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

Asymmetric oceanographic processes mediate connectivity and population genetic structure, as revealed by RADseq, in a highly dispersive marine invertebrate (Parastichopus californicus )

(2018) Amanda Xuereb et al.   MOLECULAR ECOLOGY

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

Environmental extremes drive population structure at the northern range limit of Atlantic salmon in North America

(2018) Emma V. A. Sylvester et al.   MOLECULAR ECOLOGY

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

(2018) Simon Bernatchez et al.   Evolutionary Applications

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

(2018) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Genetic diversification of intertidal gastropoda in an archipelago: the effects of islands, oceanic currents, and ecology

(2017) Daishi Yamazaki et al.   MARINE BIOLOGY

Genetic differentiation of the soft shore barnacle Fistulobalanus albicostatus (Cirripedia: Thoracica: Balanomorpha) in the West Pacific

(2017) Yen Wei Chang et al.   Marine Ecology-An Evolutionary Perspective

Development of a Medium Density Combined-Species SNP Array for Pacific and European Oysters ( Crassostrea gigas and Ostrea edulis )

(2017) Alejandro P. Gutierrez et al.   G3-Genes Genomes Genetics

Pleistocene events and present environmental factors have shaped the phylogeography of the intertidal limpetCellana toreuma(Reeve, 1855) (Gastropoda: Nacellidae) in Southeast Asia and China

(2016) Jie Wang et al.   JOURNAL OF MOLLUSCAN STUDIES

Population genomic evidence for adaptive differentiation in the Baltic Sea herring

(2016) Baocheng Guo et al.   MOLECULAR ECOLOGY

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

(2016) Laura Benestan et al.   MOLECULAR ECOLOGY

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

(2016) Keurcien Luu et al.   Molecular Ecology Resources

Bivalve-specific gene expansion in the pearl oyster genome: implications of adaptation to a sessile lifestyle

(2016) Takeshi Takeuchi et al.   Zoological Letters

Pelagic Larval Duration and Dispersal Distance Revisited

(2016) Alan L. Shanks   BIOLOGICAL BULLETIN

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

Mean Structure and Fluctuations of the Kuroshio East of Taiwan from In Situ and Remote Observations

(2015) Ying Jang Yang et al.   OCEANOGRAPHY

Isolation by resistance across a complex coral reef seascape

(2015) Luke Thomas et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

The Pliocene to recent history of the Kuroshio and Tsushima Currents: a multi-proxy approach

(2015) Stephen J. Gallagher et al.   Progress in Earth and Planetary Science

DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data

(2014) Jean-Marie Cornuet et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Population genetic structure and demographic history of the mudskipper Boleophthalmus pectinirostris on the northwestern pacific coast

(2014) Wei Chen et al.   ENVIRONMENTAL BIOLOGY OF FISHES

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

(2014) Anil Raj et al.   GENETICS

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

(2014) Pierre de Villemereuil et al.   MOLECULAR ECOLOGY

Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

(2014) Zhian N. Kamvar et al.   PeerJ

Kraken: A set of tools for quality control and analysis of high-throughput sequence data

(2013) Matthew P.A. Davis et al.   METHODS

StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations

(2013) Luke W. Pembleton et al.   Molecular Ecology Resources

Genotyping by Genome Reducing and Sequencing for Outbred Animals

(2013) Qiang Chen et al.   PLoS One

An Actin-Dependent Step in Mitochondrial Fission Mediated by the ER-Associated Formin INF2

(2013) F. Korobova et al.   SCIENCE

Determination of optimum temperature and salinity for fertilization and hatching in the Chinese pearl oyster Pinctada martensii (Dunker)

(2012) Hui Wang et al.   AQUACULTURE

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

(2012) Carsten F. Dormann et al.   ECOGRAPHY

Genetic and Morphological Differentiation of the Indo-West Pacific Intertidal Barnacle Chthamalus malayensis

(2012) Ling Ming Tsang et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

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

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

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

(2011) H. Li   BIOINFORMATICS

Phylogeography of the reef fish Cephalopholis argus(Epinephelidae) indicates Pleistocene isolation across the indo-pacific barrier with contemporary overlap in the coral triangle

(2011) Michelle R Gaither et al.   BMC EVOLUTIONARY BIOLOGY

Approximate Bayesian Computation in Evolution and Ecology

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

Evolutionary Patterns in Pearl Oysters of the Genus Pinctada (Bivalvia: Pteriidae)

(2010) Regina L. Cunha et al.   MARINE BIOTECHNOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Exploring typhoon variability over the mid-to-late Holocene: evidence of extreme coastal flooding from Kamikoshiki, Japan

(2009) Jonathan D. Woodruff et al.   QUATERNARY SCIENCE REVIEWS

The Great American Schism: Divergence of Marine Organisms After the Rise of the Central American Isthmus

(2008) H.A. Lessios   Annual Review of Ecology Evolution and Systematics

Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation

(2008) Jean-Marie Cornuet et al.   BIOINFORMATICS

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS

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

(2008) M. Foll et al.   GENETICS