J. Ross-Ibarra

Teosinte Pollen Drive guides maize diversification and domestication by RNAi

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.

A happy accident: a novel turfgrass reference genome

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

Two teosintes made modern maize

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.

Allele-specific expression reveals multiple paths to highland adaptation in maize

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

A B73 x Palomero Toluqueo mapping population reveals local adaptation in Mexican highland maize

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

Not so local: the population genetics of convergent adaptation in maize and teosinte.

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

Domestication Reshaped the Genetic Basis of Inbreeding Depression in a Maize Landrace Compared to its Wild Relative, Teosinte

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.

Analysis of genotype by environment interactions in a maize mapping population

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.

Modeling Allelic Diversity of Multi-parent Mapping Populations Affects Detection of Quantitative Trait Loci

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

Strengthened mutualistic adaptation between teosinte and its rhizosphere biota in cold climates

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.

Portrait of a genus: the genetic diversity of Zea

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

Selective sorting of ancestral introgression in maize and teosinte along an elevational cline

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 genomic signature of wild-to-crop introgression during the domestication of scarlet runner bean (Phaseolus coccineus L.)

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.

An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time

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

Conflict over fertilization underlies the transient evolution of reinforcement

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.

Molecular Parallelism Underlies Convergent Highland Adaptation of Maize Landraces

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

Constrained non-coding sequence provides insights into regulatory elements and loss of gene expression in maize

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

Evolutionary and functional genomics of DNA methylation in maize domestication and improvement

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

Selective loss of diversity in doubled-haploid linesfrom European maize landraces

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 temporal dynamics of background selection in non-equilibrium populations

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.

Single-gene resolution of locally adaptive genetic variation in Mexican maize

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 Genomic Ecosystem of Transposable Elements in Maize

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

Adaptive phenotypic divergence in an annual grass differs across biotic contexts

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

Detecting adaptive differentiation in structured populations with genomic data and common gardens

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.

Genetic architecture and selective sweeps after polygenic adaptation to distant trait optima

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.

Parallel Altitudinal Clines Reveal Adaptive Evolution Of Genome Size In Zea mays

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.

Adaptation in plant genomes: bigger is different

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.

The interplay of demography and selection during maize domestication and expansion

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

Allele specific expression analysis identifies regulatory variation associated with stress-related genes in the Mexican highland maize landrace Palomero Toluqueno

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

Evolutionary responses to conditionality in species interactions across environmental gradients

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