73 Works

Data from: Gene expression correlates of social evolution in coral reef butterflyfishes

Jessica Nowicki, Morgan Pratchett, Stefan Walker, Darren Coker & Lauren O'Connell
Animals display remarkable variation in social behavior. However, outside of rodents, little is known about the neural mechanisms of social variation, and whether they are shared across species and sexes, limiting our understanding of how sociality evolves. Using coral reef butterflyfishes, we examined gene expression correlates of social variation (i.e., pair bonding vs. solitary living) within and between species and sexes. In several brain regions, we quantified gene expression of receptors important for social variation...

Data from: Natal philopatry increases relatedness within groups of coral reef cardinalfish

Theresa Rueger, Hugo Harrison, Peter Buston, Naomi Gardiner, Michael Berumen & Geoffrey Jones
A central issue in evolutionary ecology is how patterns of dispersal influence patterns of relatedness in populations. In terrestrial organisms, limited dispersal of offspring leads to groups of related individuals. In contrast, for most marine organisms, larval dispersal in open waters is thought to minimise kin associations within populations. However, recent molecular evidence and theoretical approaches have shown that limited dispersal, sibling cohesion, and/or differential reproductive success can lead to kin-association and elevated relatedness. Here,...

Data from: Benchmarking DNA metabarcoding for biodiversity-based monitoring and assessment

Eva Aylagas, Angel Borja, Xabier Irigoien & Naiara Rodriguez-Ezpeleta
Characterization of biodiversity has been extensively used to confidently monitor and assess environmental status. Yet, visual morphology, traditionally and widely used for species identification in coastal and marine ecosystem communities, is tedious and entails limitations. Metabarcoding coupled with high-throughput sequencing represents an alternative to rapidly, accurately and cost-effectively analyze thousands of environmental samples simultaneously, and this method is increasingly used to characterize the metazoan taxonomic composition of a wide variety of environments. However, a comprehensive...

Data from: Ecomorphological convergence in planktivorous surgeonfishes

Sarah T. Friedman, Samantha A. Price, Andrew S. Hoey & Peter C. Wainwright
Morphological convergence plays a central role in the study of evolution. Often induced by shared ecological specialization, homoplasy hints at underlying selective pressures and adaptive constraints that deterministically shape the diversification of life. Though midwater zooplanktivory has arisen in adult surgeonfishes (family Acanthuridae) at least four independent times, it represents a clearly specialized state, requiring the capacity to swiftly swim in midwater locating and sucking small prey items. While this diet has commonly been associated...

Data from: Environmental switching during biofilm development in a cold seep system and functional determinants of species sorting

Weipeng Zhang, Renmao Tian, Yang Bo, Huiluo Cao, Lin Cai, Lianguo Chen, Guowei Zhou, Jin Sun, Xixiang Zhang, Abdulaziz Al-Suwailem & Pei-Yuan Qian
The functional basis for species sorting theory remains elusive, especially for microbial community assembly in deep-sea environments. Using artificial surface-based biofilm models, our recent work revealed taxonomic succession during biofilm development in a newly defined cold seep system, the Thuwal cold seeps II, which comprises a brine pool and the adjacent normal bottom water (NBW) to form a metacommunity via the potential immigration of organisms from one patch to another. Here, we designed an experiment...

Population genomic response to geographic gradients by widespread and endemic fishes of the Arabian Peninsula

Joseph DiBattista, Pablo Saenz-Agudelo, Marek Piatek, Fernando Cagua, Brian Bowen, John Choat, Luiz Rocha, Michelle Gaither, Jean-Paul Hobbs, Tane Sinclair-Taylor, Jennifer McIlwain, Mark Priest, Camrin Braun, Nigel Hussey, Steven Kessel & Michael Berumen
Genetic structure within marine species may be driven by local adaptation to their environment, or alternatively by historical processes, such as geographic isolation. The gulfs and seas bordering the Arabian Peninsula offer an ideal setting to examine connectivity patterns in coral reef fishes with respect to environmental gradients and vicariance. The Red Sea is characterized by a unique marine fauna, historical periods of desiccation and isolation, as well as environmental gradients in salinity, temperature, and...

Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning

Naveenkumar Athiyannan, Michael Abrouk, Willem H. P. Boshoff, Stéphane Cauet, Nathalie Rodde, David A. Kudrna, Nahed Mohammed, Jan Bettgenhaeuser, Kirsty Botha, Shannon Derman, Rod A. Wing, Renée Prins & Simon G. Krattinger
Cloning agronomically important genes from large, complex crop genomes remains challenging. Here, we generate a 14.7-gigabase chromosome-scale assembly of the South African bread wheat (Triticum aestivum) cultivar Kariega by combining high-fidelity long reads, optical mapping, and chromosome conformation capture. The resulting assembly is an order of magnitude more contiguous than previous wheat assemblies. Kariega shows durable resistance against the devastating fungal stripe rust disease. We identified the race-specific disease resistance gene Yr27, encoding an intracellular...

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...

Data from: Travel with your kin ship! Insights from genetic sibship among settlers of a coral damselfish

Vanessa Robitzch, Pablo Saenz-Agudelo & Michael L. Berumen
Coral reef fish larvae are tiny, exceedingly numerous, and hard to track. They are also highly capable, equipped with swimming and sensory abilities that may influence their dispersal trajectories. Despite the importance of larval input to the dynamics of a population, we remain reliant on indirect insights to the processes influencing larval behavior and transport. Here, we used genetic data (300 independent single nucleotide polymorphisms) derived from a light trap sample of a single recruitment...

Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

Michael Abrouk, Hanin Ibrahim Ahmed, Philippe Cubry, Denisa Šimoníková, Stéphane Cauet, Yveline Pailles, Jan Bettgenhaeuser, Liubov Gapa, Nora Scarcelli, Marie Couderc, Leila Zekraoui, Nagarajan Kathiresan, Jana Čížková, Eva Hřibová, Jaroslav Doležel, Sandrine Arribat, Hélène Bergès, Jan Wieringa, Mathieu Gueye, Ndjido Kane, Christian Leclerc, Sandrine Causse, Sylvie Vancoppenolle, Claire Billot, Thomas Wicker … & Simon Krattinger
Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we established high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure,...

Illumina reads for TA299

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

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: 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: 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...

Flexibility in Red Sea Tridacna maxima-Symbiodiniaceae associations supports environmental niche adaptation datasets

Benjamin Hume, Susann Rossbach, Anny Cardenas, Gabriela Perna, Christian Voolstra & Carlos Duarte
Giant clams (Tridacninae) are important members of Indo-Pacific coral reefs and among the few bivalve groups that live in a symbiosis with unicellular algae (Symbiodiniaceae). Despite the importance of these endosymbiotic dinoflagellates for clam ecology, the diversity and specificity of these associations remains relatively poorly studied, especially in the Red Sea. Here, we used the internal transcribed spacer 2 (ITS2) rDNA gene region to investigate Symbiodiniaceae communities associated with Red Sea Tridacna maxima clams. We...

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...

Data from: Empirical phylogenies and species abundance distributions are consistent with pre-equilibrium dynamics of neutral community models with gene flow

Anne-Sophie Bonnet-Lebrun, Andrea Manica, Anders Eriksson, Ana S.L. Rodrigues & Ana S. L. Rodrigues
Community characteristics reflect past ecological and evolutionary dynamics. Here, we investigate whether it is possible to obtain realistically shaped modelled communities – i.e., with phylogenetic trees and species abundance distributions shaped similarly to typical empirical bird and mammal communities – from neutral community models. To test the effect of gene flow, we contrasted two spatially explicit individual-based neutral models: one with protracted speciation, delayed by gene flow, and one with point mutation speciation, unaffected by...

Data from: Introgression and selection shaped the evolutionary history of sympatric sister-species of coral reef fishes (genus: Haemulon)

Moises A. Bernal, Michelle R. Gaither, Warren Brian Simison & Luiz A. Rocha
Closely related marine species with large sympatric ranges provide opportunities to study the mechanisms of speciation, particularly when there is evidence of gene flow between the lineages. Here we focus on a case of hybridization between the sympatric sister-species Haemulon maculicauda and H. flaviguttatum, using Sanger sequencing of mitochondrial and nuclear loci, as well as 2422 single nucleotide polymorphisms (SNPs) obtained via Restriction-site Associated DNA Sequencing (RADSeq). Mitochondrial markers revealed a shared haplotype for COI...

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: 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: 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...

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: The role of marine reserves in the replenishment of a locally-impacted population of anemonefish on the Great Barrier Reef

Mary C. Bonin, Hugo B. Harrison, David H. Williamson, Ashley J. Frisch, Pablo Saenz-Agudelo, Michael L. Berumen & Geoffrey P. Jones
The development of parentage analysis to track the dispersal of juvenile offspring has given us unprecedented insight into the population dynamics of coral reef fishes. These tools now have the potential to inform fisheries management and species conservation, particularly for small fragmented populations under threat from exploitation and disturbance. In this study we resolve patterns of larval dispersal for a population of the anemonefish Amphiprion melanopus in the Keppel Islands (southern Great Barrier Reef). Habitat...

Data from: Carotenoid metabolic profiling and transcriptome-genome mining reveal functional equivalence among blue-pigmented copepods and appendicularia

Nazia Mojib, Maan Amad, Manjula Thimma, Naroa Aldanondo, Mande Kumaran & Xabier Irigoien
The tropical oligotrophic oceanic areas are characterized by high water transparency and annual solar radiation. Under these conditions, a large number of phylogenetically diverse mesozooplankton species living in the surface waters (neuston) are found to be blue pigmented. In the present study, we focused on understanding the metabolic and genetic basis of the observed blue phenotype functional equivalence between the blue pigmented organisms from the phylum Arthropoda, subclass copepoda (Acartia fossae) and the phylum Chordata,...

Data from: Population genetics of four heavily exploited shark species around the Arabian Peninsula

Julia L. Y. Spaet, Rima W. Jabado, Aaron C. Henderson, Alec B. M. Moore & Michael L. Berumen
The northwestern Indian Ocean harbors a number of larger marine vertebrate taxa that warrant the investigation of genetic population structure given remarkable spatial heterogeneity in biological characteristics such as distribution, behavior, and morphology. Here, we investigate the genetic population structure of four commercially exploited shark species with different biological characteristics (Carcharhinus limbatus, Carcharhinus sorrah, Rhizoprionodon acutus, and Sphyrna lewini) between the Red Sea and all other water bodies surrounding the Arabian Peninsula. To assess intraspecific...

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