Natural selection shaped the rise and fall of passenger pigeon genomic diversity

Correlated patterns of genetic diversity and differentiation across an avian family

(2017) Benjamin M. Van Doren et al.   MOLECULAR ECOLOGY

Evidence that the rate of strong selective sweeps increases with population size in the great apes

(2017) Kiwoong Nam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting

(2017) Ludovic Dutoit et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Complete mitochondrial genomes of living and extinct pigeons revise the timing of the columbiform radiation

(2016) André E. R. Soares et al.   BMC EVOLUTIONARY BIOLOGY

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

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

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

Body mass-corrected molecular rate for bird mitochondrial DNA

(2016) Benoit Nabholz et al.   MOLECULAR ECOLOGY

Thromboelastography in Selected Avian Species

(2015) Sophie Strindberg et al.   JOURNAL OF AVIAN MEDICINE AND SURGERY

Recombination Rate Variation Modulates Gene Sequence Evolution Mainly via GC-Biased Gene Conversion, Not Hill–Robertson Interference, in an Avian System

(2015) Paulina Bolívar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-Wide Analysis of Positively Selected Genes in Seasonal and Non-Seasonal Breeding Species

(2015) Yuhuan Meng et al.   PLoS One

Stable recombination hotspots in birds

(2015) S. Singhal et al.   SCIENCE

Natural Selection Constrains Neutral Diversity across A Wide Range of Species

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

Present-day risk assessment would have predicted the extinction of the passenger pigeon (Ectopistes migratorius)

(2014) Jessica C. Stanton   BIOLOGICAL CONSERVATION

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

(2014) Shiping Liu et al.   CELL

Association of MEP1A gene variants with insulin metabolism in central European women with polycystic ovary syndrome

(2014) Uyen D.P. Lam et al.   GENE

Highly Variable Recombinational Landscape Modulates Efficacy of Natural Selection in Birds

(2014) Toni I. Gossmann et al.   Genome Biology and Evolution

A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution

(2014) Takeshi Kawakami et al.   MOLECULAR ECOLOGY

Drastic population fluctuations explain the rapid extinction of the passenger pigeon

(2014) C.-M. Hung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

Genetic Diversity in the Interference Selection Limit

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

Mutations in DNAH1, which Encodes an Inner Arm Heavy Chain Dynein, Lead to Male Infertility from Multiple Morphological Abnormalities of the Sperm Flagella

(2013) Mariem Ben Khelifa et al.   AMERICAN JOURNAL OF HUMAN GENETICS

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

(2013) Hákon Jónsson et al.   BIOINFORMATICS

Sleeping Giants: Emerging Roles for the Fat Cadherins in Health and Disease

(2013) Elham Sadeqzadeh et al.   MEDICINAL RESEARCH REVIEWS

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

Mutations in genes encoding the cadherin receptor-ligand pair DCHS1 and FAT4 disrupt cerebral cortical development

(2013) Silvia Cappello et al.   NATURE GENETICS

The De Novo Assembly of Mitochondrial Genomes of the Extinct Passenger Pigeon (Ectopistes migratorius) with Next Generation Sequencing

(2013) Chih-Ming Hung et al.   PLoS One

Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments

(2013) J. Dabney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Genomic Diversity and Evolution of the Head Crest in the Rock Pigeon

(2013) M. D. Shapiro et al.   SCIENCE

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

The ecology of stress: effects of the social environment

(2012) Scott Creel et al.   FUNCTIONAL ECOLOGY

Fine-Scale Maps of Recombination Rates and Hotspots in the Mouse Genome

(2012) Hadassa Brunschwig et al.   GENETICS

The Effects of Deleterious Mutations on Evolution at Linked Sites

(2012) Brian Charlesworth   GENETICS

Genomic Variation in Natural Populations of Drosophila melanogaster

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

The Effect of Variation in the Effective Population Size on the Rate of Adaptive Molecular Evolution in Eukaryotes

(2012) Toni I. Gossmann et al.   Genome Biology and Evolution

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

(2012) N. Rohland et al.   GENOME RESEARCH

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genomic landscape of species divergence in Ficedula flycatchers

(2012) Hans Ellegren et al.   NATURE

Effective/census population size ratio estimation: a compendium and appraisal

(2012) Friso P. Palstra et al.   Ecology and Evolution

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

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

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Are levels of digestive enzyme activity related to the natural diet in passerine birds?

(2011) Natalia Ramírez-Otárola et al.   BIOLOGICAL RESEARCH

Testing for Ancient Admixture between Closely Related Populations

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

Skyline-plot methods for estimating demographic history from nucleotide sequences

(2011) SIMON Y. W. HO et al.   Molecular Ecology Resources

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Meraculous: De Novo Genome Assembly with Short Paired-End Reads

(2011) Jarrod A. Chapman et al.   PLoS One

Identification of Soat1 as a Quantitative Trait Locus Gene on Mouse Chromosome 1 Contributing to Hyperlipidemia

(2011) Zongji Lu et al.   PLoS One

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Response network analysis of differential gene expression in human epithelial lung cells during avian influenza infections

(2010) Ken Tatebe et al.   BMC BIOINFORMATICS

Characterisation of sugar beet (Beta vulgaris L. ssp. vulgaris) varieties using microsatellite markers

(2010) Marinus JM Smulders et al.   BMC GENETICS

Sex-dimorphic gene expression and ineffective dosage compensation of Z-linked genes in gastrulating chicken embryos

(2010) Shaobing O Zhang et al.   BMC GENOMICS

Nebulin, a major player in muscle health and disease

(2010) Siegfried Labeit et al.   FASEB JOURNAL

The recombination landscape of the zebra finch Taeniopygia guttata genome

(2010) N. Backstrom et al.   GENOME RESEARCH

Estimation of the Neutrality Index

(2010) N. Stoletzki et al.   MOLECULAR BIOLOGY AND EVOLUTION

HapStar: automated haplotype network layout and visualization

(2010) A. G. F. TEACHER et al.   Molecular Ecology Resources

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

Multivariate analysis of male reproductive function in Inpp5b−/− mice reveals heterogeneity in defects in fertility, sperm–egg membrane interaction and proteolytic cleavage of sperm ADAMs

(2010) Matthew R. Marcello et al.   MOLECULAR HUMAN REPRODUCTION

The flight of the Passenger Pigeon: Phylogenetics and biogeographic history of an extinct species

(2010) Kevin P. Johnson et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Evolutionary stasis: the stable chromosomes of birds

(2010) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

Understanding Adaptation in Large Populations

(2010) Nick Barton   PLoS Genetics

Evidence that Adaptation in Drosophila Is Not Limited by Mutation at Single Sites

(2010) Talia Karasov et al.   PLoS Genetics

Molecular evolution of genes in avian genomes

(2010) Kiwoong Nam et al.   GENOME BIOLOGY

Apolipoprotein B levels, APOB alleles, and risk of ischemic cardiovascular disease in the general population, a review

(2009) Marianne Benn   ATHEROSCLEROSIS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Clever-1/Stabilin-1 regulates lymphocyte migration within lymphatics and leukocyte entrance to sites of inflammation

(2009) Marika Karikoski et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Differential gene-expression and host-response profiles against avian influenza virus within the chicken lung due to anatomy and airflow

(2009) S. S. Reemers et al.   JOURNAL OF GENERAL VIROLOGY

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

A rapid column-based ancient DNA extraction method for increased sample throughput

(2009) NADIN ROHLAND et al.   Molecular Ecology Resources

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

Evolution of the Drosophila Nuclear Pore Complex Results in Multiple Hybrid Incompatibilities

(2009) S. Tang et al.   SCIENCE

The Last Glacial Maximum

(2009) P. U. Clark et al.   SCIENCE

Quantifying Adaptive Evolution in the Drosophila Immune System

(2009) Darren J. Obbard et al.   PLoS Genetics

Selection on Codon Bias

(2008) Ruth Hershberg et al.   Annual Review of Genetics

The McDonald-Kreitman Test and Slightly Deleterious Mutations

(2008) J. Charlesworth et al.   MOLECULAR BIOLOGY AND EVOLUTION

The endogenous cannabinoid anandamide has effects on motivation and anxiety that are revealed by fatty acid amide hydrolase (FAAH) inhibition

(2007) Maria Scherma et al.   NEUROPHARMACOLOGY

Reduced anxiety-like behaviour induced by genetic and pharmacological inhibition of the endocannabinoid-degrading enzyme fatty acid amide hydrolase (FAAH) is mediated by CB1 receptors

(2007) Fabricio A. Moreira et al.   NEUROPHARMACOLOGY