32 Works

Data from: Spatial dynamics and mixing of bluefin tuna in the Atlantic Ocean and Mediterranean Sea revealed using next generation sequencing

Gregory Neils Puncher, Alessia Cariani, Gregory E. Maes, Jeroen Van Houdt, Koen Herten, Rita Cannas, Naiara Rodriguez-Ezpeleta, Aitor Albaina, M. Andone Estonba, Molly Lutcavage, Alex Hanke, Jay Rooker, James S. Franks, Joseph M. Quattro, Gualtiero Basilone, Igaratza Fraile, Urtzi Laconcha, Nicolas Goñi, Ai Kimoto, A. David Macías, Francisco Alemany, Simeon Deguara, Salem W. Zgozi, Fulvio Garibaldi, Isik K. Oray … & Fausto Tinti
The Atlantic bluefin tuna is a highly migratory species emblematic of the challenges associated with shared fisheries management. In an effort to resolve the species’ stock dynamics, a genome-wide search for spatially informative single nucleotide polymorphisms (SNPs) was undertaken, by way of sequencing reduced representation libraries. An allele frequency approach to SNP discovery was used, combining the data of 555 larvae and young-of-the-year (LYOY) into pools representing major geographical areas and mapping against a newly...

Data from: Rare long-distance dispersal of a marine angiosperm across the Pacific Ocean

Timothy M. Smith, Paul H. York, Bernardo R. Broitman, Martin Thiel, Graeme C. Hays, Erik Van Sebille, Nathan F. Putman, Peter I. Macreadie & Craig D. H. Sherman
Aim: Long-distance dispersal (LDD) events occur rarely but play a fundamental role in shaping species biogeography. Lying at the heart of island biogeography theory, LDD relies on unusual events to facilitate colonisation of new habitats and range expansion. Despite the importance of LDD, it is inherently difficult to quantify due to the rarity of such events. We estimate the probability of LDD of the seagrass Heterozostera nigricaulis, a common Australian species, across the Pacific Ocean...

Data from: Integrating complementary methods to improve diet analysis in fishery-targeted species

Jordan K. Matley, Gregory E. Maes, Floriaan Devloo-Delva, Roger Huerlimann, Gladys Chua, Andrew J. Tobin, Aaron T. Fisk, Colin A. Simpfendorfer & Michelle R. Heupel
Developing efficient, reliable, cost-effective ways to identify diet is required to understand trophic ecology in complex ecosystems and improve food web models. A combination of techniques, each varying in their ability to provide robust, spatially and temporally explicit information can be applied to clarify diet data for ecological research. This study applied an integrative analysis of a fishery-targeted species group - Plectropomus spp.in the central Great Barrier Reef, Australia by comparing three diet-identification approaches. Visual...

Data from: Potential of a no-take marine reserve to protect home ranges of anadromous brown trout (Salmo trutta)

Susanna H. Thorbjørnsen, Even Moland, Colin Simpfendorfer, Michelle Heupel, Halvor Knutsen & Esben M. Olsen
1. The extent to which no‐take marine reserves can benefit anadromous species requires examination. 2. Here, we used acoustic telemetry to investigate the spatial behavior of anadromous brown trout (sea trout, Salmo trutta) in relation to a small marine reserve(~1.5 km2) located inside a fjord on the Norwegian Skagerrak coast. 3. On average, sea trout spent 42.3 % (±5.0% SE) of their time in the fjord within the reserve, a proportion similar to the area...

Data from: Trade-offs for butterfly alpha and beta diversity in human-modified landscapes and tropical rainforests

Hemchandranauth Sambhu, Alliea Nankishore, Stephen M. Turton & Tobin D. Northfield
The accelerating expansion of human populations and associated economic activity across the globe have made maintaining large, intact natural areas increasingly challenging. The difficulty of preserving large intact landscapes in the presence of growing human populations has led to a growing emphasis on landscape approaches to biodiversity conservation with a complementary strategy focused on improving conservation in human-modified landscapes. This, in turn, is leading to intense debate about the effectiveness of biodiversity conservation in human-modified...


Raquel Peixoto, Phillipe Rosado, Deborah Leite, Gustavo Duarte, Ricardo Chaloub, Guillaume Jospin, Jonathan Eisen, David Bourne, Ulisses Da Rocha, João Saraiva & Francisco Dini-Andreote
Although the early coral reef-bleaching warning system (NOAA/USA) is established, there is no feasible treatment that can minimize temperature bleaching and/or disease impacts on corals in the field. Here, we present the first attempts to extrapolate the widespread and well-established use of bacterial consortia to protect or improve health in other organisms (e.g., humans and plants) to corals. Manipulation of the coral-associated microbiome was facilitated through addition of a consortium of native (isolated from Pocillopora...

Data from: Phylogenetic diversity is a better measure of biodiversity than taxon counting

Joseph T. Miller, Garry Jolley-Rogers, Brent D. Mishler & Andrew H. Thornhill
Biodiversity is most commonly measured in taxonomic richness. For example, it is common to describe how diverse a genus or a geographic area is by counting the number of species within them. Phylogenetic diversity (PD), a measurement of the branch lengths in a phylogenetic tree, is a better measure of biodiversity that provides a comparable, evolutionary measure of biodiversity not possible with species counts. Despite its advantages, PD is rarely used as the primary measure...

Data from: Australian house geckos are more aggressive than a globally successful invasive Asian house gecko

Adam Cisterne, Lin Schwarzkopf & David A. Pike
Invasive species are implicated in native species declines globally, but predicting the effect of specific invaders on a given native species remains difficult. Many successful invaders are highly aggressive, while others are not. The highly successful invasive Asian house gecko, Hemidactylus frenatus, has achieved a pan-tropical distribution. We investigated direct interactions between H. frenatus and a sympatric native Australian house gecko (Gehyra dubia) to determine the strength and nature of aggressive exclusion, and which species...

Data from: Survival, gene and metabolite responses of Litoria verreauxii alpina frogs to fungal disease chytridiomycosis

Laura Grogan, Jason Mulvenna, Joel P. A. Gummer, Benjamin C. Scheele, Lee Berger, Scott D. Cashins, Michael S. McFadden, Peter Harlow, David A. Hunter, Robert D. Trengove & Lee F. Skerratt
PLEASE NOTE, THESE DATA ARE ALSO REFERRED TO IN ANOTHER PUBLICATION. PLEASE SEE http://dx.doi.org/10.1111/mec.14493. The fungal skin disease chytridiomycosis has caused the devastating decline and extinction of hundreds of amphibian species globally, yet the potential for evolving resistance, and the underlying pathophysiological mechanisms remain poorly understood. We exposed 406 naïve, captive-raised alpine tree frogs (Litoria verreauxii alpina) from multiple populations (one evolutionarily naïve to chytridiomycosis) to the aetiological agent Batrachochytrium dendrobatidis in two concurrent and...

Data from: Blue Carbon stocks of Great Barrier Reef deep-water seagrasses

Paul York, Peter I. Macreadie & Michael A. Rasheed
Shallow-water seagrasses capture and store globally-significant quantities of organic carbon (OC), often referred to as ‘Blue Carbon’; however, data is lacking on the importance of deep-water (>15 m) seagrasses as Blue Carbon sinks. We compared OC stocks from deep-, mid- and shallow-water seagrasses at Lizard Island within the Great Barrier Reef Lagoon. We found deep-water seagrasses (Halophila species) contained similar levels of OC as shallow-water species (e.g Halodule uninervis) (0.64 ± 0.08% and 0.9 ±...

Data from: Giant coral reef fishes display markedly different susceptibility to night spearfishing

Alan R. Pearse, Richard J. Hamilton, John Howard Choat, John Pita, Glenn Almany, Nate Peterson, Grant S. Hamilton & Erin E. Peterson
The humphead wrasse (Cheilinus undulatus) and bumphead parrotfish (Bolbometopon muricatum) are two of the largest, most iconic fishes of Indo-Pacific coral reefs. Both species form prized components of subsistence and commercial fisheries and are vulnerable to overfishing. C. undulatus is listed as Endangered and B. muricatum as Vulnerable on the IUCN Red List of Threatened Species. We investigated how night spearfishing pressure and habitat associations affected both species in a relatively lightly exploited setting; the...

Data from: Latitudinal and seasonal variation in space use by a large, predatory reef fish, Plectropomus leopardus

Molly E. Scott, Michelle R. Heupel, Colin A. Simpfendorfer, Jordan K. Matley & Morgan S. Pratchett
1. Temperature directly affects the metabolic rate and resource requirements of ectothermic animals, which is likely to influence their movement and habitat use. Space use is a fundamental component of an animal’s ecology and the extent of an animal’s home range has consequences for individual distributions, community structure and ecosystem function. As ocean temperatures continue to rise as a result of global warming, determining the effects of temperature on space use and movement patterns of...

Data from: Community-wide scan identifies fish species associated with coral reef services across the Indo-Pacific

Eva Maire, Sébastien Villéger, Nicholas A.J. Graham, Andrew S. Hoey, Joshua Cinner, Sebastian C.A. Ferse, Catherine Aliaume, David J. Booth, David A. Feary, Michel Kulbicki, Stuart A. Sandin, Laurent Vigliola, David Mouillot & Sebastian C. A. Ferse
Determining whether many functionally complementary species or only a subset of key species are necessary to maintain ecosystem functioning and services is a critical question in community ecology and biodiversity conservation. Identifying such key species remains challenging, especially in the tropics where many species co-occur and can potentially support the same or different processes. Here, we developed a new community-wide scan (CWS) approach, analogous to the genome-wide scan, to identify fish species that significantly contribute,...

Data from: A framework for resolving cryptic species: a case study from the lizards of the Australian Wet Tropics

Sonal Singhal, Conrad J. Hoskin, Patrick Couper, Sally Potter & Craig Moritz
As we collect range-wide genetic data for morphologically-defined species, we increasingly unearth evidence for cryptic diversity. Delimiting this cryptic diversity is challenging, both because the divergences span a continuum and because the lack of overt morphological differentiation suggests divergence has proceeded heterogeneously. Here, we address these challenges as we diagnose and describe species in three co-occurring species groups of Australian lizards. By integrating genomic and morphological data with data on hybridization and introgression from contact...

Data from: Cell size, photosynthesis and the package effect: an artificial selection approach

Martino E. Malerba, Maria M. Palacios, Yussi M. Palacios Delgado, John Beardall & Dustin J. Marshall
Cell size correlates with most traits among phytoplankton species. Theory predicts that larger cells should show poorer photosynthetic performance, perhaps due to reduced intracellular self‐shading (i.e. package effect). Yet current theory relies heavily on interspecific correlational approaches and causal relationships between size and photosynthetic machinery have remained untested. As a more direct test, we applied 250 generations of artificial selection (c. 20 months) to evolve the green microalga Dunaliella teriolecta (Chlorophyta) toward different mean cell...

Data from: Strong effects of coral species on the diversity and structure of reef fish communities: a multi-scale analysis

Valeriya Komyakova, Geoffrey P. Jones & Philip L. Munday
While there is increasing evidence for habitat specialization in coral reef fishes, the extent to which different corals support different fish communities is not well understood. Here we quantitatively assess the relative importance of different coral species in structuring fish communities and evaluate whether sampling scale and coral colony size affect the perceived strength of fish-habitat relationships. Fish communities present on colonies of 8 coral species (Porites cylindrica, Echinopora horrida, Hydnophora rigida, Stylophora pistillata, Seriatopora...

Data from: Marginal sinks or potential refuges? Costs and benefits for coral-obligate reef fishes at deep range margins

Chancey Macdonald, Geoffrey P. Jones & Tom Bridge
Escalating climate-related disturbances and asymmetric habitat losses will increasingly result in species living in more marginal habitats. Marginal habitats may represent important refuges if individuals can acquire adequate resources to survive and reproduce. However, resources at range margins are often distributed more sparsely; therefore increased effort to acquire resources can result in sub-optimal performance and lead to marginal populations becoming non-self-sustaining sink-populations. Shifting resource availability is likely to be particularly problematic for dietary specialists. Here,...

Data from: Substantial reduction in thermo-suitable microhabitat for a rainforest marsupial under climate change

Jessica Meade, Jeremy VanDerWal, Collin Storlie, Stephen Williams, Arnaud Gourret, Andrew Krockenberger & Justin A. Welbergen
Increases in mean temperatures caused by anthropogenic climate change increases the frequency and severity of temperature extremes. Although extreme temperature events are likely to become increasingly important drivers of species’ response to climate change, the impacts are poorly understood due mainly to a lack of understanding of species’ physiological responses to extreme temperatures. The physiological response of Pseudochirops archeri (green ringtail possum) to temperature extremes has been well studied, demonstrating that heterothermy is used to...

Data from: Harvesting changes mating behavior in European lobster

Tonje K. Sørdalen, Kim T. Halvorsen, Hugo B. Harrison, Charlie D. Ellis, Leif Asbjørn Vøllestad, Halvor Knutsen, Even Moland & Esben M. Olsen
Removing individuals from a wild population can affect the availability of prospective mates and the outcome of competitive interactions, with subsequent effects on mating patterns and sexual selection. Consequently, the rate of harvest-induced evolution is predicted to be strongly dependent on the strength and dynamics of sexual selection yet, there is limited empirical knowledge on the interplay between selective harvesting and the mating systems of exploited species. In this study, we used genetic parentage assignment...

Data from: Post-Cretaceous bursts of evolution along the benthic-pelagic axis in marine fishes

Emanuell Duarte Ribeiro, Aaron M. Davis, Rafael A. Rivero-Vega, Guillermo Ortí, Ricardo Betancur-R & Emanuell Ribeiro
Ecological opportunity arising in the aftermath of mass extinction events is thought to be a powerful driver of evolutionary radiations. Here, we assessed how the wake of the Cretaceous-Paleogene (K-Pg) mass extinction shaped diversification dynamics in a clade of mostly marine fishes (Carangaria), which comprises a disparate array of benthic and pelagic dwellers including some of the most astonishing fish forms (e.g., flatfishes, billfishes, remoras, archerfishes). Analyses of lineage diversification show time-heterogeneous rates of lineage...

Data from: Rates of population differentiation and speciation are decoupled in sea snakes

Charlotte R. Nitschke, Mathew Hourston, Vinay Udyawer & Kate L. Sanders
Comparative phylogeography can inform many macroevolutionary questions, such as whether species diversification is limited by rates of geographic population differentiation. We examined the link between population genetic structure and species diversification in the fully aquatic sea snakes (Hydrophiinae) by comparing mitochondrial phylogeography in 16 species from two closely related clades that show contrasting diversification dynamics across northern Australia. Contrary to expectations from theory and several empirical studies, our results show that, at the geographic scale...

Data from: Large birds travel farther in homogeneous environments

Marlee A. Tucker, Olga Alexandrou, , Keith L. Bildstein, Katrin Böhning-Gaese, Chloe Bracis, John N. Brzorad, Evan R. Buechley, David Cabot, Justin M. Calabrese, Carlos Carrapato, André Chiaradia, Lisa C. Davenport, Sarah C. Davidson, Mark Desholm, Christopher R. DeSorbo, Robert Domenech, Peter Enggist, William F. Fagan, Nina Farwig, Wolfgang Fiedler, Christen H. Fleming, Alastair Franke, John M. Fryxell, Clara García-Ripollés … & João Paulo Silva
Aim: Animal movement is an important determinant of individual survival, population dynamics, and ecosystem structure and function. Yet it is still unclear how local movements are related to resource availability and the spatial arrangement of resources. Using resident bird species and migratory bird species outside of the migratory period, we examined how the distribution of resources affect the movement patterns of both large terrestrial birds (e.g., raptors, bustards, hornbills) and waterbirds (e.g., cranes, storks, ducks,...

Data from: Methods for normalizing microbiome data: an ecological perspective

Donald T. McKnight, Roger Huerlimann, Deborah S. Bower, Lin Schwarzkopf, Ross A. Alford & Kyall R. Zenger
1. Microbiome sequencing data often need to be normalized due to differences in read depths, and recommendations for microbiome analyses generally warn against using proportions or rarefying to normalize data and instead advocate alternatives, such as upper quartile, CSS, edgeR-TMM, or DESeq-VS. Those recommendations are, however, based on studies that focused on differential abundance testing and variance standardization, rather than community-level comparisons (i.e., beta diversity), Also, standardizing the within-sample variance across samples may suppress differences...

Data from: Parallel evolution and adaptation to environmental factors in a marine flatfish: implications for fisheries and aquaculture management of the turbot (Scophthalmus maximus)

Fernanda Dotti Do Prado, Manuel Vera, Miguel Hermida, Carmen Bouza, Belén G. Pardo, Román Vilas, Andrés Blanco, Carlos Fernández, Francesco Maroso, Gregory E. Maes, Cemal Turan, Filip A.M. Volckaert, John B. Taggart, Adrian Carr, Rob Ogden, Einar E. Nielsen, The Aquatrace Consortium, Paulino Martínez & Filip A. M. Volckaert
Unraveling adaptive genetic variation represents, in addition to the estimate of population demographic parameters, a cornerstone for the management of aquatic natural living resources, which in turn, represent the raw material for breeding programs. The turbot (Scophthalmus maximus) is a marine flatfish of high commercial value living on the European continental shelf. While wild populations are declining, aquaculture is flourishing in Southern Europe. We evaluated the genetic structure of turbot throughout its natural distribution range...

Data from: Phylogenomics of a rapid radiation: the Australian rainbow skinks

Jason G. Bragg, Sally Potter, Ana C. Afonso Silva, Conrad J. Hoskin, Benjamin Y.H. Bai & Craig Moritz
Background: The application of target capture with next-generation sequencing now enables phylogenomic analyses of rapidly radiating clades of species. But such analyses are complicated by extensive incomplete lineage sorting, demanding the use of methods that consider this process explicitly, such as the multi-species coalescent (MSC) model. However, the MSC makes strong assumptions about divergence history and population structure, and when using the full Bayesian implementation, current computational limits mean that relatively few loci and samples...

Registration Year

  • 2018

Resource Types

  • Dataset


  • James Cook University
  • Monash University
  • Australian National University
  • Australian Institute of Marine Science
  • University of Melbourne
  • Center for Human Genetics
  • University of Windsor
  • Deakin University
  • French National Centre for Scientific Research
  • Queensland Museum