The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards

Model-based approach to test hard polytomies in theEulaemusclade of the most diverse South American lizard genusLiolaemus(Liolaemini, Squamata)

(2015) Melisa Olave et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Evaluating the ability of the pairwise joint site frequency spectrum to co-estimate selection and demography

(2015) Lisha A. Mathew et al.   Frontiers in Genetics

On the Prospect of Identifying Adaptive Loci in Recently Bottlenecked Populations

(2014) Yu-Ping Poh et al.   PLoS One

On the unfounded enthusiasm for soft selective sweeps

(2014) Jeffrey D Jensen   Nature Communications

SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes

(2013) Pavlos Pavlidis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Adaptive Evolution of Multiple Traits Through Multiple Mutations at a Single Gene

(2013) C. R. Linnen et al.   SCIENCE

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

The impact of equilibrium assumptions on tests of selection

(2013) Jessica L. Crisci et al.   Frontiers in Genetics

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

(2012) X. Zheng et al.   BIOINFORMATICS

EVIDENCE OF ADAPTATION FROM ANCESTRAL VARIATION IN YOUNG POPULATIONS OF BEACH MICE

(2012) Vera S. Domingues et al.   EVOLUTION

Crossing the threshold: gene flow, dominance and the critical level of standing genetic variation required for adaptation to novel environments

(2012) S. L. Nuismer et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

A Critical Assessment of Storytelling: Gene Ontology Categories and the Importance of Validating Genomic Scans

(2012) Pavlos Pavlidis et al.   MOLECULAR BIOLOGY AND EVOLUTION

abc: an R package for approximate Bayesian computation (ABC)

(2012) Katalin Csilléry et al.   Methods in Ecology and Evolution

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

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Jaatha: a fast composite-likelihood approach to estimate demographic parameters

(2011) LISHA NADUVILEZHATH et al.   MOLECULAR ECOLOGY

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus

(2010) Gregory Ewing et al.   BIOINFORMATICS

“SAME SAME BUT DIFFERENT”: REPLICATED ECOLOGICAL SPECIATION AT WHITE SANDS

(2010) Erica Bree Rosenblum et al.   EVOLUTION

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

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

(2010) A. McKenna et al.   GENOME RESEARCH

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Adaptation genomics: the next generation

(2010) Jessica Stapley et al.   TRENDS IN ECOLOGY & EVOLUTION

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Efficient Approximate Bayesian Computation Coupled With Markov Chain Monte Carlo Without Likelihood

(2009) Daniel Wegmann et al.   GENETICS

Inferring weak population structure with the assistance of sample group information

(2009) MELISSA J. HUBISZ et al.   Molecular Ecology Resources

The genetics of quantitative traits: challenges and prospects

(2009) Trudy F. C. Mackay et al.   NATURE REVIEWS GENETICS

Molecular and functional basis of phenotypic convergence in white lizards at White Sands

(2009) E. B. Rosenblum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

(2009) Y. F. Chan et al.   SCIENCE

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

Genetic basis of fitness differences in natural populations

(2008) Hans Ellegren et al.   NATURE