467 Works

Data from: Pollen diversity matters: revealing the neglected effect of pollen diversity on fitness in fragmented landscapes

Martin F. Breed, Maria H. K. Marklund, Kym M. Ottewell, Michael G. Gardner, J. Berton C. Harris & Andrew J. Lowe
Few studies have documented the impacts of habitat fragmentation on plant mating patterns together with fitness. Yet, these processes require urgent attention to better understand the impact of contemporary landscape change on biodiversity and for guiding native plant genetic resource management. We examined these relationships using the predominantly insect-pollinated Eucalyptus socialis. Progeny were collected from trees located in three increasingly disturbed landscapes in southern Australia and were planted out in common garden experiments. We show...

Data from: Genomic evidence for the parallel evolution of coastal forms in the Senecio lautus complex

Federico Roda, Luke Ambrose, Gregory M. Walter, Huanle L. Liu, Andrea Schaul, Andrew Lowe, Pieter B. Pelser, Peter Prentis, Loren H. Rieseberg & Daniel Ortiz-Barrientos
Instances of parallel ecotypic divergence where adaptation to similar conditions repeatedly cause similar phenotypic changes in closely related organisms are useful for studying the role of ecological selection in speciation. Here we used a combination of traditional and next generation genotyping techniques to test for the parallel divergence of plants from the Senecio lautus complex, a phenotypically variable groundsel that has adapted to disparate environments in the South Pacific. Phylogenetic analysis of a broad selection...

Data from: Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species

Emese Meglécz, Gabriel Nève, Ed Biffin & Michael G. Gardner
Microsatellites are ubiquitous in Eukaryotic genomes. A more complete understanding of their origin and spread can be gained from a comparison of their distribution within a phylogenetic context. Although information for model species is accumulating rapidly, it is insufficient due to a lack of species depth, thus intragroup variation is necessarily ignored. As such, apparent differences between groups may be overinflated and generalizations cannot be inferred until an analysis of the variation that exists within...

Data from: Lean-season primary productivity and heat dissipation as key drivers of geographic body-size variation in a widespread marsupial

Rachel A. Correll, Thomas A. A. Prowse & Gavin J. Prideaux
Geographic body-size variation characterises many mammal species. Hypotheses centring around heat conservation, heat dissipation, primary productivity and seasonality have been advanced to explain geographic body-size patterns. However, identification of the primary body-size drivers has often been hampered by a paucity of data for broadly distributed species and the application of regression models that have not explicitly accounted for the spatial clustering inherent in such datasets. We used Australia's most widespread marsupial, the common brushtail possum...

Data from: Pollen flow in fragmented landscapes maintains genetic diversity following stand-replacing disturbance in a neotropical pioneer tree, Vochysia ferruginea Mart.

Andrew J. Lowe, Sam J. Davies, Stephen Cavers, Bryan Finegan, Andrew White & Martin F. Breed
In forests with gap disturbance regimes, pioneer tree regeneration is typically abundant following stand-replacing disturbances, whether natural or anthropogenic. Differences in pioneer tree density linked to disturbance regime can influence pollinator behaviour and impact on mating patterns and genetic diversity of pioneer populations. Such mating pattern shifts can manifest as higher selfing rates and lower pollen diversity in old growth forest populations. In secondary forest, where more closely related pollen donors occur, an increase in...

Data from: Gene amplification of 5-enol-pyruvylshikimate-3-phosphate synthase in glyphosate-resistant Kochia scoparia

Andrew T. Wiersma, Todd A. Gaines, Christopher Preston, John P. Hamilton, Darci Giacomini, C. Robin Buell, Jan E. Leach & Philip Westra
The widely used herbicide glyphosate inhibits the shikimate pathway enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). Globally, the intensive use of glyphosate for weed control has selected for glyphosate resistance in 31 weed species. Populations of suspected glyphosate-resistant Kochia scoparia were collected from fields located in the US central Great Plains. Glyphosate dose response verified glyphosate resistance in nine populations. The mechanism of resistance to glyphosate was investigated using targeted sequencing, quantitative PCR, immunoblotting, and whole transcriptome de...

Data from: EB Ford revisited: assessing the long-term stability of wing-spot patterns and population genetic structure of the meadow brown butterfly on the Isles of Scilly

Simon W. Baxter, Joseph I. Hoffman, Tom Tregenza, Nina Wedell & David J. Hosken
Understanding selection in the wild remains a major aim of evolutionary ecology and work by Ford and colleagues on the meadow brown butterfly Maniola jurtina did much to ignite this agenda. A great deal of their work was conducted during the 1950s on the Isles of Scilly. They documented island-specific wing-spot patterns that remained consistent over about a decade, but patterns on some islands changed after environmental perturbation. It was suggested that these wing-spot patterns...

Data from: Concordance in evolutionary history of threatened plant and insect populations warrant unified conservation management approaches

Melinda L. Moir, David J. Coates, W. Jason Kennington, Sarah Barrett, Gary S. Taylor & W. Jason Kensington
Threatened organisms may act as host to a suite of dependent organisms, which are potentially cothreatened, yet management is rarely coordinated between host and dependent species. Here, we test the congruency of patterns of genetic structure between two critically endangered interacting taxa; the feather-leaf banksia (Banksia brownii R.Br.), and its host-specific herbivorous plant-louse Trioza barrettae Taylor & Moir, to establish whether conservation actions should be implemented jointly for both species. We also examine the role...

Data from: Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas

Bastien Llamas, Lars Fehren-Schmitz, Guido Valverde, Julien Soubrier, Swapan Mallick, Nadin Rohland, Susanne Nordenfelt, Cristina Valdiosera, Stephen M. Richards, Adam Rohrlach, Maria Inés Barreto Romero, Isabel Flores Espinoza, Elsa Tomasto Cagigao, Lucía Watson Jiménez, Krzysztof Makowski, Ilán Santiago Leboreiro Reyna, Josefina Mansilla Lory, Julio Alejandro Ballivián Torrez, Mario A. Rivera, Richard L. Burger, Maria Constanza Ceruti, Johan Reinhard, R. Spencer Wells, Gustavo Politis, Calogero M. Santoro … & Wolfgang Haak
The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native...

Data from: Ocean acidification alters fish–jellyfish symbiosis

Ivan Nagelkerken, Kylie A. Pitt, Melchior D. Rutte & Robbert C. Geertsma
Symbiotic relationships are common in nature, and are important for individual fitness and sustaining species populations. Global change is rapidly altering environmental conditions, but, with the exception of coral–microalgae interactions, we know little of how this will affect symbiotic relationships. We here test how the effects of ocean acidification, from rising anthropogenic CO2 emissions, may alter symbiotic interactions between juvenile fish and their jellyfish hosts. Fishes treated with elevated seawater CO2 concentrations, as forecast for...

Data from: Evolutionary novelty in a butterfly wing pattern through enhancer shuffling

Richard W. R. Wallbank, Simon W. Baxter, Carolina Pardo-Diaz, Joseph J. Hanly, Simon H. Martin, James Mallet, Kanchon K. Dasmahapatra, Camilo Salazar, Mathieu Joron, Nicola Nadeau, W. Owen McMillan & Chris D. Jiggins
An important goal in evolutionary biology is to understand the genetic changes underlying novel morphological structures. We investigated the origins of a complex wing pattern found among Amazonian Heliconius butterflies. Genome sequence data from 142 individuals across 17 species identified narrow regions associated with two distinct red colour pattern elements, dennis and ray. We hypothesise that these modules in non-coding sequence represent distinct cis-regulatory loci that control expression of the transcription factor optix, which in...

Data from: Ocean acidification boosts larval fish development but reduces the window of opportunity for successful settlement

Tullio Rossi, Ivan Nagelkerken, Stephen D. Simpson, Jennifer C.A. Pistevos, Sue-Ann Watson, Laurene Merillet, Peter Fraser, Philip L. Munday & Sean D. Connell
Locating appropriate settlement habitat is a crucial step in the life cycle of most benthic marine animals. In marine fish, this step involves the use of multiple senses, including audition, olfaction and vision. To date, most investigations of fish audition focus on the hearing thresholds to various frequencies of sounds without testing an ecological response to such sounds. Identifying responses to biologically relevant sounds at the development stage in which orientation is most relevant is...

Data from: Diversification rates and phenotypic evolution in venomous snakes (Elapidae)

Michael S. Y. Lee, Kate L. Sanders, Benedict King & Alessandro Palci
The relationship between rates of diversification and of body size change (a common proxy for phenotypic evolution) was investigated across Elapidae, the largest radiation of highly venomous snakes. Time-calibrated phylogenetic trees for 175 species of elapids (more than 50% of known taxa) were constructed using seven mitochondrial and nuclear genes. Analyses using these trees revealed no evidence for a link between speciation rates and changes in body size. Two clades (Hydrophis, Micrurus) show anomalously high...

Data from: Direct and indirect effects of nursery habitats on coral-reef fish assemblages, grazing pressure, and benthic dynamics

Alastair R. Harborne, Ivan Nagelkerken, Nicholas H. Wolff, Yves-Marie Bozec, Martijn Dorenbosch, Monique G. G. Grol & Peter J. Mumby
Migrating species are common within seascapes, but the potential for these movements to alter the populations and functional roles of non-migrating species (e.g. by increasing predation) is rarely investigated. This study considers whether the presence of nursery habitats (mangroves and seagrass) simply enhances the abundance of nursery-using parrotfishes and piscivores on nearby coral reefs, or also affects other parrotfishes. Data from 131 reef sites and multiple seascape configurations across 13 degrees of latitude were used...

Data from: Tick exposure and extreme climate events impact survival and threaten the persistence of a long-lived lizard

Alice R. Jones, C. Michael Bull, Barry W. Brook, Konstans Wells, Kenneth H. Pollock & Damien A. Fordham
1. Assessing the impacts of multiple, often synergistic, stressors on the population dynamics of long-lived species is becoming increasingly important due to recent and future global change. 2. Tiliqua rugosa (sleepy lizard) is a long-lived skink (>30 years) that is adapted to survive in semi-arid environments with varying levels of parasite exposure and highly seasonal food availability. We used an exhaustive database of 30-years of capture-mark-recapture records to quantify the impacts of both parasite exposure...

Data from: New insights on water buffalo genomic diversity and post-domestication migration routes from medium density SNP chip data

Licia Colli, Marco Milanesi, Elia Vajana, Daniela Iamartino, Lorenzo Bomba, Francesco Puglisi, Marcello Del Corvo, Ezequiel Luis Nicolazzi, Sahar Saad El-Din Ahmed, Jesus Rommel V. Herrera, Libertado Cruz, Shuju Zhang, Aixin Liang, Gouhua Hua, Ligou Yang, Xingjie Hao, Fuyuan Zuo, Song-Jia Lai, Shuilian Wang, Ruyu Liu, Yundeng Gong, Mahdi Mokhber, Yongjiang Mao, Feng Guan, Augustin Vlaic … & Liguo Yang
The domestic water buffalo is native to the Asian continent but through historical migrations and recent importations, nowadays has a worldwide distribution. The two types of water buffalo, i.e., river and swamp, display distinct morphological and behavioral traits, different karyotypes and also have different purposes and geographical distributions. River buffaloes from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil and Colombia, and swamp buffaloes from China, Thailand, Philippines, Indonesia and Brazil were genotyped with...

The evolution of broadly polylectic behaviour in Lasioglossum (Chilalictus) (Halictidae, Apoidea)

Trace Akankunda, Carlos Rodriguez Lopez, Remko Leijs & Ken Walker
Based on the number of pollen hosts utilised, bees have been categorised as generalists (polylectic) or specialists (oligolectic). Faced with a changing habitat, polylectic bees can diversify their pollen ‘portfolio’, while oligolectic bees cannot and therefore may go locally extinct. Research into the evolution and maintenance of broad polylecty is scant. Instead, research has mainly focussed on the factors that constrain oligolectic species to a narrow diet. Here, we developed a molecular phylogeny of a...

Radiation of tropical island bees and the role of phylogenetic niche conservatism as an important driver of biodiversity

James B Dorey, Scott SVC Groom, Elisha Freedman, Cale Matthews, Olivia K Davies, Ella Deans, Celina Rebola, Mark I Stevens, Michael SY Lee & Michael P Schwarz
Island biogeography explores how biodiversity in island ecosystems arises and is maintained. The topographical complexity of islands can drive speciation by providing a diversity of niches that promote adaptive radiation and speciation. However, recent studies have argued that phylogenetic niche conservatism, combined with topographical complexity and climate change, could also promote speciation if populations are episodically fragmented into climate refugia that enable allopatric speciation. Adaptive radiation and phylogenetic niche conservatism therefore both predict that topographical...

Adaptive changes in the genomes of wild rabbits after 16 years of viral epidemics

Stephen Pederson & Nina Schwensow
Since its introduction to control overabundant alien rabbits (Oryctolagus cuniculus), the highly virulent Rabbit Haemorrhagic Disease Virus (RHDV) has caused regular annual disease outbreaks in Australian rabbit populations. Although initially reducing rabbit abundance by 60%, continent-wide, experimental evidence has since indicated increased genetic resistance in wild rabbits that have experienced RHDV-driven selection. To identify genetic adaptations, which explain the increased resistance to this biocontrol virus, we investigated genome-wide SNP (single nucleotide polymorphism) allele frequency changes...

Data from: Assessing the trophic ecology of top predators across a recolonisation frontier using DNA metabarcoding of diets

Natasha Hardy, Tina Berry, Brendan P. Kelaher, Simon D. Goldsworthy, Michael Bunce, Melinda A. Coleman, Bronwyn M. Gillanders, Sean D. Connell, Michelle Blewitt, Will Figueira, BM Gillanders, SD Connell, BP Kelaher & SD Goldsworthy
Top predator populations, once intensively hunted, are rebounding in size and geographic distribution. The cessation of sealing along coastal Australia and subsequent recovery of Australian Arctocephalus pusillus doriferus and long-nosed A. forsteri fur seals represents a unique opportunity to investigate trophic linkages at a frontier of predator recolonisation. We characterised the diets of both species across 2 locations of recolonisation, one site an established breeding colony, and the other, a new but permanent haul-out site....

Data from: Resistance to RHD virus in wild Australian rabbits: comparison of susceptible and resistant individuals using a genomewide approach

Nina I. Schwensow, Harald Detering, Stephen Pederson, Camila Mazzoni, Ron Sinclair, David Peacock, John Kovaliski, Brian Cooke, Joerns Fickel & Simone Sommer
Deciphering the genes involved in disease resistance is essential if we are to understand host–pathogen coevolutionary processes. The rabbit haemorrhagic disease virus (RHDV) was imported into Australia in 1995 as a biocontrol agent to manage one of the most successful and devastating invasive species, the European rabbit (Oryctolagus cuniculus). During the first outbreaks of the disease, RHDV caused mortality rates of up to 97%. Recently, however, increased genetic resistance to RHDV has been reported. Here,...

Data from: Long read reference genome-free reconstruction of a full-length transcriptome from Astragalus membranaceus reveals transcript variants involved in bioactive compound biosynthesis

Jun Li, Yuka Harata-Lee, Matthew D. Denton, Qianjin Feng, Judith R. Rathjen, Zhipeng Qu & David L. Adelson
Astragalus membranaceus, also known as Huangqi in China, is one of the most widely used medicinal herbs in Traditional Chinese Medicine. Traditional Chinese Medicine formulations from Astragalus membranaceus have been used to treat a wide range of illnesses, such as cardiovascular disease, type 2 diabetes, nephritis and cancers. Pharmacological studies have shown that immunomodulating, anti-hyperglycemic, anti-inflammatory, antioxidant and antiviral activities exist in the extract of Astragalus membranaceus. Therefore, characterising the biosynthesis of bioactive compounds in...

Data from: The influence of habitat accessibility on the dietary and morphological specialisation of an aquatic predator

Maria H.K. Marklund, Richard Svanbäck, Yinghua Zha, Kristin Scharnweber, Peter Eklov & Maria H. K. Marklund
Individual diet and habitat specialisation are widespread in animal taxa and often related to levels of predation and competition. Mobile consumers such as predatory fish can stabilise lake food webs by ranging over a larger area than their prey, thereby switching between habitats. Although, this switching assumes that the predator has equal preference for the available prey, individual diet specialisation and morphological adaptations to different habitats could potentially prevent individuals from switching between habitats. In...

Data from: Range-wide snow leopard phylogeography supports three subspecies

Jan E. Janecka, Yu-Quang Zhang, Di-Qiang Li, Munkhtsog Bariushaa, Bayaraa Munkhtsog, Galsandorj Naranbaatar, Wangchuk R. Tshewang, Karmacharya Dibesh, McCarthy Thomas, Li Juan, Zhi Lu, Zhumabai Uulu Kubanychbek, Gaur Ajay, Kumar Satish, B. Kumar Kesav, Hussain Shafqat, Muhammad Ghulam, Jevit Matthew, Hacker Charlotte, Burger Pamela, Wultsch Claudia, Janecka J. Mary, Helgen Kristofer, Murphy J. William & Jackson Rodney
The snow leopard, Panthera uncia, is an elusive high-altitude specialist that inhabits vast, inaccessible habitat across Asia. We conducted the first range-wide genetic assessment of snow leopards based on noninvasive scat surveys. Thirty-three microsatellites were genotyped and a total of 683-bp of mitochondrial DNA sequenced in 70 individuals. Snow leopards exhibited low genetic diversity at microsatellites (AN = 5.8, HO = 0.433, HE = 0.568), virtually no mtDNA variation, and underwent a bottleneck in the...

Data from: Rates of morphological evolution, asymmetry and morphological integration of shell shape in scallops

Emma Sherratt, Jeanne Serb & Dean Adams
Background: Rates of morphological evolution vary across different taxonomic groups, and this has been proposed as one of the main drivers for the great diversity of organisms on Earth. Of the extrinsic factors pertaining to this variation, ecological hypotheses feature prominently in observed differences in phenotypic evolutionary rates across lineages. But complex organisms are inherently modular, comprising distinct body parts that can be differentially affected by external selective pressures. Thus, the evolution of trait covariation...

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