Contrasting genomic shifts underlie parallel phenotypic evolution in response to fishing

(Non)Parallel Evolution

(2018) Daniel I. Bolnick et al.   Annual Review of Ecology Evolution and Systematics

Estimating Seven Coefficients of Pairwise Relatedness Using Population-Genomic Data

(2017) Matthew S. Ackerman et al.   GENETICS

Genomics of Parallel Experimental Evolution in Drosophila

(2017) J.L. Graves et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rapid, broad-scale gene expression evolution in experimentally harvested fish populations

(2017) Silva Uusi-Heikkilä et al.   MOLECULAR ECOLOGY

Estimating Seven Coefficients of Pairwise Relatedness Using Population-Genomic Data

(2017) Matthew S. Ackerman et al.   GENETICS

On the maintenance of genetic variation and adaptation to environmental change: considerations from population genomics in fishes

(2016) L. Bernatchez   JOURNAL OF FISH BIOLOGY

SLiM 2: Flexible, Interactive Forward Genetic Simulations

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

Practical low-coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species

(2016) Nina Overgaard Therkildsen et al.   Molecular Ecology Resources

The industrial melanism mutation in British peppered moths is a transposable element

(2016) Arjen E. van’t Hof et al.   NATURE

Human influences on evolution, and the ecological and societal consequences

(2016) Andrew P. Hendry et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish

(2016) N. M. Reid et al.   SCIENCE

Fisheries-Induced Evolution

(2015) Mikko Heino et al.   Annual Review of Ecology Evolution and Systematics

Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow

(2015) Scott P. Egan et al.   ECOLOGY LETTERS

The evolutionary legacy of size-selective harvesting extends from genes to populations

(2015) Silva Uusi-Heikkilä et al.   Evolutionary Applications

Genotype-Frequency Estimation from High-Throughput Sequencing Data

(2015) Takahiro Maruki et al.   GENETICS

Can the experimental evolution programme help us elucidate the genetic basis of adaptation in nature?

(2015) Susan F. Bailey et al.   MOLECULAR ECOLOGY

RAD sequencing reveals within-generation polygenic selection in response to anthropogenic organic and metal contamination in North Atlantic Eels

(2015) M. Laporte et al.   MOLECULAR ECOLOGY

Multi-locus fossil-calibrated phylogeny of Atheriniformes (Teleostei, Ovalentaria)

(2015) Daniela Campanella et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Elucidating the molecular architecture of adaptation via evolve and resequence experiments

(2015) Anthony Long et al.   NATURE REVIEWS GENETICS

Identification of protein coding regions in RNA transcripts

(2015) Shiyuyun Tang et al.   NUCLEIC ACIDS RESEARCH

Genotype-Frequency Estimation from High-Throughput Sequencing Data

(2015) Takahiro Maruki et al.   GENETICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

A RAD-Tag Genetic Map for the Platyfish ( Xiphophorus maculatus ) Reveals Mechanisms of Karyotype Evolution Among Teleost Fish

(2014) Angel Amores et al.   GENETICS

The kinship2 R Package for Pedigree Data

(2014) Jason P. Sinnwell et al.   HUMAN HEREDITY

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Experimental harvesting of fish populations drives genetically based shifts in body size and maturation

(2013) Serinde J van Wijk et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

A genomic island linked to ecotype divergence in Atlantic cod

(2013) Jakob Hemmer-Hansen et al.   MOLECULAR ECOLOGY

Meta-analysis reveals lower genetic diversity in overfished populations

(2013) Malin L. Pinsky et al.   MOLECULAR ECOLOGY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Assessing the Effect of Sequencing Depth and Sample Size in Population Genetics Inferences

(2013) Matteo Fumagalli   PLoS One

Spatial scale and divergent patterns of variation in adapted traits in the ocean

(2012) Lyndie A. Hice et al.   ECOLOGY LETTERS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Population genomics based on low coverage sequencing: how low should we go?

(2012) C. Alex Buerkle et al.   MOLECULAR ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Resolution of ray-finned fish phylogeny and timing of diversification

(2012) T. J. Near et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Gene function analysis in complex data sets using ErmineJ

(2010) Jesse Gillis et al.   Nature Protocols

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Human-induced evolution caused by unnatural selection through harvest of wild animals

(2009) F. W. Allendorf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reversal of evolutionary downsizing caused by selective harvest of large fish

(2009) D. O. Conover et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES