318 Works

Data from: PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses.

Robert Lanfear, Brett Calcott, Simon Y. W. Ho & Stephane Guindon
In phylogenetic analyses of molecular sequence data, partitioning involves estimating independent models of molecular evolution for different sets of sites in a sequence alignment. Choosing an appropriate partitioning scheme is an important step in most analyses because it can affect the accuracy of phylogenetic reconstruction. Despite this, partitioning schemes are often chosen without explicit statistical justification. Here, we describe two new objective methods for the combined selection of best-fit partitioning schemes and nucleotide substitution models....

Data from: Epistatic interactions determine the mutational pathways and coexistence of lineages in clonal Escherichia coli populations

Ram Prasad Maharjan & Thomas Ferenci
Understanding how diversity emerges in a single niche is not fully understood. Rugged fitness landscapes and epistasis between beneficial mutations could explain coexistence amongst emerging lineages. To provide an experimental test of this notion, we investigated epistasis amongst four pleiotropic mutations in rpoS, mglD, malT and hfq present in two coexisting lineages that repeatedly fixed in experimental populations of Escherichia coli. The mutations were transferred into the ancestral background individually or in combination of double...

Data from: Dynamics of macronutrient self-medication and illness-induced anorexia in virally-infected insects

Sonia Povey, Kenneth Wilson, Sheena C. Cotter & Stephen J. Simpson
1. Some animals change their feeding behaviour when infected with parasites, seeking out substances that enhance their ability to overcome infection. This “self-medication” is typically considered to involve the consumption of toxins, minerals or secondary compounds. However, recent studies have shown that macronutrients can influence the immune response, and that pathogen-challenged individuals can self-medicate by choosing a diet rich in protein and low in carbohydrates. Infected individuals might also reduce food intake when infected (i.e....

Data from: Anthropogenic selection enhances cancer evolution in Tasmanian devil tumours

Beata Ujvari, Anne-Maree Pearse, Kate Swift, Pamela Hodson, Bobby Hua, Stephen Pyecroft, Robyn Taylor, Rodrigo Hamede, Menna Jones, Kathy Belov, Thomas Madsen & Katherine Belov
The Tasmanian Devil Facial Tumour Disease (DFTD) provides a unique opportunity to elucidate the long-term effects of natural and anthropogenic selection on cancer evolution. Since first observed in 1996, this transmissible cancer has caused local population declines by >90%. So far, four chromosomal DFTD variants (strains) have been described and karyotypic analyses of 253 tumours showed higher levels of tetraploidy in the oldest strain. We propose that increased ploidy in the oldest strain may have...

Data from: Unexpected absence of genetic separation of a highly diverse population of hookworms from geographically isolated hosts

Benjamin T. Haynes, Alan D. Marcus, Damien P. Higgins, Jaime Gongora, Rachael Gray & Jan Slapeta
The high natal site fidelity of endangered Australian sea lions (Neophoca cinerea) along the southern Australian coast suggests that their maternally transmitted parasitic species, such as hookworms, will have restricted potential for dispersal. If this is the case, we would expect to find a hookworm haplotype structure corresponding to that of the host mtDNA haplotype structure; that is, restricted among geographically separated colonies. In this study, we used a fragment of the cytochrome c oxidase...

Data from: MHC class II diversity of koala (Phascolarctos cinereus) populations across their range

Damien P. Higgins, Quintin Lau, Weerachai Jaratlerdsiri, Joanna E. Griffith & Jaime Gongora
Major histocompatibility complex class II (MHCII) genes code for proteins that bind and present antigenic peptides and trigger the adaptive immune response. We present a broad geographical study of MHCII DA β1 (DAB) and DB β1 (DBB) variants of the koala (Phascolarctos cinereus; n=191) from 12 populations across eastern Australia, with a total of 13 DAB and 7 DBB variants found. We identified greater MHCII variation and, possibly, additional gene copies in koala populations in...

Data from: Female behavior and the interaction of male and female genital traits mediate sperm transfer during mating.

Christopher R. Friesen, Emily J. Uhrig, Robert T. Mason & Patricia L.R. Brennan
Natural selection and post-copulatory sexual selection, including sexual conflict, contribute to genital diversification. Fundamental first steps in understanding how these processes shape the evolution of specific genital traits are to determine their function experimentally and to understand the interactions between female and male genitalia during copulation. Our experimental manipulations of male and female genitalia in red-sided garter snakes (Thamnophis sirtalis parietalis) reveal that copulation duration and copulatory plug deposition, as well as total and oviductal/vaginal...

Data from: Group foraging decisions in nutritionally differentiated environments

Matthew J. Hansen, Timothy M. Schaerf, Stephen J. Simpson & Ashley J. W. Ward
Foraging behaviour must be flexible enough to adapt to heterogeneities in the distribution and quality of food resources. Accurate models of optimal foraging behaviour should acknowledge the extent to which animals can detect and regulate their intake of food based on smaller scale differences in food types. In particular, consideration of macro-nutrient distribution and how animals perceive this is limited in studies of optimal foraging, particularly in vertebrates and for animals that forage in groups....

Data from: Understanding the spatial scale of genetic connectivity at sea: unique insights from a land fish and a meta-analysis

Georgina M. Cooke, Timothy E. Schlub, William B. Sherwin & Terry J. Ord
Quantifying the spatial scale of population connectivity is important for understanding the evolutionary potential of ecologically divergent populations and for designing conservation strategies to preserve those populations. For marine organisms like fish, the spatial scale of connectivity is generally set by a pelagic larval phase. This has complicated past estimates of connectivity because detailed information on larval movements are difficult to obtain. Genetic approaches provide a tractable alternative and have the added benefit of estimating...

Data from: Age-related sex differences in body condition and telomere dynamics of red-sided garter snakes

Nicky Rollings, Emily J. Uhrig, Randolf W. Krohmer, Heather L. Waye, Robert T. Mason, Mats Olsson, Camilla M. Whittington, Christopher R. Friesen & Randolph W. Krohmer
Life-history strategies vary dramatically between the sexes, which may drive divergence in sex-specific senescence and mortality rates. Telomeres are tandem nucleotide repeats that protect the ends of chromosomes from erosion during cell division. Telomeres have been implicated in senescence and mortality because they tend to shorten with stress, growth and age. We investigated age-specific telomere length in female and male red-sided garter snakes, Thamnophis sirtalis parietalis. We hypothesized that age-specific telomere length would differ between...

Data from: Local coexistence and genetic isolation of three pollinator species on the same fig tree species

Timothy L. Sutton, Jane L. DeGabriel, Markus Riegler & James M. Cook
Molecular tools increasingly reveal cryptic lineages and species that were previously unnoticed by traditional taxonomy. The discovery of cryptic species in sympatry prompts the question of how they coexist in the apparent absence of ecological divergence. However, this assumes first that the molecular taxonomy used to identify cryptic lineages delimits species boundaries accurately. This issue is important, because many diversity studies rely heavily or solely on data from mitochondrial DNA sequences for species delimitation, and...

Data from: Can alternative mating tactics facilitate introgression across a hybrid zone by circumventing female choice?

Kathryn A. Stewart, Cameron M. Hudson & Stephen C. Lougheed
Reproductive barriers and divergence in species’ mate recognition systems underlie major models of speciation. However, hybridization between divergent species is common, and classic mechanisms to explain permeable reproductive barriers rarely consider how an individual may attain reproductive success. Alternative mating tactics exist in various forms across animal taxa. Such tactics may allow poorer quality individuals to gain mating opportunities and facilitate introgression either through asymmetrical positive selection, or by circumventing female choice altogether in areas...

Data from: Local interactions and global properties of wild, free-ranging stickleback shoals

Ashley J. W. Ward, Timothy M. Schaerf, James E. Herbert-Read, Lesley Morrell, David J.T. Sumpter, Mike M. Webster & David J. T. Sumpter
Collective motion describes the global properties of moving groups of animals and the self-organized, coordinated patterns of individual behaviour that produce them. We examined the group-level patterns and local interactions between individuals in wild, free-ranging shoals of three-spine sticklebacks, Gasterosteus aculeatus. Our data reveal that the highest frequencies of near-neighbour encounters occur at between one and two body lengths from a focal fish, with the peak frequency alongside a focal individual. Fish also show the...

Data from: Gut microbiota modifies olfactory-guided microbial preferences and foraging decisions in Drosophila

Adam Chun-Nin Wong, Qiao-Ping Wang, Juliano Morimoto, Alistair M. Senior, Mathieu Lihoreau, G. Gregory Neely, Stephen J. Simpson & Fleur Ponton
The gut microbiota affects a wide spectrum of host physiological traits, including development [ 1–5 ], germline [ 6 ], immunity [ 7–9 ], nutrition [ 4, 10, 11 ], and longevity [ 12, 13 ]. Association with microbes also influences fitness-related behaviors such as mating [ 14 ] and social interactions [ 15, 16 ]. Although the gut microbiota is evidently important for host wellbeing, how hosts become associated with particular assemblages of microbes...

Data from: Survival of the feces: does a nematode lungworm adaptively manipulate the behavior of its cane toad host?

Patrick B. Finnerty, Richard Shine & Gregory P. Brown
Parasites can enhance their fitness by modifying the behavior of their hosts in ways that increase rates of production and transmission of parasite larvae. We used an antihelminthic drug to experimentally alter infections of lungworms (Rhabdias pseudosphaerocephala) in cane toads (Rhinella marina). We then compared subsequent behaviors of dewormed toads versus toads that retained infections. Both in the laboratory and in the field, the presence of parasites induced hosts to select higher body temperatures (thereby...

Data from: Impacts of ocean acidification on sea urchin growth across the juvenile to mature adult life-stage transition is mitigated by warming

Symon A. Dworjanyn & Maria Byrne
Understanding how growth trajectories of calcifying invertebrates are affected by changing climate requires acclimation experiments that follow development across life history transitions. In a long-term acclimation study, the effects of increased acidification and temperature on survival and growth of the tropical sea urchin Tripneustes gratilla from the early juvenile (5 mm test diameter- TD) through the developmental transition to the mature adult (60 mm TD) were investigated. Juveniles were reared in a combination of three...

Data from: Nutrient-specific compensation for seasonal cold stress in a free-ranging temperate colobine monkey

Songtao Guo, Rong Hou, Paul A. Garber, David Raubenheimer, Nicoletta Righini, Weihong Ji, Ollie Jay, Shujun He, Fan Wu, Fangfang Li, Baoguo Li, Song-Tao Guo, Shu-Jun He, Fang-Fang Li, Bao-Guo Li & Wei-Hong Ji
1. Homeostatic responses of animals to environmentally-induced changes in nutrient requirements provide a powerful basis for predictive ecological models, and yet such responses are virtually unstudied in the wild. 2. We tested for macronutrient-specific compensatory feeding responses by free-ranging golden snub-nosed monkeys (Rhinopithecus roxellana) inhabiting high altitude temperate forests where they experience a substantial difference in ambient temperature in cold winters vs. warmer springs. The monkeys had free access to natural foods throughout the year,...

Data from: Unravelling species boundaries in the Aspergillus viridinutans complex (section Fumigati): opportunistic human and animal pathogens capable of interspecific hybridization

Vit Hubka, Vanessa Barrs, Zuzana Dudová, František Sklenář, Alena Kubátová, Tetsuhiro Matsuzawa, Takashi Yaguchi, Yoshikazu Horie, Alena Nováková, Jens C. Frisvad, Jessica Talbot & Miroslav Kolařík
Although Aspergillus fumigatus is the major agent of invasive aspergillosis, an increasing number of infections are caused by its cryptic species, especially A. lentulus and the A. viridinutans species complex (AVSC). Their identification is clinically relevant because of antifungal drug resistance and refractory infections. Species boundaries in the AVSC are unresolved since most species have uniform morphology and produce interspecific hybrids in vitro. Clinical and environmental strains from six continents (n = 110) were characterized...

Data from: Host provisioning behavior favors mimetic begging calls in a brood-parasitic cowbird

Cynthia A. Ursino, Ros Gloag, Juan C. Reboreda & Maria C. De Mársico
The vocalizations of some young brood-parasitic birds closely resemble those of their host’s young. Such similarities might arise because hosts bestow the greatest parental care in response to their own species’ call type. We used a playback experiment to assess the effectiveness of the nestling call structures of two brood parasites, the specialist screaming cowbird (Molothrus rufoaxillaris) and the generalist shiny cowbird (M. bonariensis), in stimulating parental provisioning in a shared host, the baywing (Agelaioides...

Data from: Sex-specific shifts in morphology and colour pattern polymorphism during range expansion of an invasive lizard

Kimberly A. Miller, Andressa Duran, Jane Melville, Michael B. Thompson & David G. Chapple
Aim: Human-assisted range expansion of animals to new environments can lead to phenotypic shifts over ecological timescales.We investigated whether phenotypic changes are sex-specific using an invasive lizard (Lampropholis delicata). Location: Pacific region (Hawaiian Islands, Lord Howe Island, New Zealand, eastern Australia) Methods: Using our knowledge of theintroduction history of L. delicata, we examined museum specimens of individuals collected across the native and introduced range to determine whether shifts in morphologyor colour pattern polymorphism had occurred...

Data from: Genomic comparisons reveal biogeographic and anthropogenic impacts in the koala (Phascolarctos cinereus); a dietary-specialist species distributed across heterogeneous environments

Shannon R. Kjeldsen, Herman W. Raadsma, Kellie A. Leigh, Jennifer R. Tobey, David Phalen, Andrew Krockenberger, William A. Ellis, Emily Hynes, Damien P. Higgins & Kyall R. Zenger
The Australian koala is an iconic marsupial with specific dietary requirements distributed across heterogeneous environments, over a large geographic range. The distribution and genetic structure of koala populations has been heavily influenced by human actions, specifically habitat modification, hunting and translocation of koalas. There is currently limited information on population diversity and gene-flow at a species-wide scale, or with consideration to the potential impacts of local adaptation. Using species-wide sampling across heterogeneous environments, and high-density...

Data from: Petrol exhaust pollution impairs honey bee learning and memory

Ryan J. Leonard, Vanina Vergoz, Nicholas Proschogo, Clare McArthur & Dieter F. Hochuli
Volatile organic compounds (VOCs) serve as important infochemicals, mediating several ecological interactions including herbivory and pollination. Atmospheric pollutants including traffic-related air pollution may impair the detection of VOCs used by insects in insect-plant interactions. We investigated the indirect effect of petrol exhaust pollution on olfactory learning and memory (short and long term) in honey bees. Using appetitive olfactory conditioning, we trained bees to learn one of four floral VOC profiles; linalool, dipentene, myrcene and geranium....

Data from: Patterns of niche filling and expansion across the invaded ranges of an Australian lizard

Reid Tingley, Michael B. Thompson, Stephen Hartley & David G. Chapple
Studies of realized niche shifts in alien species typically ignore the potential effects of intraspecific niche variation and different invaded-range environments on niche lability. We incorporate our detailed knowledge of the native-range source populations and global introduction history of the delicate skink Lampropholis delicata to examine intraspecific variation in realized niche expansion and unfilling, and investigate how alternative niche modelling approaches are affected by that variation. We analyzed the realized niche dynamics of L. delicata...

Data from: Oxidant trade-offs in immunity: an experimental test in a lizard

Michael Tobler, Cissy Ballen, Mo Healey, Mark Wilson & Mats Olsson
Immune system functioning and maintenance entails costs which may limit investment into other processes such as reproduction. Yet, the proximate mechanisms and ‘currencies’ mediating the costs of immune responses remain elusive. In vertebrates, up-regulation of the innate immune system is associated with rapid phagocytic production of pro-oxidant molecules (so-called ‘oxidative burst’ responses). Oxidative burst responses are intended to eliminate pathogens but may also constitute an immunopathological risk as they may induce oxidative damage to self...

Data from: Lack of genetic diversity across diverse immune genes in an endangered mammal, the Tasmanian devil (Sarcophilus harrisii)

Katrina M. Morris, Belinda Wright, Catherine E. Grueber, Carolyn Hogg & Katherine Belov
The Tasmanian devil (Sarcophilus harrisii) is threatened with extinction due to the spread of devil facial tumour disease. Polymorphisms in immune genes can provide adaptive potential to resist diseases. Previous studies in diversity at immune loci in wild species have almost exclusively focused on genes of the major histocompatibility complex (MHC); however, these genes only account for a fraction of immune gene diversity. Devils lack diversity at functionally important immunity loci, including MHC and Toll-like...

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