Population Genomics of Plant Species

[1]  Mathieu Blanchette,et al.  The Capsella rubella genome and the genomic consequences of rapid mating system evolution , 2013, Nature Genetics.

[2]  K. Olsen,et al.  A bountiful harvest: genomic insights into crop domestication phenotypes. , 2013, Annual review of plant biology.

[3]  Christina E. Wells,et al.  The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution , 2013, Nature Genetics.

[4]  B. Payseur,et al.  Genomic signatures of selection at linked sites: unifying the disparity among species , 2013, Nature Reviews Genetics.

[5]  Matthew D. Schultz,et al.  Patterns of Population Epigenomic Diversity , 2013, Nature.

[6]  L. Rieseberg,et al.  Association Mapping and the Genomic Consequences of Selection in Sunflower , 2013, PLoS genetics.

[7]  James K. Hane,et al.  Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement , 2013, Nature Biotechnology.

[8]  C. T. Hash,et al.  Population genomic and genome-wide association studies of agroclimatic traits in sorghum , 2012, Proceedings of the National Academy of Sciences.

[9]  S. Kalisz,et al.  COMPARATIVE POPULATION GENOMICS IN COLLINSIA SISTER SPECIES REVEALS EVIDENCE FOR REDUCED EFFECTIVE POPULATION SIZE, RELAXED SELECTION, AND EVOLUTION OF BIASED GENE CONVERSION WITH AN ONGOING MATING SYSTEM SHIFT , 2012, Evolution; international journal of organic evolution.

[10]  T. Mitchell-Olds,et al.  Environmental adaptation contributes to gene polymorphism across the Arabidopsis thaliana genome. , 2012, Molecular biology and evolution.

[11]  N. Colegrave,et al.  Estimate of the Spontaneous Mutation Rate in Chlamydomonas reinhardtii , 2012, Genetics.

[12]  W. J. Lucas,et al.  The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions , 2012, Nature Genetics.

[13]  T. Mitchell-Olds,et al.  Adaptive evolution: evaluating empirical support for theoretical predictions , 2012, Nature Reviews Genetics.

[14]  D. Charlesworth,et al.  Recent and Ancient Signature of Balancing Selection around the S-Locus in Arabidopsis halleri and A. lyrata , 2012, Molecular biology and evolution.

[15]  D. Kliebenstein,et al.  Natural Enemies Drive Geographic Variation in Plant Defenses , 2012, Science.

[16]  Thomas G. Doak,et al.  Drift-barrier hypothesis and mutation-rate evolution , 2012, Proceedings of the National Academy of Sciences.

[17]  A. Fujiyama,et al.  A map of rice genome variation reveals the origin of cultivated rice , 2012, Nature.

[18]  S. Ge,et al.  GENOME SIZE IS NOT CORRELATED WITH EFFECTIVE POPULATION SIZE IN THE ORYZA SPECIES , 2012, Evolution; international journal of organic evolution.

[19]  Andrew W George,et al.  A multiparent advanced generation inter-cross population for genetic analysis in wheat. , 2012, Plant biotechnology journal.

[20]  P. Andolfatto,et al.  Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species? , 2012, PLoS biology.

[21]  S. Wright,et al.  Signatures of balancing selection are maintained at disease resistance loci following mating system evolution and a population bottleneck in the genus Capsella , 2012, BMC Evolutionary Biology.

[22]  Xun Xu,et al.  Comparative population genomics of maize domestication and improvement , 2012, Nature Genetics.

[23]  Peter J. Bradbury,et al.  Maize HapMap2 identifies extant variation from a genome in flux , 2012, Nature Genetics.

[24]  J. Chen,et al.  Genome-wide genetic changes during modern breeding of maize , 2012, Nature Genetics.

[25]  T. Itoh,et al.  Independent domestication of Asian rice followed by gene flow from japonica to indica. , 2012, Molecular biology and evolution.

[26]  P. Andolfatto,et al.  GENETIC ARCHITECTURE AND ADAPTIVE SIGNIFICANCE OF THE SELFING SYNDROME IN CAPSELLA , 2012, Evolution; international journal of organic evolution.

[27]  P. Keightley,et al.  The Effect of Variation in the Effective Population Size on the Rate of Adaptive Molecular Evolution in Eukaryotes , 2012, Genome biology and evolution.

[28]  M. Purugganan,et al.  Natural selection in gene-dense regions shapes the genomic pattern of polymorphism in wild and domesticated rice. , 2012, Molecular biology and evolution.

[29]  Lin Fang,et al.  Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes , 2011, Nature Biotechnology.

[30]  M. Nordborg,et al.  A Map of Local Adaptation in Arabidopsis thaliana , 2011, Science.

[31]  Joy Bergelson,et al.  References and Notes Supporting Online Material Adaptation to Climate across the Arabidopsis Thaliana Genome , 2022 .

[32]  Karsten M. Borgwardt,et al.  Whole-genome sequencing of multiple Arabidopsis thaliana populations , 2011, Nature Genetics.

[33]  M. Schierup,et al.  Genomic Determinants of Protein Evolution and Polymorphism in Arabidopsis , 2011, Genome biology and evolution.

[34]  D. Charlesworth,et al.  Reduced Efficacy of Natural Selection on Codon Usage Bias in Selfing Arabidopsis and Capsella Species , 2011, Genome biology and evolution.

[35]  T. Mitchell-Olds,et al.  Evolutionary genetics of plant adaptation. , 2011, Trends in genetics : TIG.

[36]  Jeremy D. DeBarry,et al.  De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera) , 2011, Nature Biotechnology.

[37]  L. Rieseberg,et al.  Effective population size is positively correlated with levels of adaptive divergence among annual sunflowers. , 2011, Molecular biology and evolution.

[38]  Peter J. Bradbury,et al.  Genome-wide association study of leaf architecture in the maize nested association mapping population , 2011, Nature Genetics.

[39]  Joy Bergelson,et al.  Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana , 2010, Nature Reviews Genetics.

[40]  S. Wright,et al.  Genome-wide evidence for efficient positive and purifying selection in Capsella grandiflora, a plant species with a large effective population size. , 2010, Molecular biology and evolution.

[41]  D. Nelson,et al.  Ecological genetics of the Bromus tectorum (Poaceae)-Ustilago bullata (Ustilaginaceae) pathosystem: A role for frequency-dependent selection? , 2010, American journal of botany.

[42]  A. Eyre-Walker,et al.  Genome wide analyses reveal little evidence for adaptive evolution in many plant species. , 2010, Molecular biology and evolution.

[43]  S. Kalisz,et al.  A ROLE FOR NONADAPTIVE PROCESSES IN PLANT GENOME SIZE EVOLUTION? , 2010, Evolution; international journal of organic evolution.

[44]  Xinqiong Liu,et al.  The Molecular Evolution of the Rice Blast Resistance Gene Pi36 , 2010, International Journal of Plant Sciences.

[45]  Joseph K. Pickrell,et al.  The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation , 2010, Current Biology.

[46]  S. Wright,et al.  Mating-System Variation, Demographic History and Patterns of Nucleotide Diversity in the Tristylous Plant Eichhornia paniculata , 2010, Genetics.

[47]  T. Sakurai,et al.  Genome sequence of the palaeopolyploid soybean , 2010, Nature.

[48]  Richard M. Clark,et al.  The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana , 2010, Science.

[49]  M. Purugganan,et al.  Candidate Gene Association Mapping of Arabidopsis Flowering Time , 2009, Genetics.

[50]  Peter J. Bradbury,et al.  The Genetic Architecture of Maize Flowering Time , 2009, Science.

[51]  R. Mott,et al.  A Multiparent Advanced Generation Inter-Cross to Fine-Map Quantitative Traits in Arabidopsis thaliana , 2009, PLoS genetics.

[52]  Mark G. M. Aarts,et al.  What Has Natural Variation Taught Us about Plant Development, Physiology, and Adaptation? , 2009, The Plant Cell Online.

[53]  Jared L. Strasburg,et al.  Genomic patterns of adaptive divergence between chromosomally differentiated sunflower species. , 2009, Molecular biology and evolution.

[54]  T. Sang,et al.  Genetic Architecture for the Adaptive Origin of Annual Wild Rice, Oryza nivara , 2009, Evolution; international journal of organic evolution.

[55]  D. Weigel,et al.  Recent speciation of Capsella rubella from Capsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneck , 2009, Proceedings of the National Academy of Sciences.

[56]  E. Stahl,et al.  Recent speciation associated with the evolution of selfing in Capsella , 2009, Proceedings of the National Academy of Sciences.

[57]  U. Rosyara,et al.  Family-based mapping of quantitative trait loci in plant breeding populations with resistance to Fusarium head blight in wheat as an illustration , 2009, Theoretical and Applied Genetics.

[58]  B. Charlesworth.  Effective population size and patterns of molecular evolution and variation , 2009, Nature Reviews Genetics.

[59]  M. Purugganan,et al.  The evolution of plant genomes: scaling up from a population perspective. , 2008, Current opinion in genetics & development.

[60]  P. Andolfatto,et al.  The Impact of Natural Selection on the Genome: Emerging Patterns in Drosophila and Arabidopsis , 2008 .

[61]  Wei He,et al.  Control of rice grain-filling and yield by a gene with a potential signature of domestication , 2008, Nature Genetics.

[62]  B. Gaut,et al.  Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata , 2008, Proceedings of the National Academy of Sciences.

[63]  M. Schierup,et al.  Repeated Adaptive Introgression at a Gene under Multiallelic Balancing Selection , 2008, PLoS genetics.

[64]  M. Nordborg,et al.  Selection on amino acid substitutions in Arabidopsis. , 2008, Molecular biology and evolution.

[65]  S. Wright,et al.  Genomic Consequences of Outcrossing and Selfing in Plants , 2008, International Journal of Plant Sciences.

[66]  M. McMullen,et al.  Genetic Design and Statistical Power of Nested Association Mapping in Maize , 2008, Genetics.

[67]  S. Glémin.  Mating Systems and the Efficacy of Selection at the Molecular Level , 2007, Genetics.

[68]  X. Vekemans,et al.  Evolution under strong balancing selection: how many codons determine specificity at the female self-incompatibility gene SRK in Brassicaceae? , 2007, BMC Evolutionary Biology.

[69]  Richard M. Clark,et al.  Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana , 2007, Science.

[70]  R. Michelmore,et al.  Natural Variation in the Pto Disease Resistance Gene Within Species of Wild Tomato (Lycopersicon). II. Population Genetics of Pto , 2007, Genetics.

[71]  D. Charlesworth,et al.  Impact of mating systems on patterns of sequence polymorphism in flowering plants , 2006, Proceedings of the Royal Society B: Biological Sciences.

[72]  Adam Eyre-Walker,et al.  The genomic rate of adaptive evolution. , 2006, Trends in ecology & evolution.

[73]  T. Mitchell-Olds,et al.  Genetic mechanisms and evolutionary significance of natural variation in Arabidopsis , 2006, Nature.

[74]  E. Buckler,et al.  Genetic association mapping and genome organization of maize. , 2006, Current opinion in biotechnology.

[75]  D. Charlesworth.  Balancing Selection and Its Effects on Sequences in Nearby Genome Regions , 2006, PLoS genetics.

[76]  M. Purugganan,et al.  Selection Under Domestication: Evidence for a Sweep in the Rice Waxy Genomic Region , 2006, Genetics.

[77]  Jian Lu,et al.  The accumulation of deleterious mutations in rice genomes: a hypothesis on the cost of domestication. , 2006, Trends in genetics : TIG.

[78]  C. Ritland,et al.  THE GENETIC BASIS OF FLORAL TRAITS ASSOCIATED WITH MATING SYSTEM EVOLUTION IN LEPTOSIPHON (POLEMONIACEAE): AN ANALYSIS OF QUANTITATIVE TRAIT LOCI , 2006, Evolution; international journal of organic evolution.

[79]  Mattias Jakobsson,et al.  The Pattern of Polymorphism in Arabidopsis thaliana , 2005, PLoS biology.

[80]  D. Schoen,et al.  Molecular Evolution of the GapC Gene Family in Amsinckia spectabilis Populations That Differ in Outcrossing Rate , 2004, Journal of Molecular Evolution.

[81]  Michael J. Sanderson,et al.  EVOLUTION OF GENOME SIZE IN PINES (PINUS) AND ITS LIFE‐HISTORY CORRELATES: SUPERTREE ANALYSES , 2004, Evolution; international journal of organic evolution.

[82]  B. Charlesworth,et al.  Genome Size: Does Bigger Mean Worse? , 2004, Current Biology.

[83]  Joachim Messing,et al.  Pattern of diversity in the genomic region near the maize domestication gene tb1. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[84]  M. Lynch,et al.  The Origins of Genome Complexity , 2003, Science.

[85]  Alexander E Vinogradov,et al.  Selfish DNA is maladaptive: evidence from the plant Red List. , 2003, Trends in genetics : TIG.

[86]  J. Willis,et al.  PATTERNS OF NUCLEOTIDE DIVERSITY IN TWO SPECIES OF MIMULUS ARE AFFECTED BY MATING SYSTEM AND ASYMMETRIC INTROGRESSION , 2003, Evolution; international journal of organic evolution.

[87]  M. Kreitman,et al.  Fitness costs of R-gene-mediated resistance in Arabidopsis thaliana , 2003, Nature.

[88]  J. Willis,et al.  MINOR QUANTITATIVE TRAIT LOCI UNDERLIE FLORAL TRAITS ASSOCIATED WITH MATING SYSTEM DIVERGENCE IN MIMULUS , 2002, Evolution; international journal of organic evolution.

[89]  D. Charlesworth,et al.  Rates and patterns of molecular evolution in inbred and outbred Arabidopsis. , 2002, Molecular biology and evolution.

[90]  L. Rieseberg,et al.  Genetic analysis of sunflower domestication. , 2002, Genetics.

[91]  Carlos D. Bustamante,et al.  The cost of inbreeding in Arabidopsis , 2002, Nature.

[92]  Adam Eyre-Walker,et al.  Adaptive protein evolution in Drosophila , 2002, Nature.

[93]  Justin C. Fay,et al.  Testing the neutral theory of molecular evolution with genomic data from Drosophila , 2002, Nature.

[94]  W. Stephan,et al.  Species and recombination effects on DNA variability in the tomato genus. , 2001, Genetics.

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

[96]  P. Awadalla,et al.  Identification and characterization of a polymorphic receptor kinase gene linked to the self-incompatibility locus of Arabidopsis lyrata. , 2001, Genetics.

[97]  C. Langley,et al.  Contrasting patterns of nucleotide polymorphism at the alcohol dehydrogenase locus in the outcrossing Arabidopsis lyrata and the selfing Arabidopsis thaliana. , 2000, Molecular biology and evolution.

[98]  M. Nordborg.  Linkage disequilibrium, gene trees and selfing: an ancestral recombination graph with partial self-fertilization. , 2000, Genetics.

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

[100]  L. Xiong,et al.  Identification of genetic factors controlling domestication-related traits of rice using an F2 population of a cross between Oryza sativa and O. rufipogon , 1999, Theoretical and Applied Genetics.

[101]  D. Charlesworth,et al.  Genetic diversity in Leavenworthia populations with different inbreeding levels , 1998, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[102]  M. Lynch,et al.  MUTATION AND EXTINCTION: THE ROLE OF VARIABLE MUTATIONAL EFFECTS, SYNERGISTIC EPISTASIS, BENEFICIAL MUTATIONS, AND DEGREE OF OUTCROSSING , 1997, Evolution; international journal of organic evolution.

[103]  W. Beavis.  QTL Analyses: Power, Precision, and Accuracy , 1997, Molecular Dissection of Complex Traits.

[104]  K. Ritland,et al.  Quantitative trait loci differentiating the outbreeding Mimulus guttatus from the inbreeding M. platycalyx. , 1997, Genetics.

[105]  S. Muse,et al.  Comparing patterns of nucleotide substitution rates among chloroplast loci using the relative ratio test. , 1997, Genetics.

[106]  J. Hamrick,et al.  Effects of life history traits on genetic diversity in plant species , 1996 .

[107]  M T Clegg,et al.  Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[108]  D. Charlesworth,et al.  Inbreeding depression in two highly inbreeding populations of Leavenworthia , 1994, Proceedings of the Royal Society of London. Series B: Biological Sciences.

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

[110]  J. Doebley,et al.  Genetic and morphological analysis of a maize-teosinte F2 population: implications for the origin of maize. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[111]  E. Pollak,et al.  On the theory of partially inbreeding finite populations. I. Partial selfing. , 1988, Genetics.

[112]  A. Kondrashov.  Deleterious mutations as an evolutionary factor. 1. The advantage of recombination. , 1984, Genetical research.

[113]  John Maynard Smith,et al.  The hitch-hiking effect of a favourable gene. , 1974, Genetical research.

[114]  S. Wright,et al.  The Distribution of Self-Sterility Alleles in Populations. , 1939, Genetics.

[115]  S. Glémin,et al.  Male-specific DNA markers provide genetic evidence of an XY chromosome system, a recombination arrest and allow the tracing of paternal lineages in date palm. , 2013, The New phytologist.

[116]  J. Dvorak,et al.  Recombination: an underappreciated factor in the evolution of plant genomes , 2007, Nature Reviews Genetics.

[117]  S. Muse.  Examining rates and patterns of nucleotide substitution in plants , 2004, Plant Molecular Biology.

[118]  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.

[119]  S. C. Liu,et al.  Genome-wide high-resolution mapping by recurrent intermating using Arabidopsis thaliana as a model. , 1996, Genetics.

[120]  A. Paterson,et al.  Erratum: Genome-wide high-resolution mapping by recurrent intermating using Arabidopsis thaliana as a model (Genetics (January, 1996) 142 (247- 258)) , 1996 .