4.6 Article

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

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

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

Katharine E. Prata et al.

Summary: Research has found that there is no genetic structure among certain species in mesophotic coral ecosystems and there are hidden cryptic taxa. High gene flow suggests the possibility of connectivity and replenishment among these species. The study also suggests that environmental selection along shallow to mesophotic depth gradients may drive divergence in certain depth-generalist species. The research highlights the importance of gene flow in connecting different taxa within this relatively diverse Caribbean genus.

MOLECULAR ECOLOGY (2022)

Article Environmental Sciences

Genetic divergence and range expansion in a western North Pacific coral

James E. Fifer et al.

Summary: This study investigates the population genomic patterns of Acropora hyacinthus, a reef-building coral, along a latitudinal cline in Japan. The study identifies three cryptic lineages of A. hyacinthus and reveals the reduced genetic diversity, asymmetric migration, and genetic adaptation associated with range expansion. The findings provide insights into the genomic consequences of coral range expansion and the adaptive potential for further expansion.

SCIENCE OF THE TOTAL ENVIRONMENT (2022)

Article Multidisciplinary Sciences

Spatially varying selection between habitats drives physiological shifts and local adaptation in a broadcast spawning coral on a remote atoll in Western Australia

Luke Thomas et al.

Summary: This study investigates the mechanisms of coral resilience to climate change in the Rowley Shoals of Western Australia. By studying coral samples from different habitats and using various molecular techniques, the researchers found that there were genetic differences between corals living in lagoon and reef slope habitats. Corals from the lagoon were found to be more resistant to bleaching and showed distinct differences in gene expression compared to corals from the reef slope.

SCIENCE ADVANCES (2022)

Article Ecology

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

Carlos Prada et al.

Summary: Many sister species in the sea overlap geographically but are partitioned along depth gradients. Analyzing new SNP markers derived from RNAseq data revealed the history of genetic exchange, divergence, and population size of these species. The results suggest that depth-segregated populations may experience epochs of genetic exchange, divergence, and periods of isolation.

JOURNAL OF EVOLUTIONARY BIOLOGY (2021)

Article Ecology

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

Scott C. Burgess et al.

Summary: Variation among functionally similar species in their response to environmental stress plays a crucial role in buffering ecosystems from changing states. In the case of the common Indo-Pacific coral Pocillopora, cryptic species exhibited differences in their bleaching response to prolonged ocean heating, highlighting the importance of uncovering response diversity for resilience in ecosystems. The identification of morphologically similar species that differ in their response to stress has significant implications for maintaining ecological functions and driving resilience in coral-dominated systems.

ECOLOGY (2021)

Article Biology

Genomic analysis of distinct bleaching tolerances among cryptic coral species

Noah H. Rose et al.

Summary: Reef-building coral species are experiencing a significant decline due to increasing heatwaves and bleaching-induced mortality. Differences in heat tolerance and symbiont associations exist among closely related species within the Acropora hyacinthus species complex, with genetic differences observed among cryptic species during the 2015 bleaching event. Strong differences in single nucleotide polymorphisms and specific genetic regions contribute to the resilience to bleaching, with host cryptic species playing a key role in determining bleaching susceptibility during global events.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2021)

Article Biology

Twelve years of SAMtools and BCFtools

Petr Danecek et al.

Summary: SAMtools and BCFtools are widely used tools for processing high-throughput sequencing data, with a history of 12 years of continuous development and improvement. These packages have been utilized in various software projects and genomic pipelines and are freely available on GitHub.

GIGASCIENCE (2021)

Article Biochemistry & Molecular Biology

Morphological stasis masks ecologically divergent coral species on tropical reefs

Pim Bongaerts et al.

Summary: DNA sequencing studies are challenging the notion that the diversity of coral species is accurately described. Research has found that coral species can have ecological and phenotypic differences even if they are morphologically similar. This discovery highlights the potential role of temporal reproductive isolation in driving ecological and phenotypic divergence in coral species.

CURRENT BIOLOGY (2021)

Article Biochemistry & Molecular Biology

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

John P. Rippe et al.

Summary: The study revealed that two common coral species in the Florida Keys are each composed of four genetically distinct lineages, with two lineages specialized for deep habitats. Furthermore, corals migrating across reef zones are more likely to die before reaching adulthood.

MOLECULAR ECOLOGY (2021)

Article Environmental Sciences

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

Yuna Zayasu et al.

Summary: Considering genetic composition is crucial for coral restoration and new interventions to combat coral decline. A study on two acroporid species at Kume Island in Japan found higher genetic homogeneity in Acropora digitifera suitable for restoration, while Acropora tenuis showed two distinct clades with possible cryptic species, requiring cautious handling of genetic composition.

AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS (2021)

Article Biodiversity Conservation

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

Kenneth D. Hoadley et al.

Summary: This study reveals significant physiological differences even among closely related symbionts, with implications for the thermal susceptibility of reef-building Porites.

GLOBAL CHANGE BIOLOGY (2021)

Article Biochemistry & Molecular Biology

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

Bui Quang Minh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Editorial Material Biochemistry & Molecular Biology

Cryptic lineages respond differently to coral bleaching

Matias Gomez-Corrales et al.

MOLECULAR ECOLOGY (2020)

Article Biochemistry & Molecular Biology

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

Peter F. Cowman et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2020)

Article Multidisciplinary Sciences

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

Megan K. Morikawa et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Multidisciplinary Sciences

Adaptive introgression enables evolutionary rescue from extreme environmental pollution

Elias M. Oziolor et al.

SCIENCE (2019)

Review Evolutionary Biology

Delineating species in the speciation continuum: A proposal

Nicolas Galtier

EVOLUTIONARY APPLICATIONS (2019)

Article Biochemistry & Molecular Biology

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

Madeleine J. H. van Oppen et al.

MOLECULAR ECOLOGY (2018)

Article Biochemistry & Molecular Biology

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

Todd C. LaJeunesse et al.

CURRENT BIOLOGY (2018)

Article Biochemistry & Molecular Biology

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

Yafei Mao et al.

CURRENT BIOLOGY (2018)

Article Genetics & Heredity

Inferring Population Structure and Admixture Proportions in Low-Depth NGS Data

Jonas Meisner et al.

GENETICS (2018)

Review Biodiversity Conservation

Shifting paradigms in restoration of the world's coral reefs

Madeleine J. H. Van Oppen et al.

GLOBAL CHANGE BIOLOGY (2017)

Article Multidisciplinary Sciences

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

Pim Bongaerts et al.

SCIENCE ADVANCES (2017)

Article Biochemistry & Molecular Biology

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

Vimoksalehi Lukoschek et al.

MOLECULAR ECOLOGY (2016)

Article Biochemistry & Molecular Biology

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

Richard G. Harrison et al.

MOLECULAR ECOLOGY (2016)

Review Ecology

A Trait-Based Approach to Advance Coral Reef Science

Joshua S. Madin et al.

TRENDS IN ECOLOGY & EVOLUTION (2016)

Article Biochemistry & Molecular Biology

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

Camille Roux et al.

PLOS BIOLOGY (2016)

Article Biochemical Research Methods

msa: an R package for multiple sequence alignment

Ulrich Bodenhofer et al.

BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

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

Rebecca Fisher et al.

CURRENT BIOLOGY (2015)

Article Computer Science, Interdisciplinary Applications

Fitting Linear Mixed-Effects Models Using lme4

Douglas Bates et al.

JOURNAL OF STATISTICAL SOFTWARE (2015)

Article Multidisciplinary Sciences

Prevalent endosymbiont zonation shapes the depth distributions of scleractinian coral species

Pim Bongaerts et al.

ROYAL SOCIETY OPEN SCIENCE (2015)

Article Biochemistry & Molecular Biology

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

Carlos Prada et al.

MOLECULAR ECOLOGY (2014)

Review Biochemistry & Molecular Biology

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

Tami E. Cruickshank et al.

MOLECULAR ECOLOGY (2014)

Article Multidisciplinary Sciences

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

Emilia Huerta-Sanchez et al.

NATURE (2014)

Review Genetics & Heredity

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

Christian Schloetterer et al.

NATURE REVIEWS GENETICS (2014)

Article Multidisciplinary Sciences

The Naked Coral'' Hypothesis Revisited - Evidence for and Against Scleractinian Monophyly

Marcelo V. Kitahara et al.

PLOS ONE (2014)

Article Biology

Unrecognized coral species diversity masks differences in functional ecology

Jennifer N. Boulay et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2014)

Article Biochemistry & Molecular Biology

Genome-wide evidence for speciation with gene flow in Heliconius butterflies

Simon H. Martin et al.

GENOME RESEARCH (2013)

Review Genetics & Heredity

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

Vitor Sousa et al.

NATURE REVIEWS GENETICS (2013)

Article Biochemical Research Methods

phangorn: phylogenetic analysis in R

Klaus Peter Schliep

BIOINFORMATICS (2011)

Article Biochemical Research Methods

Estimation of allele frequency and association mapping using next-generation sequencing data

Su Yeon Kim et al.

BMC BIOINFORMATICS (2011)

Review Ecology

Systematic and Biogeographical Patterns in the Reproductive Biology of Scleractinian Corals

Andrew H. Baird et al.

ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS (2009)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Article Multidisciplinary Sciences

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

E. M. Sampayo et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Biochemical Research Methods

APE: Analyses of Phylogenetics and Evolution in R language

E Paradis et al.

BIOINFORMATICS (2004)

Review Ecology

Understanding and confronting species uncertainty in biology and conservation

J Hey et al.

TRENDS IN ECOLOGY & EVOLUTION (2003)

Review Multidisciplinary Sciences

The genetic legacy of the Quaternary ice ages

G Hewitt

NATURE (2000)