12 Works

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...

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...

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,...

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...

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...

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

Patricia 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 ecosystems 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 approach. Previous studies revealed the nominal species G. fascicularis included three genetically well-differentiated lineages...

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,...

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...

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: Optimising sample sizes for animal distribution analysis using tracking data

Takahiro Shimada, Michele Thums, Mark Hamann, Colin Limpus, Graeme Hays, Nancy FitzSimmons, Natalie Wildermann, Carlos Duarte & Mark Meekan
1. Knowledge of the spatial distribution of populations is fundamental to management plans for any species. When tracking data are used to describe distributions, it is sometimes assumed that the reported locations of individuals delineate the spatial extent of areas used by the target population. 2. Here, we examine existing approaches to validate this assumption, highlight caveats, and propose a new method for a more informative assessment of the number of tracked animals (i.e. sample...

Data from: High rates of carbon and dinitrogen fixation suggest a critical role of benthic pioneer communities in the energy and nutrient dynamics of coral reefs

Florian Roth, Denis Karcher, Nils Rädecker, Sönke Hohn, Susana Carvalho, Timothy Thomson, Franziska Saalmann, Christian R. Voolstra, Benjamin Kürten, Ulrich Struck, Burton Jones & Christian Wild
1. Following coral mortality in tropical reefs, pioneer communities dominated by filamentous and crustose algae efficiently colonize substrates previously occupied by coral tissue. This phenomenon is particularly common after mass coral mortality following prolonged bleaching events associated with marine heatwaves. 2. Pioneer communities play an important role for the biological succession and reorganization of reefs after disturbance. However, their significance for critical ecosystem functions previously mediated by corals, such as the efficient cycling of carbon...

Registration Year

  • 2020

Resource Types

  • Dataset


  • King Abdullah University of Science and Technology
  • James Cook University
  • University of Queensland
  • University Austral de Chile
  • Curtin University
  • University of Konstanz
  • Institute of Experimental Botany
  • University of Guam
  • National Research Institute for Agriculture, Food and Environment
  • Vrije Universiteit Brussel