Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species

How “simple” methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: A case study using the lake whitefish

(2020) Carly F. Graham et al.   PLoS One

Genetic structure is stronger across human-impacted habitats than among islands in the coral Porites lobata

(2020) Kaho H. Tisthammer et al.   PeerJ

Thermal selection as a driver of marine ecological speciation

(2019) Peter R. Teske et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genome-wide signatures of local adaptation among seven stoneflies species along a nationwide latitudinal gradient in Japan

(2019) Maribet Gamboa et al.   BMC GENOMICS

Shared genomic outliers across two divergent population clusters of a highly threatened seagrass

(2019) Nikki Leanne Phair et al.   PeerJ

Exploring a Pool‐seq‐only approach for gaining population genomic insights in nonmodel species

(2019) Sara Kurland et al.   Ecology and Evolution

Divergent northern and southern populations and demographic history of the pearl oyster in the western Pacific revealed with genomic SNPs

(2019) Takeshi Takeuchi et al.   Evolutionary Applications

Spatial genetic structure in a crustacean herbivore highlights the need for local considerations in Baltic Sea biodiversity management

(2019) Pierre De Wit et al.   Evolutionary Applications

Combining six genome scan methods to detect candidate genes to salinity in the Mediterranean striped red mullet (Mullus surmuletus)

(2018) Alicia Dalongeville et al.   BMC GENOMICS

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

(2018) Erica S. Nielsen et al.   BMC GENOMICS

Comparing methods for detecting multilocus adaptation with multivariate genotype-environment associations

(2018) Brenna R. Forester et al.   MOLECULAR ECOLOGY

Seascape genomics reveals adaptive divergence in a connected and commercially important mollusc, the greenlip abalone (Haliotis laevigata ), along a longitudinal environmental gradient

(2018) Jonathan Sandoval-Castillo et al.   MOLECULAR ECOLOGY

Contemporary and historical oceanographic processes explain genetic connectivity in a Southwestern Atlantic coral

(2018) L. Peluso et al.   Scientific Reports

Mitochondrial DNA is unsuitable to test for isolation by distance

(2018) Peter R. Teske et al.   Scientific Reports

Navigating the Interface Between Landscape Genetics and Landscape Genomics

(2018) Andrew Storfer et al.   Frontiers in Genetics

A climate-associated multispecies cryptic cline in the northwest Atlantic

(2018) Ryan R. E. Stanley et al.   Science Advances

Measuring Genetic Differentiation from Pool-seq Data

(2018) Valentin Hivert et al.   GENETICS

Discovering divergence in the thermal physiology of intertidal crabs along latitudinal gradients using an integrated approach with machine learning

(2018) Sebastian J.A. Osores et al.   JOURNAL OF THERMAL BIOLOGY

Influence of respiratory mode on the thermal tolerance of intertidal limpets

(2018) Sebbi L. Kankondi et al.   PLoS One

Seascape genomics of eastern oyster (Crassostrea virginica ) along the Atlantic coast of Canada

(2018) Simon Bernatchez et al.   Evolutionary Applications

High-frequency temperature variability mirrors fixed differences in thermal limits of the massive coral Porites lobata

(2018) Daniel J. Barshis et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Putatively adaptive genetic variation in the giant California sea cucumber ( Parastichopus californicus ) as revealed by environmental association analysis of restriction‐site associated DNA sequencing data

(2018) Amanda Xuereb et al.   MOLECULAR ECOLOGY

Local adaptation in mainland anole lizards: Integrating population history and genome-environment associations

(2018) Ivan Prates et al.   Ecology and Evolution

Seascape genetics of a flatfish reveals local selection under high levels of gene flow

(2017) Eveline Diopere et al.   ICES JOURNAL OF MARINE SCIENCE

WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas

(2017) Stephen E. Fick et al.   INTERNATIONAL JOURNAL OF CLIMATOLOGY

Deciphering the demographic history of allochronic differentiation in the pine processionary moth Thaumetopoea pityocampa

(2017) R. Leblois et al.   MOLECULAR ECOLOGY

An integrated framework to identify wildlife populations under threat from climate change

(2017) Orly Razgour et al.   Molecular Ecology Resources

Spatial detection of outlier loci with Moran eigenvector maps

(2017) Helene H. Wagner et al.   Molecular Ecology Resources

Responsible RAD: Striving for best practices in population genomic studies of adaptation

(2017) David B. Lowry et al.   Molecular Ecology Resources

Coral hybridization or phenotypic variation? Genomic data reveal gene flow between Porites lobata and P. Compressa

(2017) Z.H. Forsman et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Environmental and geographic variables are effective surrogates for genetic variation in conservation planning

(2017) Jeffrey O. Hanson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RADseq dataset with 90% missing data fully resolves recent radiation of Petalidium (Acanthaceae) in the ultra-arid deserts of Namibia

(2017) Erin A. Tripp et al.   Ecology and Evolution

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

(2016) Sophie von der Heyden   CORAL REEFS

Navigating the currents of seascape genomics: how spatial analyses can augment population genomic studies

(2016) Cynthia Riginos et al.   Current Zoology

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

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

Seascape genomics provides evidence for thermal adaptation and current-mediated population structure in American lobster (Homarus americanus )

(2016) Laura Benestan et al.   MOLECULAR ECOLOGY

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

The challenge of separating signatures of local adaptation from those of isolation by distance and colonization history: The case of two white pines

(2016) Simon Nadeau et al.   Ecology and Evolution

Suitability of Different Mapping Algorithms for Genome-wide Polymorphism Scans with Pool-Seq Data

(2016) R. Kofler et al.   G3-Genes Genomes Genetics

Navigating the currents of seascape genomics: how spatial analyses can augment population genomic studies

(2016) Cynthia Riginos et al.   Current Zoology

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

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

Assembly, Assessment, and Availability of De novo Generated Eukaryotic Transcriptomes

(2016) Joanna Moreton et al.   Frontiers in Genetics

Historical demography of southern African patellid limpets: congruence of population expansions, but not phylogeography

(2015) KL Mmonwa et al.   AFRICAN JOURNAL OF MARINE SCIENCE

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

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

Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates

(2015) M. Gautier   GENETICS

Environmental epigenetics: A promising venue for developing next-generation pollution biomonitoring tools in marine invertebrates

(2015) Victoria Suarez-Ulloa et al.   MARINE POLLUTION BULLETIN

Seascape genetics along environmental gradients in the Arabian Peninsula: insights from ddRAD sequencing of anemonefishes

(2015) Pablo Saenz-Agudelo et al.   MOLECULAR ECOLOGY

A practical guide to environmental association analysis in landscape genomics

(2015) Christian Rellstab et al.   MOLECULAR ECOLOGY

Landscape genetics in a changing world: disentangling historical and contemporary influences and inferring change

(2015) Clinton W. Epps et al.   MOLECULAR ECOLOGY

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

(2015) Mark Ravinet et al.   MOLECULAR ECOLOGY

The relative power of genome scans to detect local adaptation depends on sampling design and statistical method

(2015) Katie E. Lotterhos et al.   MOLECULAR ECOLOGY

The impact of library preparation protocols on the consistency of allele frequency estimates in Pool-Seq data

(2015) Robert Kofler et al.   Molecular Ecology Resources

Living on the Margin in the Anthropocene: engagement arenas for sustainability research and action at the ocean–land interface

(2015) BC Glavovic et al.   Current Opinion in Environmental Sustainability

LEA: AnRpackage for landscape and ecological association studies

(2015) Eric Frichot et al.   Methods in Ecology and Evolution

Rapid assessment of fisheries species sensitivity to climate change

(2014) Gretta T. Pecl et al.   CLIMATIC CHANGE

GARM: Genome Assembly, Reconciliation and Merging Pipeline

(2014) Luz Soto-Jimenez et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Emergent patterns of population genetic structure for a coral reef community

(2014) Kimberly A. Selkoe et al.   MOLECULAR ECOLOGY

Genome-wide single-generation signatures of local selection in the panmictic European eel

(2014) J. M. Pujolar et al.   MOLECULAR ECOLOGY

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

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

Advances and limits of using population genetics to understand local adaptation

(2014) Peter Tiffin et al.   TRENDS IN ECOLOGY & EVOLUTION

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Informed and automated k-mer size selection for genome assembly

(2013) R. Chikhi et al.   BIOINFORMATICS

MARSPEC: ocean climate layers for marine spatial ecology

(2013) Elizabeth J. Sbrocco et al.   ECOLOGY

Mantel test in population genetics

(2013) José Alexandre F. Diniz-Filho et al.   GENETICS AND MOLECULAR BIOLOGY

The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes

(2013)   JOURNAL OF HEREDITY

Testing for Associations between Loci and Environmental Gradients Using Latent Factor Mixed Models

(2013) Eric Frichot et al.   MOLECULAR BIOLOGY AND EVOLUTION

Stronger spatial genetic structure in recolonized areas than in refugia in the European beech

(2013) Guillaume de Lafontaine et al.   MOLECULAR ECOLOGY

Population genomic footprints of selection and associations with climate in natural populations ofArabidopsis hallerifrom the Alps

(2013) Martin C. Fischer et al.   MOLECULAR ECOLOGY

Genotyping-by-sequencing in ecological and conservation genomics

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

Signals of selection in outlier loci in a widely dispersing species across an environmental mosaic

(2013) Melissa H. Pespeni et al.   MOLECULAR ECOLOGY

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

A Coastal Seawater Temperature Dataset for Biogeographical Studies: Large Biases between In Situ and Remotely-Sensed Data Sets around the Coast of South Africa

(2013) Albertus J. Smit et al.   PLoS One

Identification of global marine hotspots: sentinels for change and vanguards for adaptation action

(2013) Alistair J. Hobday et al.   REVIEWS IN FISH BIOLOGY AND FISHERIES

Meta-analysis reveals complex marine biological responses to the interactive effects of ocean acidification and warming

(2013) Ben P. Harvey et al.   Ecology and Evolution

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

(2013) Robert J. Toonen et al.   PeerJ

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

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL 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

Seascape genetics of the New Zealand greenshell mussel: sea surface temperature explains macrogeographic scale genetic variation

(2012) K Wei et al.   MARINE ECOLOGY PROGRESS SERIES

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

(2011) R. Kofler et al.   BIOINFORMATICS

BamTools: a C++ API and toolkit for analyzing and managing BAM files

(2011) D. W. Barnett et al.   BIOINFORMATICS

Bio-ORACLE: a global environmental dataset for marine species distribution modelling

(2011) Lennert Tyberghein et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Comparing De Novo Genome Assembly: The Long and Short of It

(2011) Giuseppe Narzisi et al.   PLoS One

Seascape genetics along a steep cline: using genetic patterns to test predictions of marine larval dispersal

(2010) HEATHER M. GALINDO et al.   MOLECULAR ECOLOGY

Marine Biodiversity in South Africa: An Evaluation of Current States of Knowledge

(2010) Charles L. Griffiths et al.   PLoS One

Adaptation genomics: the next generation

(2010) Jessica Stapley et al.   TRENDS IN ECOLOGY & EVOLUTION

Habitat diversity relative to wave action on rocky shores: implications for the selection of marine protected areas

(2009) Laura K. Blamey et al.   AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Does life history predict past and current connectivity for rocky intertidal invertebrates across a marine biogeographic barrier?

(2009) D. J. AYRE et al.   MOLECULAR ECOLOGY

FORWARD SELECTION OF EXPLANATORY VARIABLES

(2008) F. Guillaume Blanchet et al.   ECOLOGY

Genetic variation across species’ geographical ranges: the central–marginal hypothesis and beyond

(2008) C. G. ECKERT et al.   MOLECULAR ECOLOGY