1,027 Works

Data from: Quantitative genetics of female mate preferences in an ancestral and a novel environment

Matthieu Delcourt, Mark W. Blows & Howard D. Rundle
A female’s mate preference is a potentially complex function relating variation in multiple male phenotypes with her probability of accepting individual males as a mate. Estimating the quantitative genetic basis of preference functions within a population is empirically challenging yet key to understanding preference evolution. We employed a recently described approach that uses random-coefficient mixed models in the analysis of function-valued traits. Using a half-sibling breeding design in a laboratory-adapted Drosophila serrata population, we estimated...

Data from: The B-matrix harbours significant and sex-specific constraints on the evolution of multi-character sexual dimorphism

Thomas P. Gosden, Krishna-Lila Shastri, Paolo Innocenti & Stephen F. Chenoweth
The extent to which sexual dimorphism can evolve within a population depends on an interaction between sexually divergent selection and constraints imposed by a genetic architecture that is shared between males and females. The degree of constraint within a population is normally inferred from the intersexual genetic correlation, rmf. However, such bivariate correlations ignore the potential constraining effect of genetic covariances between other sexually co-expressed traits. Using the fruit fly Drosophila serrata, a species that...

Data from: Diversification across a heterogeneous landscape

Gregory M. Walter, Melanie J. Wilkinson, Maddie E. James, Thomas J. Richards, J. David Aguirre, Daniel Ortiz-Barrientos & Greg M. Walter
Adaptation to contrasting environments across a heterogeneous landscape favors the formation of ecotypes by promoting ecological divergence. Patterns of fitness variation in the field can show whether natural selection drives local adaptation and ecotype formation. However, to demonstrate a link between ecological divergence and speciation, local adaptation must have consequences for reproductive isolation. Using contrasting ecotypes of an Australian wildflower, Senecio lautus in common garden experiments, hybridization experiments, and reciprocal transplants, we assessed how the...

Data from: Congruent patterns of connectivity can inform management for broadcast spawning corals on the Great Barrier Reef

Lukoschek Vimoksalehi, Cynthia Riginos, Madeleine J.H. Van Oppen, Madeleine J. H. Van Oppen & Vimoksalehi Lukoschek
Connectivity underpins the persistence and recovery of marine ecosystems. The Great Barrier Reef (GBR) is the world's largest coral reef ecosystem and managed by an extensive network of no-take zones; however, information about connectivity was not available to optimize the network's configuration. We use multivariate analyses, Bayesian clustering algorithms and assignment tests of the largest population genetic data set for any organism on the GBR to date (Acropora tenuis, >2500 colonies; >50 reefs, genotyped for...

Data from: The emergent geography of biophysical dispersal barriers across the Indo-West Pacific

Eric A. Treml, Jason Roberts, Patrick N. Halpin, Hugh P. Possingham & Cynthia Riginos
Aim: To discover and evaluate potential dispersal barriers across the Indo-West Pacific Ocean and to develop spatially explicit hypotheses regarding the location of barriers and their capacity to filter taxa. Additionally, to compare model predictions with previously described barriers and build a more thorough understanding of the region's biogeographic patterns. Location: The reefs of the Indo-West Pacific Ocean, from 100 to 170°E and from 30°N to 30°S. Methods: A biophysical larval dispersal model was used...

Data from: High-throughput genotyping for species identification and diversity assessment in germplasm collections

Annaliese S. Mason, Jing Zhang, Reece Tollenaere, Paula Vasquez Teuber, Jessica Dalton-Morgan, Liyong Hu, Guijun Yan, David Edwards, Robert Redden & Jacqueline Batley
Germplasm collections provide an extremely valuable resource for breeders and researchers. However, misclassification of accessions by species often hinders the effective use of these collections. We propose that use of high-throughput genotyping tools can provide a fast, efficient and cost-effective way of confirming species in germplasm collections, as well as providing valuable genetic diversity data. We genotyped 180 Brassicaceae samples sourced from the Australian Grains Genebank across the recently released Illumina Infinium Brassica 60K SNP...

Data from: Re-visiting the phylogeography and demography of European badgers (Meles meles) based on broad sampling, multiple markers and simulations

Alain C. Frantz, Allan D. McDevitt, Lisa C. Pope, Joanna Kochan, John Davison, Chris F. Clements, Morten Elmeros, Guillem Molina-Vacas, Aritz Ruiz-Gonzalez, Alessandro Balestrieri, Koen Van Den Berge, Peter Breyne, Emmanuel Do Linh San, Erik O. Ågren, Franz Suchentrunk, Laurent Schley, Rafał Kowalczyk, Berit I. Kostka, Dusko Ćirović, Nikica Šprem, Marc Colyn, Marco Ghirardi, Venislava Racheva, Christophe Braun, Rita Oliveira … & Terry Burke
Although the phylogeography of European mammals has been extensively investigated since the 1990s, many studies were limited in terms of sampling distribution, the number of molecular markers used and the analytical techniques employed, frequently leading to incomplete postglacial recolonisation scenarios. The broad-scale genetic structure of the European badger (Meles meles) is of interest as it may result from historic restriction to glacial refugia and/or recent anthropogenic impact. However, previous studies were based mostly on samples...

Data from: Immigrant inviability produces a strong barrier to gene flow between parapatric ecotypes of Senecio lautus

Thomas John Richards & Daniel Ortiz-Barrientos
Speciation proceeds when gene exchange is prevented between populations. Determining the different barriers preventing gene flow can therefore give insights into the factors driving and maintaining species boundaries. These reproductive barriers may result from intrinsic genetic incompatibilities between populations, from extrinsic environmental differences between populations, or a combination of both mechanisms. We investigated the potential barriers to gene exchange between three adjacent ecotypes of an Australian wildflower to determine the strength of individual barriers and...

Data from: Divergent natural selection drives the evolution of reproductive isolation in an Australian wildflower

Thomas J. Richards, Gregory M. Walter, Katrina McGuigan, Daniel Ortiz-Barrientos & Greg M. Walter
Ecological speciation occurs when reproductive isolation evolves between populations adapting to contrasting environments. A key prediction of this process is that the fitness of hybrids between divergent populations should be reduced in each parental environment as a function of the proportion of local genes they carry, a process resulting in ecologically dependent reproductive isolation (RI). To test this prediction, we use reciprocal transplant experiments between adjacent populations of an Australian wildflower, Senecio lautus, at two...

Data from: Opsins in Onychophora (velvet worms) suggest a single origin and subsequent diversification of visual pigments in arthropods

Lars Hering, Miriam J. Henze, Martin Kohler, Almut Kelber, Christoph Bleidorn, Maren Leschke, Birgit Nickel, Matthias Meyer, Martin Kircher, Paul Sunnucks & Georg Mayer
Multiple visual pigments, prerequisites for color vision, are found in arthropods, but the evolutionary origin of their diversity remains obscure. In this study, we explore the opsin genes in five distantly related species of Onychophora, using deep transcriptome sequencing and screening approaches. Surprisingly, our data reveal the presence of only one opsin gene (onychopsin) in each onychophoran species, and our behavioral experiments indicate a maximum sensitivity of onychopsin to blue–green light. In our phylogenetic analyses,...

Barriers in a sea of elasmobranchs

Maximilian Hirschfeld, Christine Dudgeon, Marcus Sheaves & Adam Barnett
Background The interplay of animal dispersal and environmental heterogeneity is fundamental for the distribution of biodiversity on earth. In the ocean, the interaction of physical barriers and dispersal has primarily been examined for organisms with planktonic larvae. Animals that lack a planktonic life stage and depend on active dispersal are however likely to produce distinctive patterns. Methods We used available literature on population genetics and phylogeography of elasmobranchs (sharks, rays and skates), to examine how...

Data from: Optimizing the spatial planning of prescribed burns to achieve multiple objectives in a fire-dependent ecosystem.

Brooke A. Williams, Luke P. Shoo, Kerrie A. Wilson & Hawthorne L. Beyer
1. There is potential for negative consequences for the ecological integrity of fire-dependent ecosystems as a result of inappropriate fire regimes. This can occur when asset (property) protection is prioritised over conservation objectives in burn programs. 2. Optimisation of fire management for multiple objectives is rarely undertaken. Here, we use integer linear programming to identify burn scheduling solutions that will cost-effectively achieve asset protection and conservation objectives. 3. An approach to burn scheduling that favours...

Data from: Mitochondrial genomes of Australian chicken Eimeria support the presence of ten species with low genetic diversity among strains

Jess A. T. Morgan, Rosamond M. Godwin & Jess A.T. Morgan
Modern molecular approaches have vastly improved diagnostic capabilities for differentiating among species of chicken infecting Eimeria. Consolidating information from multiple genetic markers, adding additional poultry Eimeria species and increasing the size of available data-sets is improving the resolving power of the DNA, and consequently our understanding of the genus. This study adds information from 25 complete mitochondrial DNA genomes from Australian chicken Eimeria isolates representing all 10 species known to occur in Australia, including OTU-X,...

Data from: Skin sloughing in susceptible and resistant amphibians regulates infection with a fungal pathogen

Michel E. B. Ohmer, Rebecca L. Cramp, Catherine J. M. Russo, Craig R. White & Craig E. Franklin
The fungal pathogen Batrachochytrium dendrobatidis (Bd) has been implicated in amphibian population declines globally. Given that Bd infection is limited to the skin in post-metamorphic amphibians, routine skin sloughing may regulate infection. Skin sloughing has been shown to reduce the number of cultivatable microbes on amphibian skin, and Bd infection increases skin sloughing rates at high loads. However, it is unclear whether species specific differences in skin sloughing patterns could regulate Bd population growth on...

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: Upwelling as the major source of nitrogen for shallow and deep reef-building corals across an oceanic atoll system

Veronica Z. Radice, Ove Hoegh-Guldberg, Brian Fry, Michael D. Fox & Sophie G. Dove
Oceanographic processes shape coral reefs worldwide by redistributing inorganic nutrients and particulate resources over depth. Deep‐water upwelling occurs frequently in coral reef ecosystems, but its impact on coral nutrition remains unclear. This study investigated the influence of upwelling on the trophic ecology of three common reef‐building corals (Galaxea fascicularis, Pachyseris speciosa and Pocillopora verrucosa) from different reef depths (shallow reef, 10 m, vs. deep reef, 30 m) and reef exposures (oceanic rim vs. Inner Sea)...

Data from: Marine environmental DNA biomonitoring reveals seasonal patterns in biodiversity and identifies ecosystem responses to anomalous climatic events

Tina E. Berry, Benjamin J. Saunders, Megan L. Coghlan, Michael Stat, Simon Jarman, Anthony J. Richardson, Claire H. Davies, Oliver Berry, Euan S. Harvey & Michael Bunce
Marine ecosystems are changing rapidly as the oceans warm and become more acidic. The physical factors and the changes to ocean chemistry that they drive can all be measured with great precision. Changes in the biological composition of communities in different ocean regions are far more challenging to measure because most biological monitoring methods focus on a limited taxonomic or size range. Environmental DNA (eDNA) analysis has the potential to solve this problem in biological...

Data from: Environmental influences and ontogenetic differences in vertical habitat use of black marlin (Istiompax indica) in the southwestern Pacific

Samuel M. Williams, Bonnie J. Holmes, Sean R. Tracey, Julian G. Pepperell, Michael L. Domeier & Michael B. Bennett
The black marlin (Istiompax indica) is a highly migratory billfish that occupies waters throughout the tropical and subtropical Indo-Pacific. To characterize the vertical habitat use of I. indica, we examined the temperature-depth profiles collected using 102 pop-up satellite archival tags deployed off the east coast of Australia. Modelling of environmental variables revealed location, sea-surface height deviation, mixed layer depth and dissolved oxygen to all be significant predictors of vertical habitat use. Distinct differences in diel...

Data from: Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement

Shan Wu, Kin H. Lau, Qinghe Cao, John P. Hamilton, Honghe Sun, Chenxi Zhou, Lauren Eserman, Dorcus Gemenet, Bode Olukolu, Haiyan Wang, Emily Crisovan, Grant T. Godden, Chen Jiao, Xin Wang, Mercy Kitavi, Norma Manrique-Carpintero, Brieanne Vaillancourt, Krystle Wiegert-Rininger, Xinsun Yang, Kan Bao, Yi Zheng, Jennifer Schaff, Jan Kreuze, Wolfgang Gruneberg, Awais Khan … & Zhangjun Fei
I_triloba_NSP323_stress_FPKM_expression_matrix_v3_anno.xlsxFPKM values of v3 high confidence gene models for 15 I. triloba abiotic and biotic stress RNA-seq libraries. The libraries are described in the 'Library Key' worksheet.I_triloba_NSP323_FPKM_expression_matrix_v3_anno.xlsxFPKM values of v3 high confidence gene models for 6 I. triloba RNA-seq libraries (flower, flowerbud, leaf, root1, root2, stem).NSP323_triloba_v3.hc.func_anno.txtPutative functional annotation of high confidence gene models.NSP323_triloba_v3.hc.gene_models.cdna.faNucleotide sequences of the high confidence gene model transcript sequences (cDNA).NSP323_triloba_v3.hc.gene_models.cds.faNucleotide sequences of the high confidence gene model coding sequences (CDS).NSP323_triloba_v3.hc.gene_models.gff3High confidence gene...

Data from: Assessment of plasma proteomics biomarker’s ability to distinguish benign from malignant lung nodules

Gerard A. Silvestri, Nichole T. Tanner, Paul Kearney, Anil Vachani, Pierre P. Massion, Alexander Porter, Steven C. Springmeyer, Kenneth C. Fang, David Midthun, Peter J. Mazzone, D. Madtes, J. Landis, A. Levesque, K. Rothe, M. Balaan, B. Dimitt, B. Fortin, N. Ettinger, A. Pierre, L. Yarmus, K. Oakjones-Burgess, N. Desai, Z. Hammoud, A. Sorenson, R. Murali … & F. Allison
Background: Lung nodules are a diagnostic challenge, with an estimated yearly incidence of 1.6 million in the United States. This study evaluated the accuracy of an integrated proteomic classifier in identifying benign nodules in patients with a pretest probability of cancer (pCA) ≤ 50%. Methods: A prospective, multicenter observational trial of 685 patients with 8- to 30-mm lung nodules was conducted. Multiple reaction monitoring mass spectrometry was used to measure the relative abundance of two...

Data from: Accurate predictions of coexistence in natural systems require the inclusion of facilitative interactions and environmental dependency

Malyon D. Bimler, Daniel B. Stouffer, Hao Ran Lai & Margaret M. Mayfield
1. Coexistence between plant species is well known to depend on the outcomes of species interactions within an environmental context. The incorporation of environmental variation into empirical studies of coexistence are rare, however, due to the complex experiments needed to do so and the lack of feasible modelling approaches for determining how environmental factors alter specific coexistence mechanisms. 2. In this paper, we present a simple modelling framework for assessing how variation in species interactions...

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: Without management interventions, endemic wet-sclerophyll forest is transitioning to rainforest in World Heritage listed K’gari (Fraser Island), Australia

Vithya Krishnan, Nicole Robinson, Jennifer Firn, Grahame Applegate, John Herbohn & Susanne Schmidt
Wet-sclerophyll forests are unique ecosystems that can transition to dry-sclerophyll forests or to rainforests. Understanding of the dynamics of these forests for conservation is limited. We evaluated the long-term succession of wet-sclerophyll forest on World Heritage listed K’gari (Fraser Island)the world’s largest sand island. We recorded the presence and growth of tree species in three 0.4 hectare plots that had been subjected to selective logging, fire, and cyclone disturbance over 65 years, from 1952 to...

Data from: Multidimensional analyses of physical performance reveal a size dependent trade-off between suites of traits

Jordan E. Charters, Jaime Heiniger, Christofer J. Clemente, Skye F. Cameron, Ami F. Amir Abdul Nasir, Amanda C. Niehaus & Robbie S. Wilson
1. Animal movement is multidimensional and complex, and to understand the motor system of wild animals in the context of their natural ecology, we must analyze how suites of performance traits both mutualistically and antagonistically affect function —a necessity highlighted by previous work on performance trade-offs. 2. Evidence from some studies of human athletes using multidimensional analyses of performance suggests that overall quality among individuals can mask functional trade-offs within them, yet no studies have...

Data from: Cyclic population dynamics and density-dependent intransitivity as pathways to coexistence between co-occurring annual plants

Daniel B. Stouffer, Claire E. Wainwright, Thomas Flanagan & Margaret M. Mayfield
1. Recent studies have brought renewed attention to the importance of complex species interactions - notably intransitive interactions - to patterns of plant community diversity. One underappreciated avenue through which intransitivity can occur is through cyclic population dynamics. Though such cyclic intransitive relationships have been extensively studied in predator-prey systems, evidence of their importance in competitive communities, notably plant communities, is more limited. Most studies of coexistence in plant communities assume fixed-point coexistence even while...

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