Complex signatures of genomic variation of two non-model marine species in a homogeneous environment

Utility of pooled sequencing for association mapping in nonmodel organisms

(2018) Steven J. Micheletti et al.   Molecular Ecology Resources

A simple molecular technique for distinguishing species reveals frequent misidentification of Hawaiian corals in the genus Pocillopora

(2018) Erika C. Johnston et al.   PeerJ

Deep transcriptome profiling sheds light on key players in nucleus implantation induced immune response in the pearl oyster Pinctada martensii

(2017) Wei Wang et al.   FISH & SHELLFISH IMMUNOLOGY

Genetic population sub-structuring of kingklip ( Genypterus capensis – Ophidiidiae), a commercially exploited demersal fish off South Africa

(2017) Romina Henriques et al.   FISHERIES RESEARCH

Fine-scale genetic structure due to adaptive divergence among microhabitats

(2017) D N Wagner et al.   HEREDITY

Transcriptomic responses to seawater acidification among sea urchin populations inhabiting a natural pH mosaic

(2017) Tyler G. Evans et al.   MOLECULAR ECOLOGY

Biodiversity redistribution under climate change: Impacts on ecosystems and human well-being

(2017) Gretta T. Pecl et al.   SCIENCE

Genotype by sequencing identifies natural selection as a driver of intraspecific divergence in Atlantic populations of the high dispersal marine invertebrate, Macoma petalum

(2017) Stacy L. Metivier et al.   Ecology and Evolution

Nimbolide upregulates RECK by targeting miR-21 and HIF-1α in cell lines and in a hamster oral carcinogenesis model

(2017) Jaganathan Kowshik et al.   Scientific Reports

A genomic glance through the fog of plasticity and diversification in Pocillopora

(2017) Erika C. Johnston et al.   Scientific Reports

Making evolutionary history count: biodiversity planning for coral reef fishes and the conservation of evolutionary processes

(2016) Sophie von der Heyden   CORAL REEFS

Migration, distribution and population (stock) structure of shallow-water hake ( Merluccius capensis ) in the Benguela Current Large Marine Ecosystem inferred using a geostatistical population model

(2016) Teunis Jansen et al.   FISHERIES RESEARCH

A decade of seascape genetics: contributions to basic and applied marine connectivity

(2016) KA Selkoe et al.   MARINE ECOLOGY PROGRESS SERIES

Next-generation biology: Sequencing and data analysis approaches for non-model organisms

(2016) Rute R. da Fonseca et al.   Marine Genomics

Population genomic evidence for adaptive differentiation in the Baltic Sea herring

(2016) Baocheng Guo et al.   MOLECULAR ECOLOGY

Genomic evidence for ecological divergence against a background of population homogeneity in the marine snail Chlorostoma funebralis

(2016) Lani U. Gleason et al.   MOLECULAR ECOLOGY

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

pcadapt: anRpackage to perform genome scans for selection based on principal component analysis

(2016) Keurcien Luu et al.   Molecular Ecology Resources

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

Comparative phylogeography of the ocean planet

(2016) Brian W. Bowen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative phylogeography clarifies the complexity and problems of continental distribution that drove A. R. Wallace to favor islands

(2016) Brett R. Riddle   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference

(2016) Aaron B. A. Shafer et al.   Methods in Ecology and Evolution

A decade of seascape genetics: contributions to basic and applied marine connectivity

(2016) KA Selkoe et al.   MARINE ECOLOGY PROGRESS SERIES

Generation and analysis of cDNA library from lipopolysaccharide-stimulated gastropod abalone (Haliotis diversicolor supertexta) hemocytes

(2016) Wu Liuji et al.   AFRICAN JOURNAL OF BIOTECHNOLOGY

Population genomic evidence for adaptive differentiation in Baltic Sea three-spined sticklebacks

(2015) Baocheng Guo et al.   BMC BIOLOGY

Genetic isolation by distance reveals restricted dispersal across a range of life histories: implications for biodiversity conservation planning across highly variable marine environments

(2015) Daniel Wright et al.   DIVERSITY AND DISTRIBUTIONS

Morphological and genomic comparisons of Hawaiian and Japanese Black-footed Albatrosses (Phoebastria nigripes) using double digest RADseq: implications for conservation

(2015) Elisa G. Dierickx et al.   Evolutionary Applications

Predicting RAD-seq Marker Numbers across the Eukaryotic Tree of Life

(2015) Santiago Herrera et al.   Genome Biology and Evolution

Seven common mistakes in population genetics and how to avoid them

(2015) Patrick G. Meirmans   MOLECULAR ECOLOGY

Shared and nonshared genomic divergence in parallel ecotypes ofLittorina saxatilisat a local scale

(2015) Mark Ravinet et al.   MOLECULAR ECOLOGY

A genomewide catalogue of single nucleotide polymorphisms in white-beaked and Atlantic white-sided dolphins

(2015) R. Fernández et al.   Molecular Ecology Resources

Genomics and the challenging translation into conservation practice

(2015) Aaron B.A. Shafer et al.   TRENDS IN ECOLOGY & EVOLUTION

New SNP markers reveal largely concordant clinal variation across the hybrid zone between Mytilus spp. in the Baltic Sea

(2014) M Zbawicka et al.   Aquatic Biology

ngsTools: methods for population genetics analyses from next-generation sequencing data

(2014) Matteo Fumagalli et al.   BIOINFORMATICS

Transcription profiling using RNA-Seq demonstrates expression differences in the body walls of juvenile albino and normal sea cucumbers Apostichopus japonicus

(2014) Deyou Ma et al.   CHINESE JOURNAL OF OCEANOLOGY AND LIMNOLOGY

Additive effects of climate change on connectivity between marine protected areas and larval supply to fished areas

(2014) Marco Andrello et al.   DIVERSITY AND DISTRIBUTIONS

Dissolved and Particulate Copper Exposure Induces Differing Gene Expression Profiles and Mechanisms of Toxicity in the Deposit Feeding Amphipod Melita plumulosa

(2014) Sharon E. Hook et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

(2014) Anil Raj et al.   GENETICS

Oligo-microarray analysis and identification of stress-immune response genes from manila clam (Ruditapes philippinarum) exposure to heat and cold stresses

(2014) Udeni Menike et al.   MOLECULAR BIOLOGY REPORTS

Genomics of the divergence continuum in an African plant biodiversity hotspot, I: drivers of population divergence inRestio capensis(Restionaceae)

(2014) C. Lexer et al.   MOLECULAR ECOLOGY

Do the same genes underlie parallel phenotypic divergence in differentLittorina saxatilispopulations?

(2014) A. M. Westram et al.   MOLECULAR ECOLOGY

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

Population Connectivity and Phylogeography of a Coastal Fish, Atractoscion aequidens (Sciaenidae), across the Benguela Current Region: Evidence of an Ancient Vicariant Event

(2014) Romina Henriques et al.   PLoS One

SNP ascertainment bias in population genetic analyses: Why it is important, and how to correct it

(2013) Joseph Lachance et al.   BIOESSAYS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Evolving coral reef conservation with genetic information

(2013) Maria Beger et al.   BULLETIN OF MARINE SCIENCE

The application of genetics to marine management and conservation: examples from the Indo-Pacific

(2013) Sophie von der Heyden et al.   BULLETIN OF MARINE SCIENCE

Evolutionary change driven by metal exposure as revealed by coding SNP genome scan in wild yellow perch (Perca flavescens)

(2013) Sébastien Bélanger-Deschênes et al.   ECOTOXICOLOGY

Climate change in the oceans: evolutionary versus phenotypically plastic responses of marine animals and plants

(2013) Thorsten B. H. Reusch   Evolutionary Applications

Natural variation and the capacity to adapt to ocean acidification in the keystone sea urchinStrongylocentrotus purpuratus

(2013) Morgan W. Kelly et al.   GLOBAL CHANGE BIOLOGY

Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius)

(2013) Ilaria Milano et al.   MOLECULAR ECOLOGY

Estimation of population allele frequencies from next-generation sequencing data: pool-versus individual-based genotyping

(2013) Mathieu Gautier et al.   MOLECULAR ECOLOGY

Going where traditional markers have not gone before: utility of and promise for RAD sequencing in marine invertebrate phylogeography and population genomics

(2013) A. M. Reitzel et al.   MOLECULAR ECOLOGY

Genotyping-by-sequencing in ecological and conservation genomics

(2013) Shawn R. Narum et al.   MOLECULAR ECOLOGY

Next-generation sequencing for molecular ecology: a caveat regarding pooled samples

(2013) Eric C. Anderson et al.   MOLECULAR ECOLOGY

Accuracy of allele frequency estimation using pooled RNA-Seq

(2013) M. Konczal et al.   Molecular Ecology Resources

Validation of SNP Allele Frequencies Determined by Pooled Next-Generation Sequencing in Natural Populations of a Non-Model Plant Species

(2013) Christian Rellstab et al.   PLoS One

Genome sequencing and population genomics in non-model organisms

(2013) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

ezRAD: a simplified method for genomic genotyping in non-model organisms

(2013) Robert J. Toonen et al.   PeerJ

DIFFERENCES IN THE REGULATION OF GROWTH AND BIOMINERALIZATION GENES REVEALED THROUGH LONG-TERM COMMON-GARDEN ACCLIMATION AND EXPERIMENTAL GENOMICS IN THE PURPLE SEA URCHIN

(2012) Melissa H. Pespeni et al.   EVOLUTION

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Long-term and trans-life-cycle effects of exposure to ocean acidification in the green sea urchin Strongylocentrotus droebachiensis

(2012) S. Dupont et al.   MARINE BIOLOGY

Oceanic circulation, local upwelling and palaeoclimatic changes linked to the phylogeography of the Cape sea urchin Parechinus angulosus

(2012) CM Muller et al.   MARINE ECOLOGY PROGRESS SERIES

Special features of RAD Sequencing data: implications for genotyping

(2012) John W. Davey et al.   MOLECULAR ECOLOGY

Transcriptome-wide polymorphisms of red abalone (Haliotis rufescens) reveal patterns of gene flow and local adaptation

(2012) Pierre De Wit et al.   MOLECULAR ECOLOGY

SNP-array reveals genome-wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar)

(2012) Vincent Bourret et al.   MOLECULAR ECOLOGY

Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

(2012) Catherine E. Wagner et al.   MOLECULAR ECOLOGY

The genetic differentiation at quantitative trait loci under local adaptation

(2012) VALÉRIE LE CORRE et al.   MOLECULAR ECOLOGY

Conservation of Gbx genes from EHG homeobox in bivalve molluscs

(2012) Crimgilt Mesías-Gansbiller et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Insights into bilaterian evolution from three spiralian genomes

(2012) Oleg Simakov et al.   NATURE

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

Multiple SNP Markers Reveal Fine-Scale Population and Deep Phylogeographic Structure in European Anchovy (Engraulis encrasicolus L.)

(2012) Iratxe Zarraonaindia et al.   PLoS One

Adaptive Capacity of the Habitat Modifying Sea Urchin Centrostephanus rodgersii to Ocean Warming and Ocean Acidification: Performance of Early Embryos

(2012) Shawna A. Foo et al.   PLoS One

The probability of genetic parallelism and convergence in natural populations

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

Harnessing genomics for delineating conservation units

(2012) W. Chris Funk et al.   TRENDS IN ECOLOGY & EVOLUTION

PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs

(2011) H. E. L. Lischer et al.   BIOINFORMATICS

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

(2011) R. Kofler et al.   BIOINFORMATICS

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

(2011) H. Li   BIOINFORMATICS

Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance

(2011) Barbara Feldmeyer et al.   BMC GENOMICS

Marine connectivity: a new look at pelagic larval duration and genetic metrics of dispersal

(2011) KA Selkoe et al.   MARINE ECOLOGY PROGRESS SERIES

Comparison ofFSToutlier tests for SNP loci under selection

(2011) SHAWN R. NARUM et al.   Molecular Ecology Resources

Outlier SNPs show more genetic structure between two Bay of Fundy metapopulations of Atlantic salmon than do neutral SNPs

(2011) HEATHER FREAMO et al.   Molecular Ecology Resources

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

(2011) Robert Kofler et al.   PLoS One

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

A review of marine phylogeography in southern Africa

(2011) Peter R. Teske et al.   SOUTH AFRICAN JOURNAL OF SCIENCE

The complex analytical landscape of gene flow inference

(2011) Peter B. Marko et al.   TRENDS IN ECOLOGY & EVOLUTION

Isolation of 12 microsatellite markers for geelbeck (Atractoscion aequidens (Cuvier, 1860), Sciaenidae), an overexploited marine fish

(2011) Romina Henriques et al.   Conservation Genetics Resources

Local Adaptation in Marine Invertebrates

(2010) Eric Sanford et al.   Annual Review of Marine Science

Tubulin evolution in insects: gene duplication and subfunctionalization provide specialized isoforms in a functionally constrained gene family

(2010) Mark G Nielsen et al.   BMC EVOLUTIONARY BIOLOGY

The Next Generation of Molecular Markers From Massively Parallel Sequencing of Pooled DNA Samples

(2010) Andreas Futschik et al.   GENETICS

Accurate detection and genotyping of SNPs utilizing population sequencing data

(2010) V. Bansal et al.   GENOME RESEARCH

Applications of next generation sequencing in molecular ecology of non-model organisms

(2010) R Ekblom et al.   HEREDITY

It's About Time: Divergence, Demography, and the Evolution of Developmental Modes in Marine Invertebrates

(2010) M. W. Hart et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Comparing three different methods to detect selective loci using dominant markers

(2010) A. PÉREZ-FIGUEROA et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

An EST-based genome scan using 454 sequencing in the marine snail Littorina saxatilis

(2010) J. GALINDO et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

SNP signatures of selection on standing genetic variation and their association with adaptive phenotypes along gradients of ecological speciation in lake whitefish species pairs (Coregonus spp.)

(2010) SÉBASTIEN RENAUT et al.   MOLECULAR ECOLOGY

Taking the chaos out of genetic patchiness: seascape genetics reveals ecological and oceanographic drivers of genetic patterns in three temperate reef species

(2010) KIMBERLY A. SELKOE et al.   MOLECULAR ECOLOGY

Parallel adaptive evolution of Atlantic cod on both sides of the Atlantic Ocean in response to temperature

(2010) I. R. Bradbury et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua)

(2009) Einar E Nielsen et al.   BMC EVOLUTIONARY BIOLOGY

Population genetics, larval dispersal, and connectivity in marine systems

(2009) K Weersing et al.   MARINE ECOLOGY PROGRESS SERIES

Genetics and ecological speciation

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

The Benguela Current: An ecosystem of four components

(2009) L. Hutchings et al.   PROGRESS IN OCEANOGRAPHY

ECOLOGICAL GENETICS IN THE NORTH ATLANTIC: ENVIRONMENTAL GRADIENTS AND ADAPTATION AT SPECIFIC LOCI

(2008) Paul S. Schmidt et al.   ECOLOGY

The Effects of Recombination Rate on the Distribution and Abundance of Transposable Elements

(2008) E. S. Dolgin et al.   GENETICS

A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective

(2008) M. Foll et al.   GENETICS

Spatial match-mismatch in the Benguela upwelling zone: should we expect chlorophyll and sea-surface temperature to predict marine predator distributions?

(2008) David Grémillet et al.   JOURNAL OF APPLIED ECOLOGY

Temperature adaptation of cytosolic malate dehydrogenases of limpets (genus Lottia): differences in stability and function due to minor changes in sequence correlate with biogeographic and vertical distributions

(2008) Y. Dong et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One

The stochastic nature of larval connectivity among nearshore marine populations

(2008) D. A. Siegel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Climate change and evolution: disentangling environmental and genetic responses

(2007) P. GIENAPP et al.   MOLECULAR ECOLOGY