Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher (Ficedula albicollis ) genome

PSMC analysis of effective population sizes in molecular ecology and its application to black-and-whiteFicedulaflycatchers

(2016) Krystyna Nadachowska-Brzyska et al.   MOLECULAR ECOLOGY

Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum ofFicedulaflycatchers

(2015) Reto Burri et al.   GENOME RESEARCH

Chromosomal patterns of diversity and differentiation in creepers: a next-gen phylogeographic investigation of Certhia americana

(2015) J D Manthey et al.   HEREDITY

Targeted capture in evolutionary and ecological genomics

(2015) Matthew R. Jones et al.   MOLECULAR ECOLOGY

Whole-genome resequencing of extreme phenotypes in collared flycatchers highlights the difficulty of detecting quantitative trait loci in natural populations

(2015) Marty Kardos et al.   Molecular Ecology Resources

Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data

(2015) Alexander Nater et al.   SYSTEMATIC BIOLOGY

Evolutionary analysis of the female-specific avian W chromosome

(2015) Linnéa Smeds et al.   Nature Communications

Natural Selection Constrains Neutral Diversity across A Wide Range of Species

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

Sampling strategies for frequency spectrum-based population genomic inference

(2014) John D Robinson et al.   BMC EVOLUTIONARY BIOLOGY

Genomic resources for the endangered Hawaiian honeycreepers

(2014) Taylor Callicrate et al.   BMC GENOMICS

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

Estimation of linkage disequilibrium and interspecific gene flow inFicedulaflycatchers by a newly developed 50k single-nucleotide polymorphism array

(2014) Takeshi Kawakami et al.   Molecular Ecology Resources

Comparative population genomics in animals uncovers the determinants of genetic diversity

(2014) J. Romiguier et al.   NATURE

Genomic identification and characterization of the pseudoautosomal region in highly differentiated avian sex chromosomes

(2014) Linnéa Smeds et al.   Nature Communications

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

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

How does ecological disturbance influence genetic diversity?

(2013) Sam C. Banks et al.   TRENDS IN ECOLOGY & EVOLUTION

Genome sequencing and population genomics in non-model organisms

(2013) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

Strong Purifying Selection at Synonymous Sites in D. melanogaster

(2013) David S. Lawrie et al.   PLoS Genetics

Genomic Patterns of Homozygosity in Worldwide Human Populations

(2012) Trevor J. Pemberton et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Effects of Deleterious Mutations on Evolution at Linked Sites

(2012) Brian Charlesworth   GENETICS

Evidence for complex selection on four-fold degenerate sites inDrosophila melanogaster

(2012) F. Clemente et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Recombination Rates and Genomic Shuffling in Human and Chimpanzee—A New Twist in the Chromosomal Speciation Theory

(2012) Marta Farré et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Quantifying the Variation in the Effective Population Size Within a Genome

(2011) Toni I. Gossmann et al.   GENETICS

Significant Selective Constraint at 4-Fold Degenerate Sites in the Avian Genome and Its Consequence for Detection of Positive Selection

(2011) Axel Künstner et al.   Genome Biology and Evolution

How closely does genetic diversity in finite populations conform to predictions of neutral theory? Large deficits in regions of low recombination

(2011) R Frankham   HEREDITY

Evolutionary Constraint in Flanking Regions of Avian Genes

(2011) Axel Künstner et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Variation in the mutation rate across mammalian genomes

(2011) Alan Hodgkinson et al.   NATURE REVIEWS GENETICS

Massive turnover of functional sequence in human and other mammalian genomes

(2010) S. Meader 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

Common SNPs explain a large proportion of the heritability for human height

(2010) Jian Yang et al.   NATURE GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Detection of nonneutral substitution rates on mammalian phylogenies

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

Distributions of Selectively Constrained Sites and Deleterious Mutation Rates in the Hominid and Murid Genomes

(2009) L. Eory et al.   MOLECULAR BIOLOGY AND EVOLUTION

The functional repertoires of metazoan genomes

(2008) Chris P. Ponting   NATURE REVIEWS GENETICS

Adaptation from standing genetic variation

(2007) R BARRETT et al.   TRENDS IN ECOLOGY & EVOLUTION