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

Estimating the parameters of background selection and selective sweeps inDrosophilain the presence of gene conversion

(2017) José Luis Campos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resolving the Conflict Between Associative Overdominance and Background Selection

(2016) L. Zhao et al.   GENETICS

Joint Prediction of the Effective Population Size and the Rate of Fixation of Deleterious Mutations

(2016) E. Santiago et al.   GENETICS

Whole-Genome Analysis of Individual Meiotic Events in Drosophila melanogaster Reveals That Noncrossover Gene Conversions Are Insensitive to Interference and the Centromere Effect

(2016) Danny E. Miller et al.   GENETICS

Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene

(2016) Simon H. Martin et al.   GENETICS

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

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

The Impact of Linked Selection in Chimpanzees: A Comparative Study

(2016) Susanne P. Pfeifer et al.   Genome Biology and Evolution

SLiM 2: Flexible, Interactive Forward Genetic Simulations

(2016) Benjamin C. Haller et al.   MOLECULAR BIOLOGY AND EVOLUTION

The potential for adaptive maintenance of diversity in insect antimicrobial peptides

(2016) Robert L. Unckless et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Deep Learning for Population Genetic Inference

(2016) Sara Sheehan et al.   PLoS Computational Biology

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

High-Resolution Mapping of Crossover and Non-crossover Recombination Events by Whole-Genome Re-sequencing of an Avian Pedigree

(2016) Linnéa Smeds et al.   PLoS Genetics

S/HIC: Robust Identification of Soft and Hard Sweeps Using Machine Learning

(2016) Daniel R. Schrider et al.   PLoS Genetics

Whole-Genome Analysis of Individual Meiotic Events in Drosophila melanogaster Reveals That Noncrossover Gene Conversions Are Insensitive to Interference and the Centromere Effect

(2016) Danny E. Miller et al.   GENETICS

Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene

(2016) Simon H. Martin et al.   GENETICS

The Effects of Background and Interference Selection on Patterns of Genetic Variation in Subdivided Populations

(2015) K. Zeng et al.   GENETICS

The Drosophila Genome Nexus: A Population Genomic Resource of 623 Drosophila melanogaster Genomes, Including 197 from a Single Ancestral Range Population

(2015) Justin B. Lack et al.   GENETICS

Recombining without Hotspots: A Comprehensive Evolutionary Portrait of Recombination in Two Closely Related Species ofDrosophila

(2015) Caiti S. Smukowski Heil et al.   Genome Biology and Evolution

The Release 6 reference sequence of theDrosophila melanogastergenome

(2015) Roger A. Hoskins et al.   GENOME RESEARCH

The Time Scale of Recombination Rate Evolution in Great Apes

(2015) Laurie S. Stevison 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

Detecting recent selective sweeps while controlling for mutation rate and background selection

(2015) Christian D. Huber et al.   MOLECULAR ECOLOGY

Nonparadoxical evolutionary stability of the recombination initiation landscape in yeast

(2015) I. Lam et al.   SCIENCE

Stable recombination hotspots in birds

(2015) S. Singhal et al.   SCIENCE

The Drosophila Genome Nexus: A Population Genomic Resource of 623 Drosophila melanogaster Genomes, Including 197 from a Single Ancestral Range Population

(2015) Justin B. Lack et al.   GENETICS

The Relations Between Recombination Rate and Patterns of Molecular Variation and Evolution in Drosophila

(2014) Brian Charlesworth et al.   Annual Review of Genetics

The Relation between Recombination Rate and Patterns of Molecular Evolution and Variation in Drosophila melanogaster

(2014) José L. Campos et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Genomic Evidence of Rapid and Stable Adaptive Oscillations over Seasonal Time Scales in Drosophila

(2014) Alan O. Bergland et al.   PLoS Genetics

Genetic Draft, Selective Interference, and Population Genetics of Rapid Adaptation

(2013) Richard A. Neher   Annual Review of Ecology Evolution and Systematics

The Drosophila early ovarian transcriptome provides insight to the molecular causes of recombination rate variation across genomes

(2013) Andrew B Adrian et al.   BMC GENOMICS

Meiotic gene-conversion rate and tract length variation in the human genome

(2013) Badri Padhukasahasram et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Crossover Heterogeneity in the Absence of Hotspots in Caenorhabditis elegans

(2013) Taniya Kaur et al.   GENETICS

Fine-Scale Heterogeneity in Crossover Rate in the garnet-scalloped Region of the Drosophila melanogaster X Chromosome

(2013) N. D. Singh et al.   GENETICS

SLiM: Simulating Evolution with Selection and Linkage

(2013) Philipp W. Messer   GENETICS

Distortions in Genealogies due to Purifying Selection and Recombination

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

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

Population genomics of rapid adaptation by soft selective sweeps

(2013) Philipp W. Messer et al.   TRENDS IN ECOLOGY & EVOLUTION

Rethinking Hardy-Weinberg and genetic drift in undergraduate biology

(2012) Joanna Masel   BIOESSAYS

The Role of Background Selection in Shaping Patterns of Molecular Evolution and Variation: Evidence from Variability on the Drosophila X Chromosome

(2012) B. Charlesworth   GENETICS

Fluctuations of Fitness Distributions and the Rate of Muller's Ratchet

(2012) R. A. Neher et al.   GENETICS

Genomic Variation in Natural Populations of Drosophila melanogaster

(2012) C. H. Langley et al.   GENETICS

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

(2012) K Zeng   HEREDITY

Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations

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

Recombination Modulates How Selection Affects Linked Sites in Drosophila

(2012) Suzanne E. McGaugh et al.   PLOS BIOLOGY

Limits to the Rate of Adaptive Substitution in Sexual Populations

(2012) Daniel B. Weissman et al.   PLoS Genetics

Genome-Wide Fine-Scale Recombination Rate Variation in Drosophila melanogaster

(2012) Andrew H. Chan et al.   PLoS Genetics

The Many Landscapes of Recombination in Drosophila melanogaster

(2012) Josep M. Comeron et al.   PLoS Genetics

Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture

(2012) John E. Pool et al.   PLoS Genetics

A Hierarchical Combination of Factors Shapes the Genome-wide Topography of Yeast Meiotic Recombination Initiation

(2011) Jing Pan et al.   CELL

The Structure of Genealogies in the Presence of Purifying Selection: A Fitness-Class Coalescent

(2011) Aleksandra M. Walczak et al.   GENETICS

The Joint Effects of Background Selection and Genetic Recombination on Local Gene Genealogies

(2011) Kai Zeng et al.   GENETICS

Genetic Draft and Quasi-Neutrality in Large Facultatively Sexual Populations

(2011) R. A. Neher et al.   GENETICS

Recombination rate variation in closely related species

(2011) C S Smukowski et al.   HEREDITY

Polymorphism, Divergence, and the Role of Recombination in Saccharomyces cerevisiae Genome Evolution

(2011) A. D. Cutter et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Genome-wide analysis reveals novel molecular features of mouse recombination hotspots

(2011) Fatima Smagulova et al.   NATURE

The landscape of recombination in African Americans

(2011) Anjali G. Hinch et al.   NATURE

Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice

(2011) M. W. Nachman et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

Contrasting Methods of Quantifying Fine Structure of Human Recombination

(2010) Andrew G. Clark et al.   Annual Review of Genomics and Human Genetics

The Effects of Demography and Linkage on the Estimation of Selection and Mutation Parameters

(2010) K. Zeng et al.   GENETICS

Muller's Ratchet and the Degeneration of the Drosophila miranda Neo-Y Chromosome

(2010) V. B. Kaiser et al.   GENETICS

Natural selection shapes nucleotide polymorphism across the genome of the nematode Caenorhabditis briggsae

(2010) A. D. Cutter et al.   GENOME RESEARCH

Extensive recombination rate variation in the house mouse species complex inferred from genetic linkage maps

(2010) B. L. Dumont et al.   GENOME RESEARCH

Shifts in the intensity of purifying selection: An analysis of genome-wide polymorphism data from two closely related yeast species

(2010) E. Elyashiv et al.   GENOME RESEARCH

Fine-scale recombination rate differences between sexes, populations and individuals

(2010) Augustine Kong et al.   NATURE

The population genetics of mutations: good, bad and indifferent

(2010) L. Loewe et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Recent Strong Positive Selection on Drosophila melanogaster HDAC6, a Gene Encoding a Stress Surveillance Factor, as Revealed by Population Genomic Analysis

(2009) N. Svetec et al.   MOLECULAR BIOLOGY AND EVOLUTION

Estimating the Rate of Adaptive Molecular Evolution in the Presence of Slightly Deleterious Mutations and Population Size Change

(2009) A. Eyre-Walker et al.   MOLECULAR BIOLOGY AND EVOLUTION

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

Population genomic inference of recombination rates and hotspots

(2009) Y. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recombinational Landscape and Population Genomics of Caenorhabditis elegans

(2009) Matthew V. Rockman 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

A flexible forward simulator for populations subject to selection and demography

(2008) R. D. Hernandez   BIOINFORMATICS

High-resolution mapping of meiotic crossovers and non-crossovers in yeast

(2008) Eugenio Mancera et al.   NATURE

Accelerated genetic drift on chromosome X during the human dispersal out of Africa

(2008) Alon Keinan et al.   NATURE GENETICS

Bayesian inference of fine-scale recombination rates using population genomic data

(2008) Y. Wang et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The effects of deleterious mutations on evolution in non-recombining genomes

(2008) Vera B. Kaiser et al.   TRENDS IN GENETICS

An Approximate Bayesian Estimator Suggests Strong, Recurrent Selective Sweeps in Drosophila

(2008) Jeffrey D. Jensen et al.   PLoS Genetics

The traveling-wave approach to asexual evolution: Muller's ratchet and speed of adaptation

(2007) Igor M. Rouzine et al.   THEORETICAL POPULATION BIOLOGY