Region-wide and ecotype-specific differences in demographic histories of threespine stickleback populations, estimated from whole genome sequences

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

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

Complete Genomes Reveal Signatures of Demographic and Genetic Declines in the Woolly Mammoth

(2015) Eleftheria Palkopoulou et al.   CURRENT BIOLOGY

Temporal Dynamics of Avian Populations during Pleistocene Revealed by Whole-Genome Sequences

(2015) Krystyna Nadachowska-Brzyska et al.   CURRENT BIOLOGY

On the importance of being structured: instantaneous coalescence rates and human evolution—lessons for ancestral population size inference?

(2015) O Mazet et al.   HEREDITY

The impact of selection, gene flow and demographic history on heterogeneous genomic divergence: three-spine sticklebacks in divergent environments

(2015) Anne-Laure Ferchaud et al.   MOLECULAR ECOLOGY

First records of three-spined stickleback Gasterosteus aculeatus in Svalbard freshwaters: An effect of climate change?

(2015) Martin-A Svenning et al.   POLAR BIOLOGY

Evolution of stickleback in 50 years on earthquake-uplifted islands

(2015) Emily A. Lescak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding

(2015) Y. Xue et al.   SCIENCE

Genomics of Divergence along a Continuum of Parapatric Population Differentiation

(2015) Philine G. D. Feulner et al.   PLoS Genetics

Admixture of ancient mitochondrial lineages in three-spined stickleback populations from the North Pacific

(2014) Emily A. Lescak et al.   JOURNAL OF BIOGEOGRAPHY

Killer Whale Nuclear Genome and mtDNA Reveal Widespread Population Bottleneck during the Last Glacial Maximum

(2014) Andre E. Moura et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genomic signature of parallel adaptation from shared genetic variation

(2014) Marius Roesti et al.   MOLECULAR ECOLOGY

Genetics of ecological divergence during speciation

(2014) Matthew E. Arnegard et al.   NATURE

A worldwide survey of genome sequence variation provides insight into the evolutionary history of the honeybee Apis mellifera

(2014) Andreas Wallberg et al.   NATURE GENETICS

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

(2014) R. E. Green et al.   SCIENCE

Unique mitochondrial DNA lineages in Irish stickleback populations: cryptic refugium or rapid recolonization?

(2014) Mark Ravinet et al.   Ecology and Evolution

Fast Evolution from Precast Bricks: Genomics of Young Freshwater Populations of Threespine Stickleback Gasterosteus aculeatus

(2014) Nadezhda V. Terekhanova et al.   PLoS Genetics

Genomic divergence between nine- and three-spined sticklebacks

(2013) Baocheng Guo et al.   BMC GENOMICS

Estimating Variable Effective Population Sizes from Multiple Genomes: A Sequentially Markov Conditional Sampling Distribution Approach

(2013) S. Sheehan et al.   GENETICS

Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products

(2013) Sergey Nurk et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

A gene with major phenotypic effects as a target for selection vs. homogenizing gene flow

(2013) Joost A. M. Raeymaekers et al.   MOLECULAR ECOLOGY

Phylogeography and adaptation genetics of stickleback from the Haida Gwaii archipelago revealed using genome-wide single nucleotide polymorphism genotyping

(2013) Bruce E. Deagle et al.   MOLECULAR ECOLOGY

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

Variation in Age and Size in Fennoscandian Three-Spined Sticklebacks (Gasterosteus aculeatus)

(2013) Jacquelin DeFaveri et al.   PLoS One

Genome sequencing and population genomics in non-model organisms

(2013) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

Genome-wide patterns of standing genetic variation in a marine population of three-spined sticklebacks

(2012) PHILINE G. D. FEULNER et al.   MOLECULAR ECOLOGY

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation

(2012) Shancen Zhao et al.   NATURE GENETICS

Fidelity of capture-enrichment for mtDNA genome sequencing: influence of NUMTs

(2012) Mingkun Li et al.   NUCLEIC ACIDS RESEARCH

The probability of genetic parallelism and convergence in natural populations

(2012) G. L. Conte et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

GLOBAL ANALYSIS OF GENES INVOLVED IN FRESHWATER ADAPTATION IN THREESPINE STICKLEBACKS (GASTEROSTEUS ACULEATUS)

(2011) Jacquelin DeFaveri et al.   EVOLUTION

Strong and consistent natural selection associated with armour reduction in sticklebacks

(2011) ARNAUD LE ROUZIC et al.   MOLECULAR ECOLOGY

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

Of glaciers and refugia: a decade of study sheds new light on the phylogeography of northwestern North America

(2010) AARON B. A. SHAFER et al.   MOLECULAR ECOLOGY

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

Statistical Phylogeography

(2009) L. Lacey Knowles   Annual Review of Ecology Evolution and Systematics

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

Genetics and ecological speciation

(2009) D. Schluter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

(2009) Y. F. Chan et al.   SCIENCE

Mitochondrial DNA phylogeography of the three-spined stickleback (Gasterosteus aculeatus) in Europe—Evidence for multiple glacial refugia

(2007) H.S. Mäkinen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION