160 Works

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...

Data from: Platelet factor 4 and Duffy antigen required for platelet killing of Plasmodium falciparum

Brendan J. McMorran, Laura Wieczorski, Karen E. Drysdale, Jo-Anne Chan, Hong Ming Huang, Clare Smith, Chalachew Mitiku, James G. Beeson, Gaetan Burgio & Simon J. Foote
Platelets restrict the growth of intraerythrocytic malaria parasites by binding to parasitized cells and killing the parasite within. Here, we show that the platelet molecule platelet factor 4 (PF4 or CXCL4) and the erythrocyte Duffy-antigen receptor (Fy) are necessary for platelet-mediated killing of Plasmodium falciparum parasites. PF4 is released by platelets on contact with parasitized red cells, and the protein directly kills intraerythrocytic parasites. This function for PF4 is critically dependent on Fy, which binds...

Data from: Promiscuity resolves constraints on social mate choice imposed by population viscosity

Geoffrey M. While, Tobias Uller, Genevieve Bordogna & Erik Wapstra
Population viscosity can have major consequences for adaptive evolution, in particular for phenotypes involved in social interactions. For example, population viscosity increases the probability of mating with close kin, resulting in selection for mechanisms that circumvent the potential negative consequences of inbreeding. Female promiscuity is often suggested to be one such mechanism. However, whether avoidance of genetically similar partners is a major selective force shaping patterns of promiscuity remains poorly supported by empirical data. Here,...

Data from: Climate, not Aboriginal landscape burning, controlled the historical demography and distribution of fire-sensitive conifer populations across Australia

Shota Sakaguchi, David M. J. S. Bowman, Lynda D. Prior, Michael D. Crisp, Celeste C. Linde, Yoshihiko Tsumura & Yuji Isagi
Climate and fire are the key environmental factors that shape the distribution and demography of plant populations in Australia. Because of limited palaeoecological records in this arid continent, however, it is unclear as to which factor impacted vegetation more strongly, and what were the roles of fire regime changes owing to human activity and megafaunal extinction (since ca 50 kya). To address these questions, we analysed historical genetic, demographic and distributional changes in a widespread...

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: Living near the edge: being close to mature forest increases the rate of succession in beetle communities

Nicholas Fountain-Jones, Gregory J. Jordan, Thomas Baker, Jayne Balmer, Timothy Wardlaw, Susan Baker, Nicholas M. Fountain-Jones, Thomas P. Baker, Jayne M. Balmer & Susan C. Baker
In increasingly fragmented landscapes, it is important to understand how mature forest affects adjacent secondary forest (forest influence). Forest influence on ecological succession of beetle communities is largely unknown. We investigated succession and forest influence using 235 m long transects across boundaries between mature and secondary forest at 15 sites, sampling a chronosequence of three forest age classes (5-10, 23-29 and 42-46 years since clearcutting) in tall eucalypt forest in Tasmania. Our results showed that...

Data from: Empirical tests of harvest-induced body-size evolution along a geographic gradient in Australian macropods

Thomas A. A. Prowse, Rachel A. Correll, Christopher N. Johnson, Gavin J. Prideaux & Barry W. Brook
1. Life-history theory predicts the progressive dwarfing of animal populations that are subjected to chronic mortality stress but the evolutionary impact of harvesting terrestrial herbivores has seldom been tested. In Australia, marsupials of the genus Macropus (kangaroos and wallabies) are subjected to size-selective commercial harvesting. Mathematical modelling suggests that harvest quotas (ca. 10–20 % of population estimates annually) could be driving body-size evolution in these species. 2. We tested this hypothesis for three harvested macropod...

Data from: Feral cats are better killers in open habitats, revealed by animal-borne video

Hugh W. McGregor, Sarah Legge, Menna E. Jones, Christopher N. Johnson & Hugh McGregor
One of the key gaps in understanding the impacts of predation by small mammalian predators on prey is how habitat structure affects the hunting success of small predators, such as feral cats. These effects are poorly understood due to the difficulty of observing actual hunting behaviours. We attached collar-mounted video cameras to feral cats living in a tropical savanna environment in northern Australia, and measured variation in hunting success among different microhabitats (open areas, dense...

Data from: Conservation of sex-linked markers among conspecific populations of a viviparous skink, Niveoscincus ocellatus, exhibiting genetic and temperature-dependent sex determination

Peta Hill, Christopher P. Burridge, Tariq Ezaz, Erik Wapstra & Peta L Hill
Sex determination systems are exceptionally diverse and have undergone multiple and independent evolutionary transitions among species, particularly reptiles. However, the mechanisms underlying these transitions have not been established. Here we tested for differences in sex-linked markers in the only known reptile that is polymorphic for sex determination system, the spotted snow skink, Niveoscincus ocellatus, to quantify the genomic differences that have accompanied this transition. In a highland population, sex is determined genetically, whilst in a...

Data from: Two-current choice flumes for testing avoidance and preference in aquatic animals

Fredrik Jutfelt, Josefin Sundin, Graham D. Raby, Anna-Sara Krång & Timothy D. Clark
Aquatic chemical ecology is an important and growing field of research that involves understanding how organisms perceive and respond to chemical cues in their environment. Research assessing the preference or avoidance of a water source containing specific chemical cues has increased in popularity in recent years, and a variety of methods have been described in the scientific literature. Two-current choice flumes have seen the greatest increase in popularity, perhaps because of their potential to address...

Data from: Avian predation intensity as a driver of clinal variation in colour morph frequency

Genevieve Matthews, Celine T. Goulet, Kaspar Delhey, Zak S. Atkins, Geoffrey M. While, Michael G. Gardner & David G. Chapple
1) Phenotypic variation provides the framework for natural selection to work upon, enabling adaptive evolution. One of the most discernible manifestations of phenotypic variability is colour variation. When this variation is discrete, genetically-based colour pattern morphs occur simultaneously within a population. 2) Why and how colour polymorphisms are maintained is an evolutionary puzzle. Several evolutionary drivers have been hypothesized as influencing clinal patterns of morph frequency, with spatial variation in climate and predation being considered...

Data from: Genetic differentiation in spite of high gene flow in the dominant rainforest tree of southeastern Australia, Nothofagus cunninghamii

Corrine J. Duncan, James R. P. Worth, Gregory J. Jordan, Rebecca C. Jones & Rene E. Vaillancourt
Nothofagus cunninghamii is a long-lived, wind-pollinated tree species that dominates the cool temperate rainforests of southeastern Australia. The species’ distribution is more or less continuous in western Tasmania but is fragmented elsewhere. However, it is unknown whether this fragmentation has affected the species’ genetic architecture. Thus, we examined N. cunninghamii using 12 nuclear microsatellites and 633 individuals from 18 populations spanning the species’ natural range. Typical of wind-pollinated trees, there was low range-wide genetic structure...

Data from: Conservation genetics of the scalloped hammerhead shark in the Pacific coast of Colombia

Sonia Quintanilla, Alberto Gomez, Camila Mariño-Ramírez, Carolina Sorzano, Sandra Bessudo, German Soler, Jaime E. Bernal & Susana Caballero
Previous investigations of the population genetics of the scalloped hammerhead sharks (Sphyrna lewini) in the Eastern Tropical Pacific have lacked information about nursery areas. Such areas are key to promoting conservation initiatives that can protect young sharks from threats such as overfishing. Here, we investigated the genetic diversity, phylogeography, and connectivity of S. lewini found in 3 areas of Colombia’s Pacific coast: around Malpelo Island and in 2 National Natural Parks on the Colombian Pacific...

Data from: Australian spiny mountain crayfish and their temnocephalan ectosymbionts: an ancient association on the edge of coextinction?

Jennifer F. Hoyal Cuthill, Kim B. Sewell, Lester R. G. Cannon, Michael A. Charleston, Susan Lawler, D. Timothy J. Littlewood, Peter D. Olson & David Blair
Australian spiny mountain crayfish (Euastacus, Parastacidae) and their ecotosymbiotic temnocephalan flatworms (Temnocephalida, Platyhelminthes) may have co-occurred and interacted through deep time, during a period of major environmental change. Therefore, reconstructing the history of their association is of evolutionary, ecological, and conservation significance. Here, time-calibrated Bayesian phylogenies of Euastacus species and their temnocephalans (Temnohaswellia and Temnosewellia) indicate near-synchronous diversifications from the Cretaceous. Statistically significant cophylogeny correlations between associated clades suggest linked evolutionary histories. However, there is...

Data from: GHOST: Recovering Historical Signal from Heterotachously-evolved Sequence Alignments

Stephen M. Crotty, Bui Quang Minh, Nigel G. Bean, Barbara R. Holland, Jonathan Tuke, Lars S. Jermiin & Arndt Von Haeseler
Molecular sequence data that have evolved under the influence of heterotachous evolutionary processes are known to mislead phylogenetic inference. We introduce the General Heterogeneous evolution On a Single Topology (GHOST) model of sequence evolution, implemented under a maximum-likelihood framework in the phylogenetic program IQ-TREE (http://www.iqtree.org). Simulations show that using the GHOST model, IQ-TREE can accurately recover the tree topology, branch lengths, and substitution model parameters from heterotachously evolved sequences. We investigate the performance of the...

Data from: Outlier SNPs detect weak regional structure against a background of genetic homogeneity in the Eastern Rock Lobster, Sagmariasus verreauxi

Laura N. Woodings, Nicholas P. Murphy, Stephen R. Doyle, Nathan E. Hall, Andrew J. Robinson, Geoffrey W. Liggins, Bridget S. Green, Ira R. Cooke, James J. Bell & Jan M. Strugnell
Genetic differentiation is characteristically weak in marine species making assessments of population connectivity and structure difficult. However the advent of genomic methods have increased genetic resolution, enabling studies to detect weak, but significant population differentiation within marine species. With an increasing number of studies employing high resolution genome-wide techniques, we are realising the connectivity of marine populations is often complex and quantifying this complexity can provide an understanding of the processes shaping marine species genetic...

Data from: Low food availability during gestation enhances offspring post-natal growth, but reduces survival, in a viviparous lizard

Thomas Botterill-James, Kirke L. Munch, Ben Halliwell, David G. Chapple, Michael G. Gardner, Erik Wapstra & Geoffrey M. While
The environment experienced by a mother can have profound effects on the fitness of her offspring (i.e., maternal effects). Maternal effects can be adaptive when the developmental environments experienced by offspring promote phenotypes that provide fitness benefits either via matching offspring phenotype to the post-developmental environment (also known as anticipatory maternal effects) or through direct effects on offspring growth and survival. We tested these hypotheses in a viviparous lizard using a factorial experimental design in...

Data from: Does migration promote or inhibit diversification? A case study involving the dominant radiation of temperate Southern Hemisphere freshwater fishes

Christopher Burridge & Jonathan M. Waters
While theory predicts that dispersal is a pivotal influence on speciation and extinction rates, it can have contradictory effects on each, such that empirical studies are needed to quantify its role. In many studies, dispersal reduction appears to promote diversification, although some analyses of migratory species suggest otherwise. Here we test for a relationship between migratory status and diversification rate within the dominant radiation of temperate Southern Hemisphere freshwater fishes, the Galaxiidae. We reconstructed a...

Data from: Greater agility increases probability of survival in the endangered northern quoll

Miranda Rew-Duffy, Skye Cameron, Natalie Freeman, Rebecca Wheatley, Jessica Latimer & Robbie Wilson
Introduced predators combined with habitat loss and modification are threatening biodiversity worldwide, particularly the ‘critical weight range’ (CWR) mammals of Australia. In order to mitigate the impacts of invasive predators on native species in different landscapes, we must understand how the prey's morphology and performance determine their survival. Here we evaluate how phenotypic traits related to escape performance predict the probability of survival for an endangered CWR mammal, the northern quoll (Dasyurus hallucatus). We measured...

rhinoceros auklet microsatellite data

Theresa Burg, Marie Prill, Katharine Studholme, Alice Domalik, Strahan Tucker, Catherine Jardine, Mark Maftei, Kenneth Wright, Jesse Beck, Russell Bradley, Ryan Carle, Thomas Good, Scott Hatch, Peter Hodum, Motohiro Ito, Scott Pearson, Nora Rojek, Leslie Slater, Yutaka Watanuki, Alexis Will, Aidan Bindoff, Glenn Crossin, Mark Drever & Mark Hipfner
We tested the hypothesis that segregation in wintering areas promotes population differentiation in a sentinel North Pacific seabird, the rhinoceros auklet (Cerorhinca monocerata). We collected tissue samples for genetic analyses on five breeding colonies in the western Pacific Ocean (Japan) and 13 in the eastern Pacific Ocean (California to Alaska), and deployed light-level geologgers on 12 eastern Pacific colonies to delineate wintering areas. Loggers were deployed previously on one colony in Japan. There was strong...

Australian fur seal foraging consistency data

Cassie Speakman, John Arnould, Sebastian Lloyd, Elodie Camprasse, Andrew Hoskins, Mark Hindell, Daniel Costa & John Arnould
Substantial variation in foraging strategies can exist within populations, even those typically regarded as generalists. Specialisations arise from the consistent exploitation of a narrow behavioural, spatial or dietary niche over time, which may reduce intra-specific competition and influence adaptability to environmental change. However, few studies have investigated whether behavioural consistency confers benefits at the individual and/or population level. While still recovering from commercial sealing over-exploitation, Australian fur seals (AUFS; Arctocephalus pusillus doriferus) represent the largest...

Data from: Climate shapes the geographic distribution and introgressive spread of colour ornamentation in common wall lizards

Maravillas Ruiz Minano, Geoffrey While, Weizhao Yang, Christopher Burridge, Roberto Sacchi, Marco Zuffi, Stefano Scali, Daniele Salvi & Tobias Uller
Climate can exert an effect on the strength of sexual selection, but empirical evidence is limited. Here, we tested if climate predicts the geographic distribution and introgressive spread of sexually selected male colour ornamentation across 114 populations of the common wall lizard, Podarcis muralis. Colouration was highly structured across the landscape, and did not reflect genetic differentiation. Instead, colour ornamentation was consistently exaggerated in hot and dry environments, suggesting that climate-driven selection maintains geographic variation...

Ice Bulletins for the Antarctic shipping season 2020–2021

Jan Lieser
The Ice Bulletins compiled in this document are weekly reports on ice conditions for predominantly East Antarctica, including sub-weekly updates. They were prepared to support ship operations in East Antarctica during the 2020/2021 shipping season.

ISIMIP3b fishing input data

Yannick Rousseau, Julia Blanchard & Derek Tittensor
The Inter-Sectoral Impact Model Intercomparison Project (ISIMIP) provides a framework for the collation of a consistent set of climate impact data across sectors and scales. It also provides a unique opportunity for considering interactions between climate change impacts across sectors through consistent scenarios.
The ISIMIP3b part of the third simulation round is dedicated to a quantification of climate-related risks at different levels of global warming and socio-economic change. ISIMIP3b group I simulations are based on historical...

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