Human demographic history has amplified the effects of background selection across the genome

Background selection as null hypothesis in population genomics: insights and challenges from Drosophila studies

(2017) Josep M. Comeron   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Temporal Perspective on the Interplay of Demography and Selection on Deleterious Variation in Humans

(2017) Evan Koch et al.   G3-Genes Genomes Genetics

Robust linear regression: A review and comparison

(2016) Chun Yu et al.   COMMUNICATIONS IN STATISTICS-SIMULATION AND COMPUTATION

The impact of recent population history on the deleterious mutation load in humans and close evolutionary relatives

(2016) Yuval B Simons et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

When Is Selection Effective?

(2016) Simon Gravel   GENETICS

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

(2016) D. R. Schrider et al.   GENETICS

Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants

(2016) Lawrence H. Uricchio et al.   GENOME RESEARCH

A Thousand Fly Genomes: An ExpandedDrosophilaGenome Nexus

(2016) Justin B. Lack et al.   MOLECULAR BIOLOGY AND EVOLUTION

Determinants of genetic diversity

(2016) Hans Ellegren et al.   NATURE REVIEWS GENETICS

The Limits of Natural Selection in a Nonequilibrium World

(2016) Yaniv Brandvain et al.   TRENDS IN GENETICS

Determining the Effect of Natural Selection on Linked Neutral Divergence across Species

(2016) Tanya N. Phung et al.   PLoS Genetics

A Genomic Map of the Effects of Linked Selection in Drosophila

(2016) Eyal Elyashiv et al.   PLoS Genetics

When Is Selection Effective?

(2016) Simon Gravel   GENETICS

Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates

(2015) Pier Francesco Palamara et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Accumulation of Deleterious Mutations as a Consequence of Domestication and Improvement in Sunflowers and Other Compositae Crops

(2015) Sebastien Renaut et al.   MOLECULAR BIOLOGY AND EVOLUTION

The consequences of not accounting for background selection in demographic inference

(2015) Gregory B. Ewing et al.   MOLECULAR ECOLOGY

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans

(2015) Ron Do et al.   NATURE GENETICS

Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs

(2015) Clare D. Marsden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distance from sub-Saharan Africa predicts mutational load in diverse human genomes

(2015) Brenna M. Henn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Natural Selection Constrains Neutral Diversity across A Wide Range of Species

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

Dominance of Deleterious Alleles Controls the Response to a Population Bottleneck

(2015) Daniel J. Balick et al.   PLoS Genetics

Contrasting X-Linked and Autosomal Diversity across 14 Human Populations

(2014) Leonardo Arbiza et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Exome capture from saliva produces high quality genomic and metagenomic data

(2014) Jeffrey M Kidd et al.   BMC GENOMICS

Population Genetic Simulations of Complex Phenotypes with Implications for Rare Variant Association Tests

(2014) Lawrence H. Uricchio et al.   GENETIC EPIDEMIOLOGY

Genome-wide signals of positive selection in human evolution

(2014) D. Enard et al.   GENOME RESEARCH

selscan: An Efficient Multithreaded Program to Perform EHH-Based Scans for Positive Selection

(2014) Z. A. Szpiech et al.   MOLECULAR BIOLOGY AND EVOLUTION

The deleterious mutation load is insensitive to recent population history

(2014) Yuval B Simons et al.   NATURE GENETICS

Recombination initiation maps of individual human genomes

(2014) F. Pratto et al.   SCIENCE

Thinking too positive? Revisiting current methods of population genetic selection inference

(2014) Claudia Bank et al.   TRENDS IN GENETICS

Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history

(2014) Hie Lim Kim et al.   Nature Communications

Distribution and Medical Impact of Loss-of-Function Variants in the Finnish Founder Population

(2014) Elaine T. Lim et al.   PLoS Genetics

Background Selection as Baseline for Nucleotide Variation across the Drosophila Genome

(2014) Josep M. Comeron   PLoS Genetics

Genetic Diversity in the Interference Selection Limit

(2014) Benjamin H. Good et al.   PLoS Genetics

Natural Selection Reduced Diversity on Human Y Chromosomes

(2014) Melissa A. Wilson Sayres et al.   PLoS Genetics

Loss and Recovery of Genetic Diversity in Adapting Populations of HIV

(2014) Pleuni S. Pennings et al.   PLoS Genetics

Distortions in Genealogies due to Purifying Selection and Recombination

(2013) L. E. Nicolaisen et al.   GENETICS

Estimating and interpreting FST: The impact of rare variants

(2013) G. Bhatia et al.   GENOME RESEARCH

Population Genetics of Rare Variants and Complex Diseases

(2013) M. Cyrus Maher et al.   HUMAN HEREDITY

Genomic signatures of selection at linked sites: unifying the disparity among species

(2013) Asher D. Cutter et al.   NATURE REVIEWS GENETICS

Frequent adaptation and the McDonald-Kreitman test

(2013) P. W. Messer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes

(2013) John A. Capra et al.   PLoS Genetics

Whole-Exome Sequencing Reveals a Rapid Change in the Frequency of Rare Functional Variants in a Founding Population of Humans

(2013) Ferran Casals et al.   PLoS Genetics

Limited Evidence for Classic Selective Sweeps in African Populations

(2012) J. M. Granka et al.   GENETICS

The Effects of Deleterious Mutations on Evolution at Linked Sites

(2012) Brian Charlesworth   GENETICS

A coalescent model of background selection with recombination, demography and variation in selection coefficients

(2012) K Zeng   HEREDITY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity

(2012) Erik C Andersen et al.   NATURE GENETICS

Genealogies of rapidly adapting populations

(2012) R. A. Neher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The great human expansion

(2012) B. M. Henn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes

(2012) J. A. Tennessen et al.   SCIENCE

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

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

Genomic Data Reveal a Complex Making of Humans

(2012) Isabel Alves et al.   PLoS Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Natural Selection in Gene-Dense Regions Shapes the Genomic Pattern of Polymorphism in Wild and Domesticated Rice

(2011) J. M. Flowers et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

Analyses of X-linked and autosomal genetic variation in population-scale whole genome sequencing

(2011) Srikanth Gottipati et al.   NATURE GENETICS

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

Demographic history and rare allele sharing among human populations

(2011) S. Gravel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Classic Selective Sweeps Were Rare in Recent Human Evolution

(2011) R. D. Hernandez et al.   SCIENCE

Natural Selection Affects Multiple Aspects of Genetic Variation at Putatively Neutral Sites across the Human Genome

(2011) Kirk E. Lohmueller et al.   PLoS Genetics

The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes

(2010) Michael F Hammer et al.   NATURE GENETICS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Genetic hitchhiking versus background selection: the controversy and its implications

(2010) W. Stephan   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds

(2009) et al.   SCIENCE

Evolutionary Processes Acting on Candidate cis-Regulatory Regions in Humans Inferred from Patterns of Polymorphism and Divergence

(2009) Dara G. Torgerson et al.   PLoS Genetics

Widespread Genomic Signatures of Natural Selection in Hominid Evolution

(2009) Graham McVicker et al.   PLoS Genetics

Pervasive Natural Selection in the Drosophila Genome?

(2009) Guy Sella et al.   PLoS Genetics

Pervasive Hitchhiking at Coding and Regulatory Sites in Humans

(2009) James J. Cai et al.   PLoS Genetics

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

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

A flexible forward simulator for populations subject to selection and demography

(2008) R. D. Hernandez   BIOINFORMATICS

Proportionally more deleterious genetic variation in European than in African populations

(2008) Kirk E. Lohmueller et al.   NATURE

Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome

(2008) Adam R. Boyko et al.   PLoS Genetics