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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
...Inference of selective forces on house mouse s during secondary contact in East Asia Kazumichi Fujiwara1,2, Shunpei Kubo2, Toshinori Endo2, Toyoyuki Takada3, Toshihiko Shiroishi4, Hitoshi Suzuki5 and Naoki Osada2 1Mouse Genomics Resource Laboratory, National Institute of Genetics, Mishima 411...
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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
...system for studying regional recombination rate variation and its potential molecular underpinnings. Here, we developed a large whole- resequencing data set from a population of wood whites to obtain high-resolution recombination maps using linkage disequilibrium information. The analyses revealed...
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Method: Fast inference of genetic recombination rates in biobank scale data
- Ardalan Naseri,
- William Yue,
- Shaojie Zhang,
- and Degui Zhi
Genome Res. July 2023 33: 1015-1022; Published in Advance June 22, 2023, doi:10.1101/gr.277676.123
...-020-0163-6 ↵Barroso GV, Puzović N, Dutheil JY. 2019. Inference of recombination maps from a single pair of s and its application to ancient samples. PLoS Genet 15: e1008449. doi:10.1371/journal.pgen.1008449 ↵Browning BL, Browning SR. 2013. Improving the accuracy and efficiency of identity-by-descent detection...
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Resource: GenomeMUSter mouse genetic variation service enables multitrait, multipopulation data integration and analysis
- Robyn L. Ball,
- Molly A. Bogue,
- Hongping Liang,
- Anuj Srivastava,
- David G. Ashbrook,
- Anna Lamoureux,
- Matthew W. Gerring,
- Alexander S. Hatoum,
- Matthew J. Kim,
- Hao He,
- Jake Emerson,
- Alexander K. Berger,
- David O. Walton,
- Keith Sheppard,
- Baha El Kassaby,
- Francisco Castellanos,
- Govindarajan Kunde-Ramamoorthy,
- Lu Lu,
- John Bluis,
- Sejal Desai,
- Beth A. Sundberg,
- Gary Peltz,
- Zhuoqing Fang,
- Gary A. Churchill,
- Robert W. Williams,
- Arpana Agrawal,
- Carol J. Bult,
- Vivek M. Philip,
- and Elissa J. Chesler
Genome Res. January 2024 34: 145-159; Published in Advance January 30, 2024, doi:10.1101/gr.278157.123
....744 to 0.963 (Supplemental Table S6).GenomeMUSter enables multipopulation, multitrait meta-analysisA major utility of GenomeMUSter is that it enables genetic discovery across the wealth of recent and historical studies of mouse population variation in a deep and extensible collection of complex disease...
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Research: The house fly Y Chromosome is young and minimally differentiated from its ancient X Chromosome partner
- Richard P. Meisel,
- Christopher A. Gonzales,
- and Hoang Luu
Genome Res. August 2017 27: 1417-1426; Published in Advance June 15, 2017, doi:10.1101/gr.215509.116
...of the gene encoding the spliceosome-associated protein CWC22 (Sharma et al. 2017), not an ancient gene as would be expected if it were the ancestral male-determining locus of brachycerans. Mdmd has been mapped to the autosomes as well as the Y Chromosome (Sharma et al. 2017), suggesting that the house fly Y...
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Research: Divergence patterns of genic copy number variation in natural populations of the house mouse (Mus musculus domesticus) reveal three conserved genes with major population-specific expansions
- Željka Pezer,
- Bettina Harr,
- Meike Teschke,
- Hiba Babiker,
- and Diethard Tautz
Genome Res. August 2015 25: 1114-1124; Published in Advance July 6, 2015, doi:10.1101/gr.187187.114
...), as well as parallel selection for some CNV regions (Hirase et al. 2014). We analyze here copy number variation in natural populations of the house mouse, with a specific focus on full genes that are located within CNVs, as these genes could be particularly relevant for population differentiation...
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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
...high-density linkage map of the collared flycatcher (Kawakami et al. 2014a, b) enabled us to examine the relationship between recombination and differentiation in more detail than previously possible. Lineage-specific differentiation (PBS) significantly increased with decreasing recombination rate...
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ARTICLE: Extensive and breed-specific linkage disequilibrium in Canis familiaris
- Nathan B. Sutter,
- Michael A. Eberle,
- Heidi G. Parker,
- Barbara J. Pullar,
- Ewen F. Kirkness,
- Leonid Kruglyak,
- and Elaine A. Ostrander
Genome Res. December 2004 14: 2388-2396; Published in Advance November 15, 2004, doi:10.1101/gr.3147604
...-sequence variation and indicate a region of extensive linkage disequilibrium. Am. J. Hum. Genet. 67 : 1437 -1451. ↵ Breen, M., Thomas, R., Binns, M.M., Carter, N.P., and Langford, C.F. 1999 . Reciprocal chromosome painting reveals detailed regions of conserved synteny between the karyotypes of the domestic dog...
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Research: The recombination landscape of the zebra finch Taeniopygia guttata genome
- Niclas Backström,
- Wolfgang Forstmeier,
- Holger Schielzeth,
- Harriet Mellenius,
- Kiwoong Nam,
- Elisabeth Bolund,
- Matthew T. Webster,
- Torbjörn Öst,
- Melanie Schneider,
- Bart Kempenaers,
- and Hans Ellegren
Genome Res. April 2010 20: 485-495; Published in Advance March 31, 2010, doi:10.1101/gr.101410.109
...of recombination is essential since this parameter is considered to affect levels of genetic variability, the efficacy of selection, and the design of association and linkage mapping studies. However, there is limited knowledge about the factors governing recombination rate variation. We genotyped 1920 single...
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LETTER: Genome-wide patterns of gene flow across a house mouse hybrid zone
- Katherine C. Teeter,
- Bret A. Payseur,
- Leslie W. Harris,
- Margaret A. Bakewell,
- Lisa M. Thibodeau,
- Janelle E. O’Brien,
- James G. Krenz,
- Maria A. Sans-Fuentes,
- Michael W. Nachman,
- and Priscilla K. Tucker
Genome Res. January 2008 18: 67-76; Published in Advance November 19, 2007, doi:10.1101/gr.6757907
...closely related species or subspecies provide useful settings for studying the genetic architecture of speciation. Using markers distributed throughout the mouse genome, we use a hybrid zone between two recently diverged species of house mice ( Mus musculus and Mus domesticus ) as a natural mapping...

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