47 Works

Data from: Efficiency of ddRAD target enriched sequencing across spiny rock lobster species (Palinuridae: Jasus)

Carla A. Souza, Nicholas Murphy, Cecilia Villacorta-Rath, Laura N. Woodings, Irina Ilyushkina, Cristian E. Hernandez, Bridget S. Green, James J. Bell & Jan M. Strugnell
Double digest restriction site-associated DNA sequencing (ddRADseq) and target capture sequencing methods are used to explore population and phylogenetic questions in non-model organisms. ddRADseq offers a simple and reliable protocol for population genomic studies, however it can result in a large amount of missing data due to allelic dropout. Target capture sequencing offers an opportunity to increase sequencing coverage with little missing data and consistent orthologous loci across samples, although this approach has generally been...

Data from: Kin recognition in embryonic damselfishes

Jennifer Ann Atherton & Mark Ian McCormick
Predator-induced mortality rates are highest in early life stages; therefore, early recognition of threats can greatly increase survival chances. Some species of coral reef fishes have been frequently found to recruit back to their natal reefs; in this instance, there is a high chance of juveniles encountering their siblings, among other kin, after hatching. Kin recognition plays an important ecological role in that it allows individuals to protect genetically similar relatives, and hence increase their...

Data from: Disentangling the pathways of land use impacts on the functional structure of fish assemblages in Amazon streams

Rafael P. Leitão, Jansen Zuanon, David Mouillot, Cecília G. Leal, Robert M. Hughes, Philip R. Kaufmann, Sébastien Villéger, Paulo S. Pompeu, Daniele Kasper, Felipe R. De Paula, Silvio F. B. Ferraz & Toby A. Gardner
Agricultural land use is a primary driver of environmental impacts on streams. However, the causal processes that shape these impacts operate through multiple pathways and at several spatial scales. This complexity undermines the development of more effective management approaches, and illustrates the need for more in-depth studies to assess the mechanisms that determine changes in stream biodiversity. Here we present results of the most comprehensive multi-scale assessment of the biological condition of streams in the...

Data from: The role of topography and plant functional traits in determining tropical reforestation success

Alexander W. Cheesman, Noel D. Preece, Penny Van Oosterzee, Peter D. Erskine & Lucas A. Cernusak
1.Early establishment and sapling growth is a key phase in ensuring cost-effective reforestation success in relation to biodiversity outcomes. Therefore species selection must consider the interaction between plant functional traits and the often-challenging and heterogeneous biophysical environment of degraded landscapes. 2.In this study, we examine how microtopography (slope) results in spatial heterogeneity of soil nutrients, especially phosphorus (P) in a degraded tropical pasture landscape in Queensland, Australia. We then explore how this small-scale heterogeneity influences...

Data from: Sibling species of mutualistic Symbiodinium clade G from bioeroding sponges in the western Pacific and western Atlantic oceans

Blake D. Ramsby, Malcolm S. Hill, Daniel J. Thornhill, Sieuwkje F. Steenuizen, Michelle Achlatis, Allison M. Lewis, Todd C. LaJeunesse & Sieuwkje F. Steenhuizen
Dinoflagellates in the genus Symbiodinium associate with a broad array of metazoan and protistian hosts. Symbiodinium-based symbioses involving bioeroding sponge hosts have received less attention than those involving scleractinian hosts. Certain species of common Cliona harbor high densities of an ecologically restricted group of Symbiodinium, referred to as Clade G. The relationships of these unusual Clade G Symbiodinium with Foraminifera, sponges, and black coral (Antipatharia) are rarely studied. Nonetheless, analyses of genetic evidence indicate that...

Data from: Idiosyncratic responses to climate-driven forest fragmentation and marine incursions in reed frogs from Central Africa and the Gulf of Guinea Islands

Rayna C. Bell, Juan L. Parra, Gabriel Badjedjea, Michael F. Barej, David C. Blackburn, Marius Burger, Alan Channing, J. Maximilian Dehling, Eli Greenbaum, Václav Gvoždík, Jos Kielgast, Chifundera Kusamba, Stefan Lötters, Patrick J. McLaughlin, Zoltán T. Nagy, Mark-Oliver Rödel, Daniel M. Portik, Bryan L. Stuart, Jeremy VanDerWal, Ange-Ghislain Zassi Boulou & Kelly R. Zamudio
Organismal traits interact with environmental variation to mediate how species respond to shared landscapes. Thus, differences in traits related to dispersal ability or physiological tolerance may result in phylogeographic discordance among co-distributed taxa, even when they are responding to common barriers. We quantified climatic suitability and stability, and phylogeographic divergence within three reed frog species complexes across the Guineo-Congolian forests and Gulf of Guinea archipelago of Central Africa to investigate how they responded to a...

Data from: Plastic waste associated with disease on coral reefs

Joleah B. Lamb, Bette L. Willis, Evan A. Fiorenza, Courtney S. Couch, Robert Howard, Douglas N. Rader, James D. True, Lisa A. Kelly, Awaludinnoer Ahmad, Jamaluddin Jompa & C. Drew Harvell
Plastic waste can promote microbial colonization by pathogens implicated in outbreaks of disease in the ocean. We assessed the influence of plastic waste on disease risk in 124,000 reef-building corals from 159 reefs in the Asia-Pacific region. The likelihood of disease increases from 4% to 89% when corals are in contact with plastic. Structurally complex corals are eight times more likely to be affected by plastic, suggesting that microhabitats for reef-associated organisms and valuable fisheries...

Data from: Warming has a greater effect than elevated CO2 on predator–prey interactions in coral reef fish

Bridie J.M. Allan, Paolo Domenici, Sue Ann Watson, Philip L. Munday, Mark I. McCormick & Bridie J. M. Allan
Ocean acidification and warming, driven by anthropogenic CO2 emissions, are considered to be among the greatest threats facing marine organisms. While each stressor in isolation has been studied extensively, there has been less focus on their combined effects, which could impact key ecological processes. We tested the independent and combined effects of short-term exposure to elevated CO2 and temperature on the predator–prey interactions of a common pair of coral reef fishes (Pomacentrus wardi and its...

Biogeography, reproductive biology and phylogenetic divergence within the Fungiidae (mushroom corals)

Mila Grinblat, Ira Cooke, Tom Shlesinger, Yossi Loya, David Miller & Peter Cowman

Data from: A global perspective on the trophic geography of sharks

Christopher Stephen Bird, Ana Veríssimo, Sarah Magozzi, Kátya G. Abrantes, Alex Aguilar, Hassan Al-Reasi, Adam Barnett, Dana M. Bethea, Gérard Biais, Asuncion Borrell, Marc Bouchoucha, Mariah Boyle, Edward J. Brooks, Juerg Brunnschweiler, Paco Bustamante, Aaron Carlisle, Diana Catarino, Stéphane Caut, Yves Cherel, Tiphaine Chouvelon, Diana Churchill, Javier Ciancio, Julien Claes, Ana Colaço, Dean L. Courtney … & Clive N. Trueman
Sharks are a diverse group of mobile predators that forage across varied spatial scales and have the potential to influence food web dynamics. The ecological consequences of recent declines in shark biomass may extend across broader geographic ranges if shark taxa display common behavioural traits. By tracking the original site of photosynthetic fixation of carbon atoms that were ultimately assimilated into muscle tissues of 5,394 sharks from 114 species, we identify globally consistent biogeographic traits...

Data from: Strong trans-Pacific break and local conservation units in the Galapagos shark (Carcharhinus galapagensis) revealed by genome-wide cytonuclear markers

Diana A. Pazmiño, Gregory E. Maes, Madeline E. Green, Colin A. Simpfendorfer, Mauricio Hoyos-Padilla, Clinton J.A. Duffy, Carl G. Meyer, Sven E. Kerwath, Pelayo Salinas-De-León & Lynne Van Herwerden
The application of genome-wide cytonuclear molecular data to identify management and adaptive units at various spatio-temporal levels is particularly important for overharvested large predatory organisms, often characterized by smaller, localized populations. Despite being “near threatened”, current understanding of habitat use and population structure of Carcharhinus galapagensis is limited to specific areas within its distribution. We evaluated population structure and connectivity across the Pacific Ocean using genome-wide Single Nucleotide Polymorphisms (~7200 SNPs) and mitochondrial Control Region...

Data from: Strong population structure deduced from genetics, otolith chemistry and parasite abundances explains vulnerability to localised fishery collapse in a large Sciaenid fish, Protonibea diacanthus

Laura Taillebois, Diane P. Barton, David A. Crook, Thor Saunders, Jonathan Taylor, Mark Hearnden, Richard J. Saunders, Stephen J. Newman, Michael J. Travers, David J. Welch, Alan Greig, Christine Dudgeon, Safia Maher & Jennifer R. Ovenden
As pressure on coastal marine resources is increasing globally, the need to quantitatively assess vulnerable fish stocks is crucial in order to avoid the ecological consequences of stock depletions. Species of Sciaenidae (croakers, drums) are important components of tropical and temperate fisheries and are especially vulnerable to exploitation. The black-spotted croaker, Protonibea diacanthus, is the only large sciaenid in coastal waters of northern Australia where it is targeted by commercial, recreational and indigenous fishers due...

Data from: Temporal and spatial activity-associated energy partitioning in free-swimming sea snakes

Vinay Udyawer, Colin A. Simpfendorfer, Michelle R. Heupel & Timothy D. Clark
1. Partitioning energy between critical basal functions and activity-associated behaviours is a primary determinant of animal survival. Consequently, habitat selection is likely to be driven by the efficiency with which resources can be acquired from a heterogeneous energy landscape. 2. Determining how energy partitioning is achieved across temporal and spatial scales is particularly challenging in aquatic animals due to the logistical limitations in estimating field metabolic rates (FMR) while simultaneously examining habitat choice. 3. Here,...

Data from: Seagrass ecosystems reduce exposure to bacterial pathogens of humans, fishes and invertebrates

Joleah B. Lamb, Jeroen A. J. M. Van De Water, David G. Bourne, Craig Altier, Margaux Y. Hein, Evan A. Fiorenza, Nur Abu, Jamaluddin Jompa & C. Drew Harvell
Plants are important in urban environments for removing pathogens and improving water quality. Seagrass meadows are the most widespread coastal ecosystem on the planet. Although these plants are known to be associated with natural biocide production, they have not been evaluated for their ability to remove microbiological contamination. Using amplicon sequencing of the 16S ribosomal RNA gene, we found that when seagrass meadows are present, there was a 50% reduction in the relative abundance of...

Data from: High intra-ocean, but limited inter-ocean genetic connectivity in populations of the deep-water oblique-banded snapper Pristipomoides zonatus (Pisces: Lutjanidae)

W. Jason Kennington, Peter W. Keron, Euan S. Harvey, Corey B. Wakefield, Ashley J. Williams, Tuikolongahau Halafihi & Stephen J. Newman
While many studies have investigated connectivity and subdivision in marine fish occupying tropical, shallow water reef habitats, relatively few have been conducted on commercially important deep-water species in the Indo-Pacific region. Here, we examine spatial and temporal genetic variation in the deep-water oblique-banded snapper Pristipomoides zonatus, collected from eight locations across the Indian and Pacific Oceans. A total of 292 individuals were screened for genetic variation at six nuclear microsatellite loci and the cytochrome c...

Data from: Functional genomic analysis of corals from natural CO2-seeps reveals core molecular responses involved in acclimatization to ocean acidification

Carly D. Kenkel, Aurelie Moya, Julia Strahl, Craig Humphrey & Line K. Bay
Little is known about the potential for acclimatization or adaptation of corals to ocean acidification and even less about the molecular mechanisms underpinning these processes. Here we examine global gene expression patterns in corals and their intracellular algal symbionts from two replicate population pairs in Papua New Guinea that have undergone long-term acclimatization to natural variation in pCO2. In the coral host, only 61 genes were differentially expressed in response to pCO2 environment, but the...

Data from: Influence of the geography of speciation on current patterns of coral reef fish biodiversity across the Indo-Pacific

Théo Gaboriau, Fabien Leprieur, David Mouillot & Nicolas Hubert
The role of speciation processes in shaping current biodiversity patterns represents a major scientific question for ecologists and biogeographers. Hence, numerous methods have been developed to determine the geography of speciation based on co-occurrence between sister-species. Most of these methods rely on the correlation between divergence time and several metrics based on the geographic ranges of sister-taxa (i.e. overlap, asymmetry). The relationship between divergence time and these metrics has scarcely been examined in a spatial...

Data from: Realistic heat pulses protect frogs from disease under simulated rainforest frog thermal regimes

Sasha E. Greenspan, Deborah S. Bower, Rebecca J. Webb, Elizabeth A. Roznik, Lisa A. Stevenson, Lee Berger, Gerry Marantelli, David A. Pike, Lin Schwarzkopf & Ross A. Alford
Recent emergences of fungal diseases have caused catastrophic global losses of biodiversity. Temperature is one of the most important factors influencing host-fungus associations but the effects of temperature variability on disease development are rarely examined. The chytrid pathogen Batrachochytrium dendrobatidis (Bd) has had severe effects on populations of hundreds of rainforest-endemic amphibian species but we know little about the effects of rainforest-specific host body temperature cycles on infection patterns. To address this challenge, we used...

Data from: Responses of neurogenesis and neuroplasticity related genes to elevated CO2 levels in the brain of three teleost species

Floriana Lai, Cathrine E. Fagernes, Nicholas J. Bernier, Gabrielle M. Miller, Philip L. Munday, Fredrik Jutfelt & Göran E. Nilsson
The continuous increase of anthropogenic CO2 in the atmosphere resulting in ocean acidification has been reported to affect brain function in some fishes. During adulthood, cell proliferation is fundamental for fish brain growth and for it to adapt in response to external stimuli, such as environmental changes. Here we report the first expression study of genes regulating neurogenesis and neuroplasticity in brains of three-spined stickleback (Gasterosteus aculeatus), cinnamon anemonefish (Amphiprion melanopus) and spiny damselfish (Acanthochromis...

Data from: Deltamethrin resistance in Aedes aegypti results in treatment failure in Merida, Mexico

Gonzalo M. Vazquez-Prokopec, Anuar Medina-Barreiro, Azael Che-Mendoza, Felipe Dzul-Manzanilla, Fabian Correa-Morales, Guillermo Guillermo-May, Wilbert Bibiano-Marin, Valentin Uc-Puc, Eduardo Geded-Moreno, Jose Vadillo-Sanches, Jorge Palacio-Vargas, Scott A. Ritchie, Audrey Lenhart, Pablo Manrique-Saide & José Vadillo-Sánchez
The operational impact of deltamethrin resistance on the efficacy of indoor insecticide applications to control Aedes aegypti was evaluated in Merida, Mexico. A randomized controlled trial quantified the efficacy of indoor residual spraying (IRS) against adult Ae. aegypti in houses treated with either deltamethrin (to which local Ae. aegypti expressed a high degree of resistance) or bendiocarb (to which local Ae. aegypti were fully susceptible) as compared to untreated control houses. All adult Ae. aegypti...

Data from: Logging and indigenous hunting impacts on persistence of large Neotropical animals

Anand Roopsind, T. Trevor Caughlin, Hemchandranauth Sambhu, Jose M.V. Fragoso, Francis E. Putz., Francis E. Putz & Jose M. V. Fragoso
Areas allocated for industrial logging and community-owned forests account for over 50% of all remaining tropical forests. Landscape-scale conservation strategies that include these forests are expected to have substantial benefits for biodiversity, especially for large mammals and birds that require extensive habitat but that are susceptible to extirpation due to synergies between logging and hunting. In addition, their responses to logging alone are poorly understood due to their cryptic behavior and low densities. In this...

Data from: Stream nitrogen concentration, but not plant N-fixing capacity, modulates litter diversity effects on decomposition

Alan M. Tonin, Luz Boyero, Silvia Monroy, Ana Basaguren, Javier Perez, Richard G. Pearson, Bradley J. Cardinale, & Jesus Pozo
1. We are facing major biodiversity loss and there is evidence that such loss can alter ecosystem functioning. However, the effects of plant diversity on decomposition – a key component of the global carbon cycle – are still unclear. A recent study suggested that a plant trait – their nitrogen (N)-fixing capacity – could mediate effects of litter diversity on decomposition by means of a microbial transfer of N from N-fixers to non-fixers. 2. We...

Data from: Reef accessibility impairs the protection of sharks

Jean-Baptiste Juhel, Laurent Vigliola, David Mouillot, Michel Kulbicki, Tom B. Letessier, Jessica J. Meeuwig & Laurent Wantiez
1. Reef sharks are declining worldwide under ever increasing fishing pressure with potential consequences on ecosystem functioning. Marine protected areas (MPAs) are currently one of the management tools to counteract the pervasive impacts of fishing. However, MPAs in which reef sharks are abundant tend to be located in remote and underexploited areas preventing a fair assessment of management effectiveness beyond remoteness from human activities. 2. Here we determine the conditions under which MPAs can effectively...

Data from: Ants as ecological indicators of rainforest restoration: community convergence and the development of an Ant Forest Indicator Index in the Australian wet tropics

Michael J. Lawes, Anthony M. Moore, Alan N. Andersen, Noel D. Preece & Donald C. Franklin
Ecosystem restoration can help reverse biodiversity loss, but whether faunal communities of forests undergoing restoration converge with those of primary forest over time remains contentious. There is a need to develop faunal indicators of restoration success that more comprehensively reflect changes in biodiversity and ecosystem function. Ants are an ecologically dominant faunal group and are widely advocated as ecological indicators. We examine ant species and functional group responses on a chronosequence of rainforest restoration in...

Data from: A unified model explains commonness and rarity on coral reefs

Sean R. Connolly, Terence P. Hughes, David R. Bellwood & Terry P. Hughes
Abundance patterns in ecological communities have important implications for biodiversity maintenance and ecosystem functioning. However, ecological theory has been largely unsuccessful at capturing multiple macroecological abundance patterns simultaneously. Here, we propose a parsimonious model that unifies widespread ecological relationships involving local aggregation, species-abundance distributions, and species associations, and we test this model against the metacommunity structure of reef-building corals and coral reef fishes across the western and central Pacific. For both corals and fishes, the...

Registration Year

  • 2017

Resource Types

  • Dataset


  • James Cook University
  • Australian Institute of Marine Science
  • University of Queensland
  • University of Western Australia
  • University of Melbourne
  • University of Tasmania
  • Hasanuddin University
  • Stanford University
  • The University of Texas at Austin
  • Murdoch University