75 Works

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,...

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...

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...

Data from: Comparative phylogeography of three host sea anemones in the Indo-Pacific

Pablo Saenz-Agudelo, Madeleine Emms, Emily Giles, Remy Gatins, Gerrit Nanninga, Anna Scott, Jean Paul Hobbs, Ashley Frisch, Suzanne Mills, Ricardo Beldade & Michael Berumen
Aim The mutualistic relationship between anemones and anemonefishes is one of the most iconic examples of symbiosis. However, while anemonefishes have been extensively studied in terms of genetic connectivity, such information is lacking entirely for host sea anemones. Here, we provide the first information on the broad-scale population structure and phylogeographic patterns of three species of host sea anemone, Heteractis magnifica, Stichodactyla mertensii, and Entacmaea quadricolor. We evaluate if there is concordance in genetic structure...

Evolutionary biogeography of the reef-building coral genus Galaxea across the Indo-Pacific ocean

Patricia Wepfer, Patricia H. Wepfer, Yuichi Nakajima, Makamas Sutthacheep, Veronica Z. Radice, Zoe Richards, Put Ang, Tullia Terraneo, Mareike Sudek, Atsushi Fujimura, Robert J. Toonen, Alexander S. Mikheyev, Evan P. Economo & Satoshi Mitarai
Stony corals (Scleractinia) form the basis for some of the most diverse ecosytems on Earth, but we have much to learn about their evolutionary history and systematic relationships. In order to improve our understanding of species in corals we here investigated phylogenetic relationships between morphologically defined species and genetic lineages in the genus Galaxea (Euphyllidae) using a combined phylogenomic and phylogeographic ap- proach. Previous studies revealed the nominal species G. fascicularis included three genetically well-differ-...

Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history

Dilan Sarange Rajapaksha Patiranage, Elodie Rey, Nazgol Emrani, Gordon Wellman, Karl Schmid, Sandra Schmöckel, Mark Tester & Christian Jung
Quinoa germplasm preserves useful and substantial genetic variation, yet it remains untapped due to a lack of implementation of modern breeding tools. We have integrated field and sequence data to characterize a large diversity panel of quinoa. Whole-genome sequencing of 310 accessions revealed 2.9 million polymorphic high confidence SNP loci. Highland and Lowland quinoa were clustered into two main groups, with FST divergence of 0.36 and fast LD decay of 6.5 and 49.8 Kb, respectively....

Data from: Seascape genetics along environmental gradients in the Arabian Peninsula: insights from ddRAD sequencing of anemonefishes

Pablo Saenz-Agudelo, Joseph D. DiBattista, Marek J. Piatek, Michelle R. Gaither, Hugo B. Harrison, Gerrit B. Nanninga & Michael L. Berumen
Understanding the processes that shape patterns of genetic structure across space is a central aim of landscape genetics. However, it remains unclear how geographic features and environmental variables shape gene flow, particularly for marine species in large complex seascapes. Here, we evaluated the genomic composition of the two-band anemonefish Amphiprion bicinctus across its entire geographic range in the Red Sea and Gulf of Aden, as well as its close relative, Amphiprion omanensis endemic to the...

Data from: Large-scale, multi-directional larval connectivity among coral reef fish populations in the Great Barrier Reef Marine Park

David H. Williamson, Hugo B. Harrison, Glenn R. Almany, Michael L. Berumen, Michael Bode, Mary C. Bonin, Severine Choukroun, Peter J. Doherty, Ashley J. Frisch, Pablo Saenz-Agudelo & Geoffrey P. Jones
Larval dispersal is the key process by which populations of most marine fishes and invertebrates are connected and replenished. Advances in larval tagging and genetics have enhanced our capacity to track larval dispersal, assess scales of population connectivity, and quantify larval exchange among no-take marine reserves and fished areas. Recent studies have found that reserves can be a significant source of recruits for populations up to 40 km away, but the scale and direction of...

Data from: Genetic structure of populations of whale sharks among ocean basins and evidence for their historic rise and recent decline

Thomas M. Vignaud, Jeffrey A. Maynard, Raphael Leblois, Mark G. Meekan, Ricardo Vázquez-Juárez, Dení Ramírez-Macías, Simon J. Pierce, David Rowat, Michael L. Berumen, Champak Beeravolu, Sandra Baksay & Serge Planes
This study presents genetic evidence that whale sharks, Rhincodon typus, are comprised of at least two populations that rarely mix and is the first to document a population expansion. Relatively high genetic structure is found when comparing sharks from the Gulf of Mexico with sharks from the Indo-Pacific. If mixing occurs between the Indian and Atlantic Oceans, it is not sufficient to counter genetic drift. This suggests whale sharks are not all part of a...

Data from: Sensitivity and acclimation of three canopy-forming seaweeds to UVB radiation and warming

Xi Xiao, Thibaut De Bettignies, Ylva S. Olsen, Susana Agusti, Carlos M. Duarte & Thomas Wernberg
Canopy-forming seaweeds, as primary producers and foundation species, provide key ecological services. Their responses to multiple stressors associated with climate change could therefore have important knock-on effects on the functioning of coastal ecosystems. We examined interactive effects of UVB radiation and warming on juveniles of three habitat-forming subtidal seaweeds from Western Australia–Ecklonia radiata, Scytothalia dorycarpa and Sargassum sp. Fronds were incubated for 14 days at 16–30°C with or without UVB radiation and growth, health status,...

Data from: Weak population structure of the Spot-tail shark Carcharhinus sorrah and the Blacktip shark C. limbatus along the coasts of the Arabian Peninsula, Pakistan and South Africa

Dareen Almojil, Geremy Cliff, Julia L.Y. Spaet & Julia L. Y. Spaet
The increase in demand for shark meat and fins has placed shark populations worldwide under high fishing pressure. In the Arabian region, the Spot-tail shark Carcharhinus sorrah and the Blacktip shark Carcharhinus limbatus are among the most exploited species. In this study we investigated the population genetic structure of C. sorrah (n= 327) along the coasts of the Arabian Peninsula and of C. limbatus (n= 525) along the Arabian coasts, Pakistan and KwaZulu-Natal, South Africa...

GLAM: Glycogen-derived Lactate Absorption Map for visual analysis of dense and sparse surface reconstructions of rodent brain structures on desktop systems and virtual environments

Marco Agus, Daniya Boges, Nicolas Gagnon, Pierre J. Magistretti, Markus Hadwiger & Corrado Cali
Human brain accounts for about one hundred billion neurons, but they cannot work properly without ultrastructural and metabolic support. For this reason, mammalian brains host another type of cells called “glial cells”, whose role is to maintain proper conditions for efficient neuronal function. One type of glial cell, astrocytes, are involved in particular in the metabolic support of neurons, by feeding them with lactate, one byproduct of glucose metabolism that they can take up from...

Data from: Entangled fates of holobiont genomes during invasion: nested bacterial and host diversities in Caulerpa taxifolia

Sophie Arnaud-Haond, Tania Aires, Rui Candeias, Sara J. L. Teixeira, Carlos M. Duarte, Myriam Valero & Ester A. Serrão
Successful prevention and mitigation of biological invasions requires retracing the initial steps of introduction, as well as understanding key elements enhancing the adaptability of invasive species. We studied the genetic diversity of the green alga Caulerpa taxifolia and its associated bacterial communities in several areas around the world. The striking congruence of α and ß diversity of the algal genome and endophytic communities reveals a tight association, supporting the holobiont concept as best describing the...

Data from: Assessing the utility of eDNA as a tool to survey reef-fish communities in the Red Sea

Joseph D. DiBattista, Darren J. Coker, Tane H. Sinclair-Taylor, Michael Stat, Michael L. Berumen & Michael Bunce
Relatively small volumes of water may contain sufficient environmental DNA (eDNA) to detect target aquatic organisms via genetic sequencing. We therefore assessed the utility of eDNA to document the diversity of coral reef fishes in the central Red Sea. DNA from seawater samples was extracted, amplified using fish-specific 16S mitochondrial DNA primers, and sequenced using a metabarcoding workflow. DNA sequences were assigned to taxa using available genetic repositories or custom genetic databases generated from reference...

Data from: Restricted grouper reproductive migrations support community-based management

Peter A. Waldie, Glenn R. Almany, Tane H. Sinclair-Taylor, Richard J. Hamilton, Tapas Potuku, Mark A. Priest, Kevin L. Rhodes, Jan Robinson, Joshua E. Cinner & Michael L. Berumen
Conservation commonly requires trade-offs between social and ecological goals. For tropical small-scale fisheries, spatial scales of socially appropriate management are generally small—the median no-take locally managed marine area (LMMA) area throughout the Pacific is less than 1 km2. This is of particular concern for large coral reef fishes, such as many species of grouper, which migrate to aggregations to spawn. Current data suggest that the catchment areas (i.e. total area from which individuals are drawn)...

Data from: Year-long monitoring of physico-chemical and biological variables provide a comparative baseline of coral reef functioning in the central Red Sea

Anna Roik, Till Röthig, Cornelia Roder, Maren Zielger, Stephan G. Kremb, Christian R. Voolstra & Maren Ziegler
Coral reefs in the central Red Sea are sparsely studied and in situ data on physico-chemical and key biotic variables are missing to provide an important comparative baseline. To fill this gap, we monitored three reefs along a cross-shelf gradient during a full year, simultaneously collecting data on currents, temperature, salinity, dissolved oxygen (DO), chlorophyll-a, turbidity, inorganic nutrients, sedimentation, bacterial communities of reef water, and bacterial and algal composition of epilithic biofilms. Some of these...

Data from: Timing of host feeding drives rhythms in parasite replication

Kimberley F. Prior, Daan R. Van Der Veen, Aidan J. O'Donnell, Katherine Cumnock, David Schneider, Arnab Pain, Amit Subudhi, Abhinay Ramaprasad, Samuel S. C. Rund, Nicholas J. Savill, Sarah E. Reece & Aidan J. O’Donnell
Circadian rhythms enable organisms to synchronise the processes underpinning survival and reproduction to anticipate daily changes in the external environment. Recent work shows that daily (circadian) rhythms also enable parasites to maximise fitness in the context of ecological interactions with their hosts. Because parasite rhythms matter for their fitness, understanding how they are regulated could lead to innovative ways to reduce the severity and spread of diseases. Here, we examine how host circadian rhythms influence...

Data from: Dominance of Endozoicomonas bacteria throughout coral bleaching and mortality suggests structural inflexibility of the Pocillopora verrucosa microbiome

Claudia Pogoreutz, Nils Rädecker, Anny Cardenas, Astrid Gärdes, Christian Wild & Christian R. Voolstra
The functional importance of Symbiodinium algal endosymbionts and a diverse suite of bacteria for coral holobiont health and functioning is widely acknowledged. Yet, we know surprisingly little about microbial community dynamics and the stability of host-microbe associations under adverse environmental conditions. To gain insight into the stability of coral host-microbe associations and holobiont structure, we assessed changes in the community structure of Symbiodinium and bacteria associated with the coral Pocillopora verrucosa under excess organic nutrient...

Data from: Two decades of genetic profiling yields first evidence of natal philopatry and long-term fidelity to parturition sites in sharks

Kevin A. Feldheim, Samuel H. Gruber, Joseph D. DiBattista, Elizabeth A. Babcock, Steven A. Kessel, Andrew P. Hendry, Ellen K. Pikitch, Mary V. Ashley & Demian D. Chapman
Sharks are a globally threatened group of marine fishes that often breed in their natal region of origin. There has even been speculation that female sharks return to their exact birthplace to breed (“natal philopatry”), which would have important conservation implications. Genetic profiling of lemon sharks (Negaprion brevirostris) from 20 consecutive cohorts (1993-2012) at Bimini, Bahamas showed that certain females faithfully gave birth at this site for nearly two decades. At least six females born...

Data from: Extra-pair mating in a socially monogamous and paternal mouthbrooding cardinalfish

Theresa Rueger, Hugo B. Harrison, Naomi M. Gardiner, Michael L. Berumen & Geoffrey P. Jones
Many vertebrates form monogamous pairs to mate and care for their offspring. However, genetic tools have increasingly shown that many offspring arise from matings outside of the monogamous pair bond. Social monogamy is relatively common in coral reef fishes, but there have been relatively few studies that have confirmed monogamy or extra-pair reproduction, either for males or females. Here long-term observations and genetic tools were applied to examine the parentage of embryos in a paternally...

Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color

Michael Abrouk, Naveenkumar Athiyannan, Thomas Müller & Simon Krattinger
The cloning of agriculturally important genes is often complicated by haplotype variation across crop cultivars. Access to pan-genome information greatly facilitates the assessment of structural variations and rapid candidate gene identification. Here, we identified the red glume 1 (Rg-B1) gene using association genetics and haplotype analyses in ten reference-grade wheat genomes. Glume color is an important trait to characterize wheat cultivars. Red glumes are frequent among Central European spelt, a dominant wheat subspecies in Europe...

A droplet reactor on a super-hydrophobic surface allows control and characterization of amyloid fibril growth

Peng Zhang, Enzo Di Fabrizio, Manola Moretti, Marco Allione, Yuansi Tian, Javier Ordonez-Loza, Davide Altamura, Cinzia Giannini, Bruno Torre, Gobind Das, Erqiang Li, Sigurdur T. Thoroddsen, Mani Sarathy, Ida Autiero, Andrea Giugni, Francesco Gentile, Natalia Malara & Monica Marini
Methods to produce protein amyloid fibrils, in vitro, and in situ structure characterization, are of primary importance in biology, medicine, and pharmacology. We first demonstrated the droplet on a super-hydrophobic substrate as the reactor to produce protein amyloid fibrils with real-time monitoring of the growth process by using combined light-sheet microscopy and thermal imaging. The molecular structures were characterized by Raman spectroscopy, X-ray diffraction and X-ray scattering. We demonstrated that the convective flow induced by...

Magellanic penguin's onland trajectory data

Flavio Quintana, Agustina Gomez-Laich, Richard Gunner, Fabian Gabelli, Giacomo Dell'Omo, Carlos Duarte, Martin Brogger & Rory Wilson
Understanding how animals move in dense environments where vision is compromised is a major challenge. We used GPS and dead-reckoning to examine the movement of Magellanic penguins commuting through vegetation that precluded long-distance vision. Birds leaving the nest followed the shortest, quickest route to the sea (the ‘ideal path’ [I-path]) but return tracks depended where the birds left the water. Penguins arriving at the beach departure spot mirrored the departure. Most of those landing at...

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