Applications of selective neutrality tests to molecular ecology

This paper reviews how statistical tests of neutrality have been used to address questions in molecular ecology are reviewed. The work consists of four major parts: a brief review of the current status of the neutral theory; a review of several particularly interesting examples of how statistical tests of neutrality have led to insight into ecological problems; a brief discussion of the pitfalls of assuming a strictly neutral model if it is false; and a discussion of some of the opportunities and problems that molecular ecologists face when using neutrality tests to study natural selection.

[1]  J. Avise Mitochondrial DNA Polymorphism and a Connection Between Genetics and Demography of Relevance to Conservation , 1995 .

[2]  D. Haydon,et al.  Evidence for positive selection in foot-and-mouth disease virus capsid genes from field isolates. , 2001, Genetics.

[3]  L. Lukens,et al.  Molecular evolution of the teosinte branched gene among maize and related grasses. , 2001, Molecular biology and evolution.

[4]  R. Hudson,et al.  How can the low levels of DNA sequence variation in regions of the drosophila genome with low recombination rates be explained? , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[5]  T. Wiehe The effect of selective sweeps on the variance of the allele distribution of a linked multiallele locus: hitchhiking of microsatellites. , 1998, Theoretical population biology.

[6]  M. Kimura The Neutral Theory of Molecular Evolution: Introduction , 1983 .

[7]  V. Vacquier,et al.  The Divergence of Species-Specific Abalone Sperm Lysins is Promoted by Positive Darwinian Selection. , 1992, The Biological bulletin.

[8]  T. Jukes,et al.  The neutral theory of molecular evolution. , 2000, Genetics.

[9]  G. A. Watterson The homozygosity test of neutrality. , 1978, Genetics.

[10]  D. Posada,et al.  Population genetics of the porB gene of Neisseria gonorrhoeae: different dynamics in different homology groups. , 2000, Molecular biology and evolution.

[11]  R. Roberts,et al.  The diversity and evolutionary relationships of the pregnancy-associated glycoproteins, an aspartic proteinase subfamily consisting of many trophoblast-expressed genes. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[12]  W. Eanes,et al.  Evidence for adaptive evolution of the G6pd gene in the Drosophila melanogaster and Drosophila simulans lineages. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Simon Easteal,et al.  Evolutionary Rate Acceleration of Cytochrome c Oxidase Subunit I in Simian Primates , 2000, Journal of Molecular Evolution.

[14]  Elizabeth Pennisi Stalking the Wild Mustard , 2000, Science.

[15]  M. Kreitman,et al.  The neutral theory is dead. Long live the neutral theory. , 1996, BioEssays : news and reviews in molecular, cellular and developmental biology.

[16]  M. Long,et al.  Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. , 1993, Science.

[17]  J. Doebley,et al.  teosinte branched1 and the origin of maize: evidence for epistasis and the evolution of dominance. , 1995, Genetics.

[18]  R. Boutilier,et al.  Genetic population structure and gene flow in the Atlantic cod Gadus morhua: a comparison of allozyme and nuclear RFLP loci. , 1995, Genetics.

[19]  R. Escalante,et al.  High DNA sequence variability at the alpha 1 Na/K-ATPase locus of Artemia franciscana (brine shrimp): polymorphism in a gene for salt-resistance in a salt-resistant organism. , 2000, Molecular biology and evolution.

[20]  M. Wilkinson,et al.  Rapid Evolution of a Homeodomain: Evidence for Positive Selection , 1997, Journal of Molecular Evolution.

[21]  M. Nachman,et al.  Microsatellite variation and recombination rate in the human genome. , 2000, Genetics.

[22]  Chung-I Wu,et al.  Positive selection driving the evolution of a gene of male reproduction, Acp26Aa, of Drosophila: II. Divergence versus polymorphism. , 1998, Molecular biology and evolution.

[23]  E. Stahl,et al.  Dynamics of disease resistance polymorphism at the Rpm1 locus of Arabidopsis , 1999, Nature.

[24]  M. Hellberg,et al.  Rapid evolution of fertilization selectivity and lysin cDNA sequences in teguline gastropods. , 1999, Molecular biology and evolution.

[25]  M. Ford TESTING MODELS OF MIGRATION AND ISOLATION AMONG POPULATIONS OF CHINOOK SALMON (ONCORHYNCHUS TSCHAWYTSCHA) , 1998, Evolution; international journal of organic evolution.

[26]  M. Ford 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 , 2000, Molecular ecology.

[27]  Andrew G. Clark,et al.  Haplotype Diversity and Linkage Disequilibrium at Human G6PD: Recent Origin of Alleles That Confer Malarial Resistance , 2001, Science.

[28]  F. Ayala,et al.  DNA variation at the Sod locus of Drosophila melanogaster: an unfolding story of natural selection. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[29]  S. Palumbi,et al.  Positive selection and sequence rearrangements generate extensive polymorphism in the gamete recognition protein bindin. , 1996, Molecular biology and evolution.

[30]  Z. Yang,et al.  Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. , 2000, Molecular biology and evolution.

[31]  M. Kreitman,et al.  Methods to detect selection in populations with applications to the human. , 2000, Annual review of genomics and human genetics.

[32]  P. Schmidt,et al.  Adaptive evolution of a candidate gene for aging in Drosophila. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[33]  W. Messier,et al.  Episodic adaptive evolution of primate lysozymes , 1997, Nature.

[34]  B. Gaut,et al.  Speciation and domestication in maize and its wild relatives: evidence from the globulin-1 gene. , 1998, Genetics.

[35]  J G Bishop,et al.  Rapid evolution in plant chitinases: molecular targets of selection in plant-pathogen coevolution. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[36]  C. Halldén,et al.  Positive correlation between recombination rates and levels of genetic variation in natural populations of sea beet (Beta vulgaris subsp. maritima). , 1998, Genetics.

[37]  The neutralist, the fly and the selectionist. , 1999, Trends in ecology & evolution.

[38]  Brandon S. Gaut,et al.  Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.) , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[39]  G. McVean,et al.  Genome sequences and evolutionary biology, a two-way interaction. , 2001, Trends in ecology & evolution.

[40]  E. Holub The arms race is ancient history in Arabidopsis, the wildflower , 2001, Nature Reviews Genetics.

[41]  M. Nei,et al.  Positive Darwinian selection promotes charge profile diversity in the antigen-binding cleft of class I major-histocompatibility-complex molecules. , 1990, Molecular biology and evolution.

[42]  T Gojobori,et al.  Large-scale search for genes on which positive selection may operate. , 1996, Molecular biology and evolution.

[43]  Jianzhi Zhang,et al.  Evolution of the rodent eosinophil-associated RNase gene family by rapid gene sorting and positive selection. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[44]  J. McDonald,et al.  Detecting non-neutral heterogeneity across a region of DNA sequence in the ratio of polymorphism to divergence. , 1996, Molecular biology and evolution.

[45]  R. El-Batsri,et al.  Enzyme Polymorphism in Mango , 1990 .

[46]  A. Blancher,et al.  Sequence, Organization, and Evolution of Rh50 Glycoprotein Genes in Nonhuman Primates , 2000, Journal of Molecular Evolution.

[47]  M. Ford,et al.  Molecular evolution of transferrin: evidence for positive selection in salmonids. , 2001, Molecular biology and evolution.

[48]  W. Stephan,et al.  Is the fast/slow allozyme variation at the Adh locus of Drosophila melanogaster an ancient balanced polymorphism? , 1999, Molecular biology and evolution.

[49]  T. Chiang,et al.  Recombination of hepatitis D virus RNA sequences and its implications. , 1999, Molecular biology and evolution.

[50]  D. A. Kirby,et al.  Multi-locus selection and the structure of variation at the white gene of Drosophila melanogaster. , 1996, Genetics.

[51]  A. Clark,et al.  Excess nonsynonymous substitution of shared polymorphic sites among self-incompatibility alleles of Solanaceae. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[52]  W. Stephan,et al.  Joint effects of genetic hitchhiking and background selection on neutral variation. , 2000, Genetics.

[53]  D. Charlesworth,et al.  The effect of mating system differences on nucleotide diversity at the phosphoglucose isomerase locus in the plant genus Leavenworthia. , 1999, Genetics.

[54]  H Baumann,et al.  Patterns of divergence during evolution of alpha 1-proteinase inhibitors in mammals. , 1996, Molecular biology and evolution.

[55]  J. Gillespie The causes of molecular evolution , 1991 .

[56]  F. Tajima Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. , 1989, Genetics.

[57]  W. Fitch,et al.  Predicting the evolution of human influenza A. , 1999, Science.

[58]  Kevin R. Thornton,et al.  Nucleotide Variation Along the Drosophila melanogaster Fourth Chromosome , 2002, Science.

[59]  C. Aquadro,et al.  Selection on X-linked genes during speciation in the Drosophila athabasca complex. , 1996, Genetics.

[60]  R. Nielsen,et al.  Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. , 1998, Genetics.

[61]  John C. Avise Molecular Markers, Natural History and Evolution , 1994, Springer US.

[62]  A. Hughes,et al.  Coordinated Amino Acid Changes in the Evolution of Mammalian Defensins , 1997, Journal of Molecular Evolution.

[63]  W. Eanes,et al.  Clinal variation for amino acid polymorphisms at the Pgm locus in Drosophila melanogaster. , 2001, Genetics.

[64]  V. Vacquier,et al.  Nonsynonymous substitution in abalone sperm fertilization genes exceeds substitution in introns and mitochondrial DNA. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[65]  Jonathan Flint,et al.  Finding the molecular basis of quatitative traits: successes and pitfalls , 2001, Nature Reviews Genetics.

[66]  F. Jiggins,et al.  Molecular evolution and phylogenetic utility of Wolbachia ftsZ and wsp gene sequences with special reference to the origin of male-killing. , 2000, Molecular biology and evolution.

[67]  E. Holmes,et al.  Genealogical evidence for positive selection in the nef gene of HIV-1. , 1999, Genetics.

[68]  R. DeSalle,et al.  Adaptive Evolution of Genes and Genomes , 2000, Heredity.

[69]  H. N. Barber Selection in natural populations , 1965, Heredity.

[70]  M W Bruford,et al.  Molecular adaptation of alanine:glyoxylate aminotransferase targeting in primates. , 2000, Molecular biology and evolution.

[71]  E. Holmes,et al.  The CD45 locus in cattle: allelic polymorphism and evidence for exceptional positive natural selection , 2000, Immunogenetics.

[72]  J. Brookfield,et al.  An investigation of the cause of low variability on the fourth chromosome of Drosophila melanogaster. , 2001, Molecular biology and evolution.

[73]  L. Bargelloni,et al.  Antarctic fish hemoglobins: evidence for adaptive evolution at subzero temperature. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[74]  M. Nachman,et al.  Single nucleotide polymorphisms and recombination rate in humans. , 2001, Trends in genetics : TIG.

[75]  E. Stahl,et al.  Evolutionary Dynamics of Plant R-Genes , 2001, Science.

[76]  L. Kann,et al.  Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans. , 1996, Molecular biology and evolution.

[77]  J. Coyne,et al.  The nucleotide changes governing cuticular hydrocarbon variation and their evolution in Drosophila melanogaster , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[78]  V. Laudet,et al.  Fast Evolution of Interleukin-2 in Mammals and Positive Selection in Ruminants , 2000, Journal of Molecular Evolution.

[79]  T. Beacham,et al.  Molecular evolution at Mhc genes in two populations of chinook salmon Oncorhynchus tshawytscha , 1997, Molecular ecology.

[80]  W. Ewens The sampling theory of selectively neutral alleles. , 1972, Theoretical population biology.

[81]  B. Cowart Let them eat soap , 1991, Nature.

[82]  M. Purugganan,et al.  Variation and selection at the CAULIFLOWER floral homeotic gene accompanying the evolution of domesticated Brassica oleracea. , 2000, Genetics.

[83]  C. Aquadro,et al.  Contrasting patterns of nucleotide sequence variation at the glucose dehydrogenase (Gld) locus in different populations of Drosophila melanogaster. , 1997, Genetics.

[84]  S. Goff,et al.  Intragenic Recombination and Diversifying Selection Contribute to the Evolution of Downy Mildew Resistance at the RPP8 Locus of Arabidopsis , 1998, Plant Cell.

[85]  C. Aquadro,et al.  Selection, Recombination, and DNA Polymorphism in Drosophila , 1994 .

[86]  R. Hudson,et al.  A test of neutral molecular evolution based on nucleotide data. , 1987, Genetics.

[87]  P. Schulte,et al.  Evolutionary adaptations 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. , 1998, The Journal of experimental zoology.

[88]  B. Charlesworth Background selection and patterns of genetic diversity in Drosophila melanogaster. , 1996, Genetical research.

[89]  Burt,et al.  Natural selection in the wild. , 2000, Trends in ecology & evolution.

[90]  M. Kreitman,et al.  Molecular analysis of an allozyme cline: alcohol dehydrogenase in Drosophila melanogaster on the east coast of North America. , 1993, Genetics.

[91]  Ziheng Yang,et al.  Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[92]  S. Saupe,et al.  Evidence for balancing selection operating at the het-c heterokaryon incompatibility locus in a group of filamentous fungi. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[93]  C. Schlötterer,et al.  Chromosomal patterns of microsatellite variability contrast sharply in African and non-African populations of Drosophila melanogaster. , 2002, Genetics.

[94]  C. Aquadro,et al.  Evolutionary inferences from DNA variation at the 6-phosphogluconate dehydrogenase locus in natural populations of drosophila: selection and geographic differentiation. , 1994, Genetics.

[95]  J. Jallon,et al.  A delta 9 desaturase gene with a different substrate specificity is responsible for the cuticular diene hydrocarbon polymorphism in Drosophila melanogaster. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[96]  R. Lewontin,et al.  Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. , 1973, Genetics.

[97]  J. Zhang,et al.  Rapid evolution of a primate sperm protein: relaxation of functional constraint or positive Darwinian selection? , 1999, Molecular biology and evolution.

[98]  J. Doebley,et al.  The evolution of apical dominance in maize , 1997, Nature.

[99]  M. Nei,et al.  Positive darwinian selection observed at the variable-region genes of immunoglobulins. , 1989, Molecular biology and evolution.

[100]  A. Hughes,et al.  Circumsporozoite protein genes of malaria parasites (Plasmodium spp.): evidence for positive selection on immunogenic regions. , 1991, Genetics.

[101]  C. Aquadro,et al.  Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster , 1992, Nature.

[102]  T. Endo,et al.  Identification of regions in which positive selection may operate in S‐RNase of Rosaceae: Implication for S‐allele‐specific recognition sites in S‐RNase , 1998, FEBS letters.

[103]  M. Nei,et al.  Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection , 1988, Nature.

[104]  A. Kawabe,et al.  DNA polymorphism at the cytosolic phosphoglucose isomerase (PgiC) locus of the wild plant Arabidopsis thaliana. , 2000, Genetics.

[105]  D. Begun,et al.  Reduced X-linked nucleotide polymorphism in Drosophila simulans. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[106]  S. Palumbi All males are not created equal: fertility differences depend on gamete recognition polymorphisms in sea urchins. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[107]  L. Andersson,et al.  Low major histocompatibility complex class II diversity in European and North American moose. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[108]  M. Nei,et al.  Positive Darwinian selection after gene duplication in primate ribonuclease genes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[109]  S. Tanksley,et al.  Seed banks and molecular maps: unlocking genetic potential from the wild. , 1997, Science.

[110]  John C. Avise,et al.  Molecular Markers, Natural History and Evolution , 1993, Springer US.

[111]  W. Eanes,et al.  Historical selection, amino acid polymorphism and lineage-specific divergence at the G6pd locus in Drosophila melanogaster and D. simulans. , 1996, Genetics.

[112]  J. Beynon,et al.  RPP13 is a simple locus in Arabidopsis thaliana for alleles that specify downy mildew resistance to different avirulence determinants in Peronospora parasitica. , 2000, The Plant journal : for cell and molecular biology.

[113]  R. Lewontin,et al.  A molecular approach to the study of genic heterozygosity in natural populations. II. Amount of variation and degree of heterozygosity in natural populations of Drosophila pseudoobscura. , 1966, Genetics.

[114]  A. Hughes Positive selection and interallelic recombination at the merozoite surface antigen-1 (MSA-1) locus of Plasmodium falciparum. , 1992, Molecular biology and evolution.

[115]  A. Clark,et al.  Molecular population genetics of male accessory gland proteins in Drosophila. , 2000, Genetics.

[116]  T. Yamazaki,et al.  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. , 2001, Genetics.

[117]  D. Schemske,et al.  Pollinator preference and the evolution of floral traits in monkeyflowers (Mimulus). , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[118]  D. Hartl,et al.  Population genetics of polymorphism and divergence. , 1992, Genetics.

[119]  J. Labavitch,et al.  Identification of target amino acids that affect interactions of fungal polygalacturonases and their plant inhibitors , 2000 .

[120]  C. Wu,et al.  Sex in Drosophila mauritiana: a very high level of amino acid polymorphism in a male reproductive protein gene, Acp26Aa. , 2001, Molecular biology and evolution.

[121]  R. Baric,et al.  Episodic evolution mediates interspecies transfer of a murine coronavirus , 1997, Journal of virology.

[122]  J. Ferveur,et al.  World-wide variation inDrosophila melanogaster sex pheromone: behavioural effects, genetic bases and potential evolutionary consequences , 2004, Genetica.

[123]  G. Churchill,et al.  Properties of statistical tests of neutrality for DNA polymorphism data. , 1995, Genetics.

[124]  A. Hughes The evolution of the type I interferon gene family in mammals , 1995, Journal of Molecular Evolution.

[125]  H. Harris C. Genetics of Man Enzyme polymorphisms in man , 1966, Proceedings of the Royal Society of London. Series B. Biological Sciences.

[126]  M. Hellberg,et al.  Positive selection and propeptide repeats promote rapid interspecific divergence of a gastropod sperm protein. , 2000, Molecular biology and evolution.

[127]  T Gojobori,et al.  A method for detecting positive selection at single amino acid sites. , 1999, Molecular biology and evolution.

[128]  D. A. Kirby,et al.  Haplotype test reveals departure from neutrality in a segment of the white gene of Drosophila melanogaster. , 1995, Genetics.

[129]  J. Gillespie,et al.  The neutral theory in an infinite population. , 2000, Gene.

[130]  F. Bonhomme,et al.  Molecular phylogeny of Fv1 , 1998, Mammalian Genome.

[131]  M. Goodman,et al.  Molecular evolution of the COX7A gene family in primates. , 1999, Molecular biology and evolution.

[132]  Y Suzuki,et al.  Reliabilities of parsimony-based and likelihood-based methods for detecting positive selection at single amino acid sites. , 2001, Molecular biology and evolution.

[133]  M. Ford,et al.  Natural selection promotes divergence of transferrin among salmonid species , 1999, Molecular ecology.

[134]  R. Lewontin,et al.  The Genetic Basis of Evolutionary Change , 2022 .

[135]  Y. Fu,et al.  Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. , 1997, Genetics.

[136]  D. Schluter,et al.  The genetic architecture of divergence between threespine stickleback species , 2001, Nature.

[137]  Chung-I Wu,et al.  A rapidly evolving homeobox at the site of a hybrid sterility gene. , 1998, Science.

[138]  M. Riley Positive selection for colicin diversity in bacteria. , 1993, Molecular biology and evolution.

[139]  W. Eanes,et al.  Analysis of Selection on Enzyme Polymorphisms , 1999 .

[140]  R. Hudson,et al.  Inferring the evolutionary histories of the Adh and Adh-dup loci in Drosophila melanogaster from patterns of polymorphism and divergence. , 1991, Genetics.

[141]  M. Kreitman,et al.  Nucleotide variation in the triosephosphate isomerase (Tpi) locus of Drosophila melanogaster and Drosophila simulans. , 1998, Molecular biology and evolution.

[142]  W. Fitch,et al.  Long term trends in the evolution of H(3) HA1 human influenza type A. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[143]  C. Biermann The molecular evolution of sperm bindin in six species of sea urchins (Echinoida: Strongylocentrotidae). , 1998, Molecular biology and evolution.

[144]  W. Stephan An improved method for estimating the rate of fixation of favorable mutations based on DNA polymorphism data. , 1995, Molecular biology and evolution.

[145]  W. Eanes,et al.  Extensive amino acid polymorphism at the pgm locus is consistent with adaptive protein evolution in Drosophila melanogaster. , 2000, Genetics.

[146]  D. Weinreich,et al.  The age of nonsynonymous and synonymous mutations in animal mtDNA and implications for the mildly deleterious theory. , 1999, Genetics.

[147]  M. Nei,et al.  Positive Selection in the Evolution of Mammalian Interleukin-2 Genes , 2000 .

[148]  L. Katz,et al.  Balancing selection on electrophoretic variation of phosphoglucose isomerase in two species of field cricket: Gryllus veletis and G. offnsylvanicus. , 1997, Genetics.

[149]  M. Nachman,et al.  Reduced nucleotide variability at an androgen-binding protein locus (Abpa) in house mice: evidence for positive natural selection. , 1999, Molecular biology and evolution.

[150]  C. Hutter,et al.  Mutation and evolution of microsatellites in Drosophila melanogaster , 2004, Genetica.

[151]  M. Aguadé Positive selection drives the evolution of the Acp29AB accessory gland protein in Drosophila. , 1999, Genetics.

[152]  T. Gojobori,et al.  Molecular evolution of myelin proteolipid protein. , 1997, Biochemical and biophysical research communications.

[153]  A. Chess,et al.  The family of genes encoding odorant receptors in the channel catfish , 1993, Cell.

[154]  W. Fitch,et al.  The Wilhelmine E. Key 1999 Invitational lecture. Predicting the evolution of human influenza A. , 2000, The Journal of heredity.

[155]  Nicholas D. Hastie,et al.  Accelerated evolution in the reactive centre regions of serine protease inhibitors , 1987, Nature.

[156]  D. Hewett‐Emmett,et al.  High polymorphism at the human melanocortin 1 receptor locus. , 1999, Genetics.

[157]  Rasmus Nielsen,et al.  The ratio of replacement to silent divergence and tests of neutrality , 1997 .

[158]  M. Nei,et al.  An unusual form of purifying selection in a sperm protein. , 2000, Molecular biology and evolution.

[159]  J. Coyne,et al.  A gene responsible for a cuticular hydrocarbon polymorphism in Drosophila melanogaster. , 1999, Genetical research.

[160]  Z. Yang,et al.  Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. , 1998, Molecular biology and evolution.

[161]  Justin C. Fay,et al.  Positive and negative selection on the human genome. , 2001, Genetics.

[162]  D. Rand Neutrality Tests of Molecular Markers and the Connection Between DNA Polymorphism, Demography, and Conservation Biology , 1996 .

[163]  W. Swanson,et al.  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. , 2001, Molecular biology and evolution.

[164]  C. Aquadro,et al.  Molecular variation at the vermilion locus in geographically diverse populations of Drosophila melanogaster and D. simulans. , 1995, Genetics.

[165]  J. McDonald,et al.  Improved tests for heterogeneity across a region of DNA sequence in the ratio of polymorphism to divergence. , 1998, Molecular biology and evolution.

[166]  C. R,et al.  Twenty-Five Years Ago in GENETICS : Electrophoresis in the Development of Evolutionary Genetics : Milestone or Millstone ? , 2022 .

[167]  Doron Lancet,et al.  Dichotomy of single-nucleotide polymorphism haplotypes in olfactory receptor genes and pseudogenes , 2000, Nature Genetics.

[168]  S. Cirera,et al.  Evolutionary history of the sex-peptide (Acp70A) gene region in Drosophila melanogaster. , 1997, Genetics.

[169]  T. Ward,et al.  Nucleotide sequence evolution at the kappa-casein locus: evidence for positive selection within the family Bovidae. , 1997, Genetics.

[170]  P. Rohani,et al.  Receptor-like Genes in the Major Resistance Locus of Lettuce Are Subject to Divergent Selection , 1998, Plant Cell.

[171]  B. Charlesworth,et al.  The effect of deleterious mutations on neutral molecular variation. , 1993, Genetics.

[172]  J. Zhang,et al.  Sequence variation at two eosinophil-associated ribonuclease loci in humans. , 2000, Genetics.

[173]  Hiroshi Akashi,et al.  Molecular Evidence for Natural Selection , 1995 .

[174]  D. Crawford,et al.  Genetic mechanisms for adapting to a changing environment. , 1991, Annual review of genetics.

[175]  D. Kordis,et al.  Adaptive evolution of animal toxin multigene families. , 2000, Gene.

[176]  M. Nachman,et al.  DNA variability and recombination rates at X-linked loci in humans. , 1998, Genetics.

[177]  M. Purugganan,et al.  Molecular population genetics of the Arabidopsis CAULIFLOWER regulatory gene: nonneutral evolution and naturally occurring variation in floral homeotic function. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[178]  A. Dean,et al.  Molecular-functional studies of adaptive genetic variation in prokaryotes and eukaryotes. , 2000, Annual review of genetics.

[179]  P. Schulte,et al.  Structural and functional differences in the promoter and 5' flanking region of Ldh-B within and between populations of the teleost Fundulus heteroclitus. , 1997, Genetics.

[180]  Leif Andersson,et al.  Genetic dissection of phenotypic diversity in farm animals , 2001, Nature Reviews Genetics.

[181]  S. Palumbi,et al.  Molecular genetics of ecological diversification: duplication and rapid evolution of toxin genes of the venomous gastropod Conus. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[182]  R. Lewontin,et al.  Twenty-five years ago in Genetics: electrophoresis in the development of evolutionary genetics: milestone or millstone? , 1991, Genetics.

[183]  Ziheng Yang,et al.  Statistical methods for detecting molecular adaptation , 2000, Trends in Ecology & Evolution.

[184]  C. Wu,et al.  Positive selection and the molecular evolution of a gene of male reproduction, Acp26Aa of Drosophila. , 1997, Molecular biology and evolution.

[185]  G. Pogson Nucleotide polymorphism and natural selection at the pantophysin (Pan I) locus in the Atlantic cod, Gadus morhua (L.). , 2001, Genetics.

[186]  M. Kreitman,et al.  Molecular population genetics of ref(2)P, a locus which confers viral resistance in Drosophila. , 1996, Molecular biology and evolution.

[187]  A. Hughes,et al.  Natural selection on Plasmodium surface proteins. , 1995, Molecular and biochemical parasitology.

[188]  J. True,et al.  PERSPECTIVE: FROM MUTANTS TO MECHANISMS? ASSESSING THE CANDIDATE GENE PARADIGM IN EVOLUTIONARY BIOLOGY , 2001, Evolution; international journal of organic evolution.

[189]  Jonathan D. G. Jones,et al.  Three Genes of the Arabidopsis RPP1 Complex Resistance Locus Recognize Distinct Peronospora parasitica Avirulence Determinants , 1998, Plant Cell.

[190]  M. Salemi,et al.  Tempo and mode of human and simian T-lymphotropic virus (HTLV/STLV) evolution revealed by analyses of full-genome sequences. , 2000, Molecular biology and evolution.

[191]  P. Schulte,et al.  Adaptive variation in lactate dehydrogenase-B gene expression: role of a stress-responsive regulatory element. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[192]  Justin C. Fay,et al.  Hitchhiking under positive Darwinian selection. , 2000, Genetics.

[193]  Trudy F. C. Mackay,et al.  Quantitative trait loci in Drosophila , 2001, Nature Reviews Genetics.

[194]  N. Goldman,et al.  A codon-based model of nucleotide substitution for protein-coding DNA sequences. , 1994, Molecular biology and evolution.

[195]  A. Clark,et al.  Evolutionary EST analysis identifies rapidly evolving male reproductive proteins in Drosophila , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[196]  D. Notter,et al.  The importance of genetic diversity in livestock populations of the future. , 1999, Journal of animal science.

[197]  P. Tucker,et al.  Episodic evolution of pyrin in primates: human mutations recapitulate ancestral amino acid states , 2001, Nature Genetics.

[198]  M. Kreitman,et al.  Adaptive protein evolution at the Adh locus in Drosophila , 1991, Nature.

[199]  Jody Hey,et al.  The limits of selection during maize domestication , 1999, Nature.