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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
....1086/418744 ↵Aguilar A, Roemer G, Debenham S, Binns M, Garcelon D, Wayne RK. 2004. High MHC diversity maintained by balancing selection in an otherwise genetically monomorphic mammal. Proc Natl Acad Sci 101: 3490–3494. doi:10.1073/pnas.0306582101 ↵Andolfatto P. 2005. Adaptive evolution of non-coding DNA in Drosophila...
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RESOURCE: A novel DNA sequence database for analyzing human demographic history
- Jeffrey D. Wall,
- Murray P. Cox,
- Fernando L. Mendez,
- August Woerner,
- Tesa Severson,
- and Michael F. Hammer
Genome Res. August 2008 18: 1354-1361; Published in Advance May 20, 2008, doi:10.1101/gr.075630.107
...ancestral structure in human populations . PLoS Genet. 2 : e105 , doi: 10.1371/journal.pgen.0020105. . ↵ Przeworski, M. , Wall, J.D. , Andolfatto, P. ( 2001 ) Recombination and the frequency spectrum in Drosophila melanogaster and Drosophila simulans . Mol. Biol. Evol. 18 : 291 – 298 . ↵ Ptak, S...
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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
...melanogaster . Mol. Biol. Evol. 6 : 123 – 130 . ↵ Akashi, H. ( 1995 ) Inferring weak selection from patterns of polymorphism and divergence at “silent” sites in Drosophila DNA . Genetics 139 : 1067 – 1076 . ↵ Akashi, H. ( 2001 ) Gene expression and molecular evolution . Curr. Opin. Genet. Dev. 11 : 660 – 666...
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Letter: Darwinian and demographic forces affecting human protein coding genes
- Rasmus Nielsen,
- Melissa J. Hubisz,
- Ines Hellmann,
- Dara Torgerson,
- Aida M. Andrés,
- Anders Albrechtsen,
- Ryan Gutenkunst,
- Mark D. Adams,
- Michele Cargill,
- Adam Boyko,
- Amit Indap,
- Carlos D. Bustamante,
- and Andrew G. Clark
Genome Res. May 2009 19: 838-849; Published in Advance March 11, 2009, doi:10.1101/gr.088336.108
...2005; Kelley et al. 2006; Sabeti et al. 2006). One special challenge when scanning a for evidence of selection is that variability in the is also strongly affected by demographic processes, such as population growth or bottlenecks, and by variation in the mutation and recombination processes (Simonsen...
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PERSPECTIVE: Drosophila melanogaster: A case study of a model genomic sequence and its consequences
- Michael Ashburner and
- Casey M. Bergman
Genome Res. December 2005 15: 1661-1667; doi:10.1101/gr.3726705
.... ↵ Green, P. 1997 . Against a whole- shotgun. Genome Res. 7 : 410 -417. ↵ Haddrill, P.R., Thornton, K.R., Charlesworth, B., and Andolfatto, P. 2005 . Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Res. 15 : 790 -799...
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Research: Genome sequencing reveals complex speciation in the Drosophila simulans clade
- Daniel Garrigan,
- Sarah B. Kingan,
- Anthony J. Geneva,
- Peter Andolfatto,
- Andrew G. Clark,
- Kevin R. Thornton,
- and Daven C. Presgraves
Genome Res. August 2012 22: 1499-1511; Published in Advance April 13, 2012, doi:10.1101/gr.130922.111
...Center for Comparative and Population Genomics, Cornell University, Ithaca, New York 14853, USA; 4 Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California 92697, USA Abstract The three species of the Drosophila simulans clade...
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Research: The influence of genomic context on mutation patterns in the human genome inferred from rare variants
- Valerie M. Schaibley,
- Matthew Zawistowski,
- Daniel Wegmann,
- Margaret G. Ehm,
- Matthew R. Nelson,
- Pamela L. St. Jean,
- Gonçalo R. Abecasis,
- John Novembre,
- Sebastian Zöllner,
- and Jun Z. Li
Genome Res. December 2013 23: 1974-1984; Published in Advance August 29, 2013, doi:10.1101/gr.154971.113
.... 2009; Lohmueller et al. 2011), Drosophila (Begun and Aquadro 1992; Begun et al. 2007; Kulathinal et al. 2008), and several plant species (Dvorak et al. 1998; Kraft et al. 1998; Stephan and Langley 1998; Tenaillon et al. 2004). Three major theories exist to explain these observations. First...
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LETTER: Fitting background-selection predictions to levels of nucleotide variation and divergence along the human autosomes
- Floyd A. Reed,
- Joshua M. Akey,
- and Charles F. Aquadro
Genome Res. September 2005 15: 1211-1221; doi:10.1101/gr.3413205
...in humans ( Nachman et al. 1998 ; Przeworski et al. 2000 ; Nachman 2001 ; Hellmann et al. 2003 ). This correlation also exists in many other eukaryotic species including Drosophila (e.g., Begun and Aquadro 1992 ; for reviews, see Andolfatto 2001 ; Aquadro et al. 2001 ; Schlötterer 2002 ). Two principal...
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Research: Shifts in the intensity of purifying selection: An analysis of genome-wide polymorphism data from two closely related yeast species
- Eyal Elyashiv,
- Kevin Bullaughey,
- Shmuel Sattath,
- Yosef Rinott,
- Molly Przeworski,
- and Guy Sella
Genome Res. November 2010 20: 1558-1573; Published in Advance September 4, 2010, doi:10.1101/gr.108993.110
.... 2005; Keightley and Eyre-Walker 2007). Some studies took a slightly different approach, inferring the DME from multilocus polymorphism data in two closely related species of Drosophila, under the assumption that all changes in f between them reflect differences in their effective population size (Loewe...
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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 population demographic history and selection on patterns of genetic variation complicate inferences of selection when a small number of loci are studied. To this end, identifying outlier loci from empirical genome-wide distributions of genetic variation is a promising strategy to detect targets of selection...

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