MD Adams SE Celniker RA Holt et al. (2000) ArticleTitleThe genome sequence of Drosophila melanogaster. Science 287 2185–2195 Occurrence Handle10.1126/science.287.5461.2185 Occurrence Handle10731132

Article  PubMed  Google Scholar 

H Akashi (1995) ArticleTitleInferring weak selection from patterns of polymorphism and divergence at “silent” sites in Drosophila DNA. Genetics 139 1067–1076

Google Scholar 

CD Bustamante R Nielsen DL Hartl (2002a) ArticleTitleA maximum likelihood method for analyzing pseudogene evolution: Implications for silent site evolution in humans and rodents. Mol Biol Evol 19 110–117 Occurrence Handle1:CAS:528:DC%2BD38XhtFCiug%3D%3D

CAS  Google Scholar 

CD Bustamante R Nielsen SA Sawyer KM Olsen MD Purugganan DL Hartl (2002b) ArticleTitleThe cost of inbreeding in Arabidopsis. Nature 416 531–534 Occurrence Handle1:CAS:528:DC%2BD38XivVOntr0%3D

CAS  Google Scholar 

BP Carlin TA Louis (2000) Bayes and empirical Bayes methods for data analysis. Chapman & Hall London

Google Scholar 

B Charlesworth D Charlesworth (1997) ArticleTitleRapid fixation of deleterious alleles can be caused by Muller’s ratchet. Genet Res 70 63–73 Occurrence Handle10.1017/S0016672397002899 Occurrence Handle1:STN:280:DyaK1c%2FjsFKjtQ%3D%3D Occurrence Handle9369098

Article  CAS  PubMed  Google Scholar 

JM Comeron M Kreitman (2002) ArticleTitlePopulation, evolutionary and genomic consequences of interference selection. Genetics 161 389–410

Google Scholar 

WJ Ewens (1972) ArticleTitleThe sampling theory of selectively neutral alleles. Theor Popul Biol 3 87–112 Occurrence Handle4667078

PubMed  Google Scholar 

JC Fay C-I Wu (2000) ArticleTitleHitchhiking under positive Darwinian selection. Genetics 155 1405–1413 Occurrence Handle1:STN:280:DC%2BD3cvgsVSntQ%3D%3D Occurrence Handle10880498

CAS  PubMed  Google Scholar 

JC Fay GJ Wyckoff C-I Wu (2002) ArticleTitleTesting the neutral theory of molecular evolution with genomic data from Drosophila. Nature 415 1024–1026 Occurrence Handle10.1038/4151024a Occurrence Handle11875569

Article  PubMed  Google Scholar 

Y-X Fu W-H Li (1993) ArticleTitleStatistical tests of neutrality of mutations. Genetics 133 693–709 Occurrence Handle1:STN:280:ByyB3c3kvVU%3D Occurrence Handle8454210

CAS  PubMed  Google Scholar 

N Galtier F Depaulis NH Barton (2000) ArticleTitleDetecting bottlenecks and selective sweeps from DNA sequence polymorphism. Genetics 155 981–987 Occurrence Handle1:CAS:528:DC%2BD3cXkslyqurc%3D Occurrence Handle10835415

CAS  PubMed  Google Scholar 

A Gelman JS Carlin HS Stern DB Rubin (1997) Bayesian data analysis. Chapman & Hall London

Google Scholar 

R Gilks S Richardson DJ Spiegelhalter (1996) Markov chain Monte Carlo in practice. Chapman & Hall London

Google Scholar 

JH Gillespie (2000) ArticleTitleGenetic drift in an infinite population. The pseudohitchhiking model. Genetics 155 909–919 Occurrence Handle1:STN:280:BymB28rlsVI%3D Occurrence Handle8685218

CAS  PubMed  Google Scholar 

SJ Gould (1989) ArticleTitleTires to sandals: As we strive to understand nature, do we seek truth or solace? Nat Hist 98 8–15

Google Scholar 

DL Hartl AG Clark (1997) Principles of population genetics. Sinauer Associates Sunderland, MA

Google Scholar 

DL Hartl CH Taubes (1996) ArticleTitleCompensatory nearly neutral mutations: Selection without adaptation. J Theor Biol 182 303–309 Occurrence Handle10.1006/jtbi.1996.0168 Occurrence Handle1:CAS:528:DyaK28XntValsrg%3D Occurrence Handle8944162

Article  CAS  PubMed  Google Scholar 

DL Hartl EN Moriyama SA Sawyer (1994) ArticleTitleSelection intensity for codon bias. Genetics 138 227–234 Occurrence Handle1:STN:280:ByqD1MrgsV0%3D Occurrence Handle8001789

CAS  PubMed  Google Scholar 

RR Hudson (1990) Gene geneologies and the coalescent process. D Futuyma J Antonovics (Eds) Oxford surveys in evolutionary biology, Oxford University Press Oxford 1–44

Google Scholar 

RR Hudson K Bailey D Skarecky J Kwiatowski FJ Ayala (1994) ArticleTitleEvidence for positive selection in the superoxide dismutase (Sod) region of Drosophila melanogaster. Genetics 136 1329–1340 Occurrence Handle1:CAS:528:DyaK2cXmslOjtLc%3D Occurrence Handle8013910

CAS  PubMed  Google Scholar 

Y Kim W Stephan (2000) ArticleTitleJoint effects of genetic hitchhiking and background selection on neutral variation. Genetics 155 1415–1427

Google Scholar 

M Kimura (1983) The neutral theory of molecular evolution. Cambridge University Press Cambridge

Google Scholar 

DA Kirby W Stephan (1996) ArticleTitleMulti-locus selection and the structure of variation at the white gene of Drosophila melanogaster. Genetics 144 635–645 Occurrence Handle1:CAS:528:DyaK28XmsVanu7o%3D Occurrence Handle8889526

CAS  PubMed  Google Scholar 

RC Lewontin (1974) The genetic basis of evolutionary change. Columbia University Press New York

Google Scholar 

JS Liu (2001) Monte Carlo strategies in scientific computing. Springer New York

Google Scholar 

J Maynard Smith J Haigh (1974) ArticleTitleThe hitch-hiking effect of a favorable gene. Genet Res 23 23–35 Occurrence Handle4407212

PubMed  Google Scholar 

JH McDonald M Kreitman (1991) ArticleTitleAdaptive protein evolution at the Adh locus in Drosophila. Nature 351 652–654 Occurrence Handle1:CAS:528:DyaK3MXks1yrtLs%3D Occurrence Handle1904993

CAS  PubMed  Google Scholar 

N Metropolis A Rosenbluth M Rosenbluth A Teller E Teller (1953) ArticleTitleEquations of state calculations by fast computing machines. J Chem Phys 21 1087–1091 Occurrence Handle1:CAS:528:DyaG3sXltlKhsw%3D%3D

CAS  Google Scholar 

R Nielsen Z Yang (1998) ArticleTitleLikelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148 929–936 Occurrence Handle1:CAS:528:DyaK1cXks1eitr8%3D Occurrence Handle9539414

CAS  PubMed  Google Scholar 

DI Nurminsky (2001) ArticleTitleGenes in sweeping competition. Cell Mol Life Sci 58 125–134 Occurrence Handle1:CAS:528:DC%2BD3MXhslKnsrs%3D Occurrence Handle11229811

CAS  PubMed  Google Scholar 

T Ohta (1992) ArticleTitleThe nearly neutral theory of molecular evolution. Annu Rev Ecol Syst 23 263–286 Occurrence Handle10.1146/annurev.es.23.110192.001403

Article  Google Scholar 

SA Sawyer DL Hartl (1992) ArticleTitlePopulation genetics of polymorphism and divergence. Genetics 132 1161–1176

Google Scholar 

KJ Schmid D Tautz (1997) ArticleTitleA screen for fast evolving genes from Drosophila. Proc Natl Acad Sci USA 94 9746–9750 Occurrence Handle10.1073/pnas.94.18.9746 Occurrence Handle1:CAS:528:DyaK2sXlvVWit7Y%3D Occurrence Handle9275195

Article  CAS  PubMed  Google Scholar 

NGC Smith A Eyre-Walker (2002) ArticleTitleAdaptive protein evolution in Drosophila. Nature 415 1022–1024 Occurrence Handle10.1038/4151022a Occurrence Handle1:CAS:528:DC%2BD38XhvVWjsLs%3D Occurrence Handle11875568

Article  CAS  PubMed  Google Scholar 

W Stephan (1996) ArticleTitleThe rate of compensatory evolution. Genetics 144 419–426 Occurrence Handle1:STN:280:ByiD3s3psFM%3D Occurrence Handle8878705

CAS  PubMed  Google Scholar 

WJ Swanson AG Clark HM Waldrip-Dail MF Wolfner CF Aquadro (2001) ArticleTitleEvolutionary EST analysis identifies rapidly evolving male reproductive proteins in Drosophila. Proc Natl Acad Sci USA 98 7375–7379 Occurrence Handle10.1073/pnas.131568198 Occurrence Handle11404480

Article  PubMed  Google Scholar 

F Tajima (1989) ArticleTitleStatistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123 585–595 Occurrence Handle1:CAS:528:DyaK3cXhslentA%3D%3D Occurrence Handle2513255

CAS  PubMed  Google Scholar 

AR Templeton (1998) ArticleTitleNested clade analysis of phylogeographical data: Testing hypotheses about gene flow and population history. Mol Ecol 7 381–397 Occurrence Handle1:CAS:528:DyaK1cXjs1Siu78%3D Occurrence Handle9627999

CAS  PubMed  Google Scholar 

AR Templeton (2002) ArticleTitleOut of Africa again and again. Nature 416 45–51 Occurrence Handle1:CAS:528:DC%2BD38XitlSitr0%3D Occurrence Handle11882887

CAS  PubMed  Google Scholar 

J Wakeley (2000) ArticleTitleThe effects of subdivision on the genetic divergence of populations and species. Evol Int J Org Evol 54 1092–1101 Occurrence Handle1:CAS:528:DC%2BD3cXntVylt7Y%3D

CAS  Google Scholar 

Z Yang (1998) ArticleTitleLikelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol 15 568–573 Occurrence Handle9580986

PubMed  Google Scholar