Jeffrey Ross-Ibarra

Professor (Evolutionary Biology)

UC Davis

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

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Co-workers & collaborators

Markus Stetter

Markus Stetter

Laura Vann

Laura Vann

Jeffrey Ross-Ibarra's public data