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Patterns of population structure and complex haplotype sharing among field isolates of the green alga Chlamydomonas reinhardtii.

Craig RJ, Böndel KB, Arakawa K, Nakada T, Ito T, Bell G, Colegrave N, Keightley PD, Ness RW.

Mol Ecol. 2019 Sep;28(17):3977-3993. doi: 10.1111/mec.15193. Epub 2019 Sep 11.


Inferring the distribution of fitness effects of spontaneous mutations in Chlamydomonas reinhardtii.

Böndel KB, Kraemer SA, Samuels T, McClean D, Lachapelle J, Ness RW, Colegrave N, Keightley PD.

PLoS Biol. 2019 Jun 26;17(6):e3000192. doi: 10.1371/journal.pbio.3000192. eCollection 2019 Jun.


Understanding the Factors That Shape Patterns of Nucleotide Diversity in the House Mouse Genome.

Booker TR, Keightley PD.

Mol Biol Evol. 2018 Dec 1;35(12):2971-2988. doi: 10.1093/molbev/msy188.


Inferring the Probability of the Derived vs. the Ancestral Allelic State at a Polymorphic Site.

Keightley PD, Jackson BC.

Genetics. 2018 Jul;209(3):897-906. doi: 10.1534/genetics.118.301120. Epub 2018 May 16.


Fitness decline under osmotic stress in Caenorhabditis elegans populations subjected to spontaneous mutation accumulation at varying population sizes.

Katju V, Packard LB, Keightley PD.

Evolution. 2018 Apr;72(4):1000-1008. doi: 10.1111/evo.13463. Epub 2018 Mar 25.


Detecting positive selection in the genome.

Booker TR, Jackson BC, Keightley PD.

BMC Biol. 2017 Oct 30;15(1):98. doi: 10.1186/s12915-017-0434-y. Review.


Fitness change in relation to mutation number in spontaneous mutation accumulation lines of Chlamydomonas reinhardtii.

Kraemer SA, Böndel KB, Ness RW, Keightley PD, Colegrave N.

Evolution. 2017 Dec;71(12):2918-2929. doi: 10.1111/evo.13360. Epub 2017 Oct 26.


The Recombination Landscape in Wild House Mice Inferred Using Population Genomic Data.

Booker TR, Ness RW, Keightley PD.

Genetics. 2017 Sep;207(1):297-309. doi: 10.1534/genetics.117.300063. Epub 2017 Jul 27.


Mitochondrial Mutation Rate, Spectrum and Heteroplasmy in Caenorhabditis elegans Spontaneous Mutation Accumulation Lines of Differing Population Size.

Konrad A, Thompson O, Waterston RH, Moerman DG, Keightley PD, Bergthorsson U, Katju V.

Mol Biol Evol. 2017 Jun 1;34(6):1319-1334. doi: 10.1093/molbev/msx051. Erratum in: Mol Biol Evol. 2017 Mar 1;34(3):778.


Global population divergence and admixture of the brown rat (Rattus norvegicus).

Puckett EE, Park J, Combs M, Blum MJ, Bryant JE, Caccone A, Costa F, Deinum EE, Esther A, Himsworth CG, Keightley PD, Ko A, Lundkvist Å, McElhinney LM, Morand S, Robins J, Russell J, Strand TM, Suarez O, Yon L, Munshi-South J.

Proc Biol Sci. 2016 Oct 26;283(1841). pii: 20161762.


Inferring the Frequency Spectrum of Derived Variants to Quantify Adaptive Molecular Evolution in Protein-Coding Genes of Drosophila melanogaster.

Keightley PD, Campos JL, Booker TR, Charlesworth B.

Genetics. 2016 Jun;203(2):975-84. doi: 10.1534/genetics.116.188102. Epub 2016 Apr 20.


Fitness effects of new mutations in Chlamydomonas reinhardtii across two stress gradients.

Kraemer SA, Morgan AD, Ness RW, Keightley PD, Colegrave N.

J Evol Biol. 2016 Mar;29(3):583-93. doi: 10.1111/jeb.12807. Epub 2016 Jan 5.


Direct Estimate of the Spontaneous Mutation Rate Uncovers the Effects of Drift and Recombination in the Chlamydomonas reinhardtii Plastid Genome.

Ness RW, Kraemer SA, Colegrave N, Keightley PD.

Mol Biol Evol. 2016 Mar;33(3):800-8. doi: 10.1093/molbev/msv272. Epub 2015 Nov 28.


The Nature of Genetic Variation for Complex Traits Revealed by GWAS and Regional Heritability Mapping Analyses.

Caballero A, Tenesa A, Keightley PD.

Genetics. 2015 Dec;201(4):1601-13. doi: 10.1534/genetics.115.177220. Epub 2015 Oct 19.


Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome.

Wiberg RA, Halligan DL, Ness RW, Necsulea A, Kaessmann H, Keightley PD.

Genome Biol Evol. 2015 Aug 12;7(8):2432-44. doi: 10.1093/gbe/evv155.


Extensive de novo mutation rate variation between individuals and across the genome of Chlamydomonas reinhardtii.

Ness RW, Morgan AD, Vasanthakrishnan RB, Colegrave N, Keightley PD.

Genome Res. 2015 Nov;25(11):1739-49. doi: 10.1101/gr.191494.115. Epub 2015 Aug 10.


Recent Evolution in Rattus norvegicus Is Shaped by Declining Effective Population Size.

Deinum EE, Halligan DL, Ness RW, Zhang YH, Cong L, Zhang JX, Keightley PD.

Mol Biol Evol. 2015 Oct;32(10):2547-58. doi: 10.1093/molbev/msv126. Epub 2015 Jun 1.


Estimation of the spontaneous mutation rate in Heliconius melpomene.

Keightley PD, Pinharanda A, Ness RW, Simpson F, Dasmahapatra KK, Mallet J, Davey JW, Jiggins CD.

Mol Biol Evol. 2015 Jan;32(1):239-43. doi: 10.1093/molbev/msu302. Epub 2014 Nov 3.


Fitness decline in spontaneous mutation accumulation lines of Caenorhabditis elegans with varying effective population sizes.

Katju V, Packard LB, Bu L, Keightley PD, Bergthorsson U.

Evolution. 2015 Jan;69(1):104-16. doi: 10.1111/evo.12554. Epub 2014 Dec 9.


Spontaneous mutation accumulation in multiple strains of the green alga, Chlamydomonas reinhardtii.

Morgan AD, Ness RW, Keightley PD, Colegrave N.

Evolution. 2014 Sep;68(9):2589-602. doi: 10.1111/evo.12448. Epub 2014 Jul 9.


Faster-X adaptive protein evolution in house mice.

Kousathanas A, Halligan DL, Keightley PD.

Genetics. 2014 Apr;196(4):1131-43. doi: 10.1534/genetics.113.158246. Epub 2013 Dec 20.


Contributions of protein-coding and regulatory change to adaptive molecular evolution in murid rodents.

Halligan DL, Kousathanas A, Ness RW, Harr B, Eöry L, Keane TM, Adams DJ, Keightley PD.

PLoS Genet. 2013;9(12):e1003995. doi: 10.1371/journal.pgen.1003995. Epub 2013 Dec 5.


Estimation of the spontaneous mutation rate per nucleotide site in a Drosophila melanogaster full-sib family.

Keightley PD, Ness RW, Halligan DL, Haddrill PR.

Genetics. 2014 Jan;196(1):313-20. doi: 10.1534/genetics.113.158758. Epub 2013 Nov 8.


A comparison of models to infer the distribution of fitness effects of new mutations.

Kousathanas A, Keightley PD.

Genetics. 2013 Apr;193(4):1197-208. doi: 10.1534/genetics.112.148023. Epub 2013 Jan 22.


Nuclear gene variation in wild brown rats.

Ness RW, Zhang YH, Cong L, Wang Y, Zhang JX, Keightley PD.

G3 (Bethesda). 2012 Dec;2(12):1661-4. doi: 10.1534/g3.112.004713. Epub 2012 Dec 1.


The maintenance of obligate sex in finite, structured populations subject to recurrent beneficial and deleterious mutation.

Hartfield M, Otto SP, Keightley PD.

Evolution. 2012 Dec;66(12):3658-69. doi: 10.1111/j.1558-5646.2012.01733.x. Epub 2012 Jul 25.


Estimate of the spontaneous mutation rate in Chlamydomonas reinhardtii.

Ness RW, Morgan AD, Colegrave N, Keightley PD.

Genetics. 2012 Dec;192(4):1447-54. doi: 10.1534/genetics.112.145078. Epub 2012 Oct 10.


Current hypotheses for the evolution of sex and recombination.

Hartfield M, Keightley PD.

Integr Zool. 2012 Jun;7(2):192-209. doi: 10.1111/j.1749-4877.2012.00284.x. Review.


A resolution of the mutation load paradox in humans.

Lesecque Y, Keightley PD, Eyre-Walker A.

Genetics. 2012 Aug;191(4):1321-30. doi: 10.1534/genetics.112.140343. Epub 2012 Jun 1.


The effect of variation in the effective population size on the rate of adaptive molecular evolution in eukaryotes.

Gossmann TI, Keightley PD, Eyre-Walker A.

Genome Biol Evol. 2012;4(5):658-67. doi: 10.1093/gbe/evs027. Epub 2012 Mar 21.


Rates and fitness consequences of new mutations in humans.

Keightley PD.

Genetics. 2012 Feb;190(2):295-304. doi: 10.1534/genetics.111.134668. Review.


Estimating the rate of adaptive molecular evolution when the evolutionary divergence between species is small.

Keightley PD, Eyre-Walker A.

J Mol Evol. 2012 Feb;74(1-2):61-8. doi: 10.1007/s00239-012-9488-1. Epub 2012 Feb 12.


A method for inferring the rate of occurrence and fitness effects of advantageous mutations.

Schneider A, Charlesworth B, Eyre-Walker A, Keightley PD.

Genetics. 2011 Dec;189(4):1427-37. doi: 10.1534/genetics.111.131730. Epub 2011 Sep 27.


Inference of site frequency spectra from high-throughput sequence data: quantification of selection on nonsynonymous and synonymous sites in humans.

Keightley PD, Halligan DL.

Genetics. 2011 Aug;188(4):931-40. doi: 10.1534/genetics.111.128355. Epub 2011 May 19.


Positive and negative selection in murine ultraconserved noncoding elements.

Halligan DL, Oliver F, Guthrie J, Stemshorn KC, Harr B, Keightley PD.

Mol Biol Evol. 2011 Sep;28(9):2651-60. doi: 10.1093/molbev/msr093. Epub 2011 Apr 8.


Inference of mutation parameters and selective constraint in mammalian coding sequences by approximate Bayesian computation.

Keightley PD, Eöry L, Halligan DL, Kirkpatrick M.

Genetics. 2011 Apr;187(4):1153-61. doi: 10.1534/genetics.110.124073. Epub 2011 Feb 1.


Positive and negative selection on noncoding DNA close to protein-coding genes in wild house mice.

Kousathanas A, Oliver F, Halligan DL, Keightley PD.

Mol Biol Evol. 2011 Mar;28(3):1183-91. doi: 10.1093/molbev/msq299. Epub 2010 Nov 8.


What can we learn about the distribution of fitness effects of new mutations from DNA sequence data?

Keightley PD, Eyre-Walker A.

Philos Trans R Soc Lond B Biol Sci. 2010 Apr 27;365(1544):1187-93. doi: 10.1098/rstb.2009.0266.


The role of advantageous mutations in enhancing the evolution of a recombination modifier.

Hartfield M, Otto SP, Keightley PD.

Genetics. 2010 Apr;184(4):1153-64. doi: 10.1534/genetics.109.112920. Epub 2010 Feb 5.


Evidence for pervasive adaptive protein evolution in wild mice.

Halligan DL, Oliver F, Eyre-Walker A, Harr B, Keightley PD.

PLoS Genet. 2010 Jan 22;6(1):e1000825. doi: 10.1371/journal.pgen.1000825.


Patterns of DNA-sequence divergence between Drosophila miranda and D. pseudoobscura.

Marion de Procé S, Halligan DL, Keightley PD, Charlesworth B.

J Mol Evol. 2009 Dec;69(6):601-11. doi: 10.1007/s00239-009-9298-2. Epub 2009 Oct 27.


Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomes.

Eory L, Halligan DL, Keightley PD.

Mol Biol Evol. 2010 Jan;27(1):177-92. doi: 10.1093/molbev/msp219.


Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change.

Eyre-Walker A, Keightley PD.

Mol Biol Evol. 2009 Sep;26(9):2097-108. doi: 10.1093/molbev/msp119. Epub 2009 Jun 17.


Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines.

Keightley PD, Trivedi U, Thomson M, Oliver F, Kumar S, Blaxter ML.

Genome Res. 2009 Jul;19(7):1195-201. doi: 10.1101/gr.091231.109. Epub 2009 May 13.


Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals.

Gaffney DJ, Keightley PD.

BMC Evol Biol. 2008 Sep 30;8:265. doi: 10.1186/1471-2148-8-265.


Direct estimation of the mitochondrial DNA mutation rate in Drosophila melanogaster.

Haag-Liautard C, Coffey N, Houle D, Lynch M, Charlesworth B, Keightley PD.

PLoS Biol. 2008 Aug 19;6(8):e204. doi: 10.1371/journal.pbio.0060204.


Analysis and implications of mutational variation.

Keightley PD, Halligan DL.

Genetica. 2009 Jun;136(2):359-69. doi: 10.1007/s10709-008-9304-4. Epub 2008 Jul 29. Review.


Evolution of genes and genomes on the Drosophila phylogeny.

Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I.

Nature. 2007 Nov 8;450(7167):203-18.


Patterns of selective constraints in noncoding DNA of rice.

Guo X, Wang Y, Keightley PD, Fan L.

BMC Evol Biol. 2007 Nov 1;7:208.

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