Res. August 2013 23: 1248-1257; Published in Advance May 14, 2013, doi:10.1101/gr.150615.112
...of the two species 13–26 million years ago (Pohl et al. 2009), both have undergone parallel radiations, such that the range of each species is composed of an identical patchwork of divergent color pattern races stitched together by a series of narrow hybrid zones. This replicate-rich and highly variable...

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