Searching journal content for articles similar to Nielsen et al. 19 (5): 838.

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  1. Research: Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection
    • PingHsun Hsieh,
    • Krishna R. Veeramah,
    • Joseph Lachance,
    • Sarah A. Tishkoff,
    • Jeffrey D. Wall,
    • Michael F. Hammer,
    • and Ryan N. Gutenkunst
    Genome Res. March 2016 26: 279-290; Published in Advance February 17, 2016, doi:10.1101/gr.192971.115
    ...Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection PingHsun Hsieh 1 , Krishna R. Veeramah 2 , 3 , Joseph Lachance 4 , 5...
  2. LETTER: Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations
    • Penelope R. Haddrill,
    • Kevin R. Thornton,
    • Brian Charlesworth,
    • and Peter Andolfatto
    Genome Res. June 2005 15: 790-799; doi:10.1101/gr.3541005
    ...Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations Penelope R. Haddrill 1 , Kevin R. Thornton 2 , Brian Charlesworth 1 , and Peter Andolfatto 3 , 4 1...
  3. Method: Inferring the mode and strength of ongoing selection
    • Gustavo V. Barroso and
    • Kirk E. Lohmueller
    Genome Res. April 2023 33: 632-643; Published in Advance April 13, 2023, doi:10.1101/gr.276386.121
    ...(Hey 1999; Kern and Hahn 2018; Jensen et al. 2019). One challenge is that genetic diversity from natural populations likely has been affected by multiple evolutionary forces simultaneously, making it hard to isolate and test for the effects of any one such force (Barroso and Dutheil 2021). However...
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  4. Method: A flexible method for estimating the fraction of fitness influencing mutations from large sequencing data sets
    • Sunjin Moon and
    • Joshua M. Akey
    Genome Res. June 2016 26: 834-843; Published in Advance April 14, 2016, doi:10.1101/gr.203059.115
    ..., Adams MD, Cargill M, Boyko A, et al. 2009. Darwinian and demographic forces affecting human protein coding genes. Genome Res 19: 838–849. ↵Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, Auton...
  5. 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
    ..., Gutenkunst R, Adams MD, Cargill M, Boyko A, et al. 2009. Darwinian and demographic forces affecting human protein coding genes. Genome Res 19: 838–849. Peng Y, Yang Z, Zhang H, Cui C, Qi X, Luo X, Tao X, Wu T, Ouzhuluobu, Basang, et al. 2011. Genetic variations in Tibetan populations and high...
  6. Research: Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis
    • Cristel G. Thomas,
    • Wei Wang,
    • Richard Jovelin,
    • Rajarshi Ghosh,
    • Tatiana Lomasko,
    • Quang Trinh,
    • Leonid Kruglyak,
    • Lincoln D. Stein,
    • and Asher D. Cutter
    Genome Res. May 2015 25: 667-678; Published in Advance March 17, 2015, doi:10.1101/gr.187237.114
    ...and demographic histories to their genomic signatures in a global sample of C. briggsae. Results Low recombination regions show drastic skews in polymorphism We sequenced 37 wild isolate s of C. briggsae to high coverage (median 32×) (Supplemental Table 1) and identified a total of 2.70 million single nucleotide...
  7. 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
    ...in comparisons between descendent lineages. Still, to further explore this possibility, we focused on SNPs unique to each species, which are expected to be highly enriched for lineage-specific mutations affected only by processes in descendent lineages. We found that lineage-specific SNPs showed strongly reduced...
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  8. 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...
  9. 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
    ...it provides a framework for understanding the distribution of genetic variability among populations and for inferring the demographic histories of natural populations from molecular data. It is also central in studies of molecular evolution, providing a foundation for understanding the contributions...
  10. 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
    ...Harbor Laboratory Press; ISSN 1088-9051/12; www..org Genome Research 1383 www..org Neutral theory for personal, population, and species differences Under the NTME, the primary forces that give rise to andmaintain variation within populations are mutation, recombination, and random genetic drift (for...
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