Cryptic diversity and spatial genetic variation in the coral Acropora tenuis and its endosymbionts across the Great Barrier Reef

Deep connections: divergence histories with gene flow in mesophotic Agaricia corals

(2022) Katharine E. Prata et al.   MOLECULAR ECOLOGY

Response diversity in corals: hidden differences in bleaching mortality among cryptic Pocillopora species

(2021) Scott C. Burgess et al.   ECOLOGY

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Morphological stasis masks ecologically divergent coral species on tropical reefs

(2021) Pim Bongaerts et al.   CURRENT BIOLOGY

Environmental specialization and cryptic genetic divergence in two massive coral species from the Florida Keys Reef Tract

(2021) John P. Rippe et al.   MOLECULAR ECOLOGY

Genome‐wide SNP genotyping reveals hidden population structure of an acroporid species at a subtropical coral island: Implications for coral restoration

(2021) Yuna Zayasu et al.   AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS

Different functional traits among closely related algal symbionts dictate stress endurance for vital Indo‐Pacific reef‐building corals

(2021) Kenneth D. Hoadley et al.   GLOBAL CHANGE BIOLOGY

Genomic analysis of distinct bleaching tolerances among cryptic coral species

(2021) Noah H. Rose et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genetic divergence and range expansion in a western North Pacific coral

(2021) James E. Fifer et al.   SCIENCE OF THE TOTAL ENVIRONMENT

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Extreme seascape drives local recruitment and genetic divergence in brooding and spawning corals in remote north‐west Australia

(2020) Jim N. Underwood et al.   Evolutionary Applications

Cryptic lineages respond differently to coral bleaching

(2020) Matías Gómez‐Corrales et al.   MOLECULAR ECOLOGY

Speciation‐by‐depth on coral reefs: Sympatric divergence with gene flow or cryptic transient isolation?

(2020) Carlos Prada et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

An enhanced target-enrichment bait set for Hexacorallia provides phylogenomic resolution of the staghorn corals (Acroporidae) and close relatives

(2020) Peter F. Cowman et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Parallel pattern of differentiation at a genomic island shared between clinal and mosaic hybrid zones in a complex of cryptic seahorse lineages

(2019) Florentine Riquet et al.   EVOLUTION

Using naturally occurring climate resilient corals to construct bleaching-resistant nurseries

(2019) Megan K. Morikawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive introgression enables evolutionary rescue from extreme environmental pollution

(2019) Elias M. Oziolor et al.   SCIENCE

Asymmetric dispersal is a critical element of concordance between biophysical dispersal models and spatial genetic structure in Great Barrier Reef corals

(2019) Cynthia Riginos et al.   DIVERSITY AND DISTRIBUTIONS

Considerations for maximizing the adaptive potential of restored coral populations in the western Atlantic

(2019) Iliana B. Baums et al.   ECOLOGICAL APPLICATIONS

Co‐dynamics of Symbiodiniaceae and bacterial populations during the first year of symbiosis with Acropora tenuis juveniles

(2019) Kate M. Quigley et al.   MicrobiologyOpen

Adaptation to reef habitats through selection on the coral animal and its associated microbiome

(2018) Madeleine J. H. van Oppen et al.   MOLECULAR ECOLOGY

Fantastic Beasts and How To Sequence Them: Ecological Genomics for Obscure Model Organisms

(2018) Mikhail V. Matz   TRENDS IN GENETICS

Systematic Revision of Symbiodiniaceae Highlights the Antiquity and Diversity of Coral Endosymbionts

(2018) Todd C. LaJeunesse et al.   CURRENT BIOLOGY

The Roles of Introgression and Climate Change in the Rise to Dominance of Acropora Corals

(2018) Yafei Mao et al.   CURRENT BIOLOGY

Delineating species in the speciation continuum: a proposal

(2018) Nicolas Galtier   Evolutionary Applications

Role of host genetics and heat tolerant algal symbionts in sustaining populations of the endangered coral Orbicella faveolata in the Florida Keys with ocean warming

(2018) Derek P. Manzello et al.   GLOBAL CHANGE BIOLOGY

Polygenic evolution drives species divergence and climate adaptation in corals

(2017) Noah H. Rose et al.   EVOLUTION

Shifting paradigms in restoration of the world's coral reefs

(2017) Madeleine J. H. van Oppen et al.   GLOBAL CHANGE BIOLOGY

Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow

(2017) M. Ravinet et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Evaluating mechanisms of diversification in a Guineo-Congolian tropical forest frog using demographic model selection

(2017) Daniel M. Portik et al.   MOLECULAR ECOLOGY

Deep reefs are not universal refuges: Reseeding potential varies among coral species

(2017) Pim Bongaerts et al.   Science Advances

Getting a grip at the edge: recolonization and introgression in eastern PacificPoritescorals

(2016) Michael E. Hellberg et al.   JOURNAL OF BIOGEOGRAPHY

Congruent patterns of connectivity can inform management for broadcast spawning corals on the Great Barrier Reef

(2016) Vimoksalehi Lukoschek et al.   MOLECULAR ECOLOGY

Heterogeneous genome divergence, differential introgression, and the origin and structure of hybrid zones

(2016) Richard G. Harrison et al.   MOLECULAR ECOLOGY

A Trait-Based Approach to Advance Coral Reef Science

(2016) Joshua S. Madin et al.   TRENDS IN ECOLOGY & EVOLUTION

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence

(2016) Camille Roux et al.   PLOS BIOLOGY

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

(2016) Nicolas Bierne et al.   Current Zoology

Species Richness on Coral Reefs and the Pursuit of Convergent Global Estimates

(2015) Rebecca Fisher et al.   CURRENT BIOLOGY

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

Niche acclimatization in Red Sea corals is dependent on flexibility of host-symbiont association

(2015) M Ziegler et al.   MARINE ECOLOGY PROGRESS SERIES

Unexpected cryptic species diversity in the widespread coralSeriatopora hystrixmasks spatial-genetic patterns of connectivity

(2015) Patricia A. Warner et al.   MOLECULAR ECOLOGY

Niche acclimatization in Red Sea corals is dependent on flexibility of host-symbiont association

(2015) M Ziegler et al.   MARINE ECOLOGY PROGRESS SERIES

Prevalent endosymbiont zonation shapes the depth distributions of scleractinian coral species

(2015) P. Bongaerts et al.   Royal Society Open Science

Cryptic diversity hides host and habitat specialization in a gorgonian-algal symbiosis

(2014) Carlos Prada et al.   MOLECULAR ECOLOGY

Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

(2014) Tami E. Cruickshank et al.   MOLECULAR ECOLOGY

Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA

(2014) Emilia Huerta-Sánchez et al.   NATURE

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

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

The “Naked Coral” Hypothesis Revisited – Evidence for and Against Scleractinian Monophyly

(2014) Marcelo V. Kitahara et al.   PLoS One

Spatio-Temporal Analyses of Symbiodinium Physiology of the Coral Pocillopora verrucosa along Large-Scale Nutrient and Temperature Gradients in the Red Sea

(2014) Yvonne Sawall et al.   PLoS One

DIVERGENCE IS FOCUSED ON FEW GENOMIC REGIONS EARLY IN SPECIATION: INCIPIENT SPECIATION OF SUNFLOWER ECOTYPES

(2013) Rose L. Andrew et al.   EVOLUTION

Estimating Individual Admixture Proportions from Next Generation Sequencing Data

(2013) Line Skotte et al.   GENETICS

Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies

(2013) Simon H. Martin et al.   GENOME RESEARCH

Spatial and temporal genetic structure ofSymbiodiniumpopulations within a common reef-building coral on the Great Barrier Reef

(2013) Emily J. Howells et al.   MOLECULAR ECOLOGY

Evidence for a host role in thermotolerance divergence between populations of the mustard hill coral (Porites astreoides ) from different reef environments

(2013) C. D. Kenkel et al.   MOLECULAR ECOLOGY

Understanding the origin of species with genome-scale data: modelling gene flow

(2013) Vitor Sousa et al.   NATURE REVIEWS GENETICS

Unrecognized coral species diversity masks differences in functional ecology

(2013) J. N. Boulay et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Environmental Factors Controlling the Distribution of Symbiodinium Harboured by the Coral Acropora millepora on the Great Barrier Reef

(2011) Timothy F. Cooper et al.   PLoS One

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Genetic Divergence across Habitats in the Widespread Coral Seriatopora hystrix and Its Associated Symbiodinium

(2010) Pim Bongaerts et al.   PLoS One

Systematic and Biogeographical Patterns in the Reproductive Biology of Scleractinian Corals

(2009) Andrew H. Baird et al.   Annual Review of Ecology Evolution and Systematics

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

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

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

Mitochondrial and Nuclear Genes Suggest that Stony Corals Are Monophyletic but Most Families of Stony Corals Are Not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria)

(2008) Hironobu Fukami et al.   PLoS One

Bleaching susceptibility and mortality of corals are determined by fine-scale differences in symbiont type

(2008) E. M. Sampayo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA