SEARCH

SEARCH BY CITATION

References

  • Aguade M (1999) Positive selection drives the evolution of the Acp29AB accessory gland protein in Drosophila. Genetics, 152, 543551.
  • Andersson L (2001) Genetic dissection of phenotypic diversity in farm animals. Nature Genetics Reviews, 2, 130138.
  • Andrews TD, Easteal S (2000) Evolutionary rate acceleration of cytochrome c oxidase subunit I in simian primates. Journal of Molecular Evolution, 50, 562568.
  • Aquadro CF, Begun DJ, Kindahl EC (1994) Selection, recombination, and DNA polymorphism in Drosophila. In: Non-Neutral Evolution: Theories and Molecular Data (ed. GoldingB), pp. 4656. Chapman & Hall, New York.
  • Araki H, Inomata N, Yamazaki T (2001) Molecular evolution of duplicated amylase gene regions in Drosophila melanogaster: evidence of positive selection in the coding regions and selective constraints in the cis-regulatory regions. Genetics, 157, 667677.
  • Avise JC (1994) Molecular Markers, Natural History and Evolution. Chapman & Hall, New York.
  • Avise JC (1995) Mitochondrial DNA polymorphism and a connection between genetics and demography of relevance to conservation. Conservation Biology, 9, 686690.
  • Ballingall KT, Waibochi L, Holmes EC et al. (2001) The CD45 locus in cattle: allelic polymorphism and evidence for exceptional positive natural selection. Immunogenetics, 52, 276283.
  • Bargelloni L, Marcato S, Patarnello T (1998) Antarctic fish hemoglobins: evidence for adaptive evolution at subzero temperature. Proceedings of the National Academy of Science USA, 95, 86708675.
  • Baric RS, Yount B, Hensley L, Peel SA, Chen W (1997) Episodic evolution mediates interspecies transfer of a murine coronavirus. Journal of Virology, 71, 19461955.
  • Begun DJ, Aquadro CF (1992) Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature, 356, 519520.
  • Begun DJ, Aquadro CF (1994) Evolutionary inferences from DNA variation at the 6-phosphogluconate dehydrogenase locus in natural populations of Drosophila: selection and geographic differentiation. Genetics, 136, 155171.
  • Begun DJ, Aquadro CF (1995) Molecular variation at the vermilion locus in geographically diverse populations of Drosophila melanogaster and D. simulans. Genetics, 140, 10191032.
  • Begun DJ, Betancourt AJ, Langley CH, Stephan W (1999) Is the fast/slow allozyme variation at the Adh locus of Drosophila melanogaster an ancient balanced polymorphism? Molecular Biology and Evolution, 16, 18161819.
  • Begun DJ, Whitley P (2000) Reduced X-linked nucleotide polymorphism in Drosophila simulans. Proceedings of the National Academy of Science USA, 97, 59605965.
  • Begun D, Whitley P, Todd BL, Waldrip-Dail HM, Clark AG (2000) Molecular population genetics of male accessory gland proteins in Drosophila. Genetics, 156, 19791888.
  • Bergelson JB, Kreitman M, Stahl EA, Tian D (2001) Evolutionary dynamics of plant R-genes. Science, 292, 22812285.
  • Berry A, Kreitman M (1993) Molecular analysis of an allozyme cline: alcohol dehydrogenase in Drosophila melanogaster on the east coast of North America. Genetics, 134, 869893.
  • Biermann CH (1998) The molecular evolution of sperm bindin in six species of sea urchins (Echinoida: Strongylocentrotidae). Molecular Biology and Evolution, 15, 17611771.
  • Bishop JG, Dean AM, Mitchell-Olds T (2000) Rapid evolution in plant chitinases: molecular targets of natural selection in plant–pathogen coevolution. Proceedings of the National Academy of Sciences USA, 97, 53225327.
  • Bittner-Eddy PD, Crute IR, Holub EB, Beynon JL (2000) RPP13 is a simple locus in Arabidopsis thaliana for alleles that specify downy mildew resistance to different avirulence determinants in Peronospora parasitica. Plant Journal, 21, 177188.
  • Botella MA, Parker JE, Frost LN et al. (1998) Three genes of the Arabidopsis RPP1 complex resistance locus recognize distinct Peronospora parasitica avirulence determinants. Plant Cell, 10, 18471860.
  • Carr M, Soloway JR, Robinson TE, Brookfield JFY (2001) An investigation of the cause of low variability on the fourth chromosome of Drosophila melanogaster. Molecular Biology and Evolution, 18, 22602269.
  • Charlesworth B (1996) Background selection and patterns of Genetic diversity in Drosophilla melanogaster. Genetical Research, 68, 131149.
  • Charlesworth D, Charlesworth B, McVean GAT (2001) Genome sequences and evolutionary biology, a two-way interaction. Trends in Ecology and Evolution, 16, 235242.
  • Charlesworth B, Morgan MT, Charlesworth D (1993) The effect of deleterious mutations on neutral molecular variation. Genetics, 134, 12891303.
  • Cirera S, Aguade M (1997) Evolutionary history of the sex-peptide (Acp70A) gene region in Drosophila melanogaster. Genetics, 147, 189197.
  • Clark AG, Kao T-H (1991) Excess nonsynonymous substitution at shared polymorphic sites among self-incompatibility alleles of Solanaceae. Proceedings of the National Academy of Sciences USA, 88, 98239827.
  • Coyne JA, Wicker-Thomas C, Jallon JM (1999) A gene responsible for a cuticular hydrocarbon polymorphism in Drosophila melanogaster. Genetical Research, 73, 189203.
  • Dallerac R, Labeur C, Jallon JM, Knipple DC, Roelofs WL, Wicker-Thomas C (2000) A delta 9 desaturase gene with a different substrate specificity is responsible for the cuticular diene hydrocarbon polymorphism in Drosophila melanogaster. Proceedings of the National Academy of Science USA, 17, 94499454.
  • Doebley J, Stec A, Gustus C (1995) Teosinte branched 1 and the origin of maize: evidence for epistasis and the evolution of dominance. Genetics, 141, 333346.
  • Doebley J, Stec A, Hubbard L (1997) The evolution of apical dominance in maize. Nature, 386, 485488.
  • Duda TF Jr, Palumbi SR (1999) Molecular genetics of ecological diversification: duplication and rapid evolution of toxin genes of the venomous gastropod Conus. Proceedings of the National Academy of Science USA, 96, 68206823.
  • Eanes WF (1999) Analysis of selection on enzyme polymorphisms. Annual Review of Ecology and Systematics, 30, 301326.
  • Eanes WF, Kirchner M, Yoon J (1993) Evidence for adaptive evolution of the G6pd gene in the Drosophila melanogaster and Drosophila simulans lineages. Proceedings of the National Academy of Sciences USA, 90, 74757479.
  • Eanes WF, Kirchner M, Yoon J et al. (1996) Historical selection, amino acid polymorphism and lineage-specific divergence at the G6pd locus in Drosophila melanogaster and D. simulans. Genetics, 144, 10271041.
  • Endler JA (1986) Natural Selection in the Wild. Princeton University Press, Princeton, New Jersey.
  • Endo T, Ikeo K, Gojobori T (1996) Large-scale search for genes on which positive selection may operate. Molecular Biology and Evolution, 13, 685690.
  • Ewens WJ (1972) The sampling theory of selectively neutral alleles. Theoretical Population Biology, 3, 87112.
  • Fay JC, Wu C-I (2000) Hitchhiking under positive Darwinian selection. Genetics, 155, 14051413.
  • Fay JC, Wyckoff GJ, Wu C-I (2001) Positive and negative selection on the human genome. Genetics, 158, 12271234.
  • Ferveur JF, Cobb M, Boukella H, Jallon JM (1996) World-wide variation in Drosophila melanogaster sex pheromone: behavioral effects, genetic bases and potential evolutionary consequences. Genetica, 97, 7380.
  • Fitch WM, Bush RM, Bender CA, Cox NJ (1997) Long term trends in the evolution of H (3) HA1 human influenza type A. Proceedings of the National Academy of Sciences USA, 94, 77127718.
  • Fitch WM, Bush RM, Bender CA, Subbarao K, Cox NJ (2000) Predicting the evolution of human influenza A. The Journal of Heredity, 91, 183185.
  • Flint J, Mott R (2001) Finding the molecular basis of quantitative traits: successes and pitfalls. Nature Genetics Reviews, 2, 437445.
  • Ford MJ (1998) Testing models of migration and isolation among populations of chinook salmon (Oncorhynchus tschawytscha). Evolution, 52, 539557.
  • Ford MJ (2000) Effects of natural selection on patterns of DNA sequence variation at the transferrin, somatolactin, and p53 genes within and among chinook salmon (Oncorhynchus tshawytscha) populations. Molecular Ecology, 9, 843855.
  • Ford MJ (2001) Molecular evolution of transferrin: evidence for positive selection in Salmonids. Molecular Biology and Evolution, 18, 639647.
  • Ford MJ, Aquadro CF (1996) Selection on X-linked genes during speciation in the Drosophila athabasca complex. Genetics, 144, 689703.
  • Ford MJ, Thornton PJ, Park LK (1999) Natural selection promotes divergence of transferrin among salmonid species. Molecular Ecology, 8, 10551061.
  • Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915925.
  • Gilad Y, Segre D, Skorecki K, Nachman MW, Lancet D, Sharon D (2000) Dichotomy of single-nucleotide polymorphism haplotypes in olfactory receptor genes and pseudogenes. Nature Genetics, 26, 221224.
  • Gillespie JH (1991) The Causes of Molecular Evolution. Oxford University Press, New York.
  • Gillespie JH (2000) The neutral theory in an infinite population. Gene, 261, 1118.
  • Goldman N, Yang Z (1994) A codon-based model of nucleotide substitution for protein-coding DNA sequences. Molecular Biology and Evolution, 11, 725736.
  • Goodwin RL, Baumann H, Berger FG (1996) Patterns of divergence during evolution of alpha 1-proteinase inhibitors in mammals. Molecular Biology and Evolution, 13, 346358.
  • Haag ES, True JR (2001) Perspective: from mutants to mechanisms? Assessing the candidate gene paradigm in evolutionary biology. Evolution, 55, 10771084.
  • Hamblin MT, Aquadro CF (1997) Contrasting patterns of nucleotide sequence variation at the glucose dehydrogenase (Gld) locus in different populations of Drosophila melanogaster. Genetics, 145, 10531062.
  • Harris H (1966) Enzyme polymorphism in man. Proceedings of the Royal Society Series B, 164, 298310.
  • Hasson E, Wang I-N, Zeng L-W, Kreitman M, Eanes WF (1998) Nucleotide variation in the triosephosphate isomerase (Tpi) locus of Drosophila melanogaster and Drosophila simulans. Molecular Biology and Evolution, 15, 756769.
  • Haydon DT, Bastos AD, Knowles NJ, Samuel AR (2001) Evidence for positive selection in foot-and-mouth disease virus capsid genes from field isolates. Genetics, 157, 715.
  • Hedrick PW, Lee RN, Parker KM (2000) Major histocompatibility complex (MHC) variation in the endangered Mexican wolf and related canids. Heredity, 85, 617624.
  • Hellberg ME, Moy GW, Vacquier VD (2000) Positive selection and propeptide repeats promote rapid interspecific divergence of a gastropod sperm protein. Molecular Biology and Evolution, 17, 458466.
  • Hellberg ME, Vacquier VD (1997) Rapid evolution of fertilization selectivity and lysin cDNA sequences in teguline gastropods. Molecular Biology and Evolution, 16, 839848.
  • Hey J (1999) The neutralist, the fly and the selectionist. Trends in Ecology and Evolution, 14, 3538.
  • Hill RE, Hastie ND (1987) Accelerated evolution in the reactive centre regions of serince protease inhibitors. Nature, 326, 9699.
  • Hilton H, Gaut B (1998) Speciation and domestication in maize and its wild relatives. Evidence from the globulin-1 gene. Genetics, 150, 863872.
  • Holbrook JD, Birdsey GM, Yang Z, Bruford MW, Danpure CJ (2000) Molecular adaptation of alanine: glyoxylate aminotransferase targeting in primates. Molecular Biology and Evolution, 17, 387400.
  • Holub EB (2001) The arms race is ancient history in Arabidopsis, the wildflower. Nature Genetics Reviews, 2, 516527.
  • Huang C-H, Liu Z, Apoil P-A, Blancher A (2000) Sequence, organization, and evolution of Rh50 glycoprotein genes in nonhuman primates. Journal of Molecular Evolution, 51, 7687.
  • Hudson RR (1994) How can the low levels of DNA sequence variation in regions of the Drosophila genome with low recombination rates be explained? Proceedings of the National Academy of Science USA, 91, 68156818.
  • Hudson RR, Kreitman M, Aguade M (1987) A test of neutral molecular evolution based on nucleotide data. Genetics, 116, 153159.
  • Hudson RR, Saez AG, Ayala FJ (1997) DNA variation at the Sod locus of Drosophila melanogaster: an unfolding story of natural selection. Proceedings of the National Academy of Sciences USA, 94, 77257729.
  • Hughes AL (1991) Circumsporozoite protein genes of malaria parasites (Plasmodium spp.): evidence for positive selection on immunogenic regions. Genetics, 127, 345353.
  • Hughes AL (1992) Positive selection and interallelic recombination at the merozoite surface antigen-1 (MSA-1) locus of Plasmodium falciparum. Molecular Biology and Evolution, 9, 381393.
  • Hughes AL (1995) The evolution of the type I interferon gene family in mammals. Journal of Molecular Evolution, 41, 539548.
  • Hughes AL (1999) Adaptive Evolution of Genes and Genomes. Oxford University Press, New York.
  • Hughes MK, Hughes AL (1995) Natural selection on Plasmodium surface proteins. Molecular and Biochemical Parasitology, 71, 99113.
  • Hughes AL, Nei M (1988) Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature, 335, 167170.
  • Hughes AL, Ota T, Nei M (1990) Positive Darwinian selection promotes charge profile diversity in the antigen-binding cleft of class I major-histocompatibility-complex molecules. Molecular Biology and Evolution, 7, 515524.
  • Hughes AL, Yeager M (1997) Coordinated amino acid changes in the evolution of mammalian defensins. Journal of Molecular Evolution, 44, 675682.
  • Ishimizu T, Endo T, Yamaguchi-Kabata Y, Nakamura KT, Sakiyama F, Norioka S (1998) Identification of regions in which positive selection may operate in S-RNase of Rosaceae: implication for S-allele-specific recognition sites in S-RNase. FEBS Letters, 440, 337342.
  • Karn RC, Nachman MW (1999) Reduced nucleotide variability at an androgen-binding protein locus (Abpa) in house mice: evidence for positive natural selection. Molecular Biology and Evolution, 16, 11921197.
  • Katz LA, Harrison RG (1997) Balancing selection on electrophoretic variation of phosphoglucose isomerase in two species of field cricket Gryllus veletis and G. pennsylvanicus. Genetics, 147, 609621.
  • Kauer M, Zangerl B, Dieringer D, Schlötterer C (2002) Chromosomal patterns of microsatellite variability contrast sharply in African and non-African populations of Drosophila melanogaster. Genetics, 160, 247256.
  • Kawabe A, Yamane K, Miyashita N (2000) DNA polymorphism at the cytosolic phosphoglucose isomerase (PgiC) locus of the wild plant Arapidopsis thaliana. Genetics, 156, 13391347.
  • Kim Y, Stephan W (2000) Joint effects of genetics hitchhiking and background selection on neutral variation. Genetics, 155, 14151427.
  • Kimura M (1983) The Neutral Theory of Molecular Evolution. Cambridge University Press, New York.
  • Kirby DA, Stephan W (1995) Haplotype test reveals departure from neutrality in a segment of the white gene of Drosophila melanogaster. Genetics, 14, 14831490.
  • Kirby DA, Stephan W (1996) Multi-locus selection and the structure of variation at the white gene of Drosophila melanogaster. Genetics, 144, 635645.
  • Kordiš D, Gubenšek F (2000) Adaptive evolution of animal toxin multigene families. Gene, 261, 4352.
  • Kraft T, Säll T, Magnusson-Rading IM, Nilsson N-O, Halldén C (1998) Positive correlation between recombination rates and levels of genetics variation in the natural populations of sea beet (Beta vulgaris subsp. maritima). Genetics, 150, 12391244.
  • Kreitman M (1996) The neutral theory is dead. Long live the neutral theory. Bioessays, 18, 678683.
  • Kreitman M (2000) Methods to detect selection in populations with applications to the human. Annual Review of Genomics and Human Genetics, 1, 539559.
  • Kreitman M, Akashi H (1995) Molecular evidence for natural selection. Annual Review of Ecology and Systematics, 26, 403422.
  • Kreitman M, Hudson RR (1991) Inferring the evolutionary histories of Adh and Adh-dup loci in Drosophila melanogaster from patterns of polymorphism and divergence. Genetics, 127, 565582.
  • Kurihara T, Sakuma M, Gojobori T (1997) Molecular evolution of myelin proteolipid protein. Biochemical and Biophysical Research Communications, 237, 559561.
  • Lee YH, Vacquier VD (1992) The divergence of species-specific abalone sperm lysins is promoted by positive Darwinian selection. Biological Bulletin, 182, 97104.
  • Lewontin RC (1974) The Genetic Basis of Evolutionary Change. Columbia University Press, New York.
  • Lewontin RC (1991) Electrophoresis in the development of evolutionary genetics: milestone or millstone? Genetics, 128, 657662.
  • Lewontin RC, Hubby JL (1966) A molecular approach to the study of genetic heterozygosity in natural populations. II. Amount of variation and degree of heterozygosity in natural populations of Drosophila pseudoobscura. Genetics, 54, 595609.
  • Lewontin RC, Krakauer J (1973) Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics, 75, 175195.
  • Liu F, Charlesworth D, Kreitman M (1999) The effect of mating system differences on nucleotide diversity at the phosphoglucose isomerase locus in the plant genus Leavenworthia. Genetics, 151, 343357.
  • Long M, Langley CH (1993) Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science, 260, 9195.
  • Lukens L, Doebley J (2001) Molecular evolution of the teosinte branched gene among maize and related grasses. Molecular Biology and Evolution, 18, 627638.
  • Mackay TFC (2001) Quantitative trait loci in Drosophila. Nature Genetics Reviews, 2, 1120.
  • McDonald JH (1996) Detecting non-neutral heterogeneity across a region of DNA sequence in the ratio of polymorphism to divergence. Molecular Biology and Evolution, 13, 253260.
  • McDonald JH (1998) Improved test for heterogeneity across a region of DNA sequence in the ratio of polymorphism to divergence. Molecular Biology and Evolution, 15, 377384.
  • McDonald JH, Kreitman M (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature, 354, 114116.
  • McDowell JM, Dhandaydham M, Long TA et al. (1998) Intragenic recombination and diversifying selection contribute to the evolution of downy mildew resistance at the RPP8 locus of Arabidopsis. Plant Cell, 10, 18611874.
  • Messier W, Stewart CB (1997) Episodic adaptive evolution of primate lysozymes. Nature, 385, 151154.
  • Metz EC, Palumbi SR (1996) Positive selection and sequence rearrangements generate extensive polymorphism in the gamete recognition protein bindin. Molecular Biology and Evolution, 13, 397406.
  • Metz EC, Robles-Sikisaka R, Vacquier VD (1998) Nonsynonymous substitution in abalone sperm fertilization genes exceeds substitution in introns and mitochondrial DNA. Proceedings of the National Academy of Science USA, 95, 1067610681.
  • Meyers BC, Shen KA, Rohani P, Gaut BS, Michelmore RW (1998) Receptor-like genes in the major resistance locus of lettuce are subject to divergent selection. Plant Cell, 11, 18331846.
  • Mikko S, Andersson L (1995) Low major histocompatibility complex class II diversity in European and North American moose. Proceedings of the National Academy of Sciences USA, 92, 42594263.
  • Miller KM, Withler RE (1996) Sequence analysis of a polymorphic Mhc class II gene in Pacific salmon. Immunogenetics, 43, 337351.
  • Miller KM, Withler RE, Beacham TD (1997) Molecular evolution at Mhc genes in two populations of chinook salmon Oncorhynchus tshawytscha. Molecular Ecology, 6, 937954.
  • Mitton JB (1997) Selection in Natural Populations. Oxford University Press, New York.
  • Nachman MW (2001) Single nucleotide polymorphisms and recombination rate in humans. Trends in Genetics, 17, 481485.
  • Nachman MW, Bauer VL, Crowell SL, Aquadro CF (1998) DNA variability and recombination rates at X-linked loci in humans. Genetics, 150, 11331141.
  • Ngai J, Dowling MM, Buck L, Axel R, Chess A (1993) The family of genes encoding odorant receptors in the channel catfish. Cell, 72, 657666.
  • Nielsen R (1997) The ratio of replacement to silent divergence and tests of neutrality. Journal of Evolutionary Biology, 10, 217231.
  • Nielsen R, Weinreich DM (1999) The age of nonsynonymous and synonymous mutations in animal mtDNA and implications for the mildly deleterious theory. Genetics, 153, 497506.
  • Nielsen R, Yang Z (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics, 148, 929936.
  • Notter DR (1999) The importance of genetic diversity in livestock populations of the future. Journal of Animal Science, 77, 6169.
  • Palumbi SR (1999) All males are not created equal: fertility differences depend on gamete recognition polymorphisms in sea urchins. Proceedings of the National Academy of Sciences USA, 96, 1263212637.
  • Payseur BA, Nachman MW (2000) Microsatellite variation and recombination rate in the human genome. Genetics, 156, 12851298.
  • Peichel CL, Nereng KS, Ohgi KA et al. (2001) The genetic architecture of divergence between threespine stickleback species. Nature, 414, 901905.
  • Pennisi E (2000) Stalking the wild mustard. Science, 290, 20552057.
  • Pogson GH (2001) Nucleotide polymorphism and natural selection at the Pantophysin (Pan I) locus in the Atlantic cod, Gadus morhua (L.). Genetics, 157, 317330.
  • Pogson GH, Mesa KA, Boutilier RG (1995) Genetic population structure and gene flow in the Atlantic cod, Gadus morhua: a comparison of allozyme and nuclear RFLP loci. Genetics, 139, 375385.
  • Posada D, Crandall KA, Nguyen M, Demma JC, Viscidi RP (2000) Population genetics of the porB gene of Neisseria gonorrhoeae: different dynamics in different homology groups. Molecular Biology and Evolution, 17, 423436.
  • Powers DA, Lauerman T, Crawford D, DiMichele L (1991) Genetic mechanisms for adapting to a changing environment. Annual Review of Genetics, 25, 629659.
  • Powers DA, Schulte PM (1998) Evolutionary adaptation of gene structure and expression in natural populations in relation to a changing environment: a multidisciplinary approach to address the million-year saga of a small fish. Journal of Experimental Zoology, 282, 7194.
  • Purugganan MD, Boyles AL, Suddith JI (2000) Variation and selection at the CAULIFLOWER floral homeotic gene accompanying the evolution of domesticated Brassica oleracea. Genetics, 155, 855862.
  • Purugganan MD, Suddith JI (1998) Molecular population genetics of the Arabidopsis CAULIFLOWER regulatory gene: nonneutral evolution and naturally occurring variation in floral homeotic function. Proceedings of the Natural Academy of Science USA, 95, 81308134.
  • Qi CF, Bonhomme F, Buckler-white A et al. (1998) Molecular phylogeny of Fv1. Mammalian Genome, 9, 10491055.
  • Rana BK, Hewett-Emmett D, Jin L et al. (1999) High polymorphism at the human melanocortin 1 receptor locus. Genetics, 151, 15471557.
  • Rand DM (1995) Neutrality tests of molecular markers and the connection between DNA polymorphism, demography, and conservation biology. Conservation Biology, 10, 665671.
  • Rand DM, Kann LM (1996) Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans. Molecular Biology and Evolution, 13, 735748.
  • Riley MA (1993) Positive selection for colicin diversity in bacteria. Molecular Biology and Evolution, 10, 10481059.
  • Rooney AP, Zhang J (1999) Rapid evolution of a primate sperm protein: relaxation of functional constraint or positive Darwinian selection? Molecular Biology and Evolution, 16, 706710.
  • Rooney AP, Zhang J, Nei M (2000) An unusual form of purifying selection in a sperm protein. Molecular Biology and Evolution, 17, 278283.
  • Saez AG, Escalante R, Sastre L (2000) High DNA sequence variability at the α1 Na/K-ATPase locus of Artemia franciscana (brine shrimp): polymorphism in a gene for salt-resistance in a salt-resistant organism. Molecular Biology and Evolution, 17, 235250.
  • Salemi M, Desmyter J, Vandamme A-M (2000) Temp and mode of human and simian T-lymphotropic virus (HTLV/STLV) evolution revealed by analyses of full-genome sequences. Molecular Biology and Evolution, 17, 374386.
  • Sawyer SA, Hartl DL (1992) Population genetics of polymorphism and divergence. Genetics, 132, 11611176.
  • Schaner P, Richards N, Wadhwa A et al. (2001) Episodic evolution of pyrin in primates: human mutations recapitulate ancestral amino acid states. Nature Genetics, 27, 318321.
  • Schemske DW, Bradshaw HDJ (1999) Pollinator preference and the evolution of floral traits in monkeyflowers (Mimulus). Proceedings of the National Academy of Science USA, 96, 1191011915.
  • Schmidt PS, Duvernell DD, Eanes WF (2000) Adaptive evolution of a candidate gene for aging in Drosophila. Proceedings of the National Academy of Science USA, 97, 1086110865.
  • Schmidt TR, Goodman M, Grossman LI (1999) Molecular evolution of the COX7A gene family in primates. Molecular Biology and Evolution, 16, 619626.
  • Schug MD, Hutter CM, Noor MA, Aquadro CF (1998) Mutation and evolution of microsatellites in Drosophila melanogaster. Genetica, 102–103, 359367.
  • Schulenburg JHG, Hurst GDD, Huigens TME, Van Meer MMM, Jiggins FM, Majerus MEN (2000) Molecular evolution and phylogenetic utility of Wolbachia ftsZ and wsp gene sequences with special reference to the origin of male-killing. Molecular Biology and Evolution, 17, 584600.
  • Schulte PM, Glemet HE, Fiebig AA, Powers DA (2000) Adaptive variation in lactate dehydrogenase-B gene expression: role of a stress-responsive regulatory element. Proceedings of the National Academy of Science USA, 97, 65976602.
  • Schulte PM, Gomez-Chiarri M, Powers DA (1997) Structural and functional differences in the promoter and 5′ flanking region of Ldh-B within and between populations of the teleost Fundulus heteroclitus. Genetics, 145, 759769.
  • Simonsen KL, Churchill GA, Aquadro CF (1995) Properties of statistical tests of neutrality for DNA polymorphism data. Genetics, 141, 413429.
  • Stahl EA, Dwyer G, Mauricio R, Kreitman M, Bergelson J (1999) Dynamics of disease resistance polymorphism at the Rpm1 locus of Arabidopsis. Nature, 400, 667671.
  • Stephan W (1995) An improved method for estimating the rate of fixation of favourable mutations based on DNA polymorphism data. Molecular Biology and Evolution, 12, 959962.
  • Stotz HU, Bishop JG, Bergmann CW et al. (2000) Identification of target amino acids that affect interactions of fungal polygalacturonases and the plant inhibitors. Physiological and Molecular Plant Pathology, 56, 117130.
  • Sutton KA, Wilkinson MF (1997) Rapid evolution of a homeodomain: evidence for positive selection. Journal of Molecular Evolution, 45, 579588.
  • Suzuki Y, Gojobori T (1999) A method for detecting positive selection at single amino acid sites. Molecular Biology and Evolution, 16, 13151328.
  • Suzuki Y, Nei M (2001) Reliabilities of parsimony-based and likelihood-based methods for detecting positive selection at single amino acid sites. Molecular Biology and Evolution, 18, 21792185.
  • Swanson WJ, Aquadro CF, Vacquir VD (2001a) Polymorphism in abalone fertilization proteins is consistent with the neutral evolution of the egg's receptor for lysin (VERL) and positive darwinian selection of sperm lysin. Molecular Biology and Evolution, 18, 376383.
  • Swanson WJ, Clark AG, Waldrip-Dail HM, Wolfner MF, Aquadro CF (2001c) Evolutionary EST analysis identifies rapidly evolving male reproductive proteins in Drosophila. Proceedings of the National Academy of Sciences USA, 98, 73757379.
  • Swanson KW, Irwin DM, Wilson AC (1991) Stomach lysozyme gene of the langur monkey: tests for convergence and positive selection. Journal of Molecular Evolution, 33, 418425.
  • Swanson WJ, Yang Z, Wolfner MF, Aquadro CF (2001b) Positive darwinian selection drives the evolution of several female reproductive proteins in mammals. Proceedings of the National Academy of Science USA, 98, 25092514.
  • Tajima F (1989) Statistical methods for testing the neutral mutation hypothesis by DNA polymorphisms. Genetics, 123, 585595.
  • Takahashi A, Tsaur S-C, Coyne JA, Wu C-I (2001) The nucleotide changes governing cuticular hydrocarbon variation and their evolution in Drosophila melanogaster. Proceedings of the National Academy of Science USA, 98, 39203925.
  • Tanaka T, Nei M (1989) Positive Darwinian selection observed at the variable-region genes of immunoglobulins. Molecular Biology and Evolution, 6, 447459.
  • Tanksley SD, McCouch SR (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science, 277, 10631066.
  • Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proceedings of the National Academy of Science USA, 98, 91619166.
  • Ting C-T, Tsaur SC, Wu M-L, Wu C-I (1998) A rapidly evolving homeobox at the site of a hybrid sterility gene. Science, 282, 15011504.
  • Tishkoff SA, Varkonyi R, Cahinhinan N et al. (2001) Haplotype diversity and linkage diequilibrium at human G6PD: recent origin of alleles that confer malarial resistance. Science, 293, 455462
  • Tsaur SC, Ting C-T, Wu C-I (1998) Positive selection driving the evolution of a gene of male reproduction, Acp26Aa, of Drosophila. II. Divergence versus polymorphism. Molecular Biology and Evolution, 15, 10401046.
  • Tsaur SC, Ting C-T, Wu C-I (2001) Sex in Drosophila mauritiana: a very high level of amino acid polymorphism in a male reproductive protein gene Acp26Aa. Molecular Biology and Evolution, 18, 2226.
  • Tsaur SC, Wu C-I (1997) Positive selection and the molecular evolution of a gene of male reproduction, Acp26Aa of Drosophila. Molecular Biology and Evolution, 14, 544549.
  • Vacquier VD, Swanson WJ, Lee YH (1997) Positive Darwinian selection on two homologous fertilization proteins: what is the selective pressure driving their divergence? Journal of Molecular Evolution, 44, S15S22.
  • Verrelli BC, Eanes WF (2000) Extensive amino acid polymorphism at the Pgm locus is consistent with adaptive protein evolution in Drosophila melanogaster. Genetics, 156, 17371752.
  • Verrelli BC, Eanes WF (2001) Clinal variation for amino acid polymorphisms at the Pgm locus in Drosophila melanogaster. Genetics, 157, 16491663.
  • Wallis M (1996) The molecular evolution of vertebrate growth hormones: a pattern of near-stasis interrupted by sustained bursts of rapid change. Journal of Molecular Evolution, 43, 93100.
  • Wang R-L, Stec A, Hey J, Lukens L, Doebley J (1999) The limits of selection during maize domestication. Nature, 398, 236239[correction, 410, 718].
  • Wang W, Thornton K, Berry A, Long M (2002) Nucleotide variation along the Drosophila melanogaster fourth chromosome. Science, 295, 134137.
  • Ward TJ, Honeycutt RL, Derr JN (1997) Nucleotide sequence evolution at the kappa-casein locus: evidence for positive selection within the family Bovidae. Genetics, 147, 18631872.
  • Watt WB, Dean AM (2000) Molecular-functional studies of adaptive genetic variation in prokaryotes and eukaryotes. Annual Review of Genetics, 34, 593622.
  • Watterson GA (1978) The homozygosity test of neutrality. Genetics, 88, 405417.
  • Wayne ML, Contamine D, Kreitman M (1996) Molecular population genetics of ref(2)P, a locus which confers viral resistance in Drosophila. Molecular Biology and Evolution, 13, 191199.
  • Wiehe T (1998) The effect of selective sweeps on the variance of the allele distribution of a linked multiallele locus: hitchhiking of microsatellites. Theoretical Population Biology, 53, 272283.
  • Wu JC, Chiang TY, Shiue WK, Wang SY, Sheen IJ, Huang YH, Syu WJ (1999) Recombination of hepatitis D virus RNA sequences and its implications. Molecular Biology and Evolution, 16, 16221632.
  • Wu J, Saupe SJ, Glass NL (1998) Evidence for balancing selection operating at the het-c heterokaryon incompatibility locus in a group of filamentous fungi. Proceedings of the National Academy of Sciences USA, 95, 1239812403.
  • Xie S, Green J, Bixby JB, Szafranska B, DeMartini JC, Hect S, Roberts RM (1997) The diversity and evolutionary relationships of the pregnancy-associated glycoproteins, and aspartic proteinase subfamily consisting of many trophoblast-expressed genes. Proceedings of the National Academy of Science USA, 94, 1280912816.
  • Yang Z (1998) Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Molecular Biology and Evolution, 15, 568573.
  • Yang Z, Bielawski JP (2000) Statistical methods for detecting molecular adaptation. Trends in Ecology and Evolution, 15, 496503.
  • Yang Z, Nielsen R (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Molecular Biology and Evolution, 17, 3243.
  • Zanotto PMA, Kallas EG, Souza RF, Holmes EC (1999) Genealogical evidence for positive selection in the nef gene of HIV-1. Genetics, 153, 10771089.
  • Zelus D, Robinson-Rechavi M, Delacre M, Auriault C, Laudet V (2000) Fast evolution of interleukin-2 in mammals and positive selection in ruminants. Journal of Molecular Evolution, 51, 234244.
  • Zhang J, Dyer KD, Rosenberg HF (2000) Evolution of the rodent eosinophil-associated RNase gene family by rapid gene sorting and positive selection. Proceedings of the National Academy of Sciences USA, 97, 47014706.
  • Zhang J, Nei M (2000) Positive selection in the evolution of mammalian interleukin-2 genes. Molecular Biology and Evolution, 17, 14131416.
  • Zhang J, Rosenberg HF (2000) Sequence variation at two eosinophil-associated ribonuclease loci in humans. Genetics, 156, 19491958.
  • Zhang J, Rosenberg HF, Nei M (1998) Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proceedings of the National Academy of Sciences USA, 95, 37083713.