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



Single gene resolution of locally adaptive genetic variation in Mexican maize [preprint]
Gates DJ, Runcie D, Janzen GM, Romero Navarro A, Willcox M, Sonder K, Snodgrass SJ, Rodríguez- Zapata F, Sawers RJH, Rubén Rellán-Álvarez, Buckler ES, Hearne S, Hufford MB, Ross-Ibarra J

We present a high-resolution genome-wide association analysis to identify loci exhibiting adaptive patterns in a large panel of more than 4500 traditional maize landraces representing the breadth of genetic diversity of maize in Mexico. We evaluate associations between genotype and plant performance in 13 common gardens across a range of environments, identifying hundreds of candidate genes underlying genotype by environment interaction. We further identify genetic associations with environment across Mexico and show that such loci are associated with variation in yield and flowering time in our field trials and predict performance in independent drought trials. Our results indicate that the variation necessary to adapt crops to changing climate exists in traditional landraces that have been subject to ongoing environmental adaptation and can be identified by both phenotypic and environmental association.”


Dynamic patterns of transcript abundance of transposable element families in maize [preprint]
Anderson SN, Stitzer MC, Zhou P, Ross-Ibarra J, Hirsch CD, Springer NM

We develop an approach to estiamte family-level expression in transposable elements. While a relatively small proportion of TE families are transcribed, expression is highly dynamic with most families exhibiting tissue-specific expression. We also assay expression among different maize genotypes and use a mapping population to identify what proportion of copies in a family contribute to expression.”


The temporal dynamics of background selection in non-equilibrium populations [preprint]
Torres R, Stetter MG, Hernandez R, Ross-Ibarra J

We use simulations to show that the effects of nonequilibrium population dynamics on linked selection differ qualitatively from predictions under equilibrium models, calling into question inferences about the efficacy of selection made from summary statistics.”


The Genomic Ecosystem of Transposable Elements in Maize [preprint]
Stitzer MC, Anderson SN, Springer NM, Ross-Ibarra J

We describe the ecosystem of transposable elements within the maize genome, revealing how different transposable element families occupy different niches, much like species within an ecosystem.”




Transposable elements contribute to dynamic genome content in maize [preprint]
Anderson SN, Stitzer MC, Brohammer AB, Peng Zhou P, Noshay JM, Hirsch CD, Ross-Ibarra J, Hirsch CN, Springer NM

We identify hundreds of thousands of variable transposable elements among a small set of maize genome assemblies. We find evidence of a large number of genes impacted by TEs, including TEs in genes and genes in TEs, and evidence of recent transposition as well.””


Hybrid decay: a transgenerational epigenetic decline in vigor and viability triggered in backcross populations of teosinte with maize [preprint]
Wei X, Anderson SN, Wang X, Yang L, Crisp PA, Li Q, Noshay J, Albert PS, Birchler JA, Bilinski P, Stitzer MC, Ross-Ibarra J, Flint-Garcia S, Chen X, Springer NM, Doebley JF

We describe a phenomenon we name ‘hybrid decay’ triggered by backcrossing between domesticated maize and a specific teosinte population, resulting in genome instability, activation of transposable elements, and altered epigenetics .”


Adaptive phenotypic divergence in teosinte differs across biotic contexts [preprint]
O’Brien AM, Sawers RJH, Strauss SY, Ross-Ibarra J

We show that rhizosphere biota impact adaptive divergence of phenotypic traits in teosinte along an environmental cline. This work suggests an important role for biotic interactions in determining the outcome of local adaptation.


Characterization of introgression from the teosinte Zea mays ssp. mexicana to Mexican highland maize [preprint]
Gonzalez-Segovia E, Pérez-Limon S, C Cíntora-Martínez C, Guerrero-Zavala A, Jansen G, Hufford MB, Ross-Ibarra J, Ruairidh J H Sawers

We look for introgression from teosinte in the genomes of two highland landraces and use QTL mapping to test for functional relevance of introgressed regions.


Detecting adaptive differentiation in structured populations with genomic data and common gardens [preprint] [github]
Josephs EB, Berg JJ, Ross-Ibarra J, Coop G

We develop methods to detect polygenic adaptation on phenotypes from common gardens and GWAS panels.



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][review]
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


Evolution and Adaptation in the Maize Genome
Manchanda N, Snodgrass SJ, Ross-Ibarra J, Hufford MB

We review progress thus far in genomic research of maize domestication and adaptation. We discuss the insights genomics has shed on our understanding of these processes and conclude with a future outlook for how genomics might be further applied.


Genomics of long- and short- term adaptation in maize and teosinte [preprint]
Lorant A, Ross-Ibarra J, Tenaillon M

We review studies on short and long term adaptation, both natural and artificial, in maize and teosinte.


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.


Other papers by lab-members

Wenbin Mei and Michelle Stitzer

Springer, Nathan M., et al. "The maize W22 genome provides a foundation for functional genomics and transposon biology." Nature genetics (2018): 1.

Markus Stetter

Joshi, Dinesh C., et al. "From zero to hero: the past, present and future of grain amaranth breeding." Theoretical and Applied Genetics (2018): 1-17.

Emily Josephs

Josephs, Emily B. "Determining the evolutionary forces shaping G× E." New Phytologist (2018).

Uzunović, Jasmina, et al. "Transposable elements are important contributors to standing variation in gene expression in Capsella grandiflora." bioRxiv (2018): 289173.

Anne Lorant

Kremling, Karl AG, et al. "Dysregulation of expression correlates with rare-allele burden and fitness loss in maize." Nature 555.7697 (2018): 520.

Daniel Gates

Gates, Daniel J., Diana Pilson, and Stacey D. Smith. "Filtering of target sequence capture individuals facilitates species tree construction in the plant subtribe Iochrominae (Solanaceae)." Molecular phylogenetics and evolution 123 (2018): 26-34.

Gates, Daniel J., et al. "A novel R3 MYB transcriptional repressor associated with the loss of floral pigmentation in Iochroma." New Phytologist 217.3 (2018): 1346-1356.  

Dianne Velasco

Riaz, Summaira, et al. "Genetic diversity analysis of cultivated and wild grapevine (Vitis vinifera L.) accessions around the Mediterranean basin and Central Asia." BMC plant biology 18.1 (2018): 137.



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



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 [] [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] [github]
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.


Other papers by lab-members

Dianne Velasco

Aradhya, Mallikarjuna, et al. "Genetic and ecological insights into glacial refugia of walnut (Juglans regia L.)." PloS one 12.10 (2017): e0185974.

Emily Josephs

Josephs, Emily B., et al. "The relationship between selection, network connectivity, and regulatory variation within a population of Capsella grandiflora." Genome biology and evolution 9.4 (2017): 1099-1109.

Josephs, Emily B., John R. Stinchcombe, and Stephen I. Wright. "What can genome‐wide association studies tell us about the evolutionary forces maintaining genetic variation for quantitative traits?." New Phytologist 214.1 (2017): 21-33.

Wenbin Mei

Mei, Wenbin, et al. "A comprehensive analysis of alternative splicing in paleopolyploid maize." Frontiers in plant science 8 (2017): 694.

Liu, Xiaoxian, et al. "Detecting alternatively spliced transcript isoforms from single‐molecule long‐read sequences without a reference genome." Molecular ecology resources 17.6 (2017): 1243-1256.

Gault, Christine M., et al. "Aberrant splicing in maize rough endosperm3 reveals a conserved role for U12 splicing in eukaryotic multicellular development." Proceedings of the National Academy of Sciences (2017): 201616173.

Feng, Guanqiao, et al. "Evolution of the 3R-MYB gene family in plants." Genome biology and evolution 9.4 (2017): 1013-1029.

Mei, Wenbin, et al. "Evolutionarily conserved alternative splicing across monocots." Genetics (2017): genetics-300189.



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



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



Other papers by lab-members

Dianne Velasco

Migicovsky, Zoë, et al. "Genomic ancestry estimation quantifies use of wild species in grape breeding." BMC genomics 17.1 (2016): 478.

Emily Josephs

Josephs, Emily B., and Stephen I. Wright. "On the Trail of Linked Selection." PLoS genetics 12.8 (2016): e1006240.

Tim Beissinger

Morota, Gota, Timothy M. Beissinger, and Francisco Peñagaricano. "MeSH-informed enrichment analysis and MeSH-guided semantic similarity among functional terms and gene products in chicken." G3: Genes, Genomes, Genetics (2016): g3-116.



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

We show how modern hybrid breeding approahces impact diversity across the genome. Using the Iowa Stiff Stalk synthetic population as an example, we track diversity across 16 generations of selection and compare with simulations. We show the vast majority of the changes in diversity observed can be explained by drift, but that fixation of large haplotypes, likley including considerable linked load, leads to selection for complementation in the recirpical populations. This work provided some of the first population genetic evidence supporting the complenmentaton model of hybrid vigor.


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



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



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



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.


Other papers by lab-members

Dianne Velasco

Aradhya, Mallikarjuna, J. E. Preece, and Dianne Velasco. "Multivariate analysis of molecular and morphological diversity in fig (Ficus carica L.)." V International Symposium on Fig 1173. 2015.

Paul Bilinski

Leung, Wilson, et al. "Drosophila Muller F elements maintain a distinct set of genomic properties over 40 million years of evolution." G3: Genes, Genomes, Genetics 5.5 (2015): 719-740.

Anna O’Brien

Persson, Tomas, et al. "Candidatus Frankia datiscae Dg1, the actinobacterial microsymbiont of Datisca glomerata, expresses the canonical nod genes nodABC in symbiosis with its host plant." PLoS One 10.5 (2015): e0127630.

Shohei Takuno

Le, Tu N., et al. "Epigenetic regulation of intragenic transposable elements impacts gene transcription in Arabidopsis thaliana." Nucleic acids research 43.8 (2015): 3911-3921.



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



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.


Other papers by lab-members



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



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



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.



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



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



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



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.



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



Other papers by lab-members

Dianne Velasco

Aradhya, Mallikarjuna, et al. "Genetic diversity, structure, and patterns of differentiation in the genus Vitis." Plant systematics and evolution 299.2 (2013): 317-330.

Zdunić, Goran, et al. "Genetic diversity and differentiation within and between cultivated (Vitis vinifera L. ssp. sativa) and wild (Vitis vinifera L. ssp. sylvestris) grapes." Vitis 52.1 (2013): 29-32.



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



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



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



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



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



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



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



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



Other papers by lab-members

Tanja Pyhäjärvi

Krutovsky, Konstantin V., et al. "Gene flow, spatial structure, local adaptation, and assisted migration in trees." Genomics of tree crops. Springer, New York, NY, 2012. 71-116.

Pyhäjärvi, Tanja, Esa Aalto, and Outi Savolainen. "Time scales of divergence and speciation among natural populations and subspecies of Arabidopsis lyrata (Brassicaceae)." American journal of botany 99.8 (2012): 1314-1322.

Matthew Hufford

Hufford, Matthew B., et al. "Inferences from the historical distribution of wild and domesticated maize provide ecological and evolutionary insight." PLoS One 7.11 (2012): e47659.



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



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



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



Other papers by lab-members

Tanja Pyhäjärvi

Savolainen, Outi, et al. "Adaptive potential of northernmost tree populations to climate change, with emphasis on Scots pine (Pinus sylvestris L.)." Journal of Heredity 102.5 (2011): 526-536.

Pyhäjärvi, Tanja, Sonja T. Kujala, and Outi Savolainen. "Revisiting protein heterozygosity in plants—nucleotide diversity in allozyme coding genes of conifer Pinus sylvestris." Tree genetics & genomes 7.2 (2011): 385-397.



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



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



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



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



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.


Other papers by lab-members

Matthew Hufford

Epanchin-Niell, Rebecca S., et al. "Controlling invasive species in complex social landscapes." Frontiers in Ecology and the Environment 8.4 (2010): 210-216.



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



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



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




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



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.



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





Mitochondrial DNA and population size
Wares JP, Barber PH, Ross-Ibarra J, Sotka EE, Toonen RJ



Quantitative trait loci and the study of plant domestication
Ross-Ibarra J



The evolution of recombination under domestication: a test of two hypotheses [data]
Ross-Ibarra J

Here I test two different hypotheses about the how recombination should relate to domestication: Does domestication itself select for increased recombination (yes), or respecies with higher recombination rates more likely to be domesticated (no).


Origen y domesticación de la chaya (Cnidoscolus aconitifolius Mill IM Johnst): La espinaca Maya
Ross-Ibarra J

I use genetic data to study the origin of a leafy shrub domesticated by the Maya


The ethnobotany of Chaya (Cnidoscolus aconitifolius ssp. aconitifolius Breckon): A nutritious Maya vegetable
Ross-Ibarra J, Molina-Cruz A



Implications of mating patterns for conservation of the endangered plant Eriogonum ovalifolium var. vineum
Neel MC, Ross-Ibarra J, Ellstrand NC


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