35 Works

Data from: Counting with DNA in metabarcoding studies: how should we convert sequence reads to dietary data?

Bruce E. Deagle, Austen C. Thomas, Julie C. McInnes, Laurence J. Clarke, Eero J. Vesterinen, Elizabeth L. Clare, Tyler R. Kartzinel & J. Paige Eveson
Advances in DNA sequencing technology have revolutionised the field of molecular analysis of trophic interactions and it is now possible to recover counts of food DNA sequences from a wide range of dietary samples. But what do these counts mean? To obtain an accurate estimate of a consumer’s diet should we work strictly with datasets summarising frequency of occurrence of different food taxa, or is it possible to use relative number of sequences? Both approaches...

Data from: Assessing bottom-trawling impacts based on the longevity of benthic invertebrates

Jan Geert Hiddink, Simon Jennings, Marija Sciberras, Stefan Bolam, Giulia Cambie, Robert McConnaughey, Tessa Mazor, Ray Hilborn, Jeremy Collie, C. Roland Pitcher, Ana Parma, Petri Suuronen, Michel Kaiser, Adriaan Rijnsdorp, Jeremy S. Collie, Michel J. Kaiser, Adriaan D. Rijnsdorp & Robert A. McConnaughey
1. Bottom trawling is the most widespread human activity directly affecting seabed habitats. Assessment and effective management of the effects of bottom trawling at the scale of fisheries requires an understanding of differences in sensitivity of biota to trawling. Responses to disturbance are expected to depend on the intrinsic rate of increase of populations (r), which is expected to be linearly related to the reciprocal of longevity. 2. We examine the relationship between the longevity...

Data from: Robust estimates of a high Ne/N ratio in a top marine predator, southern bluefin tuna

Robin S. Waples, Peter M. Grewe, Mark W. Bravington, Richard Hillarty & Pierre Feutry
Genetic studies of several marine species with high fecundity have produced “tiny” estimates (≤10−3) of the ratio of effective population size (Ne) to adult census size (N), suggesting that even very large populations might be at genetic risk. A recent study using close-kin mark-recapture methods estimated adult abundance at N ≈ 2 × 106 for southern bluefin tuna (SBT), a highly fecund top predator that supports a lucrative (~$1 billion/year) fishery. We used the same...

Data from: Groundwater enhances aboveground growth in mangroves

Matthew A. Hayes, Amber Jesse, Nina Welti, Basam Tabet, David Lockington & Catherine E. Lovelock
1. Groundwater flow through coastal wetlands plays an important role in the maintenance of productivity of intertidal ecosystems. Groundwater can reduce salinity and increase nutrient availability which can enhance plant growth and alter plant biomass allocation patterns. 2. Here, we used stable isotopes of oxygen and hydrogen to assess how groundwater influences belowground and aboveground growth in the widespread mangrove species Avicennia marina. 3. We found source water within tree stems varied seasonally, with non-saline...

Data from: Fire, fragmentation, and windstorms: a recipe for tropical forest degradation

Divino V. Silvério, Paulo M. Brando, Mercedes M.C. Bustamante, Francis E. Putz, Daniel Magnabosco Marra, Shaun R. Levick & Susan E. Trumbore
1. Widespread degradation of tropical forests is caused by a variety of disturbances that interact in ways that are not well understood. 2. To explore potential synergies between edge effects, fire and windstorm damage as causes of Amazonian forest degradation, we quantified vegetation responses to a 30-minute high-intensity windstorm that in 2012, swept through a large-scale fire experiment that borders an agricultural field. Our pre- and post-windstorm measurements include tree mortality rates and modes of...

Data from: A seascape genetic analysis of a stress-tolerant coral species along the Western Australian coast

Richard D. Evans, Nicole M. Ryan, Michael J. Travers, Ming Feng, Yvette Hitchen & W. Jason Kennington
Genetic diversity and connectivity are key factors in determining a population’s resilience to future disturbance. This is especially relevant to corals, which are in global decline due to increasing frequency and strength of thermal anomalies and severe tropical cyclones. While many studies have investigated genetic diversity and population structure in corals, they focused on species being removed at the greatest rate from coral reefs, Acroporids and Pocilloporids, and it is unclear whether the patterns observed...

Data from: Incorporating existing thermal tolerance into projections of compositional turnover under climate change

Alex Bush, Renee Catullo, Karel Mokany, Tom Harwood, Andrew Hoskins & Simon Ferrier
Aim: Observed, realized niche space often underestimates species’ physiological tolerances due to interactions with other species, dispersal constraints, and because some combinations of influential environmental factors do not currently exist in the real world. Conversely, correlative ecological niche models rely on the assumption that the range of environmental conditions encompassed by a species’ geographic distribution accurately reflects their environmental tolerances, including community-level approaches like Generalised Dissimilarity Modelling (GDM). We extend GDM to better understand what...

Data from: Reliable species distributions are obtainable with sparse, patchy and biased data by leveraging over species and data types

Samantha L. Peel, Nicole A. Hill, Scott D. Foster, Simon J. Wotherspoon, Claudio Ghiglione & Stefano Schiaparelli
1. New methods for species distribution models (SDMs) utilise presence‐absence (PA) data to correct the sampling bias of presence‐only (PO) data in a spatial point process setting. These have been shown to improve species estimates when both data sets are large and dense. However, is a PA data set that is smaller and patchier than hitherto examined able to do the same? Furthermore, when both data sets are relatively small, is there enough information contained...

Data from: Space use by 4 strains of laying hens to perch, wing flap, dust bathe, stand and lie down

Elizabeth R. Riddle, Ahmed B. A. Ali, Dana L. M. Campbell & Janice M. Siegford
The laying hen industry is implementing aviary systems intended to improve welfare by providing hens with more space and resources to perform species-specific behaviors. To date, limited research has examined spatial requirements of various strains of laying hens for performing key behaviors and none has been conducted within an alternative housing system. This study investigated the amount of space used by 4 strains of laying hens (Hy-Line Brown [HB], Bovans Brown [BB], DeKalb White [DW],...

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: Genome-wide analyses of the Bemisia tabaci species complex reveal contrasting patterns of admixture and complex demographic histories

Samia Elfekih, Paul Etter, Weetek T. Tay, Matteo Fumagalli, Karl Gordon, Eric Johnson & Paul De Barro
Once considered a single species, the whitefly, Bemisia tabaci, is a complex of numerous morphologically indistinguishable species. Within the last three decades, two of its members (MED and MEAM1) have become some of the world's most damaging agricultural pests invading countries across Europe, Africa, Asia and the Americas and affecting a vast range of agriculturally important food and fiber crops through both feeding-related damage and the transmission of numerous plant viruses. For some time now,...

Data from: Primary productivity is related to niche width in the Australian Wet Tropics

Hugh M. Burley, Karel Mokany, Shawn W. Laffan, Kristen J. Williams, Dan Metcalfe, Helen T. Murphy, Andrew Ford, Tom D. Harwood & Simon Ferrier
Aim: A key ecological debate is whether ecosystem functions are distinctly influenced by biological diversity across broad scales. Although recent work has emphasized the importance of links between ecosystem functions and measures of ecological specialization as proxies of biodiversity, few studies have analysed macroecological relationships empirically in diverse environments. We tested whether gross primary productivity (GPP) in the Australian Wet Tropics (WT) was distinctly related to community‐level measures of the ecological specialization of component tree...

Data from: Latitudinal variation in seagrass herbivory: global patterns and explanatory mechanisms

Adriana Vergés, Christopher Doropoulos, Rob Czarnik, Kathryn McMahon, Nil Llonch & Alistair G. B. Poore
Aim: The aim was to quantify latitudinal patterns in seagrass–herbivore interactions in the context of a warming climate. Location: We carried out a global meta‐analysis combined with a field experiment across 1,700 km and 12° of latitude in Western Australia. Time period: 1984–2014. Major taxa studied: Seagrasses. Methods: We first synthesized the global literature on herbivore exclusion experiments in seagrasses to test whether differences in herbivore impacts are related to latitude and sea surface temperature....

Data from: Evolutionary history of the angiosperm flora of China

Li-Min Lu, Ling-Feng Mao, Tuo Yang, Jian-Fei Ye, Bing Liu, Hong-Lei Li, Miao Sun, Joseph T. Miller, Sarah Mathews, Hai-Hua Hu, Yan-Ting Niu, Dan-Xiao Peng, You-Hua Chen, Stephen A. Smith, Min Chen, Kun-Li Xiang, Chi-Toan Le, Viet-Cuong Dang, An-Ming Lu, Pamela S. Soltis, Douglas E. Soltis, Jian-Hua Li & Zhi-Duan Chen
High species diversity may result from recent rapid speciation in a ‘cradle’ and/or the gradual accumulation and preservation of species over time in a ‘museum’1,2. China harbours nearly 10% of angiosperm species worldwide and has long been considered as both a museum, owing to the presence of many species with hypothesized ancient origins3,4, and a cradle, as many lineages have originated as recent topographic changes and climatic shifts—such as the formation of the Qinghai–Tibetan Plateau...

Data from: Herbivory and eutrophication mediate grassland plant nutrient responses across a global climatic gradient

T. Michael Anderson, Daniel M. Griffith, James B. Grace, Eric M. Lind, Peter B. Adler, Lori A. Biederman, Dana M. Blumenthal, Pedro Daleo, Jennifer Firn, Nicole Hagenah, W. Stanley Harpole, Andrew S. MacDougall, Rebecca L. McCulley, Suzanne M. Prober, Anita C. Risch, Mahesh Sankaran, Martin Schütz, Eric W. Seabloom, Carly J. Stevens, Lauren L. Sullivan, Peter D. Wragg & Elizabeth T. Borer
Plant stoichiometry, the relative concentration of elements, is a key regulator of ecosystem functioning and is also being altered by human activities. In this paper we sought to understand the global drivers of plant stoichiometry and compare the relative contribution of climatic vs. anthropogenic effects. We addressed this goal by measuring plant elemental (C, N, P and K) responses to eutrophication and vertebrate herbivore exclusion at eighteen sites on six continents. Across sites, climate and...

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: Evolution of sex determination loci in Atlantic salmon

James Kijas, Sean McWilliam, Marina Naval Sanchez, Peter Kube, Harry King, Bradley Evans, Torfin Nome, Sigbjorn Lien & Klara Verbyla
Teleost fish exhibit a remarkable diversity in the control of sex determination, offering the opportunity to identify novel differentiation mechanisms and their ecological consequences. Here, we perform GWAS using 4715 fish and 46,501 SNP to map sex determination to three separate genomic locations in Atlantic salmon (Salmo salar). To characterize each, whole genome sequencing was performed to 30-fold depth of coverage using 20 fish representing each of three identified sex lineages. SNP polymorphism reveals male...

Data from: SNP markers tightly linked to root knot nematode resistance in grapevine (Vitis cinerea) identified by a genotyping-by-sequencing approach followed by Sequenom MassARRAY validation

Harley M. Smith, Brady P. Smith, Norma B. Morales, Sam Moskwa, Peter R. Clingeleffer & Mark R. Thomas
Plant parasitic nematodes, including root knot nematode Meloidogyne species, cause extensive damage to agriculture and horticultural crops. As Vitis vinifera cultivars are susceptible to root knot nematode parasitism, rootstocks resistant to these soils pests provide a sustainable approach to maintain grapevine production. Currently, most of the commercially available root knot nematode resistant rootstocks are highly vigorous and take up excess potassium, which reduces wine quality. As a result, there is a pressing need to breed...

Data from: The search for loci under selection: trends, biases and progress

Collin W. Ahrens, Paul D. Rymer, Adam Stow, Jason Bragg, Shannon Dillon, Kate D. L. Umbers & Rachael Y. Dudaniec
Detecting genetic variants under selection using FST outlier analysis (OA) and environmental association analyses (EAA) are popular approaches that provide insight into the genetic basis of local adaptation. Despite the frequent use of OA and EAA approaches and their increasing attractiveness for detecting signatures of selection, their application to field-based empirical data have not been synthesized. Here, we review 66 empirical studies that use Single Nucleotide Polymorphisms (SNPs) in OA and EAA. We report trends...

Data from: Phylogenomic data yield new and robust insights into the phylogeny and evolution of weevils

Seunggwan Shin, Dave J. Clarke, Alan R. Lemmon, Emily Moriarty Lemmon, Alexander L. Aitken, Stephanie Haddad, Brian D. Farrell, Adriana E. Marvaldi, Rolf G. Oberprieler & Duane D. McKenna
The phylogeny and evolution of weevils (the beetle superfamily Curculionoidea) has been extensively studied, but many relationships, especially in the large family Curculionidae (true weevils; > 50000 species), remain uncertain. We used phylogenomic methods to obtain DNA sequences from 522 protein coding genes for representatives of all families of weevils and all subfamilies of Curculionidae. Most of our phylogenomic results had strong statistical support, and the inferred relationships were generally congruent with those reported in...

Data from: Functional responses of an apex predator and a mesopredator to an invading ungulate: Dingoes, red foxes and sambar deer in south-east Australia

David M. Forsyth, Peter Caley, Naomi E. Davis, A. David M. Latham, Andrew P. Woolnough, Luke P. Woodford, Kasey A. Stamation, Paul D. Moloney & Charlie Pascoe
Biological invasions by large herbivores involve the establishment of novel interactions with the receiving mammalian carnivore community, but understanding these interactions is difficult due to the large spatiotemporal scales at which such dynamics would occur. We quantified the functional responses of a native apex predator (the dingo (Canis familiaris), which includes wild dogs and their hybrids) and a non-native mesopredator (red fox; Vulpes vulpes) to an invading non-native ungulate (sambar deer; Cervus unicolor) in Australia....

Data from: Mapping phosphorus hotspots in Sydney’s organic wastes: a spatially-explicit inventory to facilitate urban phosphorus recycling

Genevieve S. Metson, Dana Cordell, Brad Ridoutt & Steve Mohr
Phosphorus is an essential element for food production whose main global sources are becoming scarce and expensive. Furthermore, losses of phosphorus throughout the food production chain can also cause serious aquatic pollution. Recycling urban organic waste resources high in phosphorus could simultaneously address scarcity concerns for agricultural producers who reply on phosphorus fertilisers, and waste managers seeking to divert waste from landfills to decrease environmental burdens. Recycling phosphorus back to agricultural lands however requires careful...

Data from: Dissection by genomic and plumage variation of a geographically complex hybrid zone between two Australian non-sister parrot species, Platycercus adscitus and P. eximius

Ashlee Shipham, Leo Joseph, Daniel J. Schmidt, Alex Drew, Ian Mason & Jane M. Hughes
The study of hybrid zones advances understanding of the speciation process, and approaches incorporating genomic data are increasingly used to draw significant conclusions about the impact of hybridisation. Despite the progress made, the complex interplay of factors that can lead to substantially variable hybridisation outcomes are still not well understood, and many systems and/or groups remain comparatively poorly studied. Our study aims to broaden the literature on avian hybrid zones, investigating a potentially geographically and...

Data from: Seascapes as drivers of herbivore assemblages in coral reef ecosystems

George Roff, Sonia Bejarano, Mark Priest, Alyssa Marshell, Iliana Chollett, Robert S. Steneck, Christopher Doropoulos, Yimnang Golbuu & Peter J. Mumby
Herbivorous fish maintain a critical ecosystem function on coral reefs by grazing algae and maintaining highly productive algal turf assemblages. Current paradigms implicate habitat complexity, predation and primary productivity as major drivers of the distribution and abundance of herbivorous fish, yet little is known about the relative contribution of these factors. Here, we compare bottom-up and top-down drivers of notional herbivore assemblages across an environmental gradient of wave exposure in the Palau archipelago. We surveyed...

Data from: Larger plants promote a greater diversity of symbiotic nitrogen-fixing soil bacteria associated with an Australian endemic legume

Russell Dinnage, Anna K. Simonsen, Luke G. Barrett, Marcel Cardillo, Nat Raisbeck-Brown, Peter H. Thrall & Suzanne M. Prober
A major goal in microbial ecology is to understand the factors that structure bacterial communities across space and time. For microbes that are plant symbionts, community assembly processes can lead to either a positive or negative relationship between plant size or age and soil microbe diversity. Here, we evaluated the extent to which such relationships exist within a single legume species (Acacia acuminata) and their naturally occurring symbiotic nitrogen-fixing bacteria (rhizobia). 2. We quantified the...

Registration Year

  • 2018
    35

Resource Types

  • Dataset
    35

Affiliations

  • Commonwealth Scientific and Industrial Research Organisation
    35
  • University of Queensland
    3
  • Australian National University
    3
  • University of Tasmania
    3
  • University of Western Australia
    3
  • University of Washington
    2
  • Utah State University
    2
  • University of Michigan-Ann Arbor
    2
  • University of Minnesota
    2
  • University of Melbourne
    2