The origin and evolution of maize in the Southwestern United States

[1]  A. Hector,et al.  Drought survival of tropical tree seedlings enhanced by non-structural carbohydrate levels , 2014 .

[2]  B. Gross,et al.  Archaeological and genetic insights into the origins of domesticated rice , 2014, Proceedings of the National Academy of Sciences.

[3]  E. Cappellini,et al.  Optimization of DNA Recovery and Amplification from Non-Carbonized Archaeobotanical Remains , 2014, PloS one.

[4]  T. Korneliussen,et al.  Estimating Individual Admixture Proportions from Next Generation Sequencing Data , 2013, Genetics.

[5]  R. Nielsen,et al.  Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data , 2013, Genetics.

[6]  Anders Albrechtsen,et al.  Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data , 2013, BMC Bioinformatics.

[7]  K. Shinozaki,et al.  Genome-Wide Analysis of ZmDREB Genes and Their Association with Natural Variation in Drought Tolerance at Seedling Stage of Zea mays L , 2013, PLoS genetics.

[8]  R. Nielsen,et al.  Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation , 2013, Genome research.

[9]  Philip L. F. Johnson,et al.  mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters , 2013, Bioinform..

[10]  G. Larson,et al.  A population genetics view of animal domestication. , 2013, Trends in genetics : TIG.

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

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

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

[14]  P. Morrell,et al.  Megabase-Scale Inversion Polymorphism in the Wild Ancestor of Maize , 2012, Genetics.

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

[16]  Joseph K. Pickrell,et al.  Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data , 2012, PLoS genetics.

[17]  M. Nei,et al.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.

[18]  M. Thomas P. Gilbert,et al.  Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA , 2011, Scientific reports.

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

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

[21]  Robert A. Edwards,et al.  Quality control and preprocessing of metagenomic datasets , 2011, Bioinform..

[22]  J. Doebley,et al.  Genetic signals of origin, spread, and introgression in a large sample of maize landraces , 2010, Proceedings of the National Academy of Sciences.

[23]  Philip L. F. Johnson,et al.  Genetic history of an archaic hominin group from Denisova Cave in Siberia , 2010, Nature.

[24]  Huanming Yang,et al.  Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants , 2010, Nature Genetics.

[25]  Philip L. F. Johnson,et al.  A Draft Sequence of the Neandertal Genome , 2010, Science.

[26]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[27]  G. Fiorentino,et al.  A multidisciplinary study of archaeological grape seeds , 2009, Naturwissenschaften.

[28]  W. L. Merrill,et al.  The diffusion of maize to the southwestern United States and its impact , 2009, Proceedings of the National Academy of Sciences.

[29]  Ryan D. Hernandez,et al.  Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data , 2009, PLoS genetics.

[30]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

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

[32]  D. Piperno,et al.  Starch grain and phytolith evidence for early ninth millennium B.P. maize from the Central Balsas River Valley, Mexico , 2009, Proceedings of the National Academy of Sciences.

[33]  J. Maguire,et al.  Solution Hybrid Selection with Ultra-long Oligonucleotides for Massively Parallel Targeted Sequencing , 2009, Nature Biotechnology.

[34]  J. Doebley,et al.  The Genetic Architecture of Complex Traits in Teosinte (Zea mays ssp. parviglumis): New Evidence From Association Mapping , 2008, Genetics.

[35]  Richard M. Clark,et al.  Major Regulatory Genes in Maize Contribute to Standing Variation in Teosinte (Zea mays ssp. parviglumis) , 2007, Genetics.

[36]  Bruce D. Smith,et al.  Documenting domestication: the intersection of genetics and archaeology. , 2006, Trends in genetics : TIG.

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

[38]  Steven G. Schroeder,et al.  A Large-Scale Screen for Artificial Selection in Maize Identifies Candidate Agronomic Loci for Domestication and Crop Improvementw⃞ , 2005, The Plant Cell Online.

[39]  L. Lukens,et al.  The origin of the naked grains of maize , 2005, Nature.

[40]  J. Doebley,et al.  The role of barren stalk1 in the architecture of maize , 2004, Nature.

[41]  T. Rocheford,et al.  Dissection of Maize Kernel Composition and Starch Production by Candidate Gene Association , 2004, The Plant Cell Online.

[42]  Michael Bunce,et al.  Ancient mitochondrial DNA from hair , 2004, Current Biology.

[43]  J. Juvik,et al.  Current models for starch synthesis and the sugary enhancer1 (se1) mutation in Zea mays. , 2004, Plant physiology and biochemistry : PPB.

[44]  N. Rosenberg distruct: a program for the graphical display of population structure , 2003 .

[45]  B. Gaut,et al.  Genetic diversity and selection in the maize starch pathway , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[46]  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.

[47]  A. Myers,et al.  Molecular structure of three mutations at the maize sugary1 locus and their allele-specific phenotypic effects. , 2001, Plant physiology.

[48]  H. Poinar,et al.  Ancient DNA: Do It Right or Not at All , 2000, Science.

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

[50]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[51]  Jenny L. Adams,et al.  Excavations in the Santa Cruz River floodplain : the Middle Archaic component at Los Pozos , 1999 .

[52]  S. Johannessen,et al.  Corn And Culture In The Prehistoric New World , 1994 .

[53]  R. Ford,et al.  Prehistoric Food Production in North America , 1989 .

[54]  C. Smith Prehistoric Food Production in North America , 1987, American Antiquity.

[55]  B S Weir,et al.  Estimation of the coancestry coefficient: basis for a short-term genetic distance. , 1983, Genetics.

[56]  P. S. Martin Mogollon Cultural Continuity and Change: the Stratigraphic Analysis of Tularosa and Cordova Caves , 1954 .

[57]  J. Doebley,et al.  The role of barren stalk 1 in the architecture of maize , 2022 .