Recent progress and challenges in population genetics of polyploid organisms: an overview of current state-of-the-art molecular and statistical tools
出版年份 2013 全文链接
标题
Recent progress and challenges in population genetics of polyploid organisms: an overview of current state-of-the-art molecular and statistical tools
作者
关键词
-
出版物
MOLECULAR ECOLOGY
Volume 23, Issue 1, Pages 40-69
出版商
Wiley
发表日期
2013-11-05
DOI
10.1111/mec.12581
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- MHC genotyping of non-model organisms using next-generation sequencing: a new methodology to deal with artefacts and allelic dropout
- (2013) Simone Sommer et al. BMC GENOMICS
- Meiosis and Its Deviations in Polyploid Animals
- (2013) P. Stenberg et al. CYTOGENETIC AND GENOME RESEARCH
- Why Comparing Polyploidy Research in Animals and Plants?
- (2013) M. Stöck et al. CYTOGENETIC AND GENOME RESEARCH
- Polyploidy and microsatellite variation in the relict treePrunus lusitanicaL.: how effective are refugia in preserving genotypic diversity of clonal taxa?
- (2013) C. García-Verdugo et al. MOLECULAR ECOLOGY
- Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing
- (2013) R. Ogden et al. MOLECULAR ECOLOGY
- RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling
- (2013) B. Arnold et al. MOLECULAR ECOLOGY
- Stacks: an analysis tool set for population genomics
- (2013) Julian Catchen et al. MOLECULAR ECOLOGY
- StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations
- (2013) Luke W. Pembleton et al. Molecular Ecology Resources
- Using high-throughput sequencing to investigate the evolution of self-incompatibility genes in the Brassicaceae: strategies and challenges
- (2013) Marte H. Jørgensen et al. Plant Ecology & Diversity
- Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations
- (2013) Florian Jupe et al. PLANT JOURNAL
- Next-generation sequencing and genome evolution in allopolyploids
- (2012) Richard J. A. Buggs et al. AMERICAN JOURNAL OF BOTANY
- Applications of next-generation sequencing in plant biology
- (2012) Ashley N. Egan et al. AMERICAN JOURNAL OF BOTANY
- Anthropogenic disturbance as a driver of microspatial and microhabitat segregation of cytotypes of Centaurea stoebe and cytotype interactions in secondary contact zones
- (2012) Patrik Mráz et al. ANNALS OF BOTANY
- Phylogeography and seed dispersal in islands: the case of Rumex bucephalophorus subsp. canariensis (Polygonaceae)
- (2012) María Talavera et al. ANNALS OF BOTANY
- Meiotic maps of sockeye salmon derived from massively parallel DNA sequencing
- (2012) Meredith V Everett et al. BMC GENOMICS
- Population genetic structure of parthenogenetic flatworm populations with occasional sex
- (2012) BEATRIZ SÁNCHEZ NAVARRO et al. FRESHWATER BIOLOGY
- Extending Coalescent Theory to Autotetraploids
- (2012) B. Arnold et al. GENETICS
- Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae)
- (2012) J Ferreira de Carvalho et al. HEREDITY
- Absence of gene flow between diploids and hexaploids of Aster amellus at multiple spatial scales
- (2012) Z Münzbergová et al. HEREDITY
- Unravelling gene expression of complex crop genomes
- (2012) R J A Buggs HEREDITY
- Reconstruction of phylogenetic relationships in a highly reticulate group with deep coalescence and recent speciation (Hieracium, Asteraceae)
- (2012) K Krak et al. HEREDITY
- Homoeolog expression bias and expression level dominance in allopolyploid cotton
- (2012) M-J Yoo et al. HEREDITY
- The effects of inheritance in tetraploids on genetic diversity and population divergence
- (2012) P G Meirmans et al. HEREDITY
- Molecular Tools for Exploring Polyploid Genomes in Plants
- (2012) Riccardo Aversano et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- Coalescent-Based Analysis Distinguishes between Allo- and Autopolyploid Origin in Shepherd's Purse (Capsella bursa-pastoris)
- (2012) K. R. St. Onge et al. MOLECULAR BIOLOGY AND EVOLUTION
- Next-Generation Sequencing Reveals the Impact of Repetitive DNA Across Phylogenetically Closely Related Genomes of Orobanchaceae
- (2012) Mathieu Piednoël et al. MOLECULAR BIOLOGY AND EVOLUTION
- Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex
- (2012) Eric M. O'Neill et al. MOLECULAR ECOLOGY
- The effect of RAD allele dropout on the estimation of genetic variation within and between populations
- (2012) Mathieu Gautier et al. MOLECULAR ECOLOGY
- Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers
- (2012) Nian Wang et al. MOLECULAR ECOLOGY
- Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensivein silicoassessment of RNA-seq experiments
- (2012) Nagarjun Vijay et al. MOLECULAR ECOLOGY
- SNP-array reveals genome-wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar)
- (2012) Vincent Bourret et al. MOLECULAR ECOLOGY
- Analysis of the bread wheat genome using whole-genome shotgun sequencing
- (2012) Rachel Brenchley et al. NATURE
- Targeted re-sequencing of the allohexaploid wheat exome
- (2012) Mark O. Winfield et al. PLANT BIOTECHNOLOGY JOURNAL
- A tailed PCR procedure for cost-effective, two-order multiplex sequencing of candidate genes in polyploid plants
- (2012) Mahmood Gholami et al. PLANT BIOTECHNOLOGY JOURNAL
- Enrichment of genomic DNA for polymorphism detection in a non-model highly polyploid crop plant
- (2012) Peter C. Bundock et al. PLANT BIOTECHNOLOGY JOURNAL
- Single nucleotide polymorphism discovery from wheat next-generation sequence data
- (2012) Kaitao Lai et al. PLANT BIOTECHNOLOGY JOURNAL
- Efficient Exact Maximum a Posteriori Computation for Bayesian SNP Genotyping in Polyploids
- (2012) Oliver Serang et al. PLoS One
- Exploring the Switchgrass Transcriptome Using Second-Generation Sequencing Technology
- (2012) Yixing Wang et al. PLoS One
- Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species
- (2012) Brant K. Peterson et al. PLoS One
- Bringing Together Evolution on Serpentine and Polyploidy: Spatiotemporal History of the Diploid-Tetraploid Complex of Knautia arvensis (Dipsacaceae)
- (2012) Filip Kolář et al. PLoS One
- The mode of inheritance in tetraploid cut roses
- (2012) C. F. S. Koning-Boucoiran et al. THEORETICAL AND APPLIED GENETICS
- Accessing complex crop genomes with next-generation sequencing
- (2012) David Edwards et al. THEORETICAL AND APPLIED GENETICS
- Targeted Capture of Homoeologous Coding and Noncoding Sequence in Polyploid Cotton
- (2012) Armel Salmon et al. G3-Genes Genomes Genetics
- Recent Loss of Self-Incompatibility by Degradation of the Male Component in Allotetraploid Arabidopsis kamchatica
- (2012) Takashi Tsuchimatsu et al. PLoS Genetics
- Genetic Adaptation Associated with Genome-Doubling in Autotetraploid Arabidopsis arenosa
- (2012) Jesse D. Hollister et al. PLoS Genetics
- adegenet 1.3-1: new tools for the analysis of genome-wide SNP data
- (2011) Thibaut Jombart et al. BIOINFORMATICS
- Genetic diversity and multiple origins of polyploid Atriplex nummularia Lindl. (Chenopodiaceae)
- (2011) JANE F. SAMPSON et al. BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
- Genotype calling in tetraploid species from bi-allelic marker data using mixture models
- (2011) Roeland E Voorrips et al. BMC BIOINFORMATICS
- Removing Noise From Pyrosequenced Amplicons
- (2011) Christopher Quince et al. BMC BIOINFORMATICS
- A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses
- (2011) Philippa C Griffin et al. BMC BIOLOGY
- Interspecific and interploidal gene flow in Central European Arabidopsis (Brassicaceae)
- (2011) Marte H Jørgensen et al. BMC EVOLUTIONARY BIOLOGY
- Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence
- (2011) Frank M You et al. BMC GENOMICS
- WIDE VARIATION IN PLOIDY LEVEL AND GENOME SIZE IN A NEW ZEALAND FRESHWATER SNAIL WITH COEXISTING SEXUAL AND ASEXUAL LINEAGES
- (2011) Maurine Neiman et al. EVOLUTION
- Next-generation hybridization and introgression
- (2011) A D Twyford et al. HEREDITY
- Genome duplication in amphibians and fish: an extended synthesis
- (2011) B. K. Mable et al. JOURNAL OF ZOOLOGY
- Reticulate evolution of the Daphnia pulex complex as revealed by nuclear markers
- (2011) ROLAND VERGILINO et al. MOLECULAR ECOLOGY
- The Rift Valley is a major barrier to dispersal of African clawed frogs (Xenopus) in Ethiopia
- (2011) BEN J. EVANS et al. MOLECULAR ECOLOGY
- and D do not replace FST
- (2011) MICHAEL C. WHITLOCK MOLECULAR ECOLOGY
- Short reads and nonmodel species: exploring the complexities of next-generation sequence assembly and SNP discovery in the absence of a reference genome
- (2011) M. V. EVERETT et al. Molecular Ecology Resources
- Current trends in microsatellite genotyping
- (2011) E. GUICHOUX et al. Molecular Ecology Resources
- Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms
- (2011) J. E. SEEB et al. Molecular Ecology Resources
- polysat: an R package for polyploid microsatellite analysis
- (2011) LINDSAY V. CLARK et al. Molecular Ecology Resources
- Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout
- (2011) PAUL A. HOHENLOHE et al. Molecular Ecology Resources
- A framework for variation discovery and genotyping using next-generation DNA sequencing data
- (2011) Mark A DePristo et al. NATURE GENETICS
- Unlocking the Barley Genome by Chromosomal and Comparative Genomics
- (2011) Klaus F.X. Mayer et al. PLANT CELL
- Evidence for non-disomic inheritance in a Citrus interspecific tetraploid somatic hybrid between C. reticulata and C. limon using SSR markers and cytogenetic analysis
- (2011) Mourad Kamiri et al. PLANT CELL REPORTS
- Genomic and Resistance Gene Homolog Diversity of the Dominant Tallgrass Prairie Species across the U.S. Great Plains Precipitation Gradient
- (2011) Matthew N. Rouse et al. PLoS One
- Stacks : Building and Genotyping Loci De Novo From Short-Read Sequences
- (2011) Julian M. Catchen et al. G3-Genes Genomes Genetics
- Other tetraploid species and conspecific diploids as sources of genetic variation for an autotetraploid
- (2010) Marc Stift et al. AMERICAN JOURNAL OF BOTANY
- Allopolyploid speciation and ongoing backcrossing between diploid progenitor and tetraploid progeny lineages in the Achillea millefolium species complex: analyses of single-copy nuclear genes and genomic AFLP
- (2010) Jin-Xiu Ma et al. BMC EVOLUTIONARY BIOLOGY
- Discriminant analysis of principal components: a new method for the analysis of genetically structured populations
- (2010) Thibaut Jombart et al. BMC GENETICS
- The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
- (2010) A. McKenna et al. GENOME RESEARCH
- Two reproductively isolated cytotypes and a swarm of highly inbred, disconnected populations: a glimpse into Salicornia’s evolutionary history and challenging taxonomy
- (2010) A. VANDERPOORTEN et al. JOURNAL OF EVOLUTIONARY BIOLOGY
- Homoplasy and Distribution of AFLP Fragments: An Analysis In Silico of the Genome of Different Species
- (2010) A. Caballero et al. MOLECULAR BIOLOGY AND EVOLUTION
- In defence of model-based inference in phylogeography
- (2010) MARK A. BEAUMONT et al. MOLECULAR ECOLOGY
- Multiple autopolyploidizations and range expansion ofAllium przewalskianumRegel. (Alliaceae) in the Qinghai-Tibetan Plateau
- (2010) LI-LI WU et al. MOLECULAR ECOLOGY
- Characterization of duplicate gene evolution in the recent natural allopolyploidTragopogon miscellusby next-generation sequencing and Sequenom iPLEX MassARRAY genotyping
- (2010) RICHARD J. A. BUGGS et al. MOLECULAR ECOLOGY
- Transcriptome sequencing and high-resolution melt analysis advance single nucleotide polymorphism discovery in duplicated salmonids
- (2010) J. E. SEEB et al. Molecular Ecology Resources
- Assessing population structure: FST and related measures
- (2010) PATRICK G. MEIRMANS et al. Molecular Ecology Resources
- Extensive hybridization and tetrapolyploidy in spined loach fish
- (2010) Kenji Saitoh et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- Focus on polyploidy
- (2010) Malika L. Ainouche et al. NEW PHYTOLOGIST
- Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina × townsendii and Spartina anglica (Poaceae)
- (2010) Houda Chelaifa et al. NEW PHYTOLOGIST
- Differential sensitivity of the Arabidopsis thaliana transcriptome and enhancers to the effects of genome doubling
- (2010) Daniela Pignatta et al. NEW PHYTOLOGIST
- Evolutionary consequences of autopolyploidy
- (2010) Christian Parisod et al. NEW PHYTOLOGIST
- Approximate Bayesian Computation (ABC) in practice
- (2010) Katalin Csilléry et al. TRENDS IN ECOLOGY & EVOLUTION
- Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags
- (2010) Paul A. Hohenlohe et al. PLoS Genetics
- Genome size evolution and polyploidy in the Daphnia pulex complex (Cladocera: Daphniidae)
- (2009) ROLAND VERGILINO et al. BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
- Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery
- (2009) Matthew C Hale et al. BMC GENOMICS
- Genomic and expression plasticity of polyploidy
- (2009) Scott Jackson et al. CURRENT OPINION IN PLANT BIOLOGY
- Estimation of Allele Frequencies From High-Coverage Genome-Sequencing Projects
- (2009) M. Lynch GENETICS
- Genetic markers in the playground of multivariate analysis
- (2009) T Jombart et al. HEREDITY
- Gene loss and silencing in Tragopogon miscellus (Asteraceae): comparison of natural and synthetic allotetraploids
- (2009) R J A Buggs et al. HEREDITY
- Major disruption of gene expression in hybrids between young sympatric anadromous and resident populations of brook charr (Salvelinus fontinalisMitchill)
- (2009) JESUS MAVAREZ et al. JOURNAL OF EVOLUTIONARY BIOLOGY
- Genetic structure and evolution of Alpine polyploid complexes:Ranunculus kuepferi(Ranunculaceae) as a case study
- (2009) J. BURNIER et al. MOLECULAR ECOLOGY
- Extreme changes to gene expression associated with homoploid hybrid speciation
- (2009) MATTHEW J. HEGARTY et al. MOLECULAR ECOLOGY
- The allopolyploidArabidopsis kamchaticaoriginated from multiple individuals ofArabidopsis lyrataandArabidopsis halleri
- (2009) RIE SHIMIZU-INATSUGI et al. MOLECULAR ECOLOGY
- Population genetic structure of diploid sexual and polyploid apomictic hawthorns (Crataegus; Rosaceae) in the Pacific Northwest
- (2009) EUGENIA Y. Y. LO et al. MOLECULAR ECOLOGY
- Genetic similarity of polyploids: a new version of the computer program POPDIST (version 1.2.0) considers intraspecific genetic differentiation
- (2009) JÜRGEN TOMIUK et al. Molecular Ecology Resources
- atetra, a new software program to analyse tetraploid microsatellite data: comparison with tetra and tetrasat
- (2009) K. VAN PUYVELDE et al. Molecular Ecology Resources
- Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation
- (2009) Lex E. Flagel et al. NEW PHYTOLOGIST
- Fall and rise of satellite repeats in allopolyploids of Nicotiana over c. 5 million years
- (2009) Blazena Koukalova et al. NEW PHYTOLOGIST
- Rapid structural and epigenetic reorganization near transposable elements in hybrid and allopolyploid genomes in Spartina
- (2009) Christian Parisod et al. NEW PHYTOLOGIST
- Homoeologous nonreciprocal recombination in polyploid cotton
- (2009) Armel Salmon et al. NEW PHYTOLOGIST
- Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing
- (2009) Peter C. Bundock et al. PLANT BIOTECHNOLOGY JOURNAL
- Phylogeographic implications for the North American boreal-arcticArabidopsis lyratacomplex
- (2009) Roswitha Schmickl et al. Plant Ecology & Diversity
- Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event
- (2009) J. A. Fawcett et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- adegenet: a R package for the multivariate analysis of genetic markers
- (2008) Thibaut Jombart BIOINFORMATICS
- Hybridization, polyploidy and invasion: lessons from Spartina (Poaceae)
- (2008) M. L. Ainouche et al. BIOLOGICAL INVASIONS
- Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution
- (2008) Lex Flagel et al. BMC BIOLOGY
- Segregation Models for Disomic, Tetrasomic and Intermediate Inheritance in Tetraploids: A General Procedure Applied to Rorippa (Yellow Cress) Microsatellite Data
- (2008) M. Stift et al. GENETICS
- Quality scores and SNP detection in sequencing-by-synthesis systems
- (2008) W. Brockman et al. GENOME RESEARCH
- Towards natural polyploid model organisms
- (2008) RICHARD J. A. BUGGS MOLECULAR ECOLOGY
- GSTand its relatives do not measure differentiation
- (2008) LOU JOST MOLECULAR ECOLOGY
- High genetic diversity and connectivity in the polyploid invasive seaweedAsparagopsis taxiformis(Bonnemaisoniales) in the Mediterranean, explored with microsatellite alleles and multilocus genotypes
- (2008) NIKOS ANDREAKIS et al. MOLECULAR ECOLOGY
- Changes to gene expression associated with hybrid speciation in plants: further insights from transcriptomic studies in Senecio
- (2008) M. J Hegarty et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- The origin and evolution of a unisexual hybrid: Poecilia formosa
- (2008) K.P Lampert et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Two distinct AFLP types in three populations of marram grass ( Ammophila arenaria) in Wales
- (2008) W. H. Gera Hol et al. Plant Genetic Resources-Characterization and Utilization
- Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers
- (2008) Nathan A. Baird et al. PLoS One
- Genomic Plasticity and the Diversity of Polyploid Plants
- (2008) A. R. Leitch et al. SCIENCE
- High resolution melting analysis of almond SNPs derived from ESTs
- (2008) Shu-Biao Wu et al. THEORETICAL AND APPLIED GENETICS
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