J. Ross-Ibarra

The paper identifies Teosinte Pollen Drive, an RNAi-based gene drive in maize-teosinte hybrids, and shows its role in maize domestication and diversification through linked genetic elements.

The paper reports a novel reference genome for Poa pratensis, demonstrating its utility in studying genetic diversity and population structure.

This study clarifies the origin of modern maize by showing it resulted from an ancient admixture between domesticated maize and Zea mays ssp. mexicana around 5300 years ago, contributing to genetic and phenotypic diversity.

This study identifies convergent cis-regulatory variation in maize landraces adapted to highland environments through allele-specific expression analysis.

The paper identifies genomic regions linked to yield and morphological traits in a maize mapping population, revealing local adaptation in highland environments.

The paper investigates local and convergent adaptation in maize and teosinte, finding intermediate geographic scales for adaptive genetic sharing.

This study compares inbreeding depression in maize and teosinte, finding greater depression in maize due to polygenic small-effect recessive variation and reduced large-effect variants after domestication.

This study examines genotype by environment interactions in a maize population across five environments, finding that these interactions contribute significantly to trait variation and that genetic covariances change across environments.

The paper compares QTL detection methods in a MAGIC maize population, showing varying power to detect QTL depending on the assumed allelic model.

The paper investigates how abiotic stress gradients affect mutualistic adaptation between teosinte and its rhizosphere biota, finding stronger local adaptation in colder sites but greater average benefits from less stressful biota.

This study maps genetic diversity across Zea species, identifying millions of variants and adaptive genes, and demonstrates their utility in breeding.

This study examines introgression patterns between maize and mexicana teosinte across an elevational gradient, finding ancient introgression from mexicana into maize that contributes to adaptation to high elevation environments.

The paper analyzes genomic data from wild and cultivated scarlet runner beans to show introgression from wild to domesticated populations during domestication, contributing to genetic diversity.

This study identifies an introgression from teosinte mexicana that affects HPC1, modulating phosphatidylcholine levels and influencing maize flowering time under low-temperature conditions.

This paper models interspecific conflict over reinforcement, showing that sexual conflict over fertilization can lead to transient evolution of prezygotic isolation before it is lost.

This study identifies molecular parallelism in highland maize landraces, showing convergent adaptation through shared SNPs, genes, and pathways related to flowering time.

The paper identifies constrained non-coding sequences in maize, showing their role in gene regulation and phenotypic variation through evolutionary analysis.

This study investigates DNA methylation variation during maize domestication using WGS and WGBS, identifying DMRs linked to gene regulation and adaptation.

The paper analyzes the genetic diversity loss in doubled-haploid lines derived from European maize landraces using SNP data, finding significant haplotype and SNP diversity reduction.

The paper uses forward simulations to study how background selection affects genetic diversity in non-equilibrium populations over time, finding that initial dynamics often oppose long-term trends and classical models are inadequate.

The paper identifies adaptive genetic loci in Mexican maize landraces by analyzing genotype-environment interactions across multiple environments, showing their potential for climate adaptation.

The paper analyzes the ecological and evolutionary dynamics of transposable element families in maize genomes, revealing diverse strategies and interactions among TE families.

This study shows that rhizosphere biota alter trait expression and covariance in teosinte, influencing local adaptation and responses to environmental changes.

The paper develops methods to detect polygenic adaptation using genomic data and common garden trait measurements in structured populations, applying them to maize lines and landraces.

This study uses simulations and machine learning to analyze how genetic architecture and selective sweeps change during polygenic adaptation to new trait optima, showing that sweeps occur even under weak selection and that demography and mutation effects are key factors.

The paper investigates genome size variation in Zea mays across altitudinal gradients, finding natural selection drives genome size changes through repeat content and linking it to flowering time and cell division rates.

The paper proposes the functional space hypothesis, suggesting genome size affects mutational targets and adaptation patterns in plants, but more data are needed for validation.

This study examines how demographic changes and selection shaped maize domestication and spread using genomic data from landraces and wild progenitors.

The paper identifies regulatory variation in stress-related genes in Mexican highland maize using allele-specific expression analysis under benign conditions.

The paper proposes the CoCoA hypothesis, predicting adaptation and co-adaptation in species interactions along environmental gradients based on interaction conditionality.