Genome-Wide Analysis of Colonization History and Concomitant Selection in Arabidopsis lyrata

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions

(2016) Sean Hoban et al.   AMERICAN NATURALIST

Selection for population-specific adaptation shaped patterns of variation in the photoperiod pathway genes inArabidopsis lyrataduring post-glacial colonization

(2016) Tiina M. Mattila et al.   MOLECULAR ECOLOGY

A genomic history of Aboriginal Australia

(2016) Anna-Sapfo Malaspinas et al.   NATURE

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

The role of climate adaptation in colonization success inArabidopsis thaliana

(2015) Jill A. Hamilton et al.   MOLECULAR ECOLOGY

Exploring population size changes using SNP frequency spectra

(2015) Xiaoming Liu et al.   NATURE GENETICS

Long-distance plant dispersal to North Atlantic islands: colonization routes and founder effect

(2015) Inger Greve Alsos et al.   AoB Plants

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

A recent local sweep at thePHYAlocus in the Northern European Spiterstulen population ofArabidopsis lyrata

(2014) Tuomas Toivainen et al.   MOLECULAR ECOLOGY

Contrasting Patterns of Genetic Structuring in Natural Populations of Arabidopsis lyrata Subsp. petraea across Different Regions in Northern Europe

(2014) Mohsen Falahati-Anbaran et al.   PLoS One

Evidence for Widespread Positive and Negative Selection in Coding and Conserved Noncoding Regions of Capsella grandiflora

(2014) Robert J. Williamson et al.   PLoS Genetics

Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data

(2013) Matteo Fumagalli et al.   GENETICS

Estimating Individual Admixture Proportions from Next Generation Sequencing Data

(2013) Line Skotte et al.   GENETICS

Characterizing Bias in Population Genetic Inferences from Low-Coverage Sequencing Data

(2013) Eunjung Han et al.   MOLECULAR BIOLOGY AND EVOLUTION

Understanding the origin of species with genome-scale data: modelling gene flow

(2013) Vitor Sousa et al.   NATURE REVIEWS GENETICS

Genetic roadmap of the Arctic: plant dispersal highways, traffic barriers and capitals of diversity

(2013) Pernille Bronken Eidesen et al.   NEW PHYTOLOGIST

Ensembl Genomes 2013: scaling up access to genome-wide data

(2013) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

Signatures of Demography and Recombination at Coding Genes in Naturally-Distributed Populations of Arabidopsis Lyrata Subsp. Petraea

(2013) Cynthia C. Vigueira et al.   PLoS One

Cryptic or mystic? Glacial tree refugia in northern Europe

(2013) P.C. Tzedakis et al.   TRENDS IN ECOLOGY & EVOLUTION

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

Time scales of divergence and speciation among natural populations and subspecies of Arabidopsis lyrata (Brassicaceae)

(2012) Tanja Pyhäjärvi et al.   AMERICAN JOURNAL OF BOTANY

Genetic basis of local adaptation and flowering time variation inArabidopsis lyrata

(2012) PÄIVI H. LEINONEN et al.   MOLECULAR ECOLOGY

Adaptation at range margins: common garden trials and the performance ofArabidopsis lyrataacross its northwestern European range

(2012) Philippine Vergeer et al.   NEW PHYTOLOGIST

SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data

(2012) Rasmus Nielsen et al.   PLoS One

Glacial Survival of Boreal Trees in Northern Scandinavia

(2012) L. Parducci et al.   SCIENCE

fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios

(2011) Laurent Excoffier et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Variation in tolerance to drought among Scandinavian populations of Arabidopsis lyrata

(2011) Nina Sletvold et al.   EVOLUTIONARY ECOLOGY

Testing for Ancient Admixture between Closely Related Populations

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

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

(2011) Tina T Hu et al.   NATURE GENETICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Investigating the effects of topography and clonality on genetic structuring within a large Norwegian population of Arabidopsis lyrata

(2010) Sverre Lundemo et al.   ANNALS OF BOTANY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The evolutionary history of the Arabidopsis lyrata complex: a hybrid in the amphi-Beringian area closes a large distribution gap and builds up a genetic barrier

(2010) Roswitha Schmickl et al.   BMC EVOLUTIONARY BIOLOGY

LOCAL ADAPTATION, PHENOTYPIC DIFFERENTIATION, AND HYBRID FITNESS IN DIVERGED NATURAL POPULATIONS OF ARABIDOPSIS LYRATA

(2010) Päivi H. Leinonen et al.   EVOLUTION

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

(2010) A. McKenna et al.   GENOME RESEARCH

Population structure and historical biogeography of European Arabidopsis lyrata

(2010) S W Ansell et al.   HEREDITY

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

(2010) LAURENT EXCOFFIER et al.   Molecular Ecology Resources

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

(2010) X. Yi et al.   SCIENCE

Local adaptation in European populations of Arabidopsis lyrata (Brassicaceae)

(2009) P. H. Leinonen et al.   AMERICAN JOURNAL OF BOTANY

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

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

The allopolyploidArabidopsis kamchaticaoriginated from multiple individuals ofArabidopsis lyrataandArabidopsis halleri

(2009) RIE SHIMIZU-INATSUGI et al.   MOLECULAR ECOLOGY

Intraspecfic variation in cold-temperature metabolic phenotypes of Arabidopsis lyrata ssp. petraea

(2008) Matthew P. Davey et al.   Metabolomics

Selection on Amino Acid Substitutions in Arabidopsis

(2008) J. P. Foxe et al.   MOLECULAR BIOLOGY AND EVOLUTION

Patterns of Polymorphism and Demographic History in Natural Populations of Arabidopsis lyrata

(2008) Jeffrey Ross-Ibarra et al.   PLoS One