The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history

Natural selection interacts with recombination to shape the evolution of hybrid genomes

(2018) Molly Schumer et al.   SCIENCE

Ancient hybridization and strong adaptation to viruses across African vervet monkey populations

(2017) Hannes Svardal et al.   NATURE GENETICS

Unstable Inheritance of 45S rRNA Genes in Arabidopsis thaliana

(2017) Fernando A. Rabanal et al.   G3-Genes Genomes Genetics

B chromosomes: from cytogenetics to systems biology

(2016) Guilherme T. Valente et al.   CHROMOSOMA

Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data

(2016) George P. Tiley et al.   Genome Biology and Evolution

Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism

(2016) Polina Yu Novikova et al.   NATURE GENETICS

Subfamilial and tribal relationships of Ranunculaceae: evidence from eight molecular markers

(2016) Guillaume Cossard et al.   PLANT SYSTEMATICS AND EVOLUTION

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

(2016) James B. Pease et al.   PLOS BIOLOGY

How reticulated are species?

(2015) James Mallet et al.   BIOESSAYS

Chromosome-Specific Painting in Cucumis Species Using Bulked Oligonucleotides

(2015) Yonghua Han et al.   GENETICS

Evolution of Darwin’s finches and their beaks revealed by genome sequencing

(2015) Sangeet Lamichhaney et al.   NATURE

Extreme selective sweeps independently targeted the X chromosomes of the great apes

(2015) Kiwoong Nam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular basis for three-dimensional elaboration of the Aquilegia petal spur

(2015) L. Yant et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Natural Selection Constrains Neutral Diversity across A Wide Range of Species

(2015) Russell B. Corbett-Detig et al.   PLOS BIOLOGY

Chromosome-Specific Painting in Cucumis Species Using Bulked Oligonucleotides

(2015) Yonghua Han et al.   GENETICS

Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes

(2015) Michael Baym et al.   PLoS One

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Genomic variability as a driver of plant–pathogen coevolution?

(2014) Talia L Karasov et al.   CURRENT OPINION IN PLANT BIOLOGY

Localization of 45S and 5S rDNA on Chromosomes of Nigella damascena, Ranunculaceae

(2014) Masahiro Hizume et al.   CYTOLOGIA

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

(2014) Kevin Vanneste et al.   GENOME RESEARCH

Genomics and the origin of species

(2014) Ole Seehausen et al.   NATURE REVIEWS GENETICS

Phenotypic and genetic evidence for ecological speciation ofAquilegia japonicaandA. oxysepala

(2014) Lin-Feng Li et al.   NEW PHYTOLOGIST

Methods for the Preparation of Large Quantities of Complex Single-Stranded Oligonucleotide Libraries

(2014) Yusuf E. Murgha et al.   PLoS One

Reversal of an ancient sex chromosome to an autosome in Drosophila

(2013) Beatriz Vicoso et al.   NATURE

Spatiotemporal reconstruction of theAquilegiarapid radiation through next-generation sequencing of rapidly evolving cpDNA regions

(2013) Simone Fior et al.   NEW PHYTOLOGIST

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

(2013) Daniël P Melters et al.   GENOME BIOLOGY

Distribution of 45S rDNA sites in chromosomes of plants: Structural and evolutionary implications

(2012) Fernando Roa et al.   BMC EVOLUTIONARY BIOLOGY

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Origins of Shared Genetic Variation in African Cichlids

(2012) Yong-Hwee E. Loh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic insights into the correlates of dioecy in meadow-rues (Thalictrum, Ranunculaceae)

(2012) Valerie L. Soza et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?

(2012) Ellen M. Leffler et al.   PLOS BIOLOGY

Nuclear DNA amounts in angiosperms: targets, trends and tomorrow

(2011) M. D. Bennett et al.   ANNALS OF BOTANY

Sex Chromosomes in Land Plants

(2011) Ray Ming et al.   Annual Review of Plant Biology

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Are ribosomal DNA clusters rearrangement hotspots? A case study in the genus Mus (Rodentia, Muridae)

(2011) Benoîte Cazaux et al.   BMC EVOLUTIONARY BIOLOGY

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

ReadDepth: A Parallel R Package for Detecting Copy Number Alterations from Short Sequencing Reads

(2011) Christopher A. Miller et al.   PLoS One

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Retrogenes Reveal the Direction of Sex-Chromosome Evolution in Mosquitoes

(2010) M. A. Toups et al.   GENETICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Early Inbreeding Depression Selects for High Outcrossing Rates in Aquilegia formosa and Aquilegia pubescens

(2010) Ji Y. Yang et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Aquilegia as a model system for the evolution and ecology of petals

(2010) E. M. Kramer et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genetic Variation at Nuclear Loci Fails to Distinguish Two Morphologically Distinct Species of Aquilegia

(2010) Elizabeth A. Cooper et al.   PLoS One

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Aquilegia: A New Model for Plant Development, Ecology, and Evolution

(2009) Elena M. Kramer   Annual Review of Plant Biology

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Phylogeny and classification of Ranunculales: Evidence from four molecular loci and morphological data

(2009) Wei Wang et al.   PERSPECTIVES IN PLANT ECOLOGY EVOLUTION AND SYSTEMATICS

Extended phylogeny of Aquilegia: the biogeographical and ecological patterns of two simultaneous but contrasting radiations

(2009) Jesús M. Bastida et al.   PLANT SYSTEMATICS AND EVOLUTION

Adaptive radiations: From field to genomic studies

(2009) S. A. Hodges et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetics and ecological speciation

(2009) D. Schluter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How to usefully compare homologous plant genes and chromosomes as DNA sequences

(2008) Eric Lyons et al.   PLANT JOURNAL

Multiple hybridization origin of Ranunculus cantoniensis (4x): evidence from trnL-F and ITS sequences and fluorescent in situ hybridization (FISH)

(2008) Liang Liao et al.   PLANT SYSTEMATICS AND EVOLUTION

45S rDNA Regions Are Chromosome Fragile Sites Expressed as Gaps In Vitro on Metaphase Chromosomes of Root-Tip Meristematic Cells in Lolium spp

(2008) Jing Huang et al.   PLoS One

Hemiplasy: A New Term in the Lexicon of Phylogenetics

(2008) John C. Avise et al.   SYSTEMATIC BIOLOGY