268 Works

Data from: Phylogenetic variation in hind-limb bone scaling of flightless theropods

Nicholas R. Chan
The robusticity of the weight-bearing limbs of large terrestrial animals is expected to increase at a more rapid rate than in their smaller relatives. This scaling has been hypothesized to allow large species to maintain stresses in the limb bones that are similar to those seen in smaller ones. Curvilinear scaling has previously been found in mammals and nonavian theropods but has not been demonstrated in birds. In this study, polynomial regressions of leg-bone length...

Data from: Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria)

David W. Bapst, April M. Wright, Nick J. Matzke & Graeme T. Lloyd
Dated phylogenies of fossil taxa allow palaeobiologists to estimate the timing of major divergences and placement of extinct lineages, and to test macroevolutionary hypotheses. Recently developed Bayesian ‘tip-dating’ methods simultaneously infer and date the branching relationships among fossil taxa, and infer putative ancestral relationships. Using a previously published dataset for extinct theropod dinosaurs, we contrast the dated relationships inferred by several tip-dating approaches and evaluate potential downstream effects on phylogenetic comparative methods. We also compare...

Data from: Learning and robustness to catch-and-release fishing in a shark social network

Johann Mourier, Culum Brown & Serge Planes
Individuals can play different roles in maintaining connectivity and social cohesion in animal populations and thereby influence population robustness to perturbations. We performed a social network analysis in a reef shark population to assess the vulnerability of the global network to node removal under different scenarios. We found that the network was generally robust to the removal of nodes with high centrality. The network appeared also highly robust to experimental fishing. Individual shark catchability decreased...

Data from: Genetic structure and signatures of selection in grey reef sharks (Carcharhinus amblyrhynchos)

Paolo Momigliano, Robert Harcourt, William D. Robbins, Vanessa Jaiteh, Gusti N. Mahardika, Andriuanus Sembiring & Adam Stow
With overfishing reducing the abundance of marine predators in multiple marine ecosystems, knowledge of genomic structure and local adaptation may provide valuable information to assist sustainable management. Despite recent technological advances, most studies on sharks have used small sets of neutral markers to describe their genetic structure. We used 5517 nuclear SNPs and a mtDNA gene to characterize patterns of genetic structure and detect signatures of selection in grey reef sharks (Carcharhinus amblyrhynchos). Using samples...

Data from: Temporal variability in the environmental and geographic predictors of spatial-recruitment in nearshore rockfishes

Russell W. Markel, Katie E. Lotterhos, Clifford L. K. Robinson, RW Markel, KE Lotterhos & CLK Robinson
Geography and habitat availability may be key drivers underlying spatial patterns of larval supply and recruitment success of nearshore marine fishes, but they are poorly understood. We assessed spatial recruitment patterns of nearshore young-of-the-year Pacific rockfishes Sebastes spp. in kelp forest and eelgrass meadow habitats from 2004 to 2014 on the west coast of Vancouver Island, British Columbia. Our sites varied in habitat area, wave exposure, sea surface temperature, and distance from the open coast....

Data from: Abiotic and biotic predictors of macroecological patterns in bird and butterfly coloration

Rhiannon L. Dalrymple, Habacuc Flores-Moreno, Darrell J. Kemp, Thomas E. White, Shawn W. Laffan, Frank A. Hemmings, Timothy D. Hitchcock & Angela T. Moles
Animal color phenotypes are invariably influenced by both their biotic community and the abiotic environments. A host of hypotheses have been proposed for how variables such as solar radiation, habitat shadiness, primary productivity, temperature, rainfall and community diversity might affect animal color traits. However, while individual factors have been linked to coloration in specific contexts, little is known about which factors are most important across broad taxonomic and geographic scales. Using data collected from 570...

Data from: The colour of paternity: extra-pair paternity in the wild Gouldian finch does not appear to be driven by genetic incompatibility between morphs

Peri E. Bolton, Lee Ann Rollins, James Brazill-Boast, Kang-Wook Kim, Terry Burke, Simon C. Griffith & K-W. Kim
In socially monogamous species, individuals can use extra-pair paternity and offspring sex allocation as adaptive strategies to ameliorate costs of genetic incompatibility with their partner. Previous studies on domesticated Gouldian finches (Erythrura gouldiae) demonstrated a genetic incompatibility between head colour morphs, the effects of which are more severe in female offspring. Domesticated females use differential sex allocation, and extra-pair paternity with males of compatible head colour, to reduce fitness costs associated with incompatibility in mixed-morph...

Data from: Body mass-corrected molecular rate for bird mitochondrial DNA

Benoit Nabholz, Robert Lanfear & Jérome Fuchs
Mitochondrial DNA remains one of the most widely used molecular markers to reconstruct the phylogeny and phylogeography of closely related birds. It has been proposed that bird mitochondrial genomes evolve at a constant rate of ~0.01 substitution per site per million years, that is that they evolve according to a strict molecular clock. This molecular clock is often used in studies of bird mitochondrial phylogeny and molecular dating. However, rates of mitochondrial genome evolution vary...

Data from: Unusual but consistent latitudinal patterns in macroalgal habitats and their invertebrate communities across two countries

Hannah Lloyd, Juan Cruz-Motta, Tim Glasby, Pat Hutchings & Paul Gribben
Aim: The physical characteristics of biogenic habitats and environmental conditions are important determinants of biodiversity, yet their relative importance can change across spatial scales. We aimed to understand how relationships between the physical characteristics of macroalgal habitats and their invertebrate communities varied across spatial scales and whether general ecological patterns occurred across two countries. Location: 18 sites across the temperate east coasts of Australia (over 1,300 km) and New Zealand (over 1,000 km), with the...

The apparent exponential radiation of Phanerozoic land vertebrates is an artefact of spatial sampling biases

Roger Close, Roger Benson, John Alroy, Matthew Carrano, Terri Cleary, Emma Dunne, Philip Mannion, Mark Uhen & Richard Butler
There is no consensus about how terrestrial biodiversity was assembled through deep time, and in particular whether it has risen exponentially over the Phanerozoic. Using a database of 38,711 fossil occurrences, we show that the spatial extent of the ‘global’ terrestrial tetrapod fossil record itself expands exponentially through the Phanerozoic, and that this spatial variation explains around 75% of the variation in known fossil species counts. Controlling for this bias, we find that regional-scale terrestrial...

Urbanization and translocation disrupt the relationship between host density and parasite abundance

Jayna L. DeVore, Richard Shine & Simon Ducatez
1.) The species interactions that structure natural communities are increasingly disrupted by radical habitat change resulting from the widespread processes of urbanization and species translocations. Although many species are disadvantaged by these changes, others thrive in these new environments, achieving densities exceeding those found in natural habitats. Often the same species that benefit from urbanization are successful invaders in introduced habitats, suggesting that similar processes promote these species in both environments. 2.) Both processes may...

Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems

Joseph DiBattista, James Reimer, Michael Stat, Giovanni Masucci, Piera Biondi, Maarten De Brauwer, Shaun Wilkinson, Anthony Chariton & Michael Bunce
Loss of biodiversity from lower to upper trophic levels reduces overall productivity and stability of coastal ecosystems in our oceans, but rarely are these changes documented across both time and space. The characterisation of environmental DNA (eDNA) from sediment and seawater using metabarcoding offers a powerful molecular lens to observe marine biota and provides a series of ‘snapshots’ across a broad spectrum of eukaryotic organisms. Using these next-generation tools and downstream analytical innovations including machine...

Data from: It’s not all black and white: investigating colour polymorphism in manta rays across Indo-Pacific populations

Stephanie Venables, Andrea Marshall, Elitza Germanov, Robert Perryman, Ricardo Tapilatu, I. Gede Hendrawan, Anna Flam, Mike Van Keulen, Joseph Tomkins & Jason Kennington
Intraspecific colour polymorphisms have been the focus of numerous studies, yet processes affecting melanism in the marine environment remain poorly understood. Arguably the most prominent example of melanism in marine species occurs in manta rays (Mobula birostris and M. alfredi). Here, we use photo identification catalogues to document the frequency variation of melanism across Indo-Pacific manta ray populations and test for evidence of selection by predation acting on colour morph variants. We use mark-recapture modeling...

Data from: Unscrambling variation in avian eggshell colour and patterning in a continent-wide study

Kiara L. L'Herpiniere, Louis G. O'Neill, Andrew F. Russell, Daisy E. Duursma & Simon C. Griffith
The evolutionary drivers underlying marked variation in the pigmentation of eggs within many avian species remains unclear. The leading hypotheses proposed to explain such variation advocate the roles of genetic differences, signalling and/or structural integrity. One means of testing amongst these hypotheses is to capitalise on museum collections of eggs obtained throughout a broad geographic range of a species to ensure sufficient variation in predictors pertaining to each hypothesis. Here we measured colouration and patterning...

Data from: Detection of environmental and morphological adaptation despite high landscape genetic connectivity in a pest grasshopper (Phaulacridium vittatum)

Sonu Yadav, Adam J. Stow & Rachael Y. Dudaniec
Widespread species that exhibit both high gene flow and the capacity to occupy heterogeneous environments make excellent models for examining local selection processes along environmental gradients. Here we evaluate the influence of temperature and landscape variables on genetic connectivity and signatures of local adaptation in Phaulacridium vittatum, a widespread agricultural pest grasshopper, endemic to Australia. With sampling across a 900 km latitudinal gradient, we genotyped 185 P. vittatum from 19 sites at 11,408 single nucleotide...

Genomic and transcriptomic data for the frog Platyplectrum ornatum

Scott Edwards, Sangeet Lamichhaney, Renee Catullo, Scott Keogh, Simon Clulow & Tariq Ezaz
The diversity of genome sizes across the tree of life is of key interest in evolutionary biology. Various correlates of variation in genome size, such as accumulation of transposable elements or rate of DNA gain and loss, are well known, but the underlying molecular mechanisms that drive or constrain genome size are poorly understood. Here we study one of the smallest genomes among frogs characterized thus far, that of the ornate burrowing frog (Platyplectrum ornatum)...

Morphology of parotoid glands in cane toads

Richard Shine, Gregory Brown, Ryann Blennerhassett & Cameron Hudson
If optimal investment in anti-predator defences depends on predation risk, invading new regions (and thus, encountering different predators) may favour shifts in that investment. Cane toads offer an ideal system to test this prediction: expensive anti-predator toxins are stored mainly in parotoid glands whose dimensions are easy to measure, and toad invasions have changed the suites of predators they encounter. Although plasticity may influence parotoid morphology, comparisons between parents and progeny revealed that gland dimensions...

Kin-mediated plasticity in alternative reproductive tactics

Samuel James Lymbery, Joseph Tomkins, Bruno Buzatto & David Hosken
Conditional strategies occur when the fitness payoff an individual receives from expressing a given phenotype (from a range of two or more possible phenotypes) is contingent upon that individual’s environmental circumstances. This conditional strategy model underlies many cases of alternative reproductive tactics, in which individuals of one sex employ different means to obtain reproductive opportunities. How genetic relatedness and indirect fitness effects could affect the expression of alternative reproductive tactics remains unexplored. Here, we address...

Population dynamics of the sea snake Emydocephalus annulatus

Richard Shine, Gregory Brown & Claire Goiran
For sea snakes as for many types of animals, long-term studies on population biology are rare and hence, we do not understand the degree to which annual variation in population sizes is driven by density-dependent regulation versus by stochastic abiotic factors. We monitored three populations of turtle-headed sea snakes (Emydocephalus annulatus) in New Caledonia over an 18-year period. Annual recruitment (% change in numbers) showed negative density-dependence: that is, recruitment increased when population densities were...

High fire frequency and the impact of the 2019–2020 megafires on Australian plant diversity

Rachael Gallagher, Stuart Allen, Berin MacKenzie, Colin Yates, Gosper Carl, David Keith, Cory Merow, Matthew White, Elizabeth Wenk, Brian Maitner, Kang He, Vanessa Adams, Tony Auld, Rachael V. Gallagher, Berin D. E. Mackenzie, Colin J. Yates, Carl R. Gosper, David A. Keith, Matthew D. White, Brian S. Maitner, Vanessa M. Adams & Tony D. Auld
This dataset details the proportion of the geographic range of 26,062 Australian plant species burnt in the 2019-2020 megafire; threatened listing status on state and Commonwealth threatened species legislation; species endemic status in each state/territory according to the Australian Plant Census; and risk ranking for exposure to high fire frequency (short intervals between fires) and cumulative impacts of fire (populations dominated by immature individuals). Further details are provided in the users should consult and cite...

A fossil-calibrated time-tree of all Australian freshwater fishes

Amy Tims, Simon Ho & Peter Unmack
Australian freshwater fishes are a relatively species-poor assemblage, comprising a small number of Gondwanan lineages and a number of groups derived from repeated freshwater invasions by marine ancestors. In addition to being a comparatively small assemblage, they are both highly endemic and highly threatened. However, a comprehensive phylogeny for these taxa is lacking, which has hampered efforts to study their phylogenetic diversity, distribution of extinction risk, speciation rate, and rates of trait evolution. Here, we...

Avian vampire fly (Philornis downsi) intensity and mortality

Lauren K Common, Petra Sumasgutner, Rachael Y Dudaniec, Diane Colombelli-Negrel & Sonia Kleindorfer
In invasive parasites, generalism is considered advantageous during the initial phase of introduction. Thereafter, fitness costs to parasites, such as host-specific mortality, can drive parasites towards specialism to avoid costly hosts. It is important to determine changes in host specificity of invasive populations to understand host-parasite dynamics and their effects on vulnerable host populations. We examined changes in mortality in the introduced avian vampire fly (Philornis downsi) (Diptera: Muscidae), a generalist myasis-causing ectoparasite, between 2004...

Evaluating evidence of mitonuclear incompatibilities with the sex chromosomes in an avian hybrid zone

Daniel Hooper, Kelsie A Lopez, Callum S McDiarmid, Simon Griffith & Irby Lovette
The exploration of hybrid zones and the intergenomic conflicts exposed through hybridization provide windows into the processes of divergence and speciation. Sex chromosomes and mitonuclear incompatibilities have strong associations with the genetics of hybrid dysfunction. In ZW sex-determining systems, maternal co-inheritance of the mitochondrial and W chromosomes immediately exposes incompatibilities between these maternal contributions of one species and the Z chromosome of another. We analyze mitochondrial and Z chromosome admixture in the long-tailed finch (Poephila...

Rates of attraction of cane toad tadpoles to chemicals

Richard Shine
Chemical cues produced by late-stage embryos of the cane toad (Rhinella marina) attract older conspecific larvae, which are highly cannibalistic and can consume an entire clutch. To clarify the molecular basis of this attraction response, we presented captive tadpoles with components present in toad eggs. As previously reported, attractivity arises from the distinctive toxins (bufadienolides) produced by cane toads, with some toxins (e.g., bufagenins) much stronger attractants than others (e.g., bufotoxins). Extracts of frozen toad...

Colour polymorphism in the sea snake Emydocephalus annulatus

Richard Shine, Greg Brown & Claire Goiran
Evolutionary theory suggests that polymorphic traits can be maintained within a single population only under specific conditions, such as negative frequency-dependent selection or heterozygote advantage. Non-venomous turtle-headed sea snakes (Emydocephalus annulatus) living in shallow bays near Noumea in New Caledonia exhibit three colour morphs: black, black-and-white banded, and an intermediate (grey-banded) morph that darkens with age. We recorded morph frequencies during 18 consecutive years of surveys, and found that the numbers of recruits (neonates plus...

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