Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa

[1]  A. Venkat,et al.  Multinucleotide mutations cause false inferences of lineage-specific positive selection , 2018, Nature Ecology & Evolution.

[2]  B. Hunter,et al.  Genetic basis and evolution of rapid cycling in railway populations of tetraploid Arabidopsis arenosa , 2018, PLoS genetics.

[3]  A. Venkat,et al.  Multinucleotide mutations cause false inferences of lineage-specific positive selection , 2018, Nature Ecology & Evolution.

[4]  N. Galtier,et al.  Overestimation of the adaptive substitution rate in fluctuating populations , 2018, Biology Letters.

[5]  P. Schönswetter,et al.  Mixed-Ploidy Species: Progress and Opportunities in Polyploid Research. , 2017, Trends in plant science.

[6]  L. Yant,et al.  Hybrids and horizontal transfer: introgression allows adaptive allele discovery. , 2017, Journal of experimental botany.

[7]  M. Arnold,et al.  Adaptive Genetic Exchange: A Tangled History of Admixture and Evolutionary Innovation. , 2017, Trends in ecology & evolution.

[8]  N. Johnson.  Faculty Opinions recommendation of Adaptive genetic exchange: A tangled history of admixture and evolutionary innovation. , 2017 .

[9]  K. A. Segraves.  The effects of genome duplications in a community context. , 2017, The New phytologist.

[10]  Y. Peer,et al.  The evolutionary significance of polyploidy , 2017, Nature Reviews Genetics.

[11]  L. Yant,et al.  Genomic studies of adaptive evolution in outcrossing Arabidopsis species. , 2017, Current opinion in plant biology.

[12]  Katrine N. Bjerkan,et al.  Endosperm-based hybridization barriers explain the pattern of gene flow between Arabidopsis lyrata and Arabidopsis arenosa in Central Europe , 2017, Proceedings of the National Academy of Sciences.

[13]  Simon H. Martin,et al.  Exploring Evolutionary Relationships Across the Genome Using Topology Weighting , 2016, Genetics.

[14]  Marek Svitok,et al.  Ecological segregation does not drive the intricate parapatric distribution of diploid and tetraploid cytotypes of the Arabidopsis arenosa group (Brassicaceae) , 2016 .

[15]  A. Nagano,et al.  Northern glacial refugia and altitudinal niche divergence shape genome‐wide differentiation in the emerging plant model Arabidopsis arenosa , 2016, Molecular ecology.

[16]  I. Mayrose,et al.  Whole-genome duplication as a key factor in crop domestication , 2016, Nature Plants.

[17]  J. Sese,et al.  Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism , 2016, Nature Genetics.

[18]  Karsten M. Borgwardt,et al.  1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana , 2016, Cell.

[19]  Caroline M. Weisman,et al.  Borrowed alleles and convergence in serpentine adaptation , 2016, Proceedings of the National Academy of Sciences.

[20]  R. Nichols,et al.  Unidirectional diploid–tetraploid introgression among British birch trees with shifting ranges shown by restriction site‐associated markers , 2016, Molecular ecology.

[21]  Camilo Salazar,et al.  Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene , 2016, Genetics.

[22]  B. Arnold,et al.  Habitat-Associated Life History and Stress-Tolerance Variation in Arabidopsis arenosa1[OPEN] , 2016, Plant Physiology.

[23]  H. Ellegren,et al.  PSMC analysis of effective population sizes in molecular ecology and its application to black‐and‐white Ficedula flycatchers , 2016, Molecular ecology.

[24]  L. Yant,et al.  Genome management and mismanagement—cell-level opportunities and challenges of whole-genome duplication , 2015, Genes & development.

[25]  Jerome Kelleher,et al.  Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes , 2015, bioRxiv.

[26]  D. Bates,et al.  Linear Mixed-Effects Models using 'Eigen' and S4 , 2015 .

[27]  F. Allendorf,et al.  Spatial sorting promotes the spread of maladaptive hybridization. , 2015, Trends in ecology & evolution.

[28]  B. Arnold,et al.  Single Geographic Origin of a Widespread Autotetraploid Arabidopsis arenosa Lineage Followed by Interploidy Admixture. , 2015, Molecular biology and evolution.

[29]  Phillip A. Richmond,et al.  Polyploidy can drive rapid adaptation in yeast , 2015, Nature.

[30]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[31]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[32]  Matthew W. Hahn,et al.  Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow , 2014, Molecular ecology.

[33]  K. Bomblies,et al.  Polyploidy in the Arabidopsis genus , 2014, Chromosome Research.

[34]  M. Stephens,et al.  fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets , 2014, Genetics.

[35]  Michael I. Love,et al.  Differential analysis of count data – the DESeq2 package , 2013 .

[36]  Matthew Stephens,et al.  Variational Inference of Population Structure in Large SNP Datasets , 2013, bioRxiv.

[37]  B. Arnold,et al.  Meiotic Adaptation to Genome Duplication in Arabidopsis arenosa , 2013, Current Biology.

[38]  L. Excoffier,et al.  Robust Demographic Inference from Genomic and SNP Data , 2013, PLoS genetics.

[39]  N. Cogan,et al.  StAMPP: an R package for calculation of genetic differentiation and structure of mixed‐ploidy level populations , 2013, Molecular ecology resources.

[40]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[41]  K. Katoh,et al.  Improvements in Performance and Usability , 2013 .

[42]  J. Suda,et al.  The Incidence of Polyploidy in Natural Plant Populations: Major Patterns and Evolutionary Processes , 2013 .

[43]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[44]  B. Arnold,et al.  Genetic Adaptation Associated with Genome-Doubling in Autotetraploid Arabidopsis arenosa , 2012, PLoS genetics.

[45]  Roman Yukilevich.  ASYMMETRICAL PATTERNS OF SPECIATION UNIQUELY SUPPORT REINFORCEMENT IN DROSOPHILA , 2012, Evolution; international journal of organic evolution.

[46]  Jan Suda,et al.  The more the better? The role of polyploidy in facilitating plant invasions. , 2012, Annals of botany.

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

[48]  R. Schmickl,et al.  Arabidopsis hybrid speciation processes , 2011, Proceedings of the National Academy of Sciences.

[49]  R. Durbin,et al.  Inference of human population history from individual whole-genome sequences. , 2011, Nature.

[50]  R. Durbin,et al.  Inference of Human Population History From Whole Genome Sequence of A Single Individual , 2011, Nature.

[51]  Martin Goodson,et al.  Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. , 2011, Genome research.

[52]  Marcel Martin.  Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[53]  M. DePristo,et al.  A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.

[54]  Richard M. Clark,et al.  The Arabidopsis lyrata genome sequence and the basis of rapid genome size change , 2011, Nature Genetics.

[55]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

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

[57]  Christian Parisod,et al.  Evolutionary consequences of autopolyploidy. , 2010, The New phytologist.

[58]  Emmanuel Paradis,et al.  pegas: an R package for population genetics with an integrated-modular approach , 2010, Bioinform..

[59]  P. Keightley,et al.  Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change. , 2009, Molecular biology and evolution.

[60]  S. Otto,et al.  Ploidy and the Causes of Genomic Evolution Background: Variation in Ploidy Level , 2009 .

[61]  Itay Mayrose,et al.  The frequency of polyploid speciation in vascular plants , 2009, Proceedings of the National Academy of Sciences.

[62]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[63]  M. Lascoux,et al.  Polyploid speciation did not confer instant reproductive isolation in Capsella (Brassicaceae). , 2008, Molecular biology and evolution.

[64]  Thibaut Jombart,et al.  adegenet: a R package for the multivariate analysis of genetic markers , 2008, Bioinform..

[65]  J. Haldane.  Theoretical genetics of autopolyploids , 1930, Journal of Genetics.

[66]  P. Keightley,et al.  Joint Inference of the Distribution of Fitness Effects of Deleterious Mutations and Population Demography Based on Nucleotide Polymorphism Frequencies , 2007, Genetics.

[67]  Anne-Béatrice Dufour,et al.  The ade4 Package: Implementing the Duality Diagram for Ecologists , 2007 .

[68]  L. Rieseberg,et al.  Plant Speciation , 2007, Science.

[69]  P. Keightley,et al.  A Comparison of Models to Infer the Distribution of Fitness Effects of New Mutations , 2013, Genetics.

[70]  Pär K Ingvarsson,et al.  Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula. , 2006, Molecular biology and evolution.

[71]  J. Mallet.  Hybrid speciation , 2007, Nature.

[72]  Kai Zeng,et al.  Statistical Tests for Detecting Positive Selection by Utilizing High-Frequency Variants , 2006, Genetics.

[73]  P. Smouse,et al.  genalex 6: genetic analysis in Excel. Population genetic software for teaching and research , 2006 .

[74]  T. Borza,et al.  Evolutionary Rates and Expression Level in Chlamydomonas , 2006, Genetics.

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

[76]  D. Crawford.  The Role of Chromosomal Change in Plant Evolution.Oxford Series in Ecology and Evolution.ByDonald A Levin.Oxford and New York: Oxford University Press. $75.00 (hardcover); $35.00 (paper). ix + 230 p; ill.; index. ISBN: 0–19–513859–7 (hc); 0–19–513860–0 (pb). 2002. , 2004 .

[77]  Blake C Meyers,et al.  Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata. , 2004, Molecular biology and evolution.

[78]  Inger Greve Alsos,et al.  Polyploidy in arctic plants , 2004 .

[79]  B. Husband,et al.  Reproductive isolation between autotetraploids and their diploid progenitors in fireweed, Chamerion angustifolium (Onagraceae). , 2003, The New phytologist.

[80]  D. Pellman,et al.  From polyploidy to aneuploidy, genome instability and cancer , 2004, Nature Reviews Molecular Cell Biology.

[81]  R. Hill.  Selection in autotetraploids , 2004, Theoretical and Applied Genetics.

[82]  Eduardo P C Rocha,et al.  An analysis of determinants of amino acids substitution rates in bacterial proteins. , 2004, Molecular biology and evolution.

[83]  O. Hardy,et al.  spagedi: a versatile computer program to analyse spatial genetic structure at the individual or population levels , 2002 .

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

[85]  D. Levin.  The Role of Chromosomal Change in Plant Evolution , 2002 .

[86]  L. Boiteux,et al.  Selection-mutation balance in polysomic tetraploids: impact of double reduction and gametophytic selection on the frequency and subchromosomal localization of deleterious mutations. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[87]  P. Donnelly,et al.  Inference of population structure using multilocus genotype data. , 2000, Genetics.

[88]  L. Duret,et al.  Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. , 2000, Molecular biology and evolution.

[89]  S. Otto,et al.  Polyploid incidence and evolution. , 2000, Annual review of genetics.

[90]  J. Willis,et al.  Inbreeding load, average dominance and the mutation rate for mildly deleterious alleles in Mimulus guttatus. , 1999, Genetics.

[91]  D. Soltis,et al.  Polyploidy: recurrent formation and genome evolution. , 1999, Trends in ecology & evolution.

[92]  J. Ronfort.  The mutation load under tetrasomic inheritance and its consequences for the evolution of the selfing rate in autotetraploid species , 1999 .

[93]  L. Kruglyak.  Prospects for whole-genome linkage disequilibrium mapping of common disease genes , 1999, Nature Genetics.

[94]  F Rousset,et al.  Analysis of population structure in autotetraploid species. , 1998, Genetics.

[95]  Daniel H. Huson,et al.  SplitsTree: analyzing and visualizing evolutionary data , 1998, Bioinform..

[96]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[97]  B. Weir,et al.  ESTIMATING F‐STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE , 1984, Evolution; international journal of organic evolution.

[98]  C. Favarger.  Cytogeography and Biosystematics , 1984 .

[99]  E. Pahlich,et al.  A rapid DNA isolation procedure for small quantities of fresh leaf tissue , 1980 .

[100]  J. Harborne,et al.  Phytochemical Ecology, Phytochemical Society Symposia Series no. 8 , 1973 .

[101]  Masatoshi Nei,et al.  Genetic Distance between Populations , 1972, The American Naturalist.

[102]  G. Ledyard Stebbins,et al.  Chromosomal evolution in higher plants , 1971 .

[103]  N. Hylander.  Cardaminopsis suecica (fr.) Hiit., a Northern Amphidiploid species , 1957 .

[104]  R. Fisher.  THE THEORETICAL CONSEQUENCES OF POLYPLOID INHERITANCE FOR THE MID STYLE FORM OF LYTHRUM SALICARIA , 1941 .

[105]  S Wright,et al.  The Distribution of Gene Frequencies in Populations of Polyploids. , 1938, Proceedings of the National Academy of Sciences of the United States of America.

[106]  W. E. Ritter.  AS TO THE CAUSES OF EVOLUTION. , 1923, Science.