A beginner's guide to low‐coverage whole genome sequencing for population genomics

Genomic signatures of selection in bats surviving white‐nose syndrome

(2021) Sarah A. Gignoux‐Wolfsohn et al.   MOLECULAR ECOLOGY

High genetic diversity and low differentiation reflect the ecological versatility of the African leopard

(2021) Patrícia Pečnerová et al.   CURRENT BIOLOGY

Haplotype tagging reveals parallel formation of hybrid races in two butterfly species

(2021) Joana I. Meier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional colour genes and signals of selection in colour‐polymorphic salamanders

(2020) James D. Burgon et al.   MOLECULAR ECOLOGY

Versatile simulations of admixture and accurate local ancestry inference with mixnmatch and ancestryinfer

(2020) Molly Schumer et al.   Molecular Ecology Resources

Natural hybridization reveals incompatible alleles that cause melanoma in swordtail fish

(2020) Daniel L. Powell et al.   SCIENCE

Optimized and affordable high‐throughput sequencing workflow for preserved and nonpreserved small zooplankton specimens

(2020) Jannik Beninde et al.   Molecular Ecology Resources

Evaluating the effect of reference genome divergence on the analysis of empirical RADseq datasets

(2020) Justin Bohling   Ecology and Evolution

Population genomics of the Viking world

(2020) Ashot Margaryan et al.   NATURE

Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome

(2020) Aryn P. Wilder et al.   Evolution Letters

LFMM 2: Fast and accurate inference of gene-environment associations in genome-wide studies

(2019) Kevin Caye et al.   MOLECULAR BIOLOGY AND EVOLUTION

Minor allele frequency thresholds strongly affect population structure inference with genomic datasets

(2019) Ethan Linck et al.   Molecular Ecology Resources

Genotype-free estimation of allele frequencies reduces bias and improves demographic inference from RADSeq data

(2019) Vera M. Warmuth et al.   Molecular Ecology Resources

The future is now: amplicon sequencing and sequence capture usher in the conservation genomics era

(2019) Mariah H. Meek et al.   Molecular Ecology Resources

ngsLD: evaluating linkage disequilibrium using genotype likelihoods

(2019) Emma A Fox et al.   BIOINFORMATICS

Allele Frequency Difference AFD–An Intuitive Alternative to FST for Quantifying Genetic Population Differentiation

(2019) Berner   Genes

Adaptive genetic variation underlies biocomplexity of Atlantic Cod in the Gulf of Maine and on Georges Bank

(2019) G. V. Clucas et al.   PLoS One

Contrasting genomic shifts underlie parallel phenotypic evolution in response to fishing

(2019) Nina O. Therkildsen et al.   SCIENCE

Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole‐genome sequencing

(2019) Gemma V. Clucas et al.   Evolutionary Applications

An Ultra High-Density Arabidopsis thaliana Crossover Map That Refines the Influences of Structural Variation and Epigenetic Features

(2019) Beth A. Rowan et al.   GENETICS

Using Haplotype Information for Conservation Genomics

(2019) Maeva Leitwein et al.   TRENDS IN ECOLOGY & EVOLUTION

A flicker of hope: Genomic data distinguish Northern Flicker taxa despite low levels of divergence

(2018) Stepfanie M. Aguillon et al.   AUK

Linkage Disequilibrium Estimation in Low Coverage High-Throughput Sequencing Data

(2018) Timothy P. Bilton et al.   GENETICS

Inferring Continuous and Discrete Population Genetic Structure Across Space

(2018) Gideon S. Bradburd et al.   GENETICS

Full mitochondrial genome sequences reveal new insights about post-glacial expansion and regional phylogeographic structure in the Atlantic silverside (Menidia menidia)

(2018) Runyang Nicolas Lou et al.   MARINE BIOLOGY

Extended and Continuous Decline in Effective Population Size Results in Low Genomic Diversity in the World’s Rarest Hyena Species, the Brown Hyena

(2018) Michael V Westbury et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparing methods for detecting multilocus adaptation with multivariate genotype-environment associations

(2018) Brenna R. Forester et al.   MOLECULAR ECOLOGY

Expressed exome capture sequencing: A method for cost-effective exome sequencing for all organisms

(2018) Jonathan B. Puritz et al.   Molecular Ecology Resources

Linkage Disequilibrium Estimation in Low Coverage High-Throughput Sequencing Data

(2018) Timothy P. Bilton et al.   GENETICS

Inferring Continuous and Discrete Population Genetic Structure Across Space

(2018) Gideon S. Bradburd et al.   GENETICS

SLiM 3: Forward Genetic Simulations Beyond the Wright–Fisher Model

(2018) Benjamin C Haller et al.   MOLECULAR BIOLOGY AND EVOLUTION

New Approaches for Genome Assembly and Scaffolding

(2018) Edward S. Rice et al.   Annual Review of Animal Biosciences

Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

(2017) Angela P. Fuentes-Pardo et al.   MOLECULAR ECOLOGY

RADseq provides unprecedented insights into molecular ecology and evolutionary genetics: comment on Breaking RAD by Lowry et al . (2016)

(2017) Garrett J. McKinney et al.   Molecular Ecology Resources

Large-Scale Low-Cost NGS Library Preparation Using a Robust Tn5 Purification and Tagmentation Protocol

(2017) Bianca P. Hennig et al.   G3-Genes Genomes Genetics

Repeated divergent selection on pigmentation genes in a rapid finch radiation

(2017) Leonardo Campagna et al.   Science Advances

Complex modular architecture around a simple toolkit of wing pattern genes

(2017) Steven M. Van Belleghem et al.   Nature Ecology & Evolution

Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia

(2016) Kevin J. Galinsky et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Estimating IBD tracts from low coverage NGS data

(2016) Filipe G. Vieira et al.   BIOINFORMATICS

SweepFinder2: increased sensitivity, robustness and flexibility

(2016) Michael DeGiorgio et al.   BIOINFORMATICS

Improvement in detection of minor alleles in next generation sequencing by base quality recalibration

(2016) Shengyu Ni et al.   BMC GENOMICS

Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples

(2016) N. Snyder-Mackler et al.   GENETICS

Inferring Heterozygosity from Ancient and Low Coverage Genomes

(2016) Athanasios Kousathanas et al.   GENETICS

Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation

(2016) David B. Lowry et al.   Molecular Ecology Resources

Practical low-coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species

(2016) Nina Overgaard Therkildsen et al.   Molecular Ecology Resources

Exon capture optimization in amphibians with large genomes

(2016) Evan McCartney-Melstad et al.   Molecular Ecology Resources

Rapid genotype imputation from sequence without reference panels

(2016) Robert W Davies et al.   NATURE GENETICS

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

Genome-culture coevolution promotes rapid divergence of killer whale ecotypes

(2016) Andrew D. Foote et al.   Nature Communications

Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species

(2016) Eric T Domyan et al.   eLife

Inferring Heterozygosity from Ancient and Low Coverage Genomes

(2016) Athanasios Kousathanas et al.   GENETICS

Reliable Detection of Loci Responsible for Local Adaptation: Inference of a Null Model through Trimming the Distribution of FST

(2015) Michael C. Whitlock et al.   AMERICAN NATURALIST

Fast imputation using medium or low-coverage sequence data

(2015) Paul M. VanRaden et al.   BMC GENETICS

Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates

(2015) M. Gautier   GENETICS

Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation

(2015) Leonardo Campagna et al.   MOLECULAR ECOLOGY

Visualizing spatial population structure with estimated effective migration surfaces

(2015) Desislava Petkova et al.   NATURE GENETICS

Fast and accurate site frequency spectrum estimation from low coverage sequence data

(2014) Eunjung Han et al.   BIOINFORMATICS

ngsTools: methods for population genetics analyses from next-generation sequencing data

(2014) Matteo Fumagalli et al.   BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears

(2014) Shiping Liu et al.   CELL

A field guide to whole-genome sequencing, assembly and annotation

(2014) Robert Ekblom et al.   Evolutionary Applications

Genome-Wide Estimation of Linkage Disequilibrium from Population-Level High-Throughput Sequencing Data

(2014) Takahiro Maruki et al.   GENETICS

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

(2014) Simone Picelli et al.   GENOME RESEARCH

Resequencing studies of nonmodel organisms using closely related reference genomes: optimal experimental designs and bioinformatics approaches for population genomics

(2014) B. Nevado et al.   MOLECULAR ECOLOGY

WFABC: a Wright-Fisher ABC-based approach for inferring effective population sizes and selection coefficients from time-sampled data

(2014) Matthieu Foll et al.   Molecular Ecology Resources

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

Advances and limits of using population genetics to understand local adaptation

(2014) Peter Tiffin et al.   TRENDS IN ECOLOGY & EVOLUTION

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

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation

(2013) Filipe G. Vieira et al.   GENOME RESEARCH

Next-generation sequencing for molecular ecology: a caveat regarding pooled samples

(2013) Eric C. Anderson et al.   MOLECULAR ECOLOGY

Assessing the Effect of Sequencing Depth and Sample Size in Population Genetics Inferences

(2013) Matteo Fumagalli   PLoS One

Uninformative polymorphisms bias genome scans for signatures of selection

(2012) Marius Roesti et al.   BMC EVOLUTIONARY BIOLOGY

Association Testing for Next-Generation Sequencing Data Using Score Statistics

(2012) Line Skotte et al.   GENETIC EPIDEMIOLOGY

Population genomics based on low coverage sequencing: how low should we go?

(2012) C. Alex Buerkle et al.   MOLECULAR ECOLOGY

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Extremely low-coverage sequencing and imputation increases power for genome-wide association studies

(2012) Bogdan Pasaniuc et al.   NATURE GENETICS

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

(2012) Rasmus Nielsen et al.   PLoS One

Synthetic Spike-in Standards Improve Run-Specific Systematic Error Analysis for DNA and RNA Sequencing

(2012) Justin M. Zook et al.   PLoS One

Empirical Validation of Pooled Whole Genome Population Re-Sequencing in Drosophila melanogaster

(2012) Yuan Zhu et al.   PLoS One

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

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

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

(2011) Laurent Excoffier et al.   BIOINFORMATICS

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Estimation of allele frequency and association mapping using next-generation sequencing data

(2011) Su Kim et al.   BMC BIOINFORMATICS

Low-coverage sequencing: Implications for design of complex trait association studies

(2011) Y. Li et al.   GENOME RESEARCH

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

optix Drives the Repeated Convergent Evolution of Butterfly Wing Pattern Mimicry

(2011) R. D. Reed et al.   SCIENCE

The Next Generation of Molecular Markers From Massively Parallel Sequencing of Pooled DNA Samples

(2010) Andreas Futschik et al.   GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Simultaneous Genotype Calling and Haplotype Phasing Improves Genotype Accuracy and Reduces False-Positive Associations for Genome-wide Association Studies

(2009) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Linkage disequilibrium estimates of contemporaryNeusing highly variable genetic markers: a largely untapped resource for applied conservation and evolution

(2009) Robin S. Waples et al.   Evolutionary Applications

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

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

A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective

(2008) M. Foll et al.   GENETICS

Linkage disequilibrium — understanding the evolutionary past and mapping the medical future

(2008) Montgomery Slatkin   NATURE REVIEWS GENETICS