159 Works

Beyond leaf habit: generalities in plant function across 97 tropical dry forest tree species

German Vargas G., Tim J. Brodribb, Juan M. Dupuy, Roy González‐M., Catherine M. Hulshof, David Medvigy, Tristan A. P. Allerton, Camila Pizano, Beatriz Salgado‐Negret, Naomi B. Schwartz, Skip J. Van Bloem, Bonnie G. Waring & Jennifer S. Powers
Leaf habit has been hypothesized to define a linkage between the slow-fast plant economic spectrum and the drought resistance-avoidance trade-off in tropical forests (‘slow-safe versus fast-risky’). However, variation in hydraulic traits as a function of leaf habit has rarely been explored for a large number of species. We sampled leaf and branch functional traits of 97 tropical dry forest tree species from four sites to investigate whether patterns of trait variation varied consistently in relation...

Data from: Going with the flow: the role of ocean circulation in global marine ecosystems under a changing climate

Simon J. Van Gennip, Ekaterina E. Popova, Andrew Yool, Gretta T. Pecl, Alistair J. Hobday & Cascade J. B. Sorte
Ocean warming, acidification, deoxygenation and reduced productivity are widely considered to be the major stressors to ocean ecosystems induced by emissions of CO2. However, an overlooked stressor is the change in ocean circulation in response to climate change. Strong changes in the intensity and position of the western boundary currents have already been observed, and the consequences of such changes for ecosystems are beginning to emerge. In this study, we address climatically induced changes in...

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: Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales)

Hervé Sauquet, Simon Y. W. Ho, Maria A. Gandolfo, Gregory J. Jordan, Peter Wilf, David J. Cantrill, Michael J. Bayly, Lindell Bromham, Gillian K. Brown, Raymond J. Carpenter, Daphne M. Lee, Daniel J. Murphy, J. M. Kale Sniderman & Frank Udovicic
Although temporal calibration is widely recognized as critical for obtaining accurate divergence-time estimates using molecular dating methods, few studies have evaluated the variation resulting from different calibration strategies. Depending on the information available, researchers have often used primary calibrations from the fossil record or secondary calibrations from previous molecular dating studies. In analyses of flowering plants, primary calibration data can be obtained from macro- and mesofossils (e.g., leaves, flowers, and fruits) or microfossils (e.g., pollen)....

Data from: The identification of concerted convergence in insect heads corroborates Palaeoptera

Alexander Blanke, Carola Greve, Benjamin Wipfler, Rolf Beutel, Barbara Holland & Bernhard Misof
The relationships of the three major clades of winged insects - Ephemeroptera, Odonata and Neoptera - are still unclear. Many morphologists favor a clade Metapterygota (Odonata+Neoptera), but Chiastomyaria (Ephemeroptera+Neoptera) or Palaeoptera (Ephemeroptera+Odonata) have also been supported in some older and more recent studies. A possible explanation for the difficulties in resolving these relationships is concerted convergence - the convergent evolution of entire character complexes under the same or similar selective pressures. In this study we...

Data from: Sand lizard (Lacerta agilis) phenology in a warming world

Gabriella Ljungström, Erik Wapstra & Mats Olsson
Background: Present-day climate change has altered the phenology (the timing of periodic life cycle events) of many plant and animal populations worldwide. Some of these changes have been adaptive, leading to an increase in population fitness, whereas others have been associated with fitness decline. Representing short-term responses to an altered weather regime, hitherto observed changes are largely explained by phenotypic plasticity. However, to track climatically induced shifts in optimal phenotype as climate change proceeds, evolutionary...

Data from: Anthropogenic debris ingestion by avifauna in eastern Australia

Lauren Roman, Qamar A. Schuyler, Britta Denise Hardesty & Kathy A. Townsend
Anthropogenic debris in the world’s oceans and coastal environments is a pervasive global issue that has both direct and indirect impacts on avifauna. The number of bird species affected, the feeding ecologies associated with an increased risk of debris ingestion, and selectivity of ingested debris have yet to be investigated in most of Australia’s coastal and marine birds. With this study we aim to address the paucity of data regarding marine debris ingestion in Australian...

Data from: Inferring contemporary and historical genetic connectivity from juveniles

Pierre Feutry, Oliver Berry, Peter M. Kyne, Richard D. Pillans, Rich Hillary, Peter M. Grewe, James R. Marthick, Grant Johnson, Rasanthi M. Gunasekera, Nicholas J. Bax, Mark Bravington & Richard M. Hillary
Measuring population connectivity is a critical task in conservation biology. While genetic markers can provide reliable long-term historical estimates of population connectivity, scientists are still limited in their ability to determine contemporary patterns of gene flow, the most practical time frame for management. Here, we tackled this issue by developing a new approach that only requires juvenile sampling at a single time period. To demonstrate the usefulness of our method, we used the Speartooth shark...

Data from: Rapid evolutionary response to a transmissible cancer in Tasmanian devils

Brendan Epstein, Menna Jones, Rodrigo Hamede, Sarah Hendricks, Hamish McCallum, Elizabeth P. Murchison, Barbara Schönfeld, Cody Wiench, Paul Hohenlohe & Andrew Storfer
Although cancer rarely acts as an infectious disease, a recently emerged transmissible cancer in Tasmanian devils (Sarcophilus harrisii) is virtually 100% fatal. Devil facial tumour disease (DFTD) has swept across nearly the entire species’ range, resulting in localized declines exceeding 90% and an overall species decline of more than 80% in less than 20 years. Despite epidemiological models that predict extinction, populations in long-diseased sites persist. Here we report rare genomic evidence of a rapid,...

Data from: Relating trophic resources to community structure: a predictive index of food availability

Valerio Zupo, Timothy J. Alexander & Graham J. Edgar
The abundance and the distribution of trophic resources available for consumers influence the productivity and the diversity of natural communities. Nevertheless, assessment of the actual abundance of food items available for individual trophic groups has been constrained by differences in methods and metrics used by various authors. Here we develop an index of food abundance, the framework of which can be adapted for different ecosystems. The relative available food index (RAFI) is computed by considering...

Data from: Genome-wide scans detect adaptation to aridity in a widespread forest tree species.

Dorothy A. Steane, Brad M. Potts, Elizabeth McLean, Suzanne M. Prober, William D. Stock, René E. Vaillancourt & Margaret Byrne
Patterns of adaptive variation within plant species are best studied through common garden experiments, but these are costly and time-consuming, especially for trees that have long generation times. We explored whether genome-wide scanning technology combined with outlier marker detection could be used to detect adaptation to climate and provide an alternative to common garden experiments. As a case study, we sampled nine provenances of the widespread forest tree species, Eucalyptus tricarpa, across an aridity gradient...

Data from: Molecular genetics to inform spatial management in benthic invertebrate fisheries: a case study using the Australian greenlip abalone

Karen J. Miller, Craig N. Mundy & Stephen Mayfield
Hierarchical sampling and subsequent microsatellite genotyping of >2,300 Haliotis laevigata (greenlip abalone) from 19 locations distributed across five biogeographic regions has substantially advanced our knowledge of population structure and connectivity in this commercially-important species. The study has found key differences in stock structure of H. laevigata compared with the sympatric and con-generic Haliotis rubra (blacklip abalone) and yielded valuable insights into the management of fisheries targeting species characterised by spatial structure at small scales (i.e....

Data from: Development of 15 nuclear EST microsatellite markers for the palaeoendemic conifer Pherosphaera hookeriana (Podocarpaceae)

James R. P. Worth, James R. Marthick, Maurizio Rossetto, Joel Cohen, Greg Bourke & Gregory J. Jordan
Premise of the study: Nuclear microsatellite markers were developed for population genetic analysis of the threatened palaeoendemic conifer Pherosphaera hookeriana W. Archer (Podocarpaceae). Methods and Results: Fifteen variable loci were identified showing 1 to 13 alleles per population with seven loci displaying over four alleles in all populations and the average number of alleles per locus ranging from 4.8 to 5.93 per population. The observed heterozygosity per locus varied from 0.00 to 0.91 and overall...

Data from: Genetic monitoring of open ocean biodiversity: an evaluation of DNA metabarcoding for processing continuous plankton recorder samples

Bruce E. Deagle, Laurence J. Clarke, John A. Kitchener, Andrea M. Polanowski & Andrew T. Davidson
DNA metabarcoding is an efficient method for measuring biodiversity, but the process of initiating long-term DNA-based monitoring programs, or integrating with conventional programs, is only starting. In marine ecosystems, plankton surveys using the continuous plankton recorder (CPR) have characterised biodiversity along transects covering millions of kilometres with time-series spanning decades. We investigated the potential for use of metabarcoding in CPR surveys. Samples (n= 53) were collected in two Southern Ocean transects and metazoans identified using...

Data from: Retention forestry influences understory diversity and functional identity

Miranda Curzon, Christel Kern, Susan Baker, Brian Palik & Anthony D'Amato
In recent decades, a paradigm shift in forest management and associated policies has led to greater emphasis on harvest practices that retain mature, overstory trees in forest stands that would otherwise be clearcut. While it is often assumed that the maintenance of compositional and structural complexity, such as that achieved through retention forestry approaches, will also mitigate negative impacts to functional diversity, empirical evidence of this relationship is sparse. We examined the effects of an...

Data from: Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (Sarcophilus harrisii) populations

Alexandra Kaye Fraik, Mark Margres, Brendan Epstein, Soraia Barbosa, Menna Jones, Sarah Hendricks, Barbara Schonfeld, Amanda R. Stahlke, Anne Veillet, Rodrigo Hamede, Hamish McCallum, Elisa Lopez-Contreras, Samantha J Kallinen, Paul A Hohenlohe, Joanna Kelley & Andrew Storfer
Landscape genomics studies focus on identifying candidate genes under selection via spatial variation in abiotic environmental variables, but rarely by biotic factors such as disease. The Tasmanian devil (Sarcophilus harrisii) is found only on the environmentally heterogeneous island of Tasmania and is threatened with extinction by a nearly 100% fatal, transmissible cancer, devil facial tumor disease (DFTD). Devils persist in regions of long-term infection despite epidemiological model predictions of species’ extinction, suggesting possible adaptation to...

A catastrophic tropical drought kills hydraulically vulnerable tree species

Jennifer Powers, German Vargas-G, Timothy Brodribb, Naomi Schwartz, Daniel Perez-Aviles, Chris Smith-Martin, Justin Becknell, Filippo Aureli, Roger Blanco, Erick Calderón-Morales, Julio César Calvo-Alvarado, Ana Julieta Calvo-Obando, María Marta Chavarría, Dorian Carvajal-Vanegas, César Dionisio Jiménez-Rodríguez, Evin Murillo Chacon, Colleen Schaffner, Leland Werden, Xiangtao Xu & David Medvigy
Drought-related tree mortality is now a widespread phenomenon predicted to increase in magnitude with climate change. However, the patterns of which species and trees are most vulnerable to drought, and the underlying mechanisms have remained elusive, in part due to the lack of relevant data and difficulty of predicting the location of catastrophic drought years in advance. We used long‐term demographic records and extensive databases of functional traits and distribution patterns to understand the responses...

Urbanization impacts apex predator gene flow but not genetic diversity across an urban-rural divide

Daryl R Trumbo, Patricia E Salerno, Kenneth Logan, Mat Alldredge, Roderick B Gagne, Christopher P Kozakiewicz, Simona Kraberger, Nick Fountain-Jones, Meggan E Craft, Scott Carver, Holly B Ernest, Kevin Crooks, Sue VandeWoude & W. Chris Funk
Apex predators are important indicators of intact natural ecosystems. They are also sensitive to urbanization because they require broad home ranges and extensive contiguous habitat to support their prey base. Pumas (Puma concolor) can persist near human developed areas, but urbanization may be detrimental to their movement ecology, population structure, and genetic diversity. To investigate potential effects of urbanization in population connectivity of pumas, we performed a landscape genomics study of 130 pumas on the...

Data from: Temporal genetic patterns of diversity and structure evidence sweepstakes in reproductive success of a spiny lobster

Cecilia Villacorta-Rath, Carla A. Souza, Nicholas P. Murphy, Bridget S. Green, Caleb Gardner & Jan M. Strugnell
Population structure of many marine organisms is spatially patchy and varies within and between years, a phenomenon defined as chaotic genetic patchiness. This results from the combination of planktonic larval dispersal and environmental stochasticity. Additionally, in species with bi-partite life, post-settlement selection can magnify these genetic differences. The high fecundity (up to 500,000 eggs annually) and protracted larval duration (12-24 months) and dispersal of the southern rock lobster, Jasus edwardsii, make it a good test...

Data from: Chemical communication, sexual selection, and introgression in wall lizards

Hannah Elizabeth Alexandra MacGregor, Rachel Alison Margaret Lewandowsky, Patrizia D'Ettorre, Chloé Leroy, Noel W. Davies, Geoffrey M. While & Tobias Uller
Divergence in communication systems should influence the likelihood that individuals from different lineages interbreed, and consequently shape the direction and rate of hybridization. Here, we studied the role of chemical communication in hybridization, and its contribution to asymmetric and sexually selected introgression, between two lineages of the common wall lizard (Podarcis muralis). Males of the two lineages differed in the chemical composition of their femoral secretions. Chemical profiles provided information regarding male secondary sexual characters,...

Data from: Bacterial epibiont communities of panmictic Antarctic krill are spatially structured

Laurence Clarke, Leonie Suter, Rob King, Andrew Bissett, Sophie Bestley & Bruce Deagle
Antarctic krill (Euphausia superba) are amongst the most abundant animals on Earth, with a circumpolar distribution in the Southern Ocean. Genetic and genomic studies have failed to detect any population structure for the species, suggesting a single panmictic population. However, the hyper-abundance of krill slows the rate of genetic differentiation, masking potential underlying structure. Here we use high-throughput sequencing of bacterial 16S rRNA genes to show that krill bacterial epibiont communities exhibit spatial structuring, driven...

Protein structure alignments and structural similarity score code for: Benchmarking methods of protein structure alignment

Janan Sykes
The function of a protein is primarily determined by its structure and amino acid sequence. Many biological questions of interest rely on being able to accurately determine the group of structures to which domains of a protein belong (often referred to as their `fold'); this can be done through alignment and comparison of protein structures. This fundamental task underpins predicting function, identification of homology, and testing hypotheses about the way "protein-space'' is organised. Dozens of...

CPR dataset for: Testing Bergmann's Rule in Marine Copepods

Max D. Campbell, David S. Schoeman, William Venables, Rana Abu-Alhaija, Sonia D. Batten, Sanae Chiba, Frank Coman, Claire H. Davies, Martin Edwards, Ruth Eriksen, Jason D. Everett, Yutaka Fukai, Mitsuo Fukuchi, Octavio Esquivel Garrote, Graham Hosie, Jenny Huggett, David G. Johns, John A. Kitchener, Philippe Koubbi, Felicity R. McEnnulty, Erik Muxagata, Clare Ostle, Karen V. Robinson, Anita Slotwinski, Kerrie M. Swadling … & Anthony J. Richardson
This is the global dataset used for the Campbell et al. (2021) paper “Testing Bergmann’s Rule in marine copepods”. The dataset includes the mean length of copepods weighted by abundance found in 97,830 continuous plankton recorder (CPR) samples. Further, it contains satellite observations for sea surface temperature, chlorophyll-a, and dissolved oxygen (see paper for details). It was a massive collaborative effort to get this dataset assembled by the Global Alliance of CPR Surveys (GACS 2011,...

Pleistocene divergence in the absence of gene flow among populations of a viviparous reptile with intraspecific variation in sex determination

Peta Hill, Erik Wapstra, Tariq Ezaz & Christopher Burridge
Polymorphisms can lead to speciation if there is differential mating success among conspecifics divergent for a trait. Polymorphism for sex determining system might be particularly expected to isolate gene pools, given strong selection for the production of viable males and females and the low success of heterogametic hybrids when sex chromosomes differ (Haldane’s rule). We investigated this question using a rare example of a species exhibiting polymorphism for sex determination: the viviparous snow skink Carinascincus...

Data from: Novel distances for Dollo data

Michael Woodhams, Dorothy A. Steane, Rebecca C. Jones, Dean Nicolle, Vincent Moulton & Barbara R. Holland
We investigate distances on binary (presence/absence) data in the context of a Dollo process, where a trait can only arise once on a phylogenetic tree but may be lost many times. We introduce a novel distance, the Additive Dollo Distance (ADD), that applies to data generated under a Dollo model, and show that it has some useful theoretical properties including an intriguing link to the LogDet/paralinear distance. Simulations of Dollo data are used to compare...

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