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

Detecting polygenic selection in marine populations by combining population genomics and quantitative genetics approaches

(2016) Pierre-Alexandre Gagnaire 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

New view of population genetics of zooplankton: RAD-seq analysis reveals population structure of the North Atlantic planktonic copepod Centropages typicus

(2016) L. Blanco-Bercial et al.   MOLECULAR ECOLOGY

Parallel genetic divergence among coastal-marine ecotype pairs of European anchovy explained by differential introgression after secondary contact

(2016) A. Le Moan et al.   MOLECULAR ECOLOGY

Detecting polygenic selection in marine populations by combining population genomics and quantitative genetics approaches

(2016) Pierre-Alexandre Gagnaire 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

The geography of introgression in a patchy environment and the thorn in the side of ecological speciation

(2016) Nicolas Bierne et al.   Current Zoology

Reliable Detection of Loci Responsible for Local Adaptation: Inference of a Null Model through Trimming the Distribution of FST

(2015) Michael C. Whitlock et al.   AMERICAN NATURALIST

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

(2015) Baocheng Guo et al.   BMC BIOLOGY

The emergent geography of biophysical dispersal barriers across the Indo-West Pacific

(2015) Eric A. Treml et al.   DIVERSITY AND DISTRIBUTIONS

Latitude-wide genetic patterns reveal historical effects and contrasting patterns of turnover and nestedness at the range peripheries of a tropical marine fish

(2015) Libby Liggins et al.   ECOGRAPHY

Using neutral, selected, and hitchhiker loci to assess connectivity of marine populations in the genomic era

(2015) Pierre-Alexandre Gagnaire et al.   Evolutionary Applications

Adaptation to Low Salinity Promotes Genomic Divergence in Atlantic Cod ( Gadus morhua L.)

(2015) Paul R. Berg et al.   Genome Biology and Evolution

Detecting adaptive evolution based on association with ecological gradients: Orientation matters!

(2015) E Frichot et al.   HEREDITY

Seascape features, rather than dispersal traits, predict spatial genetic patterns in co-distributed reef fishes

(2015) Libby Liggins et al.   JOURNAL OF BIOGEOGRAPHY

Is there such a thing as landscape genetics?

(2015) Rodney J. Dyer   MOLECULAR ECOLOGY

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

Multicollinearity in spatial genetics: separating the wheat from the chaff using commonality analyses

(2015) J. G. Prunier et al.   MOLECULAR ECOLOGY

The aggregate site frequency spectrum for comparative population genomic inference

(2015) Alexander T. Xue et al.   MOLECULAR ECOLOGY

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

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

A new FST-based method to uncover local adaptation using environmental variables

(2015) Pierre de Villemereuil et al.   Methods in Ecology and Evolution

Should the Mantel test be used in spatial analysis?

(2015) Pierre Legendre et al.   Methods in Ecology and Evolution

Archived DNA reveals fisheries and climate induced collapse of a major fishery

(2015) Sara Bonanomi et al.   Scientific Reports

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

(2014) Deren A. R. Eaton   BIOINFORMATICS

So, you want to use next-generation sequencing in marine systems? Insight from the Pan-Pacific Advanced Studies Institute

(2014) DA Willette et al.   BULLETIN OF MARINE SCIENCE

Genome Scans for Detecting Footprints of Local Adaptation Using a Bayesian Factor Model

(2014) Nicolas Duforet-Frebourg et al.   MOLECULAR BIOLOGY AND EVOLUTION

Detecting genotypic changes associated with selective mortality at sea in Atlantic salmon: polygenic multilocus analysis surpasses genome scan

(2014) Vincent Bourret et al.   MOLECULAR ECOLOGY

ABC inference of multi-population divergence with admixture from unphased population genomic data

(2014) John D. Robinson et al.   MOLECULAR ECOLOGY

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

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

Evaluation of demographic history and neutral parameterization on the performance ofFSToutlier tests

(2014) Katie E. Lotterhos et al.   MOLECULAR ECOLOGY

Genome scan methods against more complex models: when and how much should we trust them?

(2014) Pierre de Villemereuil et al.   MOLECULAR ECOLOGY

Restriction site-associated DNA sequencing, genotyping error estimation andde novoassembly optimization for population genetic inference

(2014) A. Mastretta-Yanes et al.   Molecular Ecology Resources

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

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

(2014) Jonathan B. Puritz et al.   PeerJ

Inference of historical migration rates via haplotype sharing

(2013) P. F. Palamara et al.   BIOINFORMATICS

Dispersal potential and population genetic structure in the marine intertidal of the eastern North Pacific

(2013) Michael N. Dawson et al.   ECOLOGICAL MONOGRAPHS

DETECTING RANGE EXPANSIONS FROM GENETIC DATA

(2013) Benjamin M. Peter et al.   EVOLUTION

HETEROGENEOUS GENOMIC DIFFERENTIATION IN MARINE THREESPINE STICKLEBACKS: ADAPTATION ALONG AN ENVIRONMENTAL GRADIENT

(2013) Jacquelin DeFaveri et al.   EVOLUTION

Spatiotemporal SNP analysis reveals pronounced biocomplexity at the northern range margin of Atlantic codGadus morhua

(2013) Nina Overgaard Therkildsen et al.   Evolutionary Applications

Oceanographic connectivity and environmental correlates of genetic structuring in Atlantic herring in the Baltic Sea

(2013) Amber GF Teacher et al.   Evolutionary Applications

Robust Identification of Local Adaptation from Allele Frequencies

(2013) T. Gunther et al.   GENETICS

Origins of species richness in the Indo-Malay-Philippine biodiversity hotspot: evidence for the centre of overlap hypothesis

(2013) Michelle R. Gaither et al.   JOURNAL OF BIOGEOGRAPHY

Crossing the Species Barrier: Genomic Hotspots of Introgression between Two Highly Divergent Ciona intestinalis Species

(2013) Camille Roux et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

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

(2013) Ilaria Milano et al.   MOLECULAR ECOLOGY

Optimizing the trade-off between spatial and genetic sampling efforts in patchy populations: towards a better assessment of functional connectivity using an individual-based sampling scheme

(2013) J. G. Prunier et al.   MOLECULAR ECOLOGY

Using multilevel models to identify drivers of landscape-genetic structure among management areas

(2013) Rachael Y. Dudaniec et al.   MOLECULAR ECOLOGY

Regional environmental pressure influences population differentiation in turbot (Scophthalmus maximus)

(2013) S. G. Vandamme et al.   MOLECULAR ECOLOGY

Dismantling the Mantel tests

(2013) Gilles Guillot et al.   Methods in Ecology and Evolution

Global imprint of climate change on marine life

(2013) Elvira S. Poloczanska et al.   Nature Climate Change

Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales

(2012) Ke Bi et al.   BMC GENOMICS

Collinearity: a review of methods to deal with it and a simulation study evaluating their performance

(2012) Carsten F. Dormann et al.   ECOGRAPHY

Reproductive Output and Duration of the Pelagic Larval Stage Determine Seascape-Wide Connectivity of Marine Populations

(2012) Eric A. Treml et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Population connectivity: recent advances and new perspectives

(2012) Johnathan T. Kool et al.   LANDSCAPE ECOLOGY

Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

Coalescent and biophysical models of stepping-stone gene flow in neritid snails

(2012) Eric D. Crandall et al.   MOLECULAR ECOLOGY

Theoretical limits to the correlation between pelagic larval duration and population genetic structure

(2012) SØREN FAURBY et al.   MOLECULAR ECOLOGY

Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus)

(2012) MORTEN T. LIMBORG et al.   MOLECULAR ECOLOGY

Connectivity of Caribbean coral populations: complementary insights from empirical and modelled gene flow

(2012) NICOLA L. FOSTER 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

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

RADSeq: next-generation population genetics

(2011) J. W. Davey et al.   Briefings in Functional Genomics

The coupling hypothesis: why genome scans may fail to map local adaptation genes

(2011) NICOLAS BIERNE et al.   MOLECULAR ECOLOGY

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

(2011) Tim R Mercer et al.   NATURE BIOTECHNOLOGY

Molecular spandrels: tests of adaptation at the genetic level

(2011) Rowan D. H. Barrett et al.   NATURE REVIEWS GENETICS

Controlling for non-independence in comparative analysis of patterns across populations within species

(2011) G. N. Stone et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2011) Robert Kofler et al.   PLoS One

Single-Nucleotide Polymorphic Genotypes Reveal Patterns of Early Juvenile Migration of Sockeye Salmon in the Eastern Bering Sea

(2011) Lisa W. Seeb et al.   TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY

The complex analytical landscape of gene flow inference

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

Approximate Bayesian Computation in Evolution and Ecology

(2010) Mark A. Beaumont   Annual Review of Ecology Evolution and Systematics

THE DISTINCTIVE FOOTPRINTS OF LOCAL HITCHHIKING IN A VARIED ENVIRONMENT AND GLOBAL HITCHHIKING IN A SUBDIVIDED POPULATION

(2010) Nicolas Bierne   EVOLUTION

Unified Framework to Evaluate Panmixia and Migration Direction Among Multiple Sampling Locations

(2010) P. Beerli et al.   GENETICS

Using Environmental Correlations to Identify Loci Underlying Local Adaptation

(2010) G. Coop et al.   GENETICS

New insights into global patterns of ocean temperature anomalies: implications for coral reef health and management

(2010) Elizabeth R. Selig et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

INVITED REVIEW: Spatial modelling and landscape-level approaches for visualizing intra-specific variation

(2010) HENRI A. THOMASSEN et al.   MOLECULAR ECOLOGY

Landscape modelling of gene flow: improved power using conditional genetic distance derived from the topology of population networks

(2010) RODNEY J. DYER et al.   MOLECULAR ECOLOGY

Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field

(2010) STÉPHANIE MANEL et al.   MOLECULAR ECOLOGY

Assessing population structure: FST and related measures

(2010) PATRICK G. MEIRMANS et al.   Molecular Ecology Resources

Statistical Phylogeography

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

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

Genetic markers in the playground of multivariate analysis

(2009) T Jombart et al.   HEREDITY

Geographical patterns of genetic structure in marine species with contrasting life histories

(2009) R. A. Pelc et al.   JOURNAL OF BIOGEOGRAPHY

An information-theoretical approach to phylogeography

(2009) BRYAN C. CARSTENS et al.   MOLECULAR ECOLOGY

A landscape genetics approach for quantifying the relative influence of historic and contemporary habitat heterogeneity on the genetic connectivity of a rainforest bird

(2009) DAVID C. PAVLACKY JR et al.   MOLECULAR ECOLOGY

Statistical methods in spatial genetics

(2009) GILLES GUILLOT et al.   MOLECULAR ECOLOGY

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

Population genomics of marine fishes: identifying adaptive variation in space and time

(2009) EINAR E. NIELSEN et al.   MOLECULAR ECOLOGY

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

Larval Dispersal and Marine Population Connectivity

(2008) Robert K. Cowen et al.   Annual Review of Marine Science

Modelling directional spatial processes in ecological data

(2008) F. Guillaume Blanchet et al.   ECOLOGICAL MODELLING

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

(2008) Paul S. Schmidt et al.   ECOLOGY

Seascape genetics and the spatial ecology of marine populations

(2008) Kimberly A Selkoe et al.   FISH AND FISHERIES

Inference of Historical Changes in Migration Rate From the Lengths of Migrant Tracts

(2008) J. E. Pool 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 analysis method (sam): a software tool combining molecular and environmental data to identify candidate loci for selection

(2008) STÉPHANE JOOST et al.   Molecular Ecology Resources

A consumer's guide to nestedness analysis

(2008) Werner Ulrich et al.   OIKOS