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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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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
...Compensatory evolution associated with misexpression. dAssociation between misexpression and compensatory evolution not formally tested. eGenome-wide analysis (RNA-seq or microarray). fHybrids are allopolyploids. Gene regulation and speciation in house mice Genome Research 453 www..org changes acting in the same...
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Research: A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids
- Bridgett M. vonHoldt,
- John P. Pollinger,
- Dent A. Earl,
- James C. Knowles,
- Adam R. Boyko,
- Heidi Parker,
- Eli Geffen,
- Malgorzata Pilot,
- Wlodzimierz Jedrzejewski,
- Bogumila Jedrzejewska,
- Vadim Sidorovich,
- Claudia Greco,
- Ettore Randi,
- Marco Musiani,
- Roland Kays,
- Carlos D. Bustamante,
- Elaine A. Ostrander,
- John Novembre,
- and Robert K. Wayne
Genome Res. August 2011 21: 1294-1305; Published in Advance May 12, 2011, doi:10.1101/gr.116301.110
...(Supplemental Table S1). Map depicts historic species distributions and admixture zone (data from Nowak 2009; Rutledge et al. 2010b). Genome Research 1295 www..org Genome-wide analysis of enigmatic wolf-like canids We found considerable -wide SNP variation at the population level in graywolves and coyotes...
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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
.... 2015). Previous analyses in collared flycatcher (F. albicollis) and pied flycatcher (F. hypoleuca) revealed a highly heterogeneous differentiation landscape across the (Ellegren et al. 2012). An involvement of gene flow in its evolution would be plausible, as hybrids between these species occur at low...
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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
...relationships vary considerably across the , primarily as a function of gene flow/introgression and incomplete lineage sorting (Li et al. 2019). The relationships and species divergence times are derived from a consensus of regions of the with low recombination and of recent studies incorporating complete...
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LETTER: Genetic and Haplotype Diversity Among Wild-Derived Mouse Inbred Strains
- Folami Y. Ideraabdullah,
- Elena de la Casa-Esperón,
- Timothy A. Bell,
- David A. Detwiler,
- Terry Magnuson,
- Carmen Sapienza,
- and Fernando Pardo-Manuel de Villena
Genome Res. October 2004 14: 1880-1887; doi:10.1101/gr.2519704
...between subspecies is common in hybrid zones and in classical strains ( Guenet and Bonhomme 2003 ), but our approach specifically excludes the use of strains derived from hybrid populations in the identification of ancient polymorphisms (Methods). Therefore, gene flow is unlikely to contribute...
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LETTER: Global organization of replication time zones of the mouse genome
- Shlomit Farkash-Amar,
- Doron Lipson,
- Andreas Polten,
- Alon Goren,
- Charles Helmstetter,
- Zohar Yakhini,
- and Itamar Simon
Genome Res. October 2008 18: 1562-1570; Published in Advance July 30, 2008, doi:10.1101/gr.079566.108
...), demonstrating the uniform loading of newly replicated DNA ( Buzina et al. 2005 ). On the other hand, the early replicating gene ( Actb ) is enriched in the early samples and the late replicating regions ( Hbb and X141) in late samples. Genome-wide mapping of the mouse replication time zones In order to obtain...
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ARTICLE: Identification of Multiple Genetic Loci Linked to the Propensity for “Behavioral Despair” in Mice
- Takeo Yoshikawa,
- Akiko Watanabe,
- Yuichi Ishitsuka,
- Akihiro Nakaya,
- and Noriaki Nakatani
Genome Res. March 1, 2002 12: 357-366; doi:10.1101/gr.222602
...for whole- scans and radiation hybrid mapping and a mouse family tree. Genome Res. 9 : 878 – 887 . ↵ Shimomura K. , Low-Zeddies S.S. , King D.P. , Steeves T.D. , Whiteley A. , Kushla J. , Zemenides P.D. , Lin A. , Vitaterna M.H. , Churchill G.A. , et al. ( 2001 ) Genome-wide epistatic interaction analysis...
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Research: Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early- and late-firing origins
- Larry D. Mesner,
- Veena Valsakumar,
- Marcin Cieślik,
- Rebecca Pickin,
- Joyce L. Hamlin,
- and Stefan Bekiranov
Genome Res. November 2013 23: 1774-1788; Published in Advance July 16, 2013, doi:10.1101/gr.155218.113
...depth (RD), defined as the number of reads in each EcoRI fragment diGenome Research 1775 www..org Genome-wide map of human replication origins vided by the fragment length in base pairs.We then fit the low end of the RD distribution (background or noise) to a negative binomial distribution, and defined...
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Research: Restless Legs Syndrome-associated intronic common variant in Meis1 alters enhancer function in the developing telencephalon
- Derek Spieler,
- Maria Kaffe,
- Franziska Knauf,
- José Bessa,
- Juan J. Tena,
- Florian Giesert,
- Barbara Schormair,
- Erik Tilch,
- Heekyoung Lee,
- Marion Horsch,
- Darina Czamara,
- Nazanin Karbalai,
- Christine von Toerne,
- Melanie Waldenberger,
- Christian Gieger,
- Peter Lichtner,
- Melina Claussnitzer,
- Ronald Naumann,
- Bertram Müller-Myhsok,
- Miguel Torres,
- Lillian Garrett,
- Jan Rozman,
- Martin Klingenspor,
- Valérie Gailus-Durner,
- Helmut Fuchs,
- Martin Hrabě de Angelis,
- Johannes Beckers,
- Sabine M. Hölter,
- Thomas Meitinger,
- Stefanie M. Hauck,
- Helmut Laumen,
- Wolfgang Wurst,
- Fernando Casares,
- Jose Luis Gómez-Skarmeta,
- and Juliane Winkelmann
Genome Res. April 2014 24: 592-603; Published in Advance March 18, 2014, doi:10.1101/gr.166751.113
...These authors contributed equally to this work. Abstract Genome-wide association studies (GWAS) identified the MEIS1 locus for Restless Legs Syndrome (RLS), but causal single nucleotide polymorphisms (SNPs) and their functional relevance remain unknown. This locus contains a large number of highly...
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