Timothy G. Stephens
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View article: Green fluorescent proteins show divergent patterns among species and strains of Porites from the Great Barrier Reef
Green fluorescent proteins show divergent patterns among species and strains of Porites from the Great Barrier Reef Open
GFP-like and RFP-like proteins serve diverse functional roles in corals, including photoprotection, prey capture, and algal symbiont attraction. This study investigated the diversity of biofluorescence patterns in 27 coral colonies of Pori…
View article: Green fluorescent proteins show divergent patterns among species and strains of Porites from the Great Barrier Reef
Green fluorescent proteins show divergent patterns among species and strains of Porites from the Great Barrier Reef Open
GFP-like and RFP-like proteins serve diverse functional roles in corals, including photoprotection, prey capture, and algal symbiont attraction. This study investigated the diversity of biofluorescence patterns in 27 coral colonies of Pori…
View article: Stony coral tissue loss disease (SCTLD) destabilizes the coral microbiome
Stony coral tissue loss disease (SCTLD) destabilizes the coral microbiome Open
Stony coral tissue loss disease (SCTLD) is a rapidly spreading lethal coral disease, the etiology of which remains poorly understood. In this study, using deep metagenomic sequencing, we investigate microbial and viral community dynamics a…
View article: Gene transfer drives community cooperation in geothermal habitats
Gene transfer drives community cooperation in geothermal habitats Open
Cyanidiophyceae red algae dominate many geothermal habitats and provide important tools for investigating the evolution of extremophilic eukaryotes and associated microbial communities. We propose that resource sharing drove genome reducti…
View article: Coral Restoration in the Omics Era: Development of Point‐of‐Care Tools for Monitoring Disease, Reproduction, and Thermal Stress
Coral Restoration in the Omics Era: Development of Point‐of‐Care Tools for Monitoring Disease, Reproduction, and Thermal Stress Open
Coral reef degradation has captured global attention from governments, conservationists, and researchers, who are making concerted efforts to develop sustainable solutions to support reef resilience in the face of environmental degradation…
View article: Metaproteome analysis of short-term thermal stress in three sympatric coral species reveals divergent host responses
Metaproteome analysis of short-term thermal stress in three sympatric coral species reveals divergent host responses Open
The accelerating loss of coral reefs worldwide due to anthropogenic climate change has led to a myriad of studies aimed at understanding the basis of coral resilience to support reef conservation. Here, we integrate physiological measureme…
View article: Genetic Transfer in Action: Uncovering <scp>DNA</scp> Flow in an Extremophilic Microbial Community
Genetic Transfer in Action: Uncovering <span>DNA</span> Flow in an Extremophilic Microbial Community Open
Horizontal genetic transfer (HGT) is a significant driver of genomic novelty in all domains of life. HGT has been investigated in many studies however, the focus has been on conspicuous protein‐coding DNA transfers that often prove to be a…
View article: Fpa (YlaN) is an iron(II) binding protein that functions to relieve Fur-mediated repression of gene expression in <i>Staphylococcus aureus</i>
Fpa (YlaN) is an iron(II) binding protein that functions to relieve Fur-mediated repression of gene expression in <i>Staphylococcus aureus</i> Open
Iron (Fe) is a trace nutrient required by nearly all organisms. As a result of the demand for Fe and the toxicity of non-chelated cytosolic ionic Fe, regulatory systems have evolved to tightly balance Fe acquisition and usage while limitin…
View article: Community-wide interactions sustain life in geothermal spring habitats
Community-wide interactions sustain life in geothermal spring habitats Open
We investigated an alga-dominated geothermal spring community in Yellowstone National Park, USA. Our goal was to determine how cells cope with abiotic stressors during diurnal sampling that spanned over two orders of magnitude in solar irr…
View article: Gene expression response under thermal stress in two Hawaiian corals is dominated by ploidy and genotype
Gene expression response under thermal stress in two Hawaiian corals is dominated by ploidy and genotype Open
Transcriptome data are frequently used to investigate coral bleaching; however, the factors controlling gene expression in natural populations of these species are poorly understood. We studied two corals, Montipora capitata and Pocillopor…
View article: Evidence of a putative CO <sub>2</sub> delivery system to the chromatophore in the photosynthetic amoeba <i>Paulinella</i>
Evidence of a putative CO <sub>2</sub> delivery system to the chromatophore in the photosynthetic amoeba <i>Paulinella</i> Open
The photosynthetic amoeba, Paulinella provides a recent (ca. 120 Mya) example of primary plastid endosymbiosis. Given the extensive data demonstrating host lineage‐driven endosymbiont integration, we analysed nuclear genome and transcripto…
View article: Diverse fates of ancient horizontal gene transfers in extremophilic red algae
Diverse fates of ancient horizontal gene transfers in extremophilic red algae Open
Horizontal genetic transfer (HGT) is a common phenomenon in eukaryotic genomes. However, the mechanisms by which HGT‐derived genes persist and integrate into other pathways remain unclear. This topic is of significant interest because, ove…
View article: Hot springs viruses at Yellowstone National Park have ancient origins and are adapted to thermophilic hosts
Hot springs viruses at Yellowstone National Park have ancient origins and are adapted to thermophilic hosts Open
Geothermal springs house unicellular red algae in the class Cyanidiophyceae that dominate the microbial biomass at these sites. Little is known about host-virus interactions in these environments. We analyzed the virus community associated…
View article: Temporal dynamics in a red alga dominated geothermal feature in Yellowstone National Park
Temporal dynamics in a red alga dominated geothermal feature in Yellowstone National Park Open
Alga-dominated geothermal spring communities in Yellowstone National Park (YNP), USA, have been the focus of many studies, however, relatively little is known about the composition and community interactions which underpin these ecosystems…
View article: Hot springs viruses at Yellowstone National Park have ancient origins and are adapted to their thermophilic hosts
Hot springs viruses at Yellowstone National Park have ancient origins and are adapted to their thermophilic hosts Open
Geothermal springs in areas such as Yellowstone National Park (YNP), USA house unicellular red algae that dominate the microbial biomass. Little is known about the viruses that infect the biota. Here we used metagenomics to characterize th…
View article: YlaN is an iron(II) binding protein that functions to relieve Fur-mediated repression of gene expression in<i>Staphylococcus aureus</i>
YlaN is an iron(II) binding protein that functions to relieve Fur-mediated repression of gene expression in<i>Staphylococcus aureus</i> Open
Iron (Fe) is a trace nutrient required by nearly all organisms. As a result of the demand for Fe and the toxicity of non-chelated cytosolic ionic Fe, regulatory systems have evolved to tightly balance Fe acquisition and usage while limitin…
View article: Peeling back the layers of coral holobiont multi-omics data
Peeling back the layers of coral holobiont multi-omics data Open
The integration of multiple 'omics' datasets is a promising avenue for answering many important and challenging questions in biology, particularly those relating to complex ecological systems. Although multi-omics was developed using data …
View article: Ploidy Variation and Its Implications for Reproduction and Population Dynamics in Two Sympatric Hawaiian Coral Species
Ploidy Variation and Its Implications for Reproduction and Population Dynamics in Two Sympatric Hawaiian Coral Species Open
Standing genetic variation is a major driver of fitness and resilience and therefore of fundamental importance for threatened species such as stony corals. We analyzed RNA-seq data generated from 132 Montipora capitata and 119 Pocillopora …
View article: Building consensus around the assessment and interpretation of Symbiodiniaceae diversity
Building consensus around the assessment and interpretation of Symbiodiniaceae diversity Open
Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at mul…
View article: Peer Review #1 of "Building consensus around the assessment and interpretation of Symbiodiniaceae diversity (v0.1)"
Peer Review #1 of "Building consensus around the assessment and interpretation of Symbiodiniaceae diversity (v0.1)" Open
Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences.To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at mult…
View article: Algae obscura: The potential of rare species as model systems
Algae obscura: The potential of rare species as model systems Open
Model organism research has provided invaluable knowledge about foundational biological principles. However, most of these studies have focused on species that are in high abundance, easy to cultivate in the lab, and represent only a small…
View article: Montipora capitata multi-omics supplemental tables
Montipora capitata multi-omics supplemental tables Open
Supplemental tables for Montipora capitata multi-omics study. Table S1. Read statistics for the microbiome 16S rRNA data from the four M. capitata colonies (n=3 per treatment/time point/colony). Table S2. Protein and transcript FC values f…
View article: Montipora capitata multi-omics supplemental tables
Montipora capitata multi-omics supplemental tables Open
Supplemental tables for Montipora capitata multi-omics study. Table S1. Read statistics for the microbiome 16S rRNA data from the four M. capitata colonies (n=3 per treatment/time point/colony). Table S2. Protein and transcript FC values f…
View article: Montipora capitata multi-omics supplemental tables
Montipora capitata multi-omics supplemental tables Open
Supplemental tables for Montipora capitata multi-omics study. Table S1. Read statistics for the microbiome 16S rRNA data from the four M. capitata colonies (n=3 per treatment/time point/colony). Table S2. Protein and transcript FC values f…
View article: Differential Gene Expression Analysis and Gene Ontology in Triploid and Diploid Pocillopora Acuta
Differential Gene Expression Analysis and Gene Ontology in Triploid and Diploid Pocillopora Acuta Open
Corals are marine invertebrates that are facing life-threatening environmental stressors due to climate change. Polyploidy can, in such cases, be an important source of variation and adaptation in corals and other species. Polyploidy is th…
View article: A k-mer-based approach for phylogenetic classification of taxa in environmental genomic data
A k-mer-based approach for phylogenetic classification of taxa in environmental genomic data Open
In the age of genome sequencing, whole genome data is readily and frequently generated, leading to a wealth of new information that can be used to advance various fields of research. New approaches, such as alignment-free phylogenetic meth…
View article: Endosymbiotic ratchet accelerates divergence after organelle origin
Endosymbiotic ratchet accelerates divergence after organelle origin Open
We hypothesize that as one of the most consequential events in evolution, primary endosymbiosis accelerates lineage divergence, a process we refer to as the endosymbiotic ratchet . Our proposal is supported by recent work on the photosynth…
View article: Development of a portable toolkit to diagnose coral thermal stress
Development of a portable toolkit to diagnose coral thermal stress Open
Coral bleaching, precipitated by the expulsion of the algal symbionts that provide colonies with fixed carbon is a global threat to reef survival. To protect corals from anthropogenic stress, portable tools are needed to detect and diagnos…