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Method: Identifying loci under positive selection in complex population histories
- Alba Refoyo-Martínez,
- Rute R. da Fonseca,
- Katrín Halldórsdóttir,
- Einar Árnason,
- Thomas Mailund,
- and Fernando Racimo
Genome Res. September 2019 29: 1506-1520; Published in Advance July 30, 2019, doi:10.1101/gr.246777.118
...Consortium 2015) and a SNP capture data set (Human Origins) (Patterson et al. 2012) from different populations sampled around the world (Fig. 4) and obtained the top candidate regions from the scan (P-value < 10−7). Many of these have been identified in previous world-wide positive selection scans, and some...
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Research: Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans
- James A. Cahill,
- Joel Armstrong,
- Alden Deran,
- Carolyn J. Khoury,
- Benedict Paten,
- David Haussler,
- and Erich D. Jarvis
Genome Res. November 2021 31: 2035-2049; Published in Advance October 19, 2021, doi:10.1101/gr.275989.121
.... 2014), one or more episodes of positive selection or an overarching loss of constraint might produce similar signatures of acceleration. In either case, it would represent a probable deviation in the function of the conserved element so that even a loss of constraint would still be indicative a likely...
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Methods: Tracking the Evolution of the SARS Coronavirus Using High-Throughput, High-Density Resequencing Arrays
- Christopher W. Wong,
- Thomas J. Albert,
- Vinsensius B. Vega,
- Jason E. Norton,
- David J. Cutler,
- Todd A. Richmond,
- Lawrence W. Stanton,
- Edison T. Liu,
- and Lance D. Miller
Genome Res. March 2004 14: 398-405; doi:10.1101/gr.2141004
...-CoV , the iterative design flexibility and high density of probes makes this a highly attractive platform for gene expression analysis, comparative genomic hybridization, SNP discovery, and other genomic applications. METHODS Amplification of SARS Viral RNA A detailed protocol is published on our Web site. Briefly...
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Method: Genome-wide detection of natural selection in African Americans pre- and post-admixture
- Wenfei Jin,
- Shuhua Xu,
- Haifeng Wang,
- Yongguo Yu,
- Yiping Shen,
- Bailin Wu,
- and Li Jin
Genome Res. March 2012 22: 519-527; Published in Advance November 29, 2011, doi:10.1101/gr.124784.111
...regions that deviated from -wide ancestral contributions or with extremely high FST were annotated based on the HapMap website (Thorisson et al. 2005). The SNPs showing substantial population differentiation were interrogated for network and functional interrelatedness using the IPA version 8.5 software...
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Method: A probabilistic method for testing and estimating selection differences between populations
- Yungang He,
- Minxian Wang,
- Xin Huang,
- Ran Li,
- Hongyang Xu,
- Shuhua Xu,
- and Li Jin
Genome Res. December 2015 25: 1903-1909; Published in Advance October 13, 2015, doi:10.1101/gr.192336.115
...gain? Eur J Hum Genet 9: 291–300. Akey JM, Zhang G, Zhang K, Jin L, Shriver MD. 2002. Interrogating a highdensity SNP map for signatures of natural selection. Genome Res 12: 1805–1814. Bagos PG. 2012. On the covariance of two correlated log-odds ratios. Stat Med 31: 1418–1431. Basu Mallick C, Iliescu...
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Resource: Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines
- Wen Huang,
- Andreas Massouras,
- Yutaka Inoue,
- Jason Peiffer,
- Miquel Ràmia,
- Aaron M. Tarone,
- Lavanya Turlapati,
- Thomas Zichner,
- Dianhui Zhu,
- Richard F. Lyman,
- Michael M. Magwire,
- Kerstin Blankenburg,
- Mary Anna Carbone,
- Kyle Chang,
- Lisa L. Ellis,
- Sonia Fernandez,
- Yi Han,
- Gareth Highnam,
- Carl E. Hjelmen,
- John R. Jack,
- Mehwish Javaid,
- Joy Jayaseelan,
- Divya Kalra,
- Sandy Lee,
- Lora Lewis,
- Mala Munidasa,
- Fiona Ongeri,
- Shohba Patel,
- Lora Perales,
- Agapito Perez,
- LingLing Pu,
- Stephanie M. Rollmann,
- Robert Ruth,
- Nehad Saada,
- Crystal Warner,
- Aneisa Williams,
- Yuan-Qing Wu,
- Akihiko Yamamoto,
- Yiqing Zhang,
- Yiming Zhu,
- Robert R.H. Anholt,
- Jan O. Korbel,
- David Mittelman,
- Donna M. Muzny,
- Richard A. Gibbs,
- Antonio Barbadilla,
- J. Spencer Johnston,
- Eric A. Stone,
- Stephen Richards,
- Bart Deplancke,
- and Trudy F.C. Mackay
Genome Res. July 2014 24: 1193-1208; Published in Advance April 8, 2014, doi:10.1101/gr.171546.113
...sequence reads to the D. melanogaster using BWA (Li and Durbin 2010) and Novoalign (Novocraft.com), recalibrated base quality scores, and locally realigned reads. The average mapped sequence coverage was 273 per line (Supplemental Data File S1). There are many algorithms for detecting SNP and non-SNP...
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LETTER: Genomic signatures of positive selection in humans and the limits of outlier approaches
- Joanna L. Kelley,
- Jennifer Madeoy,
- John C. Calhoun,
- Willie Swanson,
- and Joshua M. Akey
Genome Res. August 2006 16: 980-989; Published in Advance July 6, 2006, doi:10.1101/gr.5157306
...) Interrogating a high-density SNP map for signatures of natural selection. Genome Res. 12 : 1805 – 1814 . ↵ Akey J.M. , Zhang K. , Xiong M. , Jin L. ( 2003 ) The effect of single nucleotide polymorphism identification strategies on estimates of linkage disequilibrium. Mol. Biol. Evol. 20 : 232 – 242 . ↵ Akey J...
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Methods: Genomic scans for selective sweeps using SNP data
- Rasmus Nielsen,
- Scott Williamson,
- Yuseob Kim,
- Melissa J. Hubisz,
- Andrew G. Clark,
- and Carlos Bustamante
Genome Res. November 2005 15: 1566-1575; doi:10.1101/gr.4252305
...Type I error). Our new test also provides estimates of the location of the selective sweep(s) and the magnitude of the selection coefficient. To illustrate the method, we apply our approach to data from the Seattle SNP project and to Chromosome 2 data from the HapMap project. In Chromosome 2, the most...
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Research: Adaptive selection of an incretin gene in Eurasian populations
- Chia Lin Chang,
- James J. Cai,
- Chiening Lo,
- Jorge Amigo,
- Jae-Il Park,
- and Sheau Yu Teddy Hsu
Genome Res. January 2011 21: 21-32; Published in Advance October 26, 2010, doi:10.1101/gr.110593.110
..., Zhang K, Jin L, Shriver MD. 2002. Interrogating a highdensity SNP map for signatures of natural selection. Genome Res 12: 1805–1814. Allison AC. 1956. The sickle-cell and haemoglobin C genes in some African populations. Ann Hum Genet 21: 67–89. Amigo J, Salas A, Phillips C, Carracedo A. 2008. SPSmart...
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Perspective: Constructing genomic maps of positive selection in humans: Where do we go from here?
- Joshua M. Akey
Genome Res. May 2009 19: 711-722; doi:10.1101/gr.086652.108
...’Reilly et al. (2008) SNP LD HapMap, Perlegen aStudies included in the analysis of the integrated map of positive selection are shown in bold. Inclusion criteria were that the study was performed in the HapMap or Perlegen data, lists of all loci deemed as outlier were available as supplemental data...

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