Population genomics unravels the Holocene history of bread wheat and its relatives

[1]  Mingming Xin,et al.  Dispersed emergence and protracted domestication of polyploid wheat uncovered by mosaic ancestral haploblock inference , 2022, Nature Communications.

[2]  M. Feldman,et al.  Evolution and origin of bread wheat , 2022, The Plant cell.

[3]  Robert P. Davey,et al.  Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement , 2021, Nature biotechnology.

[4]  B. Gaut,et al.  The evolutionary genomics of species’ responses to climate change , 2021, Nature Ecology & Evolution.

[5]  Changsong Zou,et al.  Introgressing the Aegilops tauschii genome into wheat as a basis for cereal improvement , 2021, Nature Plants.

[6]  Xiangdong Fu,et al.  Wheat speciation and adaptation: perspectives from reticulate evolution , 2021, aBIOTECH.

[7]  L. Excoffier,et al.  Demographic inference , 2021, Current Biology.

[8]  Jianbing Yan,et al.  Natural Variation in Crops: Realized Understanding, Continuing Promise. , 2021, Annual review of plant biology.

[9]  D. Soltis,et al.  Polyploidy: an evolutionary and ecological force in stressful times , 2020, The Plant cell.

[10]  Haofeng Chen,et al.  Triticum population sequencing provides insights into wheat adaptation , 2020, Nature Genetics.

[11]  Mingming Xin,et al.  Origin and adaptation to high altitude of Tibetan semi-wild wheat , 2020, Nature Communications.

[12]  Emily B Josephs,et al.  Molecular Parallelism Underlies Convergent Highland Adaptation of Maize Landraces , 2020, bioRxiv.

[13]  P. Bayer,et al.  Climate change and the need for agricultural adaptation. , 2020, Current opinion in plant biology.

[14]  Xiaoqiang Li,et al.  5,200-year-old cereal grains from the eastern Altai Mountains redate the trans-Eurasian crop exchange , 2020, Nature Plants.

[15]  Sandra L. Kennedy,et al.  Multiregional origins of the domesticated tetraploid wheats , 2020, PloS one.

[16]  K. Jordan,et al.  Genomic Patterns of Introgression in Interspecific Populations Created by Crossing Wheat with Its Wild Relative , 2019, G3.

[17]  Elizabeth A. Ainsworth,et al.  Genetic strategies for improving crop yields , 2019, Nature.

[18]  R. Mott,et al.  A 3,000-year-old Egyptian emmer wheat genome reveals dispersal and domestication history , 2019, Nature Plants.

[19]  R. Kyle Bocinsky,et al.  Genomic history and ecology of the geographic spread of rice , 2019, Nature Plants.

[20]  M. Purugganan.  Evolutionary Insights into the Nature of Plant Domestication , 2019, Current Biology.

[21]  Zhonghua Wang,et al.  Frequent intra- and inter-species introgression shapes the landscape of genetic variation in bread wheat , 2019, Genome Biology.

[22]  V. Brendel,et al.  SRAssembler: Selective Recursive local Assembly of homologous genomic regions , 2019, BMC Bioinformatics.

[23]  M. Tester,et al.  Breeding crops to feed 10 billion , 2019, Nature Biotechnology.

[24]  S. Dyer,et al.  Tracing the ancestry of modern bread wheats , 2019, Nature Genetics.

[25]  G. Spangenberg,et al.  Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome , 2019, Nature Genetics.

[26]  Arthur T. O. Melo,et al.  Durum wheat genome highlights past domestication signatures and future improvement targets , 2019, Nature Genetics.

[27]  N. Zimmermann,et al.  Uncertainty in ensembles of global biodiversity scenarios , 2019, Nature Communications.

[28]  D. Lister,et al.  From ecological opportunism to multi-cropping: Mapping food globalisation in prehistory , 2019, Quaternary Science Reviews.

[29]  Xiao Hu,et al.  SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier , 2019, bioRxiv.

[30]  Andrew J. Blumberg,et al.  Genomic architecture and introgression shape a butterfly radiation , 2018, Science.

[31]  F. Choulet,et al.  Worldwide phylogeography and history of wheat genetic diversity , 2018, Science Advances.

[32]  Huanming Yang,et al.  Origin and evolution of qingke barley in Tibet , 2018, Nature Communications.

[33]  Jonathan D. G. Jones,et al.  Shifting the limits in wheat research and breeding using a fully annotated reference genome , 2018, Science.

[34]  B. Gaut,et al.  Demography and its effects on genomic variation in crop domestication , 2018, Nature Plants.

[35]  O. François,et al.  The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes , 2018, Current Biology.

[36]  B. Pickersgill.  Parallel vs. Convergent Evolution in Domestication and Diversification of Crops in the Americas , 2018, Front. Ecol. Evol..

[37]  Bin Ma,et al.  Genome sequence of the progenitor of wheat A subgenome Triticum urartu , 2018, Nature.

[38]  G. Jin,et al.  The early history of wheat in China from 14C dating and Bayesian chronological modelling , 2018, Nature Plants.

[39]  Adam M. Phillippy,et al.  MUMmer4: A fast and versatile genome alignment system , 2018, PLoS Comput. Biol..

[40]  R. Allaby,et al.  Geographic mosaics and changing rates of cereal domestication , 2017, Philosophical Transactions of the Royal Society B: Biological Sciences.

[41]  Jianbing Yan,et al.  Contributions of Zea mays subspecies mexicana haplotypes to modern maize , 2017, Nature Communications.

[42]  Karl G. Kugler,et al.  Genome sequence of the progenitor of the wheat D genome Aegilops tauschii , 2017, Nature.

[43]  Axel Himmelbach,et al.  Wild emmer genome architecture and diversity elucidate wheat evolution and domestication , 2017, Science.

[44]  John K. McCooke,et al.  A chromosome conformation capture ordered sequence of the barley genome , 2017, Nature.

[45]  E. Buckler,et al.  Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation , 2017, Nature Genetics.

[46]  Timothy M. Beissinger,et al.  The interplay of demography and selection during maize domestication and expansion , 2017, bioRxiv.

[47]  Joe Hereford,et al.  Precipitation drives global variation in natural selection , 2017, Science.

[48]  Thomas Mailund,et al.  admixturegraph: an R package for admixture graph manipulation and fitting , 2017, Bioinform..

[49]  Yun S. Song,et al.  Robust and scalable inference of population history from hundreds of unphased whole genomes , 2016, Nature Genetics.

[50]  J. Ibáñez,et al.  Regional diversity on the timing for the initial appearance of cereal cultivation and domestication in southwest Asia , 2016, Proceedings of the National Academy of Sciences.

[51]  Brett R. Scheffers,et al.  The broad footprint of climate change from genes to biomes to people , 2016, Science.

[52]  D. Fuller,et al.  Between China and South Asia: A Middle Asian corridor of crop dispersal and agricultural innovation in the Bronze Age , 2016, The Holocene.

[53]  Peer Bork,et al.  Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees , 2016, Nucleic Acids Res..

[54]  Chrystian C. Sosa,et al.  Global conservation priorities for crop wild relatives , 2016, Nature Plants.

[55]  J. Ibáñez,et al.  Crop husbandry activities and wild plant gathering, use and consumption at the EPPNB Tell Qarassa North (south Syria) , 2016, Vegetation History and Archaeobotany.

[56]  B. Peter,et al.  Admixture, Population Structure, and F-Statistics , 2015, Genetics.

[57]  Matthew Stephens,et al.  Visualizing spatial population structure with estimated effective migration surfaces , 2014, Nature Genetics.

[58]  Joshua M. Akey,et al.  Methods and models for unravelling human evolutionary history , 2015, Nature Reviews Genetics.

[59]  T. Komatsuda,et al.  Evolution of the Grain Dispersal System in Barley , 2015, Cell.

[60]  Stephen R Keller,et al.  Ecological genomics meets community-level modelling of biodiversity: mapping the genomic landscape of current and future environmental adaptation. , 2015, Ecology letters.

[61]  A. Betts,et al.  The origins of wheat in China and potential pathways for its introduction: A review , 2014 .

[62]  Simon H. Martin,et al.  Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci , 2014, bioRxiv.

[63]  K. Jakobsen,et al.  Ancient hybridizations among the ancestral genomes of bread wheat , 2014, Science.

[64]  Robin G. Allaby,et al.  Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record , 2014, Proceedings of the National Academy of Sciences.

[65]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[66]  Rachel S. Meyer,et al.  Evolution of crop species: genetics of domestication and diversification , 2013, Nature Reviews Genetics.

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

[68]  J. Foley,et al.  Yield Trends Are Insufficient to Double Global Crop Production by 2050 , 2013, PloS one.

[69]  J. Dvorak,et al.  Aegilops tauschii single nucleotide polymorphisms shed light on the origins of wheat D-genome genetic diversity and pinpoint the geographic origin of hexaploid wheat. , 2013, The New phytologist.

[70]  G. Coop,et al.  Robust Identification of Local Adaptation from Allele Frequencies , 2012, Genetics.

[71]  M. Hufford,et al.  The Genomic Signature of Crop-Wild Introgression in Maize , 2012, PLoS genetics.

[72]  Melinda Smale,et al.  Crops that feed the world 10. Past successes and future challenges to the role played by wheat in global food security , 2013, Food Security.

[73]  Swapan Mallick,et al.  Ancient Admixture in Human History , 2012, Genetics.

[74]  Pablo Cingolani,et al.  © 2012 Landes Bioscience. Do not distribute. , 2022 .

[75]  M. Suchard,et al.  Bayesian Phylogenetics with BEAUti and the BEAST 1.7 , 2012, Molecular biology and evolution.

[76]  R. Allaby,et al.  Early agricultural pathways: moving outside the 'core area' hypothesis in Southwest Asia. , 2012, Journal of experimental botany.

[77]  Stephen J. Smith,et al.  Gradient forests: calculating importance gradients on physical predictors. , 2012, Ecology.

[78]  K. Tanno,et al.  Distinguishing wild and domestic wheat and barley spikelets from early Holocene sites in the Near East , 2012, Vegetation History and Archaeobotany.

[79]  A. Thomson,et al.  The representative concentration pathways: an overview , 2011 .

[80]  Y. Matsuoka.  Evolution of polyploid triticum wheats under cultivation: the role of domestication, natural hybridization and allopolyploid speciation in their diversification. , 2011, Plant & cell physiology.

[81]  J. Jia,et al.  Discovery, evaluation and distribution of haplotypes of the wheat Ppd-D1 gene. , 2010, The New phytologist.

[82]  M. Balter.  Archaeology. The tangled roots of agriculture. , 2010, Science.

[83]  David Reich,et al.  Population differentiation as a test for selective sweeps. , 2010, Genome research.

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

[85]  B. Kilian,et al.  Geographic distribution and domestication of wild emmer wheat (Triticum dicoccoides) , 2010, Genetic Resources and Crop Evolution.

[86]  David H. Alexander,et al.  Fast model-based estimation of ancestry in unrelated individuals. , 2009, Genome research.

[87]  J. Elith,et al.  Species Distribution Models: Ecological Explanation and Prediction Across Space and Time , 2009 .

[88]  Terence A Brown,et al.  The complex origins of domesticated crops in the Fertile Crescent. , 2009, Trends in ecology & evolution.

[89]  Dorian Q. Fuller,et al.  The nature of selection during plant domestication , 2009, Nature.

[90]  Luay Nakhleh,et al.  PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships , 2008, BMC Bioinformatics.

[91]  D. Laurie,et al.  A Pseudo-Response Regulator is misexpressed in the photoperiod insensitive Ppd-D1a mutant of wheat (Triticum aestivum L.) , 2007, Theoretical and Applied Genetics.

[92]  T. Komatsuda,et al.  A Phylogenetic Analysis Based on Nucleotide Sequence of a Marker Linked to the Brittle Rachis Locus Indicates a Diphyletic Origin of Barley , 2007, Annals of botany.

[93]  J. Dvorak,et al.  The structure of wild and domesticated emmer wheat populations, gene flow between them, and the site of emmer domestication , 2007, Theoretical and Applied Genetics.

[94]  K. Tanno,et al.  How Fast Was Wild Wheat Domesticated? , 2006, Science.

[95]  D. Laurie,et al.  The Pseudo-Response Regulator Ppd-H1 Provides Adaptation to Photoperiod in Barley , 2005, Science.

[96]  Richard M. Clark,et al.  Estimating a nucleotide substitution rate for maize from polymorphism at a major domestication locus. , 2005, Molecular biology and evolution.

[97]  G. Willcox.  The distribution, natural habitats and availability of wild cereals in relation to their domestication in the Near East: multiple events, multiple centres , 2005 .

[98]  A. Brandolini,et al.  A reconsideration of the domestication geography of tetraploid wheats , 2005, Theoretical and Applied Genetics.

[99]  A. Brandolini,et al.  AFLP analysis of a collection of tetraploid wheats indicates the origin of emmer and hard wheat domestication in southeast Turkey. , 2002, Molecular biology and evolution.

[100]  Andrea Brandolini,et al.  Genetics and geography of wild cereal domestication in the near east , 2002, Nature Reviews Genetics.

[101]  J. Doebley,et al.  A single domestication for maize shown by multilocus microsatellite genotyping , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[102]  G. Coupland,et al.  Functional importance of conserved domains in the flowering-time gene CONSTANS demonstrated by analysis of mutant alleles and transgenic plants. , 2002, The Plant journal : for cell and molecular biology.

[103]  J. Araus,et al.  FOCUS: Estimated Wheat Yields During the Emergence of Agriculture Based on the Carbon Isotope Discrimination of Grains: Evidence from a 10th Millennium BP Site on the Euphrates , 2001 .

[104]  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.

[105]  E. R. Sears,et al.  The origin of Triticum spelta and its free-threshing hexaploid relatives. , 1946, The Journal of heredity.