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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
...-Sánchez E, Sousa VC, Foll M. 2013. Robust demographic inference from genomic and SNP data. PLoS Genet 9: e1003905. doi:10.1371/journal.pgen.1003905 ↵Fraïsse C, Sachdeva H. 2021. The rates of introgression and barriers to genetic exchange between hybridizing species: sex chromosomes vs autosomes. Genetics...
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LETTER: How reliable are empirical genomic scans for selective sweeps?
- Kosuke M. Teshima,
- Graham Coop,
- and Molly Przeworski
Genome Res. June 2006 16: 702-712; Published in Advance May 10, 2006, doi:10.1101/gr.5105206
...are not directly applicable to genotyping studies, which type a pre-ascertained set of SNPs. Given the huge genotyping data sets now available for humans ( Hinds et al. 2005 ; International HapMap Consortium 2005 ), as well as increasingly for other organisms, it will be of interest to assess the reliability...
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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
...-rumped and fat-tailed sheep breeds. (C) Genome-wide selection sweep tests (the FST-based and π-ratio-based methods) for the tail configuration between fat-rumped and fat-tailed sheep breeds. (D) Calculation of Tajima's D-values and π and FST values for SNPs in the candidate genomic region Chr 8: 87.56–87.88 Mb...
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Research: Genomic analyses provide insights into peach local adaptation and responses to climate change
- Yong Li,
- Ke Cao,
- Nan Li,
- Gengrui Zhu,
- Weichao Fang,
- Changwen Chen,
- Xinwei Wang,
- Jian Guo,
- Qi Wang,
- Tiyu Ding,
- Jiao Wang,
- Liping Guan,
- Junxiu Wang,
- Kuozhan Liu,
- Wenwu Guo,
- Pere Arús,
- Sanwen Huang,
- Zhangjun Fei,
- and Lirong Wang
Genome Res. April 2021 31: 592-606; Published in Advance March 9, 2021, doi:10.1101/gr.261032.120
...encodes the epidermal patterning factor 1 (PpEPF1) involved in stomatal development (Hara et al. 2009), showed strong selection signals, based on the high Tajima's D and μ values (Fig. 5K,L). By scanning the variants in PpEPF1, we found that SNPs with functional significance were absent. Through further...
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Methods: Population differentiation as a test for selective sweeps
- Hua Chen,
- Nick Patterson,
- and David Reich
Genome Res. March 2010 20: 393-402; Published in Advance January 19, 2010, doi:10.1101/gr.100545.109
..., Bustamante CD. 2005. Genomic scans for selective sweeps using SNP data. Genome Res 15: 1566–1575. Nielsen R, Hubisz MJ, Hellmann I, Torgerson D, Andres AM, Albrechtsen A, Gutenkunst R, Adams MD, Cargill M, Boyko A, et al. 2009. Darwinian and demographic forces affecting human protein coding genes. Genome Res...
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Research: Natural genetic variation in C. elegans identified genomic loci controlling metabolite levels
- Arwen W. Gao,
- Mark G. Sterken,
- Jelmi uit de Bos,
- Jelle van Creij,
- Rashmi Kamble,
- Basten L. Snoek,
- Jan E. Kammenga,
- and Riekelt H. Houtkooper
Genome Res. September 2018 28: 1296-1308; Published in Advance August 14, 2018, doi:10.1101/gr.232322.117
...) and CB4856 (Hawaii), which is suitable for studying -to-phenome relations (Li et al. 2006; Andersen et al. 2012; Sterken et al. 2015). The segregating population consists of 199 homozygous recombinant inbred lines (RILs) that have been SNP genotyped and phenotyped for several traits, including gene...
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Research: Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches
- Fan Han,
- Sangeet Lamichhaney,
- B. Rosemary Grant,
- Peter R. Grant,
- Leif Andersson,
- and Matthew T. Webster
Genome Res. June 2017 27: 1004-1015; Published in Advance April 25, 2017, doi:10.1101/gr.212522.116
...were included in this study. We selected nine species from six islands from the Galápagos archipelago and one from Cocos Island and designed 12 species pairs based on the ranges of sympatry and allopatry and their beak haplogroups (Tables 1, 2). About 7 million SNPs were retained in each species pair...
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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
...to limit sharing of the DNA. Whole- resequencing was performed with Illumina paired-end sequencing technology, using a HiSeq 2000 instrument at the SNP&Seq Technology Platform of Uppsala University. Individually tagged libraries with insert sizes of ∼450 Evolution of differentiation Genome Research 1661...
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Perspective: Human genomic disease variants: A neutral evolutionary explanation
- Joel T. Dudley,
- Yuseob Kim,
- Li Liu,
- Glenn J. Markov,
- Kristyn Gerold,
- Rong Chen,
- Atul J. Butte,
- and Sudhir Kumar
Genome Res. August 2012 22: 1383-1394; Published in Advance June 4, 2012, doi:10.1101/gr.133702.111
...functional regions does not appear to be substantially different than the genomic background, nor are these regions enriched for alleles that segregate among populations (Hernandez et al. 2011). These observations suggest that classic selective sweeps for adaptive alleles may not be frequent in human...
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Review: Population genetic inference from genomic sequence variation
- John E. Pool,
- Ines Hellmann,
- Jeffrey D. Jensen,
- and Rasmus Nielsen
Genome Res. March 2010 20: 291-300; Published in Advance January 12, 2010, doi:10.1101/gr.079509.108
...affected by recent selective sweeps. For example, several studies (e.g., Carlson et al. 2005; Williamson et al. 2007; Nielsen et al. 2009) have used the distribution of human SNP frequencies along chromosomes to scan for completed sweeps. Whole- sequence polymorphism data should includemany rare SNPs...

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