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Research: Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation
- Xin Li,
- San-Gang He,
- Wen-Rong Li,
- Ling-Yun Luo,
- Ze Yan,
- Dong-Xin Mo,
- Xing Wan,
- Feng-Hua Lv,
- Ji Yang,
- Ya-Xi Xu,
- Juan Deng,
- Qiang-Hui Zhu,
- Xing-Long Xie,
- Song-Song Xu,
- Chen-Xi Liu,
- Xin-Rong Peng,
- Bin Han,
- Zhong-Hui Li,
- Lei Chen,
- Jian-Lin Han,
- Xue-Zhi Ding,
- Renqing Dingkao,
- Yue-Feng Chu,
- Jin-Yan Wu,
- Li-Min Wang,
- Ping Zhou,
- Ming-Jun Liu,
- and Meng-Hua Li
Genome Res. September 2022 32: 1669-1684; Published in Advance August 10, 2022, doi:10.1101/gr.276769.122
...of the worldwide populations and the F2 intercross confirmed the previously reported association between the two mutations in TBXT and the number of caudal vertebrae (Han et al. 2019).View larger version: In this window In a new window Figure 5. Genome-wide selection sweep test, -wide association study (GWAS...
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Research: Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants
- Kazumasa Shirai,
- Mitsuhiko P. Sato,
- Ranko Nishi,
- Masahide Seki,
- Yutaka Suzuki,
- and Kousuke Hanada
Genome Res. June 2021 31: 1060-1068; Published in Advance May 18, 2021, doi:10.1101/gr.271726.120
...regions of genes associated with specialized metabolites show a selective sweep signature in the A. thaliana population. Thus, naturally selected mCGs appear to be key mutations that cause the expressional diversity associated with specialized metabolites during plant evolution.All living organisms use...
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Method: Identifying chromosomal subpopulations based on their recombination histories advances the study of the genetic basis of phenotypic traits
- Carlos Ruiz-Arenas,
- Alejandro Cáceres,
- Marcos López,
- Dolors Pelegrí-Sisó,
- Josefa González,
- and Juan R. González
Genome Res. December 2020 30: 1802-1814; Published in Advance November 17, 2020, doi:10.1101/gr.258301.119
...in Drosophila melanogaster and human, and the chromosomes under selective pressure at the lactase locus in humans. We then applied recombClust to the complex human 1q21.1 region, where nonallelic homologous recombination produces deleterious phenotypes. We discovered and validated the presence of two different...
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Research: The circular RNome of primary breast cancer
- Marcel Smid,
- Saskia M. Wilting,
- Katharina Uhr,
- F. Germán Rodríguez-González,
- Vanja de Weerd,
- Wendy J.C. Prager-Van der Smissen,
- Michelle van der Vlugt-Daane,
- Anne van Galen,
- Serena Nik-Zainal,
- Adam Butler,
- Sancha Martin,
- Helen R. Davies,
- Johan Staaf,
- Marc J. van de Vijver,
- Andrea L. Richardson,
- Gaëten MacGrogan,
- Roberto Salgado,
- Gert G.G.M. van den Eynden,
- Colin A. Purdie,
- Alastair M. Thompson,
- Carlos Caldas,
- Paul N. Span,
- Fred C.G.J. Sweep,
- Peter T. Simpson,
- Sunil R. Lakhani,
- Steven Van Laere,
- Christine Desmedt,
- Angelo Paradiso,
- Jorunn Eyfjord,
- Annegien Broeks,
- Anne Vincent-Salomon,
- Andrew P. Futreal,
- Stian Knappskog,
- Tari King,
- Alain Viari,
- Anne-Lise Børresen-Dale,
- Hendrik G. Stunnenberg,
- Mike Stratton,
- John A. Foekens,
- Anieta M. Sieuwerts,
- and John W.M. Martens
Genome Res. March 2019 29: 356-366; Published in Advance January 28, 2019, doi:10.1101/gr.238121.118
.... Richardson6,7, Gaëten MacGrogan8, Roberto Salgado9,10, Gert G.G.M. van den Eynden10,11, Colin A. Purdie12, Alastair M. Thompson12, Carlos Caldas13, Paul N. Span14, Fred C.G.J. Sweep15, Peter T. Simpson16, Sunil R. Lakhani16,17, Steven Van Laere18, Christine Desmedt9, Angelo Paradiso19, Jorunn Eyfjord20...
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Research: Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles
- Xuejing Wang and
- Gerald Heckel
Genome Res. June 2024 34: 851-862; Published in Advance July 2, 2024, doi:10.1101/gr.278487.123
.... 1B), showing the importance of purifying selection across the (Kimura 1977; Kryazhimskiy and Plotkin 2008).Relaxed selection and the island syndromeRelaxation from selection may have contributed to the island syndrome phenotype of Orkney voles. We detected signatures of hard sweeps related to body...
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Review: Origins, evolution, and phenotypic impact of new genes
- Henrik Kaessmann
Genome Res. October 2010 20: 1313-1326; Published in Advance July 22, 2010, doi:10.1101/gr.101386.109
...by a selective sweep in Mus musculus musculus populations. Remarkably, knocking out Pldi led to reduced sperm motility and reduced testis weight, suggesting that Pldi contributed to enhanced fertility of the mice carrying it. Gene expression analyses indicate that the molecular basis of this phenotype is related...
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Research: Analysis of canine gene constraint identifies new variants for orofacial clefts and stature
- Reuben M. Buckley,
- Nüket Bilgen,
- Alexander C. Harris,
- Peter Savolainen,
- Cafer Tepeli,
- Metin Erdoğan,
- Aitor Serres Armero,
- Dayna L. Dreger,
- Frank G. van Steenbeek,
- Marjo K. Hytönen,
- Heidi G. Parker,
- Jessica Hale,
- Hannes Lohi,
- Bengi Çınar Kul,
- Adam R. Boyko,
- and Elaine A. Ostrander
Genome Res. May 2025 35: 1080-1093; Published in Advance March 24, 2025, doi:10.1101/gr.280092.124
...variation. This indicates trait selection in dogs is likely a balancing act between preserving essential gene functions and maximizing regulatory variation to drive phenotypic extremes.The s of domestic species hold immense promise for the discovery of novel genotype–phenotype associations (Andersson...
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Method: A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
- Meilin Zhang,
- Heng Du,
- Yu Zhang,
- Yue Zhuo,
- Zhen Liu,
- Yahui Xue,
- Lei Zhou,
- Sixuan Zhou,
- Wanying Li,
- and Jian-Feng Liu
Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
...filtration, such as the fixation index (FST) (Weir and Cockerham 1984), informativeness (In) (Kosoy et al. 2009; Nassir et al. 2009), selective sweep (SS) (Yan et al. 2020; Yang et al. 2022), and principal component analysis (PCA) (Paschou et al. 2007, 2008). In addition, with the development of machine...
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Research: Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana
- Viola Nolte,
- Ram Vinay Pandey,
- Robert Kofler,
- and Christian Schlötterer
Genome Res. January 2013 23: 99-110; Published in Advance October 10, 2012, doi:10.1101/gr.139873.112
...Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana Viola Nolte , Ram Vinay Pandey , Robert Kofler and Christian Schlötterer 1 Institut für Populationsgenetik...
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Method: Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle
- Sotiria Milia,
- Alexander S. Leonard,
- Xena Marie Mapel,
- Sandra Milena Bernal Ulloa,
- Cord Drögemüller,
- and Hubert Pausch
Genome Res. April 2025 35: 1041-1052; Published in Advance December 18, 2024, doi:10.1101/gr.279064.124
.... Signature of selection analyses using these short-read sequencing-derived variants revealed a strong selective sweep near KIT in both white-headed breeds (Supplemental Fig. S1). This finding corroborates previous mapping attempts and suggests a shared genetic origin of the white-headed phenotype (Fontanesi...

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