75 Works

In situ monitoring reveals cellular environmental instabilities in human pluripotent stem cell culture

Shannon Klein, Samhan Alsolami, Silvia Arossa, Gerardo Ramos Mandujano, Anieka Parry, Alexandra Steckbauer, Carlos Duarte & Mo Li
Mammalian cell cultures are a keystone resource in biomedical research, but the results of published experiments often suffer from reproducibility challenges. This has led to a focus on the influence of cell culture conditions on cellular responses and reproducibility of experimental findings. Here, we perform frequent in situ monitoring of dissolved O2 and CO2 with optical sensor spots and contemporaneous evaluation of cell proliferation and medium pH in standard batch cultures of three widely used...

Assembly of Aegilops comosa chromosomes

Mahmoud Said, Kateřina Holušová, András Farkas, László Ivanizs, Eszter Gaál, Petr Cápal, Michael Abrouk, Mihaela Martis-Thiele, Balázs Kalapos, Jan Bartoš, Bernd Friebe, Jaroslav Doležel & István Molnár
We sequenced and assembled seven chromosomes of Aegilops comosa. The assembly with Meraculous resulted in ~ 50k - 186k scaffolds per chromosome with N50 size 6.4kb - 20.2kb. The scaffold sequences were used for development of molecular markers specific for cDNAs sequences mapped on Ae. comosa chromosomes Pairwise alignment of wheat cDNA-sequences and the chromosomal scaffolds of Ae. comosa identified candidate sequences. In order to analyze the structure and homeology of Aegilops chromosomes, forty-three mapped...

Illumina reads for TA299

Hanin Ibrahim Ahmed
Raw Illumina short reads (~40x) for TA299 Triticum monococcum subsp. aegilopoides.

Pieces in a global puzzle: Population genetics at two whale shark aggregations in the western Indian Ocean

Royale Hardenstine, Song He, Jesse Cochran, Camrin Braun, E. Fernando Cagua, Simon Pierce, Clare Prebble, Christoph Rohner, Pablo Saenz-Agudelo, Tane Sinclair-Taylor, Gregory Skomal, Simon Thorrold, Alexandra Watts, Casey Zakroff & Michael Berumen
The whale shark Rhincodon typus is found throughout the world’s tropical and warm-temperate ocean basins. Despite their broad physical distribution, research on the species has been concentrated at a few aggregation sites. Comparing DNA sequences from sharks at different sites can provide a demographically neutral understanding of the whale shark’s global ecology. Here, we created genetic profiles for 84 whale sharks from the Saudi Arabian Red Sea and 72 individuals from the coast of Tanzania...

Data from: Relative accuracy of three common methods of parentage analysis in natural populations

Hugo B. Harrison, Pablo Saenz-Agudelo, Serge Planes, Michael L. Berumen & Geoffrey P. Jones
Parentage studies and family reconstructions have become increasingly popular for investigating a range of evolutionary, ecological and behavioral processes in natural populations. However, a number of different assignment methods have emerged in common use, and the accuracy of each may differ in relation to the number of loci examined, allelic diversity, incomplete sampling of all candidate parents, and the presence of genotyping errors. Here we examine how these factors affect the accuracy of three popular...

Data from: Global ecological success of Thalassoma fishes in extreme coral reef habitats

Christopher J. Fulton, Peter C. Wainwright, Andrew S. Hoey & David R. Bellwood
Phenotypic adaptations can allow organisms to relax abiotic selection and facilitate their ecological success in challenging habitats, yet we have relatively little data for the prevalence of this phenomenon at macroecological scales. Using data on the relative abundance of coral reef wrasses and parrotfishes (f. Labridae) spread across three ocean basins and the Red Sea, we reveal the consistent global dominance of extreme wave-swept habitats by fishes in the genus Thalassoma, with abundances up to...

Data from: Systematic revision of Symbiodiniaceae highlights the antiquity and diversity of coral endosymbionts

Todd C. LaJeunesse, John Everett Parkinson, Paul W. Gabrielson, Hae Jin Jeong, James Davis Reimer, Christian R. Voolstra & Scott R. Santos
The advent of molecular data has transformed the science of organizing and studying life on Earth. Genetics-based evidence provides fundamental insights into the diversity, ecology, and origins of many biological systems, including the mutualisms between metazoan hosts and their micro-algal partners. A well-known example is the dinoflagellate endosymbionts (“zooxanthellae”) that power the growth of stony corals and coral reef ecosystems. Once assumed to encompass a single panmictic species, genetic evidence has revealed a divergent and...

Data from: Assessing the effects of iron enrichment across holobiont compartments reveals reduced microbial nitrogen fixation in the Red Sea coral Pocillopora verrucosa

Nils Rädecker, Claudia Pogoreutz, Maren Ziegler, Ananya Ashok, Marcelle M. Barreto, Veronica Chaidez, Carsten G. B. Grupstra, Yi Mei Ng, Gabriela Perna, Manuel Aranda & Christian R. Voolstra
The productivity of coral reefs in oligotrophic tropical waters is sustained by an efficient uptake and recycling of nutrients. In reef-building corals, the engineers of these ecosystems, this nutrient recycling is facilitated by a constant exchange of nutrients between the animal host and endosymbiotic photosynthetic dinoflagellates (zooxanthellae), bacteria, and other microbes. Due to the complex interactions in this so-called coral holobiont, it has proven difficult to understand the environmental limitations of productivity in corals. Among...

Data from: Blind to morphology: genetics identifies several widespread ecologically common species and few endemics among Indo-Pacific cauliflower corals (Pocillopora, Scleractinia)

Jorge H. Pinzón, Eugenia Sampayo, Evelyn Cox, Leonard J. Chauka, Chaolun Allen Chen, Christian R. Voolstra & Todd C. LaJeunesse
AIM: Using high-resolution genetic markers on samples gathered from across their wide distributional range, we endeavoured to delimit species diversity in reef-building Pocillopora corals. They are common, ecologically important, and widespread throughout the Indo-Pacific, but their phenotypic plasticity in response to environmental conditions and their nearly featureless microskeletal structures confound taxonomic assignments and limit an understanding of their ecology and evolution. LOCATION: Indo-Pacific, Red Sea, Arabian/Persian Gulf. METHODS: Sequence analysis of nuclear ribosomal (internal transcribed...

Data from: Acoustic telemetry reveals cryptic residency of whale sharks

Edgar Fernando Cagua, Jesse E. M. Cochran, Christoph A. Rohner, Clare E. M. Prebble, Tane H. Sinclair-Taylor, Simon J. Pierce & Michael L. Berumen
Although whale sharks (Rhincodon typus) have been documented to move thousands of kilometres, they are most frequently observed at a few predictable seasonal aggregation sites. The absence of sharks at the surface during visual surveys has led to the assumption that sharks disperse to places unknown during the long ‘off-seasons’ at most of these locations. Here we compare 2 years of R. typus visual sighting records from Mafia Island in Tanzania to concurrent acoustic telemetry...

Moderate pH deviations trigger transcriptome-wide responses in human cells cultured in physioxia and physiological buffers

Silvia Arossa, Samhan M Alsolami, Shannon Grace Klein, Alexandra Steckbauer, Anieka Janice Parry, Yingzi Zhang, Gerardo Ramos Mandujano, Juan Carlos Izpisua-Belmonte, Carlos Manauel Duarte & Mo Li
Although pH instability is emerging as a potential driver of changes in cell physiology, pH is still poorly controlled during cell culture and in vitro experiments. Standard procedures include the use of chemicals usually not present in the primary physiological buffering system (CO2/HCO3-), such as acids and bases, to manipulate pH levels. This, however, leads to artifacts that potentially affect scientists’ findings. Here, we propose a novel method for controlling pH levels by relying only...

A high-quality genome assembly and annotation of the gray mangrove, Avicennia marina

Guillermo Friis, Joel Vizueta, David R. Nelson, Basel Khraiwesh, Enas Qudeimat, Kourosh Salehi-Ashtiani, Alejandra Ortega, Alyssa Marshell, Carlos M. Duarte & Edward Smith
The gray mangrove [Avicennia marina (Forsk.) Vierh.] is the most widely distributed mangrove species, ranging throughout the Indo-West Pacific. It presents remarkable levels of geographic variation both in phenotypic traits and habitat, often occupying extreme environments at the edges of its distribution. However, subspecific evolutionary relationships and adaptive mechanisms remain understudied, especially across populations of the West Indian Ocean. High-quality genomic resources accounting for such variability are also sparse. Here we report the first chromosome-level...

Data for: Are feeding modes concealing morphofunctional diversity? The case of the New World Parrotfishes

Lucía Pombo-Ayora & Jose Tavera
In functional ecology, morphology is expected to reflect function, however, occasional decoupling of these two can be found. We did not find a relationship between feeding functional morphology and feeding modes of the American parrotfishes of the genera Scarus and Sparisoma. We explore some possible morpho-functional reasons for this phenomenon and reconsider the functional diversity within the scrapers. A phylogenetic tree including 50 species of parrotfishes, based on 12 genes, was reconstructed over which all...

Horizontal acquisition of Symbiodiniaceae in the Anemonia viridis genetic data

Barbara Porro, Thamilla Zamoum, Cédric Mallien, Benjamin C.C. Hume, Christian R. Voolstra, Eric Röttinger, Paola Furla & Didier Forcioli
All metazoans are in fact holobionts, resulting from the association of several organisms, and organismal adaptation is then due to the composite response of this association to the environment. Deciphering the mechanisms of symbiont acquisition in a holobiont is therefore essential to understanding the extent of its adaptive capacities. In cnidarians, some species acquire their photosynthetic symbionts directly from their parents (vertical transmission) but may also acquire symbionts from the environment (horizontal acquisition) at the...

Data from: Applied phenomics and genomics for improving barley yellow dwarf resistance in winter wheat

Paula Silva, Byron Evers, Alexandria Kieffaber, Xu Wang, Allan Fritz, Jared Crain, Jesse Poland & Liangliang Gao
Barley yellow dwarf is one of the major viral diseases of cereals. Phenotyping barley yellow dwarf in wheat is extremely challenging due to similarities to other biotic and abiotic stresses. Breeding for resistance is additionally challenging as the wheat primary germplasm pool lacks genetic resistance, with most of the few resistance genes named to date originating from a wild relative species. The objectives of this study were to (1) evaluate the use of high-throughput phenotyping...

Data from: Larval dispersal and fishing pressure influence recruitment in a coral reef fishery

Richard J. Hamilton, Diego Lozano-Cortés, Michael Bode, Glenn Almany, Hugo B. Harrison, John Pita, Pablo Saenz-Agudelo, Colin Gereniu, Nate Peterson, Howard Choat, Peter A. Waldie & Michael L. Berumen
Understanding larval connectivity patterns in exploited fishes is a fundamental prerequisite for developing effective management strategies and assessing the vulnerability of a fishery to recruitment overfishing and localised extinction. To date however, researchers have not considered how regional variations in fishing pressure also influence recruitment. We used genetic parentage analyses and modelling to infer the dispersal patterns of bumphead parrotfish (Bolbometopon muricatum) larvae in the Kia fishing grounds, Isabel Province, Solomon Islands. We then extrapolated...

Microsatellite genotypes and ITS2 DNA sequence data for Seriatopora hystrix

Rosa Maria Van Der Ven, Jean-François Flot, Carol Buitrago-López & Marc Kochzius
Coral reefs provide essential goods and services but are degrading at an alarming rate due to local and global anthropogenic stressors. The main limitation that prevents the implementation of adequate conservation measures is that connectivity and genetic structure of populations are poorly known. Here, the genetic diversity and connectivity of the brooding scleractinian coral, Seriatopora hystrix were assessed at two scales by genotyping ten microsatellite markers for 356 individual colonies. Seriatopora hystrix showed high differentiation,...

Amino acid d13C dataset for nearshore marine primary producers

Emma Elliott Smith, Michael Fox, Marilyn Fogel & Seth Newsome
Carbon isotope fingerprinting, or multivariate analysis using δ13C values of individual compounds, is a powerful tool in ecological studies, particularly measurements of essential amino acids (EAA δ13C). Despite the widespread application of this technique, there has been little methodological validation to determine (1) whether multivariate EAA δ13C signatures (fingerprints) of primary producer groups vary across space and time, and (2) what biochemical mechanisms drive these patterns. Here, we evaluate the spatiotemporal consistency in EAA δ13C...

Data from: Widespread hybridization and bidirectional introgression in sympatric species of coral reef fish

Hugo B. Harrison, Michael L. Berumen, Pablo Saenz-Agudelo, Eva Salas, David H. Williamson & Geoffrey P. Jones
Coral reefs are highly diverse ecosystems, where numerous closely related species often coexist. How new species arise and are maintained in these high geneflow environments have been long-standing conundrums. Hybridization and patterns of introgression between sympatric species provide a unique insight into the mechanisms of speciation and the maintenance of species boundaries. In this study, we investigate the extent of hybridization between two closely related species of coral reef fish: the common coral trout (Plectropomus...

Data from: An in situ approach for measuring biogeochemical fluxes in structurally complex benthic communities

Florian Roth, Christian Wild, Susana Carvalho, Nils Rädecker, Christian R. Voolstra, Benjamin Kurten, Holger Anlauf, Yusuf C. El-Khaled, Ronan Carolan, Burton H. Jones & Yusuf C. El‐Khaled
1. The exchange of energy and nutrients are integral components of ecological functions of benthic shallow-water ecosystems and are directly dependent on in situ environmental conditions. Traditional laboratory experiments cannot account for the multidimensionality of interacting processes when assessing metabolic rates and biogeochemical fluxes of structurally complex benthic communities. Current in situ chamber systems are expensive, limited in their functionality, and the deployment is often restricted to planar habitats (e.g., sediments or seagrass meadows) only....

Data from: Coral reef carbonate budgets and ecological drivers in the central Red Sea – a naturally high temperature and high total alkalinity environment

Anna Roik, Till Röthig, Claudia Pogoreutz, Vincent Saderne, Christian R. Voolstra & Till Roethig
The structural framework provided by corals is crucial for reef ecosystem function and services, but high seawater temperatures can be detrimental to the calcification capacity of reef-building organisms. The Red Sea is very warm, but total alkalinity (TA) is naturally high and beneficial for reef accretion. To date, we know little about how such detrimental and beneficial abiotic factors affect each other and the balance between calcification and erosion on Red Sea coral reefs, i.e.,...

Data from: Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish

Joseph D. DiBattista, Pablo Saenz-Agudelo, Marek J. Piatek, Xin Wang, Manuel Aranda & Michael L. Berumen
Data from a large-scale restriction site associated DNA (RAD-Seq) study of nine butterflyfish species in the Red Sea and Arabian Sea provided a means to test the utility of a recently published draft genome (Chaetodon austriacus) and assess apparent bias in this method of isolating nuclear loci. We here processed double-digest restriction-site (ddRAD) associated DNA sequencing data to identify single nucleotide polymorphism (SNP) markers and their associated function with and without our reference genome to...

Data from: Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes

Guillem Salazar Guiral, Francisco Cornejo-Castillo, Encarna Borrull, Cristina Díez-Vives, Elena Lara, Dolors Vaqué, Jesús Arrieta, Carlos Duarte, Josep Gasol & Silvia Acinas
The free-living (FL) and particle-attached (PA) marine microbial communities have repeatedly been proved to differ in their diversity and composition in the photic ocean and also recently in the bathypelagic ocean at a global scale. However, although high taxonomic ranks have been proved to exhibit preferences for a PA or FL mode of life, it remains poorly understood whether two clear lifestyles do exist and how these are distributed across the prokaryotic phylogeny. We studied...

Data from: Group elicitations yield more consistent, yet more uncertain experts in understanding risks to ecosystem services in New Zealand bays

Gerald G. Singh, Jim Sinner, Joanne Ellis, Milind Kandlikar, Benjamin S. Halpern, Terre Satterfield & Kai Chan
The elicitation of expert judgment is an important tool for assessment of risks and impacts in environmental management contexts, and especially important as decision-makers face novel challenges where prior empirical research is lacking or insufficient. Evidence-driven elicitation approaches typically involve techniques to derive more accurate probability distributions under fairly specific contexts. Experts are, however, prone to overconfidence in their judgements. Group elicitations with diverse experts can reduce expert overconfidence by allowing cross-examination and reassessment of...

Data from: Pushing the limits of photoreception in twilight conditions: The rod-like cone retina of the deep-sea pearlsides

Fanny De Busserolles, Fabio Cortesi, Jon Vidar Helvik, Wayne I. L. Davies, Rachel M. Templin, Robert K. P. Sullivan, Craig T. Michell, Jessica K. Mountford, Shaun P. Collin, Xabier Irigoien, Stein Kaartvedt & Justin Marshall
Most vertebrates have a duplex retina comprising two photoreceptor types, rods for dim-light (scotopic) vision and cones for bright-light (photopic) and color vision. However, deep-sea fishes are only active in dim-light conditions; hence, most species have lost their cones in favor of a simplex retina composed exclusively of rods. Although the pearlsides, Maurolicus spp., have such a pure rod retina, their behavior is at odds with this simplex visual system. Contrary to other deep-sea fishes,...

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