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

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

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

A supermatrix phylogeny of corvoid passerine birds (Aves: Corvides)

(2016) Knud Andreas Jønsson et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Determinants of genetic diversity

(2016) Hans Ellegren et al.   NATURE REVIEWS GENETICS

Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex

(2016) Nagarjun Vijay et al.   Nature Communications

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

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

Transcriptomics of colour patterning and coloration shifts in crows

(2015) J. W. Poelstra et al.   MOLECULAR ECOLOGY

Detecting balancing selection in genomes: limits and prospects

(2015) Anna Fijarczyk et al.   MOLECULAR ECOLOGY

Genetic rescue of small inbred populations: meta-analysis reveals large and consistent benefits of gene flow

(2015) Richard Frankham   MOLECULAR ECOLOGY

Fifteen years of genomewide scans for selection: trends, lessons and unaddressed genetic sources of complication

(2015) Ryan J. Haasl et al.   MOLECULAR ECOLOGY

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

(2015) Richard O. Prum et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

The effects of chromatin organization on variation in mutation rates in the genome

(2015) Kateryna D. Makova et al.   NATURE REVIEWS GENETICS

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

Genomic resources for the endangered Hawaiian honeycreepers

(2014) Taylor Callicrate et al.   BMC GENOMICS

The impact of linked selection on plant genomic variation

(2014) T. Slotte   Briefings in Functional 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

Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

(2014) Tami E. Cruickshank et al.   MOLECULAR ECOLOGY

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

(2014) J. W. Poelstra et al.   SCIENCE

Genome-wide analysis in chicken reveals that local levels of genetic diversity are mainly governed by the rate of recombination

(2013) Carina F Mugal et al.   BMC GENOMICS

Twisted Signatures of GC-Biased Gene Conversion Embedded in an Evolutionary Stable Karyotype

(2013) Carina F. Mugal et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data

(2013) Krystyna Nadachowska-Brzyska et al.   PLoS Genetics

Genomic Variation in Natural Populations of Drosophila melanogaster

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

The genomic landscape of species divergence in Ficedula flycatchers

(2012) Hans Ellegren et al.   NATURE

Quantifying the Variation in the Effective Population Size Within a Genome

(2011) Toni I. Gossmann et al.   GENETICS

Dynamic Evolution of Base Composition: Causes and Consequences in Avian Phylogenomics

(2011) B. Nabholz 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

The recombination landscape of the zebra finch Taeniopygia guttata genome

(2010) N. Backstrom et al.   GENOME RESEARCH

Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution

(2010) M. Volker 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

Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow

(2010) JOCHEN B. W. WOLF et al.   MOLECULAR ECOLOGY

Evolutionary stasis: the stable chromosomes of birds

(2010) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

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

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS