Genome-wide SNP analysis explains coral diversity and recovery in the Ryukyu Archipelago

Population Genomics of Marine Fishes: Next-Generation Prospects and Challenges

(2016) Jakob Hemmer-Hansen et al.   BIOLOGICAL BULLETIN

Trans-Pacific RAD-Seq population genomics confirms introgressive hybridization in Eastern Pacific Pocillopora corals

(2015) David J. Combosch et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A population genetic assessment of coral recovery on highly disturbed reefs of the Keppel Island archipelago in the southern Great Barrier Reef

(2015) Madeleine J.H. van Oppen et al.   PeerJ

Population Genomics Reveals Seahorses (Hippocampus erectus) of the Western Mid-Atlantic Coast to Be Residents Rather than Vagrants

(2015) J. T. Boehm et al.   PLoS One

Regional population structure of Montipora capitata across the Hawaiian Archipelago

(2014) GT Concepcion et al.   BULLETIN OF MARINE SCIENCE

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

(2014) Anil Raj et al.   GENETICS

Ancient human genomes suggest three ancestral populations for present-day Europeans

(2014) Iosif Lazaridis et al.   NATURE

The genetic prehistory of the New World Arctic

(2014) M. Raghavan et al.   SCIENCE

Genotyping-by-sequencing in ecological and conservation genomics

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

Genomic divergence between the migratory and stationary ecotypes of Atlantic cod

(2013) Bård O. Karlsen et al.   MOLECULAR ECOLOGY

Species-Specific Responses of Corals to Bleaching Events on Anthropogenically Turbid Reefs on Okinawa Island, Japan, over a 15-year Period (1995–2009)

(2013) Chuki Hongo et al.   PLoS One

Regional genetic differentiation among northern high-latitude island populations of a broadcast-spawning coral

(2012) Y. Nakajima et al.   CORAL REEFS

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

2b-RAD: a simple and flexible method for genome-wide genotyping

(2012) Shi Wang et al.   NATURE METHODS

The 27-year decline of coral cover on the Great Barrier Reef and its causes

(2012) G. De'ath et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

RADSeq: next-generation population genetics

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

Revisiting the winners and the losers a decade after coral bleaching

(2011) R van Woesik et al.   MARINE ECOLOGY PROGRESS SERIES

Using the Acropora digitifera genome to understand coral responses to environmental change

(2011) Chuya Shinzato et al.   NATURE

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Data quality control in genetic case-control association studies

(2010) Carl A Anderson et al.   Nature Protocols

Gene Flow and Genetic Diversity of a Broadcast-Spawning Coral in Northern Peripheral Populations

(2010) Yuichi Nakajima et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Restoration of coral populations in light of genetic diversity estimates

(2009) T. L. Shearer et al.   CORAL REEFS

Connectivity, biodiversity conservation and the design of marine reserve networks for coral reefs

(2009) G. R. Almany et al.   CORAL REEFS

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Reconstructing Indian population history

(2009) David Reich et al.   NATURE

Doom and Boom on a Resilient Reef: Climate Change, Algal Overgrowth and Coral Recovery

(2009) Guillermo Diaz-Pulido et al.   PLoS One

Genetic diversity and connectivity in a brooding reef coral at the limit of its distribution

(2009) A. M. E. Noreen et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Population structure is not a simple function of reproductive mode and larval type: insights from tropical corals

(2008) Karen J. Miller et al.   JOURNAL OF ANIMAL ECOLOGY

A restoration genetics guide for coral reef conservation

(2008) ILIANA B. BAUMS   MOLECULAR ECOLOGY