Jeffrey Ross-Ibarra

Publications

• Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution DOI: 10.1186/gb-2013-14-1-r10
• Comparative population genomics of maize domestication and improvement DOI: 10.1038/ng.2309
• Crop genomics: Advances and applications DOI: 10.1038/nrg3097
• Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels DOI: 10.1104/pp.111.185033
• Historical genomics of North American maize DOI: 10.1073/pnas.1209275109
• Maize HapMap2 identifies extant variation from a genome in flux DOI: 10.1038/ng.2313
• Megabase-scale inversion polymorphism in the wild ancestor of maize DOI: 10.1534/genetics.112.138578
• Reshaping of the maize transcriptome by domestication DOI: 10.1073/pnas.1201961109
• Teosinte as a model system for population and ecological genomics DOI: 10.1016/j.tig.2012.08.004
• Genetic signals of origin, spread, and introgression in a large sample of maize landraces DOI: 10.1073/pnas.1013011108
• Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians DOI: 10.1093/gbe/evr008
• Identification of a functional transposon insertion in the maize domestication gene tb1 DOI: 10.1038/ng.942
• Influence of cryptic population structure on observed mating patterns in the wild progenitor of maize (Zea mays ssp. parviglumis) DOI: 10.1111/j.1365-294X.2010.04924.x
• A role for nonadaptive processes in plant genome size evolution? DOI: 10.1111/j.1558-5646.2010.00967.x
• Fine scale genetic structure in the wild ancestor of maize (Zea mays ssp. parviglumis) DOI: 10.1111/j.1365-294X.2010.04559.x
• Genetic diversity in a crop metapopulation DOI: 10.1038/hdy.2009.110
• Indel-associated mutation rate varies with mating system in flowering plants DOI: 10.1093/molbev/msp249
• Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae) DOI: 10.1534/genetics.110.115543
• Reproductive biology of macleania rupestris (ericaceae), a pollen-limited neotropical cloud-forest species in Costa Rica DOI: 10.1017/S0266467410000064
• Widespread gene conversion in centromere cores DOI: 10.1371/journal.pbio.1000327
• A first-generation haplotype map of maize DOI: 10.1126/science.1177837
• A pleistocene clone of palmer's oak persisting in Southern California DOI: 10.1371/journal.pone.0008346
• Historical divergence and gene flow in the genus Zea DOI: 10.1534/genetics.108.097238
• Selection on grain shattering genes and rates of rice domestication DOI: 10.1111/j.1469-8137.2009.02984.x
• Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata DOI: 10.1073/pnas.0804671105
• Multiple domestications do not appear monophyletic DOI: 10.1073/pnas.0809042105
• Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata DOI: 10.1371/journal.pone.0002411
• Selection on major components of angiosperm genomes DOI: 10.1126/science.1153586
• Genome size and recombination in angiosperms: A second look DOI: 10.1111/j.1420-9101.2006.01275.x
• Plant domestication, a unique opportunity to identify the genetic basis of adaptation DOI: 10.1073/pnas.0700643104
• Mitochondrial DNA and population size [4] DOI: 10.1126/science.314.5804.1388
• Quantitative trait loci and the study of plant domestication DOI: 10.1007/s10709-004-2744-6
• The Evolution of Recombination under Domestication: A Test of Two Hypotheses DOI: 10.1086/380606
• Origin and domestication of the chaya (Cnidoscolus aconitifolius Mill I. M. Johnst): The Mayan spinach | Origen y domesticación de la chaya (Cnidoscolus aconitifolius Mill I. M. Johnst): La espinaca Maya DOI: 10.1525/msem.2003.19.2.287
• Genetic Data Analysis II. Methods for Discrete Population Genentic Data DOI: 10.1663/0013-0001(2002)056[0216:GDAIMF]2.0.CO;2
• The ethnobotany of chaya (Cnidoscolus aconitifolius ssp. aconitifolius Breckon): A nutritious Maya vegetable
• Implications of mating patterns for conservation of the endangered plant Eriogonum ovalifolium var. vineum (Polygonaceae)
• Using Nextgen Sequencing to Investigate Genome Size Variation and Transposable Element Content DOI: 10.1007/978-3-642-31842-9_3
• Adaptation in plant genomes: bigger is different
• Diversity and evolution of centromere repeats in the maize genome
• Adaptation in plant genomes: Bigger is different
• The pattern and distribution of deleterious mutations in maize
• Seed filling in domesticated maize and rice depends on SWEET-mediated hexose transport
• Extending the Stress-Gradient hypothesis: increased local adaptation between teosinte and soil biota at the stressful end of a climate gradient
• Agriculture: feeding the future
• A test of ecological and ethnolinguistic determinants of maize diversity in southern Mexico
• Transposable elements contribute to activation of maize genes in response to abiotic stress
• Reply to Brush et al.: Wake-up call for crop conservation science
• Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species
• Advances and limits of using population genetics to understand local adaptation
• From Many, One: Genetic Control of Prolificacy during Maize Domestication
• Diversity and abundance of the abnormal chromosome 10 meiotic drive complex in Zea mays
• Complex patterns of local adaptation in teosinte
• The origin and evolution of maize in the Southwestern United States
• Natural variation in teosinte at the domestication locus teosinte branched1 (tb1)
• Construction of the third generation Zea mays haplotype map
• ANGSD-wrapper
• Genetic, evolutionary and plant breeding insights from the domestication of maize
• Diversity and evolution of centromere repeats in the maize genome
• Parallel altitudinal clines reveal trends in adaptive evolution of genome size in Zea mays
• Not so local: the population genetics of convergent adaptation in maize and teosinte
• The Temporal Dynamics of Background Selection in Nonequilibrium Populations
• Evolutionary Genomics of Peach and Almond Domestication
• Evolutionary insights into plant breeding
• Genetic architecture and selective sweeps after polygenic adaptation to distant trait optima
• Genetic architecture and selective sweeps after polygenic adaptation to distant trait optima
• Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution
• The Genomic Ecosystem of Transposable Elements in Maize
• Detecting Adaptive Differentiation in Structured Populations with Genomic Data and Common Gardens
• The temporal dynamics of background selection in non-equilibrium populations
• Dynamic patterns of transcript abundance of transposable element families in maize
• Natural variation in teosinte at the domestication locus teosinte branched1 (tb1)
• The genomic impacts of drift and selection for hybrid performance in maize
• Selective sorting of ancestral introgression in maize and teosinte along an elevational cline
• High quality maize centromere 10 sequence reveals evidence of frequent recombination events
• Construction of the third generation Zea mays haplotype map
• Evolutionary and functional genomics of DNA methylation in maize domestication and improvement
• Modeling Allelic Diversity of Multi-parent Mapping Populations Affects Detection of Quantitative Trait Loci
• Selective Loss of Diversity in Doubled-Haploid Lines from European Maize Landraces
• Genetic, evolutionary and plant breeding insights from the domestication of maize
• Dynamic Patterns of Transcript Abundance of Transposable Element Families in Maize
• ANGSD-wrapper: utilities for analyzing next generation
• Transposable elements contribute to dynamic genome content in maize
• Independent molecular basis of convergent highland adaptation in maize
• Evolutionary genomics of peach and almond domestication
• Allele specific expression analysis identifies regulatory variation associated with stress-related genes in the Mexican highland maize landrace Palomero Toluqueño
• Transposable elements contribute to dynamic genome content in maize
• Selective loss of diversity in doubled-haploid lines from European maize landraces
• Quantitative trait loci and the study of plant domestication
• Teosinte as a model system for population and ecological genomics
• Genetic signals of origin, spread, and introgression in a large sample of maize landraces
• Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels
• A role for nonadaptive processes in plant genome size evolution?
• Genome size and recombination in angiosperms: A second look
• Historical divergence and gene flow in the genus Zea
• Identification of a functional transposon insertion in the maize domestication gene tb1
• Indel-associated mutation rate varies with mating system in flowering plants
• Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata
• The genomic signature of crop-wild introgression in maize
• Crop genomics: advances and applications
• Population genetics and ethnobotany of cultivated Diospyros riojae Gómez Pompa (Ebenaceae), an endangered fruit crop from Mexico
• Historical genomics of North American maize
• Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels
• Genome size and recombination in angiosperms: a second look
• Historical divergence and gene flow in the genus Zea
• Genetic signals of origin, spread, and introgression in a large sample of maize landraces
• Multiple domestications do not appear monophyletic
• Maize HapMap2 identifies extant variation from a genome in flux
• Comparative population genomics of maize domestication and improvement
• Genetic diversity in a crop metapopulation
• The genomic impacts of drift and selection for hybrid performance in maize
• Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae)
• Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians
• Mitochondrial DNA and population size
• Identification of a functional transposon insertion in the maize domestication gene tb1
• Widespread gene conversion in centromere cores
• Indel-associated mutation rate varies with mating system in flowering plants
• Megabase-scale inversion polymorphism in the wild ancestor of maize
• Reproductive biology of macleania rupestris (ericaceae), a pollen-limited neotropical cloud-forest species in Costa Rica
• A first-generation haplotype map of maize
• A pleistocene clone of palmer's oak persisting in Southern California
• Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae)
• Fine scale genetic structure in the wild ancestor of maize (Zea mays ssp. parviglumis)
• Historical genomics of North American maize
• Mitochondrial DNA and population size [4]
• Crop genomics: Advances and applications
• Genetic diversity in a crop metapopulation
• Influence of cryptic population structure on observed mating patterns in the wild progenitor of maize (Zea mays ssp. parviglumis)
• Selection on major components of angiosperm genomes
• Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata
• Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians
• Multiple domestications do not appear monophyletic
• Maize HapMap2 identifies extant variation from a genome in flux
• Reshaping of the maize transcriptome by domestication
• Plant domestication, a unique opportunity to identify the genetic basis of adaptation
• Selection on grain shattering genes and rates of rice domestication
• Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata
• Comparative population genomics of maize domestication and improvement
• Genetic Data Analysis II. Methods for Discrete Population Genentic Data
• Origin and domestication of the chaya (Cnidoscolus aconitifolius Mill I. M. Johnst): The Mayan spinach | Origen y domesticación de la chaya (Cnidoscolus aconitifolius Mill I. M. Johnst): La espinaca Maya
• The Evolution of Recombination under Domestication: A Test of Two Hypotheses
• Using Nextgen Sequencing to Investigate Genome Size Variation and Transposable Element Content
• GBS of highland and lowland maize
• Gene Popgen Stats from Hufford et al. 2012 Nat. Gen.
• Population Genetics and Ethnobotany of Cultivated Diospyros riojae Gómez Pompa (Ebenaceae), an Endangered Fruit Crop from Mexico
• Recombination rho in maize
• The evolution of recombination under domestication: a test of two hypotheses
• Origen y domesticación de la chaya (Cnidoscolus aconitifolius Mill IM Johnst): La espinaca Maya
• Not so local: the population genetics of convergent adaptation in maize and teosinte.
• Analysis of genotype-by-environment interactions in a maize mapping population
• Controlling for Variable Transposition Rate with an Age-Adjusted Site Frequency Spectrum
• HERITABILITY AND QTL MAPPING OF AERIAL ROOTS AND OTHER YIELD COMPONENT TRAITS WITH IMPLICATIONS FOR N2 FIXATION IN ZEA MAYS
• Unraveling Prevalence and Effects of Deleterious Mutations in Maize Elite Lines across Decades of Modern Breeding
• Genome sequencing reveals evidence of adaptive variation in the genus Zea
• A happy accident: a novel turfgrass reference genome
• Comparative evolutionary genetics of deleterious load in sorghum and maize
• Diamonds in the not-so-rough: Wild relative diversity hidden in crop genomes
• An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time
• Gene body methylation is under selection in Arabidopsis thaliana
• The genomic ecosystem of transposable elements in maize
• Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize (vol 13, e1007019, 2017)
• Two teosintes made modern maize
• Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize
• Genomic insights into historical improvement of heterotic groups during modern hybrid maize breeding
• De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes
• Allele-specific Expression Reveals Multiple Paths to Highland Adaptation in Maize
• Modeling allelic diversity of multiparent mapping populations affects detection of quantitative trait loci
• Domestication reshaped the genetic basis of inbreeding depression in a maize landrace compared to its wild relative, teosinte
• The genomic signature of wild-to-crop introgression during the domestication of scarlet runner bean (Phaseolus coccineus L.)
• Conflict over fertilization underlies the transient evolution of reinforcement
• Molecular Parallelism Underlies Convergent Highland Adaptation of Maize Landraces
• Allele-specific expression reveals multiple paths to highland adaptation in maize
• A B73xPalomero Toluqueno mapping population reveals local adaptation in Mexican highland maize
• Portrait of a genus: the genetic diversity of Zea
• Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize
• Teosinte Pollen Drive guides maize domestication and evolution by RNAi
• Teosinte Pollen Drive guides maize diversification and domestication by RNAi
• Teosinte populations exhibit weak local adaptation to their rhizosphere biota despite strong effects of biota source on teosinte fitness and traits
• A unified VCF dataset from nearly 1,500 diverse maize accessions and resources to explore the genomic landscape of maize
• An ancient origin of the naked grains of maize
• Molecular evolution of a reproductive barrier in maize and related species
• The population genetics of convergent adaptation in maize and teosinte is not locally restricted
• Using nextgen sequencing to investigate genome size variation and transposable element content