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Resource: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
- Wenyu Zhang,
- Anja Guenther,
- Yuanxiao Gao,
- Kristian Ullrich,
- Bruno Huettel,
- Aftab Ahmad,
- Lei Duan,
- Kaizong Wei,
- and Diethard Tautz
Genome Res. November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124
...roughly half a million years ago, are distinguished as subspecies (Harr et al. 2016): the Western European house mouse M. musculus domesticus, the Eastern European house mouse M. musculus musculus, and the Southeast Asian house mouse M. musculus castaneus. With a divergence time of fewer than 2 million...
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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
...of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan Corresponding author: nosada@ist.hokudai.ac.jpAbstractThe house mouse (Mus musculus), which is commensal to humans, has spread globally via human activities, leading to secondary contact between genetically divergent subspecies. This pattern...
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Research: Gene regulation and speciation in house mice
- Katya L. Mack,
- Polly Campbell,
- and Michael W. Nachman
Genome Res. April 2016 26: 451-461; Published in Advance February 1, 2016, doi:10.1101/gr.195743.115
.... As gene regulation requires interactions between loci, negative epistatic interactions between divergent regulatory elements might underlie hybrid incompatibilities and contribute to reproductive isolation. Here, we take advantage of a cross between house mouse subspecies, where hybrid dysfunction...
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LETTER: Contribution of Asian mouse subspecies Mus musculus molossinus to genomic constitution of strain C57BL/6J, as defined by BAC-end sequence–SNP analysis
- Kuniya Abe,
- Hideki Noguchi,
- Keiko Tagawa,
- Misako Yuzuriha,
- Atsushi Toyoda,
- Toshio Kojima,
- Kiyoshi Ezawa,
- Naruya Saitou,
- Masahira Hattori,
- Yoshiyuki Sakaki,
- Kazuo Moriwaki,
- and Toshihiko Shiroishi
Genome Res. December 2004 14: 2439-2447; doi:10.1101/gr.2899304
...mice bred at the beginning of the 20th century ( Morse III 1981 ; Silver 1995 ). The house mouse, Mus musculus , is a complex species comprised of several subspecies. Results of our past studies (Yonekawa et al. 1980 , 1982 ; Moriwaki 1994 ) and those of others ( Ferris et al. 1982 ; Bonhomme et al...
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Research: Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F₁ hybrids
- Carina F. Mugal,
- Mi Wang,
- Niclas Backström,
- David Wheatcroft,
- Murielle Ålund,
- Marie Sémon,
- S. Eryn McFarlane,
- Ludovic Dutoit,
- Anna Qvarnström,
- and Hans Ellegren
Genome Res. December 2020 30: 1727-1739; Published in Advance November 3, 2020, doi:10.1101/gr.254508.119
...in the HP comparison but only 485 in the interspecific CP comparison of the same tissue. In contrast, for testis the number of differently expressed genes was vastly higher in the interspecific CP (965) than in the HP (61) or HC (61) comparisons. Again, this suggests that regulatory evolution is highly...
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Research: Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells
- Tate Tunstall,
- Richard Kock,
- Jiri Vahala,
- Mark Diekhans,
- Ian Fiddes,
- Joel Armstrong,
- Benedict Paten,
- Oliver A. Ryder,
- and Cynthia C. Steiner
Genome Res. June 2018 28: 780-788; Published in Advance May 24, 2018, doi:10.1101/gr.227603.117
...population history and demography of these two white rhinoceros subspecies and identified potential regions of selection in the NWR that may suggest local adaptation and divergent evolution from the SWR. Because of the comparative approach we employed using two closely related populations, this work may...
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Research: Evolutionary conservation of Y Chromosome ampliconic gene families despite extensive structural variation
- Wesley A. Brashear,
- Terje Raudsepp,
- and William J. Murphy
Genome Res. December 2018 28: 1841-1851; Published in Advance October 31, 2018, doi:10.1101/gr.237586.118
...of eutherian Y Chromosomes due to strong purifying selection to retain dosage-sensitive genes. In contrast, the ampliconic regions of the Y Chromosome, which contain testis-specific genes that encode the majority of the transcripts on eutherian Y Chromosomes, are rapidly evolving and are thought to undergo...
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RESOURCE: Mouse inter-subspecific consomic strains for genetic dissection of quantitative complex traits
- Toyoyuki Takada,
- Akihiko Mita,
- Akiteru Maeno,
- Takahiro Sakai,
- Hiroshi Shitara,
- Yoshiaki Kikkawa,
- Kazuo Moriwaki,
- Hiromichi Yonekawa,
- and Toshihiko Shiroishi
Genome Res. March 2008 18: 500-508; Published in Advance February 6, 2008, doi:10.1101/gr.7175308
...organs. By contrast, several consomic strains show reduced testis and liver weights, although the relative weights of these organs in MSM/Ms are indistinguishable from those of the B6 strain ( Fig. 2 ). We also carried out extensive phenotyping of fat pad weight. We measured epididymal, perirenal...
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LETTER: A genome-wide survey of structural variation between human and chimpanzee
- Tera L. Newman,
- Eray Tuzun,
- V. Anne Morrison,
- Karen E. Hayden,
- Mario Ventura,
- Sean D. McGrath,
- Mariano Rocchi,
- and Evan E. Eichler
Genome Res. October 2005 15: 1344-1356; Published in Advance September 16, 2005, doi:10.1101/gr.4338005
...-specific evolution because of their potential for dramatic and irreversible mutation. The low-quality nature of the current chimpanzee genome assembly precludes the reliable identification of many of these differences. To circumvent this, we applied a method to optimally map chimpanzee fosmid paired-end sequences...
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Research: The Y chromosome as a regulatory element shaping immune cell transcriptomes and susceptibility to autoimmune disease
- Laure K. Case,
- Emma H. Wall,
- Julie A. Dragon,
- Naresha Saligrama,
- Dimitry N. Krementsov,
- Mohamad Moussawi,
- James F. Zachary,
- Sally A. Huber,
- Elizabeth P. Blankenhorn,
- and Cory Teuscher
Genome Res. September 2013 23: 1474-1485; Published in Advance June 25, 2013, doi:10.1101/gr.156703.113
...; Case et al. 2012; Charchar et al. 2012). Like autosomal chromosomes, ChrX and ChrYare thought to have once been identical pairs that were free to recombine and exchange genetic material. Over the course of evolution, ChrY became unique from all other chromosomes due to the acquisition of a dominant sex...

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