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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
...be explained by variation in recombination rate and the density of targets for selection. We thus conclude that the heterogeneous landscape of differentiation in Ficedula flycatchers evolves mainly as the result of background selection and selective sweeps in genomic regions of low recombination. Our results...
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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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Dog Special/Letters: Selective sweep mapping of genes with large phenotypic effects
- John P. Pollinger,
- Carlos D. Bustamante,
- Adi Fledel-Alon,
- Sheila Schmutz,
- Melissa M. Gray,
- and Robert K. Wayne
Genome Res. December 2005 15: 1809-1819; doi:10.1101/gr.4374505
...-specific phenotypes. In this study, we test the assumptions of the selective sweep approach in dogs by using simulations and empirical marker surveys. First, we simulate the process of breed formation and assess the probability that in a moderate-density genomic scan, a single marker or two or three adjacent markers...
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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
..., until recently, been frustratingly slow, relying on the analysis of individual candidate genes. Genomics, however, has provided the necessary resources to systematically interrogate the entire genome for signatures of natural selection. To date, 21 genome-wide scans for recent or ongoing positive...
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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
...of the observed correlation, particularly in the EA sample, implies that the Perlegen data is suitable for identifying candidate selection genes based on the empirical distribution of TDGen. Genome-wide analysis of the site frequency spectrum We pursed a gene-centric -wide scan for positive selection...
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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
...,000 or 150,000 yr ago. We also find that bidirectional asymmetric gene flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested. We then applied complementary statistics to scan the genome for evidence of selective sweeps...
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Letter: Signals of recent positive selection in a worldwide sample of human populations
- Joseph K. Pickrell,
- Graham Coop,
- John Novembre,
- Sridhar Kudaravalli,
- Jun Z. Li,
- Devin Absher,
- Balaji S. Srinivasan,
- Gregory S. Barsh,
- Richard M. Myers,
- Marcus W. Feldman,
- and Jonathan K. Pritchard
Genome Res. May 2009 19: 826-837; Published in Advance March 23, 2009, doi:10.1101/gr.087577.108
...Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, USA Abstract Genome-wide scans for recent positive selection in humans have yielded insight into the mechanisms underlying the extensive phenotypic diversity in our species, but have focused on a limited number...
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LETTER: Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome
- Peter Andolfatto
Genome Res. December 2007 17: 1755-1762; Published in Advance November 7, 2007, doi:10.1101/gr.6691007
.... Recurrent selective sweeps associated with adaptive substitutions should leave a characteristic signature in genome variability data that contains information about the frequency and strength of selection. Here, I document a significant negative correlation between the level and the frequency of synonymous...
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Method: Ultrafast genome-wide inference of pairwise coalescence times
- Regev Schweiger and
- Richard Durbin
Genome Res. July 2023 33: 1023-1031; Published in Advance August 10, 2023, doi:10.1101/gr.277665.123
...of European individuals from the 1000 Genomes Project data, at Chr 2: 500,000. Coalescence times are estimated by taking posterior means, measured in years ago. Times were converted from generations to years using a generation time of 30 yr.We then performed a selection scan by looking for genomic regions...
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Methods: Confounding between recombination and selection, and the Ped/Pop method for detecting selection
- Paul F. O’Reilly,
- Ewan Birney,
- and David J. Balding
Genome Res. August 2008 18: 1304-1313; Published in Advance July 10, 2008, doi:10.1101/gr.067181.107
...to confounding by the other. We illustrate here that even modest levels of positive selection can substantially reduce population-based recombination rate estimates. We also show that genome-wide scans to detect loci under recent selection in humans have tended to highlight loci in regions of low recombination...

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