Migration without interbreeding: Evolutionary history of a highly selfing Mediterranean grass inferred from whole genomes

Functional variants of DOG1 control seed chilling responses and variation in seasonal life-history strategies in Arabidopsis thaliana

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Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors

(2020) Sean P. Gordon et al.   Nature Communications

Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations

(2020) Aleksandra Skalska et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Evolutionary processes from the perspective of flowering time diversity

(2019) Allison Gaudinier et al.   NEW PHYTOLOGIST

Advancing an interdisciplinary framework to study seed dispersal ecology

(2019) Noelle G Beckman et al.   AoB Plants

Diversity, dynamics and effects of long terminal repeat retrotransposons in the model grass Brachypodium distachyon

(2019) Christoph Stritt et al.   NEW PHYTOLOGIST

Brachypodium: A monocot grass model system for plant biology

(2018) Karen-Beth G. Scholthof et al.   PLANT CELL

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent

(2018) Tomáš Flouri et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon

(2018) Yann Bourgeois et al.   PLANT JOURNAL

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files

(2018) Chi Zhang et al.   BIOINFORMATICS

Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon

(2017) Christoph Stritt et al.   Genome Biology and Evolution

Comparative plastome genomics and phylogenomics of Brachypodium : flowering time signatures, introgression and recombination in recently diverged ecotypes

(2017) Rubén Sancho et al.   NEW PHYTOLOGIST

The Evolutionary Interplay between Adaptation and Self-Fertilization

(2017) Matthew Hartfield et al.   TRENDS IN GENETICS

Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure

(2017) Sean P. Gordon et al.   Nature Communications

Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts

(2017) Jean-Tristan Brandenburg et al.   PLoS Genetics

A Flowering Locus C Homolog Is a Vernalization-Regulated Repressor in Brachypodium and Is Cold Regulated in Wheat

(2016) Neha Sharma et al.   PLANT PHYSIOLOGY

Recreating Stable Brachypodium hybridum Allotetraploids by Uniting the Divergent Genomes of B. distachyon and B. stacei

(2016) Vinh Ha Dinh Thi et al.   PLoS One

Environmental niche variation and evolutionary diversification of the Brachypodium distachyon grass complex species in their native circum-Mediterranean range

(2015) D. Lopez-Alvarez et al.   AMERICAN JOURNAL OF BOTANY

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

LEA: AnRpackage for landscape and ecological association studies

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MCMC Methods for Multi-Response Generalized Linear Mixed Models: TheMCMCglmmRPackage

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Targeting environmental adaptation in the monocot model Brachypodium distachyon: a multi-faceted approach

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SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data

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Evolutionary shifts to self-fertilisation restricted to geographic range margins in North AmericanArabidopsis lyrata

(2014) P. C. Griffin et al.   ECOLOGY LETTERS

Patterns and processes in plant phylogeography in the Mediterranean Basin. A review

(2014) Gonzalo Nieto Feliner   PERSPECTIVES IN PLANT ECOLOGY EVOLUTION AND SYSTEMATICS

Classification and mapping of the ecoregions of Italy

(2014) C. Blasi et al.   PLANT BIOSYSTEMS

Challenges in analysis and interpretation of microsatellite data for population genetic studies

(2014) Alexander I. Putman et al.   Ecology and Evolution

Evolution in subdivided plant populations: concepts, recent advances and future directions

(2013) John R. Pannell et al.   NEW PHYTOLOGIST

Interaction of Photoperiod and Vernalization Determines Flowering Time of Brachypodium distachyon

(2013) T. S. Ream et al.   PLANT PHYSIOLOGY

Evolutionary consequences of self-fertilization in plants

(2013) S. I. Wright et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evolution and taxonomic split of the model grass Brachypodium distachyon

(2012) Pilar Catalán et al.   ANNALS OF BOTANY

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

ADAPTATION AND MALADAPTATION IN SELFING AND OUTCROSSING SPECIES: NEW MUTATIONS VERSUS STANDING VARIATION

(2012) Sylvain Glémin et al.   EVOLUTION

Validation of microsatellite markers for cytotype discrimination in the model grass Brachypodium distachyon

(2012) Patricia Giraldo et al.   GENOME

A DNA Barcoding Method to Discriminate between the Model Plant Brachypodium distachyon and Its Close Relatives B. stacei and B. hybridum (Poaceae)

(2012) Diana López-Alvarez et al.   PLoS One

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

Inference of Population Structure using Dense Haplotype Data

(2012) Daniel John Lawson et al.   PLoS Genetics

Time-dependent rates of molecular evolution

(2011) SIMON Y. W. HO et al.   MOLECULAR ECOLOGY

Comparison of a high-density genetic linkage map to genome features in the model grass Brachypodium distachyon

(2011) Naxin Huo et al.   THEORETICAL AND APPLIED GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

Darwin's legacy: the forms, function and sexual diversity of flowers

(2010) S. C. H. Barrett   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

The Scale of Population Structure in Arabidopsis thaliana

(2010) Alexander Platt et al.   PLoS Genetics

Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon

(2009) John P Vogel et al.   BMC PLANT BIOLOGY

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS