Publications

Journal names have been intentionally excluded. Lab member names are in bold. Links are provided to the published article and when possible an open-access version (pre- or post-print) of the paper. Hover over article links for a brief synopsis of the paper.

Click on a triangle for a brief summary of each paper.

Preprints

Genetic architecture and selective sweeps after polygenic adaptation to distant trait optima [preprint] [Shiny app]
Stetter MG, Thornton K, Ross-Ibarra J

We use simulations to study the population genetics of selection on a quantitative trait and learn which parameters drive quantitative trait evollution.

Evolutionary responses to conditionality in species interactions across environmental gradients [preprint]
O’Brien AM, Sawers RJH, Ross-Ibarra J, Strauss SY

We present the CoCoA hypothesis which describes how patterns of biotic coadpation change across varying abiotic environments

2018

Maize domestication and gene interaction [preprint]
Stitzer MC, Ross-Ibarra J

We review genetic work looking at the role of dominance, epistasis, and pleiotropy during maize domestication.

A novel maize kinesin causes neocentromere activity and meiotic drive, altering inheritance patterns across the genome [pdf] [YouTube]
Dawe RK, Lowry EG, Gent JI, Stitzer MC, Higgins DM, Ross-Ibarra J, Wallace J, Kanizay LB … [7 authors]

We identify a small gene family Kindr as the causal locus for meiotic drive in maize.

Parallel altitudinal clines reveal adaptive evolution of genome size in Zea mays [perspective] [preprint] [github] [slides]
Bilinski P, Albert P, Berg JJ, Birchler JA, Grote M, Lorant A, Quezada J, Swarts K, Yang J, Ross-Ibarra J

We show that genome size can be analyzed as a quantitative trait and that selection on flowering time in maize has likely driven adaptive changes in genome size along multiple altitudinal clines.

Adaptation in plant genomes: bigger is different [preprint][github][YouTube][slides]
Mei W, Stetter MG, Gates DJ, Stitzer MC, Ross-Ibarra J

We develop the functional space hypothesis in which we posit that adaptation in large genomes uses more noncoding variation and is more likely to proceed via soft sweeps.

Harnessing cross-border resources to confront climate change
Aburto-Oropeza O …[Ross-Ibarra J and 85 authors in alphabetical order]… Taylor JE

Discusses the challenges of changing climates pose for society and the environment along the Mexican-US border.

2017

Construction of the third generation Zea mays haplotype map [preprint] [sequence data] [genotype data] [alignment data] [code]
Bukowski R …[16 authors]… Ross-Ibarra J, Lorant A, Buffalo V, Romay MC, Buckler ES, Ware D, Lai J, Sun Q, Xu Y

We present a SNP dataset of 80M variants from a sample of 1200 maize and teosinte genomes.

The interplay of demography and selection during maize domestication and diffusion [preprint][github][YouTube]
Wang L, Beissinger TM, Lorant A, Ross-Ibarra C, Ross-Ibarra J, Hufford MB.

We show how population bottlenecks and gene flow have shaped patterns of genetic load across the maize genome and among populatons.

Incomplete dominance of deleterious alleles contribute substantially to trait variation and heterosis in maize [preprint] [github]
Yang J, Mezmouk S, Baumgarten A, Buckler ES, Guill KE, McMullen MD, Mumm RH, Ross-Ibarra J

We combine phenotypic data from crosses between multiple maize inbred lines and genome-wide characterization of deleterious alleles to show that a simple model of incomplete dominance may help explain hybrid vigor.

The potential role of genetic assimilation during maize domestication [preprint]
Lorant A, Pedersen, S, Holst I, Hufford MB, Winter K, Piperno D, Ross-Ibarra J

Gene expression data from maize and teosinte grown in mid-Holocene environments suggests that for some genes plastic changes in expression may have preceded genetic changes during domestication.

Allele specific expression analysis identifies regulatory variation associated with stress-related genes in the Mexican highland maize landrace Palomero Toluqueño [preprint]
Aguilar-Rangel MR, Chávez Montes RA, Gonzalez-Segovia E, Ross-Ibarra J, Simpson JK, Sawers RJH

SUMMARY

Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America
Swarts K, Gutaker RM …[Ross-Ibarra J and 14 authors in alphabetical order]… Krause J, Matson RG, Weigel D, Buckler ES, Burbano HA

SUMMARY Nature News Phys.org Science Daily

How to make a domesticate [preprint]
Stetter MG, Gates DJ, Mei W, Ross-Ibarra J

A perspective that seeks to predict what factors influence the success of domestication, how many genes contributed to the process, where these genes originated and the implications for de novo domestication.

Improved maize reference genome with single-molecule technologies [preprint] [github]
Jiao Y, Peluso P, Shi J, Liang T, Stitzer MC, …[18 authors]… Ross-Ibarra J, Dawe K, Hastie A, Rank DR, Ware D

We present a high-quality long-read reference genome of the maize inbred B73 and the first detailed annotation of retroelements in any grass species. [NSF research news] [UCD press release]

Gene fractionation and function in the ancient subgenomes of maize [preprint]
Renny-Byfield S, Rodgers-Melnick E, Ross-Ibarra J

We show that the two subgenomes of maize differentially contribute to functional variation in phenotypes.

Genomic abundance is not predictive of tandem repeat localization in grass genomes [preprint]
Bilinski P, Han Y, Hufford MB, Lorant A, Zhang P, Estep MC, Jiang J, Ross-Ibarra J

We show that short read sequence data allows discovery of novel tandem repeats in grass species but, unlike many other species, the most abundant repeat is frequently not centromeric.

2016

Genome sequence of a 5310-year-old maize cob provides insights into the early stages of maize domestication
Ramos-Madrigal J, Smith BD, Moreno-Mayar JV, Gopalakrishnan S, Ross-Ibarra J, Gilbert MTP, Wales N

Genome sequence of a 5,000 year old maize cob reveals it was partially domesticated and helps identify the timing of adaptation during domestication.

Evolutionary genomics of peach and almond domestication [preprint]
Velasco D, Hough J, Aradhya M, Ross-Ibarra J

Resequencing data from a number of peach and almond varieties show differences in population size and mating system, but little evidence for convergent selection during domestication.

ANGSD-wrapper: utilities for analyzing next generation sequencing data [github] [preprint]
Durvasula A, Hoffman PJ, Kent TV, Liu C, Kono TJY, Morrell PL, Ross-Ibarra J

We provide a set of scripts and configuration files to facilitate easy popgen analysis of short-read sequencing data.

Recent demography drives changes in linked selection across the maize genome [github] [preprint]
Beissinger TM, Wang L, Crosby K, Durvasula A, Hufford MB, Ross-Ibarra J

We find little evidence for widespread hard sweeps in maize or teosinte and show that differences in demography during maize domestication and subsequent expansion have have changed the impacts of linked selection on surrounding diversity in the maize genome.

Maize diversity associated with social origin and environmental variation in southern Mexico [preprint]
Orozco-Ramírez Q, Santacruz-Varela A, Ross-Ibarra J, Brush S

SUMMARY

High quality maize centromere 10 sequence reveals evidence of frequent recombination events
Wolfgruber TK, Nakashima MM …(5 authors)… Bilinski P, Dawe RK, Ross-Ibarra J, Birchler JA, Presting G

SUMMARY

2015

The genomic impacts of drift and selection for hybrid performance in maize [preprint]
Gerke JP, Edwards JW, Guill KE, Ross-Ibarra J, McMullen MD

SUMMARY

Seed filling in domesticated maize and rice depends on SWEET-mediated hexose transport
Sosso D, Luo D, Li Q-B, Sasse J, Yang J …[6 authors]… Ross-Ibarra J, Yang B, Frommer WB

SUMMARY

Independent molecular basis of convergent highland adaptation in maize [preprint] [github] [data]
Takuno S, Ralph P, Swarts K, Elshire RJ, Glaubitz JC, Buckler ES, Hufford MB, Ross-Ibarra J

We find that maize adaptation to the highlands in Mexico and South America is largely independent and has made considerable use of standing genetic variation.

Natural variation in teosinte at the domestication locus teosinte branched1 (tb1) [preprint]
Vann LE, Kono TJ, Pyhäjärvi T, Hufford MB, Ross-Ibarra J.

We find that variation in the domestication locus tb1 does not explain a substantial proportion of phenotypic variation for tillering in natural populations of teosinte.

Genetic, evolutionary and plant breeding insights from the domestication of maize
Hake S, Ross-Ibarra J

SUMMARY

The origin and evolution of maize in the American Southwest [preprint] [data]
Fonseca RR, Smith B, Wales N, Cappellini E …[12 authors]… Hufford MB, Albrechtsen A, Ross-Ibarra J, Gilbert MT

We use sequence data from ancient maize cobs to reveal the timing and geography of maize introduction into the Southwest US. One of the most read papers from the last four years of the journal! UC Davis Press Release Science World Report Archaeology SiNC, Science magazine Nature Plants commentary The Scientist

Reply to Brush et al.: Wake-up call for crop conservation science
Dyer GA, Lopez-Feldman A, Yunez-Naude A, Taylor JE, Ross-Ibarra J

SUMMARY

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress [preprint]
Makarevitch I, Waters M, West P, Stitzer M, Ross-Ibarra J, Springer NM

We show that transposable elements can act as regulatory sequences that up- or down-regulate genes in maize in response to abiotic stress.

2014

Advances and limits of using population genetics to understand local adaptation [preprint]
Tiffin P, Ross-Ibarra J

We discuss some of the outstanding questions and key challenges facing the use of population genetics to study local adaptation.

Diversity and evolution of centromere repeats in the maize genome [preprint]
Bilinski P, Distor KD, Gutierez-Lopez J, Mendoza Mendoza G, Shi J, Dawe K, Ross-Ibarra J

SUMMARY

The pattern and distribution of deleterious mutations in maize [preprint] [github]
Mezmouk S, Ross-Ibarra J

We show that deleterious mutations are abundant in modern maize breeding material and that genes with deleterious mutations are likely important contributors to phenotypic variation.

2013

Comprehensive analysis of imprinted genes in maize reveals allelic variation and limited conservation with other species [preprint] [github]
Waters AJ, Bilinski P, Eichten SR, Vaugh MW, Ross-Ibarra J, Gehring M, Springer NM

SUMMARY

Complex patterns of local adaptation in teosinte [data] [preprint]
Pyhäjärvi T, Hufford MB, Mezmouk S, Ross-Ibarra J

SUMMARY

From many, one: genetic control of prolificacy during maize domestication [data] [preprint]
Wills DM, Whipple C, Takuno S, Kursel LE, Shannon LM, Ross-Ibarra J, Doebley JF.

SUMMARY

Agriculture: Feeding the future
McCouch S, Baute GJ, Bradeen J, Bramel P …[36 authors]… Ward J, Waugh R, Wenzl P, Zamir.

SUMMARY

The genomic signature of crop-wild introgression in maize [data] [preprint]
Hufford MB, Lubinsky P, Pyhäjärvi T, Devengenzo MT, Ellstrand NC, Ross-Ibarra J

SUMMARY

Population genetics and ethnobotany of cultivated Diospyros riojae (Ebenaceae), an endangered fruit crop from Mexico [preprint]
Provance MC, Garcia Ruiz I, Thommes C, Ross-Ibarra J

SUMMARY

Patterns of centromere tandem repeat evolution in 282 animal and plant genomes [preprint]
Melters DP, Bradnam KR, Young HA, Telis N …[9 authors]… Tobias C, Ross-Ibarra J, Korf IF, Chan SW-L.

SUMMARY

Diversity and abundance of the Abnormal chromosome 10 meiotic drive complex in Zea mays [preprint]
Kanizay LB, Pyhäjärvi T, Lowry E, Hufford MB, Peterson DG, Ross-Ibarra J, Dawe RK

SUMMARY

2012

Teosinte as a model system for population and ecological genomics
Hufford MB, Bilinski P, Pyhäjärvi T, Ross-Ibarra J

SUMMARY

Comparative population genomics of maize domestication and improvement [data]
Hufford MB, Xun X, van Heerwaarden J, Pyhäjärvi T …[17 authors]… Ware D, Buckler ES, Yang S, Ross-Ibarra J

SUMMARY

Using nextgen sequencing to investigate genome size variation and transposable element content
Munoz Diez C, Vitte C, Ross-Ibarra J, Gaut BS, Tenaillon MI

SUMMARY

Historical genomics of North American maize [data]
van Heerwaarden J, Hufford MB, Ross-Ibarra J

SUMMARY

Reshaping of the maize transcriptome by domestication
Swanson-Wagner R, Briskine R, Schaefer R, Hufford MB, Ross-Ibarra J, Myers CL, Tiffin P, Springer NM

SUMMARY

Maize HapMap2 identifies extant variation from a genome in flux
Chia J-M, Song C, …[Hufford, MB, Pyhäjärvi T, and 27 authors]… Ross-Ibarra, J, McMullen MD, Buckler ES, Zhang G, Xu Y, Ware, D

SUMMARY

Megabase-scale inversion polymorphism in the wild ancestor of maize [data]
Fang Z, Pyhäjärvi T, Weber AL, Dawe RK, …[2 authors]… Ross-Ibarra C, Doebley J, Morrell PL, Ross-Ibarra J

We identify and study the evolutionary genetics of a 50Mb inversion in natural populations of teosinte

Genetic architecture of maize kernel composition in the Nested Association Mapping and Inbred Association panels
Cook JP, McMullen MD, Holland JB, Tian F, Bradbury P, Ross-Ibarra J, Buckler ES, Flint-Garcia SA

SUMMARY

Crop genomics: advances and applications
Morrell PL, Buckler ES, Ross-Ibarra J

SUMMARY

2011

Identification of a functional transposon insertion in the maize domestication gene tb1 [data]
Studer A, Zhao Q, Ross-Ibarra J, Doebley J

SUMMARY

Genetic signals of origin, spread and introgression in a large sample of maize landraces [data]
van Heerwaarden J, Doebley J, Briggs WH, Glaubitz JC, Goodman MM, Sanchez Gonzalez JJ, Ross-Ibarra J

We resolve the conflict between genetic, ecological, and achaeological data regarding the geographic location of maize domestication.

Influence of cryptic population structure on observed mating patterns in the wild progenitor of maize [data]
Hufford MB, Gepts P, Ross-Ibarra J

SUMMARY

Genome size and TE content as determined by high-throughput sequencing in maize and Zea luxurians
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J

SUMMARY

2010

Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda)
Eckert AJ, van Heerwaarden J, Wegrzyn JL, Nelson CD, Ross-Ibarra J, Gonzalez-Martinez SC, and Neale DB

SUMMARY

Reproductive biology of Macleania rupestris (Ericaceae): a pollen-limited Neotropical cloud-forest species in Costa Rica
Fuchs EJ, Ross-Ibarra J, Barrantes G

SUMMARY

A role for nonadaptive processes in plant genome size evolution?
Whitney KD, Baack EJ, Hamrick JL, Godt, MJW …[3 authors]… Goodwillie C, Kalisz S, Leitch I, Ross-Ibarra J

SUMMARY

Fine scale genetic structure in the wild ancestor of maize (Zea mays ssp. parviglumis)
van Heerwaarden J, Ross-Ibarra J, Doebley J, Glaubitz JC, Sanchez Gonzalez J, Gaut BS, Eguiarte LE

SUMMARY

Widespread gene conversion in centromere cores
Shi J, Wolf S, Burke J, Presting G, Ross-Ibarra J, Dawe RK

[plos biology commentary]

Indel-associated mutation rate varies with mating system in flowering plants
Hollister JD, Ross-Ibarra J, Gaut BS

We show that mating system differences in heterozygosity mitigate the effects of insertion and deletion polymorphisms on nucleotide diversity.

Genetic diversity in a crop metapopulation
van Heerwaarden J, van Eeuwijk FA, Ross-Ibarra J

We develop a coalescent model to predict genetic structure and diversity of a crop plant in an agronomic ecosystem.

2009

A first-generation haplotype map of maize
Gore MA, Chia JM, Elshire RJ, Sun Q …[4 authors]… Grills GS, Ross-Ibarra J, Ware DH, Buckler ES

SUMMARY

A pleistocene clone of Palmer’s Oak persisting in Southern California May MR, Provance MC, Sanders AC, Ellstrand NC, Ross-Ibarra J

We discover a 13,000 year old oak clone in the hilss of Southern California

Selection on grain shattering genes and rates of rice domestication
Zhang LB, Zhu Q, Wu ZQ, Ross-Ibarra J, Gaut BS, Ge S, Sang T

SUMMARY

Historical divergence and gene flow in the genus Zea
Ross-Ibarra J, Tenaillon M, Gaut BS

SUMMARY

2008

Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata
Ross-Ibarra J, Wright SI, Foxe JP, Kawabe A, DeRose-Wilson L, Gos G, Charlesworth D, Gaut BS

SUMMARY

Demography and weak selection drive patterns of TE diversity in natural populations of A. lyrata
Lockton S, Ross-Ibarra J, Gaut BS

We show that differences in demographic history among populations of have changed the abundance and freqeuncy of transposable elements in the A lyrata genome.

Multiple domestications do not appear monophyletic
Ross-Ibarra J, Gaut BS

A rebuttal showing that genetic data can indeed successfully recover multiple independent domestications.

Selection on major components of angiosperm genomes
Gaut BS, Ross-Ibarra J

Discusses some of the evolutionary forces responsible for shaping genome size across plants.

2007

Plant domestication, a unique opportunity to identify the genetic basis of adaptation
Ross-Ibarra J, Morrell PL, Gaut BS

Presents plant domestication as an ideal system in which to study the genetics of adaptation.

Genome size and recombination in angiosperms: a second look
Ross-Ibarra J

SUMMARY