Niche-based approach to explore the impacts of environmental disturbances on biodiversity.

Globally, species are increasingly at risk from compounding threatening processes, an increasingly prominent driver of which is environmental disturbances. To facilitate effective conservation efforts following such events, methods that evaluate potential impacts across multiple species and provide landscape-scale information are needed to guide targeted responses. Often, the geographic overlap between a disturbance and species' distribution is calculated and then used as a proxy for potential impact.

Estimates of heterozygosity from single nucleotide polymorphism markers are context-dependent and often wrong.

Genetic diversity is frequently described using heterozygosity, particularly in a conservation context. Often, it is estimated using single nucleotide polymorphisms (SNPs); however, it has been shown that heterozygosity values calculated from SNPs can be biased by both study design and filtering parameters. Though solutions have been proposed to address these issues, our own work has found them to be inadequate in some circumstances.

Population genomics and sexual signals support reproductive character displacement in Uperoleia (Anura: Myobatrachidae) in a contact zone.

When closely related species come into contact via range expansion, both may experience reduced fitness as a result of the interaction. Selection is expected to favour traits that minimize costly interspecies reproductive interactions (such as mismating) via a phenomenon called reproductive character displacement (RCD). Research on RCD frequently assumes secondary contact between species, but the geographical history of species interactions is often unknown.

Phylogenomic analyses of the genus Drosophila reveals genomic signals of climate adaptation.

Many Drosophila species differ widely in their distributions and climate niches, making them excellent subjects for evolutionary genomic studies. Here, we have developed a database of high-quality assemblies for 46 Drosophila species and one closely related Zaprionus. Fifteen of the genomes were newly sequenced, and 20 were improved with additional sequencing.

Seen only once: an evolutionarily distinct species of Toadlet (Uperoleia: Myobatrachidae) from the Wessel Islands of northern Australia.

There is a high rate of recent species discovery in remote regions of northern Australia, especially for amphibians and reptiles. The Wessel Islands, located in the northeastern corner of the Northern Territory, has recently been identified as a region of high species and phylogenetic endemism based on samples collected during the sole reptile and amphibian survey there in 1993. Using a phylogenetic approach, we describe a new, evolutionarily distinct species of Uperoleia endemic to the Wessel Islands.

A bird-like genome from a frog: Mechanisms of genome size reduction in the ornate burrowing frog, .

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 (TEs) or rate of DNA gain and loss, are well known, but the underlying molecular mechanisms driving or constraining genome size are poorly understood. Here, we study one of the smallest genomes among frogs characterized thus far, that of the ornate burrowing frog () from Australia, and compare it to other published frog and vertebrate genomes to examine the forces driving reduction in genome size.

A new phylogenetic protocol: dealing with model misspecification and confirmation bias in molecular phylogenetics.

Molecular phylogenetics plays a key role in comparative genomics and has increasingly significant impacts on science, industry, government, public health and society. In this paper, we posit that the current phylogenetic protocol is missing two critical steps, and that their absence allows model misspecification and confirmation bias to unduly influence phylogenetic estimates. Based on the potential offered by well-established but under-used procedures, such as assessment of phylogenetic assumptions and tests of goodness of fit, we introduce a new phylogenetic protocol that will reduce confirmation bias and increase the accuracy of phylogenetic estimates.

Genome-wide patterns of differentiation over space and time in the Queensland fruit fly.

The Queensland fruit fly, Bactrocera tryoni, is a major pest of Australian horticulture which has expanded its range in association with the spread of horticulture over the last ~ 150 years. Its distribution in northern Australia overlaps that of another fruit fly pest to which some authors accord full species status, Bactrocera aquilonis. We have used reduced representation genome-wide sequencing to genotype 359 individuals taken from 35 populations from across the current range of the two taxa, plus a further 73 individuals from six of those populations collected 15-22 years earlier.

Ecological Drivers and Sex-Based Variation in Body Size and Shape in the Queensland Fruit Fly, (Diptera: Tephritidae).

The Queensland fruit fly (; Q-fly) is an Australian endemic horticultural pest species, which has caused enormous economic losses. It has the potential to expand its range to currently Q-fly-free areas and poses a serious threat to the Australian horticultural industry. A large number of studies have investigated the correlation between environmental factors and Q-fly development, reproduction, and expansion.

Publisher Correction: Open Science principles for accelerating trait-based science across the Tree of Life.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Open Science principles for accelerating trait-based science across the Tree of Life.

Synthesizing trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Species traits are widely used in ecological and evolutionary science, and new data and methods have proliferated rapidly. Yet accessing and integrating disparate data sources remains a considerable challenge, slowing progress toward a global synthesis to integrate trait data across organisms.

The Potential for Rapid Evolution under Anthropogenic Climate Change.

Understanding how natural populations will respond to rapid anthropogenic climate change is one of the greatest challenges for ecologists and evolutionary biologists. Much research has focussed on whether physiological traits can evolve quickly enough under rapidly increasing temperatures. While the simple Breeder's equation helps to understand how extreme temperatures and genetic variation might drive within-population evolution under climate change, it does not consider two key areas: how different forms of phenotypic plasticity interact and variation among populations.

Correction: Lineage Range Estimation Method Reveals Fine-Scale Endemism Linked to Pleistocene Stability in Australian Rainforest Herpetofauna.

[This corrects the article DOI: 10.1371/journal.pone.

Incorporating evolutionary adaptation in species distribution modelling reduces projected vulnerability to climate change.

Based on the sensitivity of species to ongoing climate change, and numerous challenges they face tracking suitable conditions, there is growing interest in species' capacity to adapt to climatic stress. Here, we develop and apply a new generic modelling approach (AdaptR) that incorporates adaptive capacity through physiological limits, phenotypic plasticity, evolutionary adaptation and dispersal into a species distribution modelling framework. Using AdaptR to predict change in the distribution of 17 species of Australian fruit flies (Drosophilidae), we show that accounting for adaptive capacity reduces projected range losses by up to 33% by 2105.

Resources for phylogenomic analyses of Australian terrestrial vertebrates.

High-throughput sequencing methods promise to improve our ability to infer the evolutionary histories of lineages and to delimit species. These are exciting prospects for the study of Australian vertebrates, a group comprised of many globally unique lineages with a long history of isolation. The evolutionary relationships within many of these lineages have been difficult to resolve with small numbers of loci, and we now know that many lineages also exhibit substantial cryptic diversity.

A new species of Australian frog (Myobatrachidae: Uperoleia) from the New South Wales mid-north coast sandplains.

The discovery of new vertebrate species in developed countries is still occurring at surprising rates for some taxonomic groups, especially the amphibians and reptiles. While this most often occurs in under-explored areas, it occasionally still happens in well-inhabited regions. We report such a case with the discovery and description of U.

Phylogeographic structure across one of the largest intact tropical savannahs: Molecular and morphological analysis of Australia's iconic frilled lizard Chlamydosaurus kingii.

The spectacular threat display of the savannah specialist Australo-Papuan frilled lizards has made them one of the world's most iconic reptiles. They are increasingly used as a model system for research in evolutionary biology and ecology but little is known of their population structure. Their distribution across northern Australia and southern New Guinea also provides an opportunity to examine biogeographic patterns as they relate to the large-scale movement of savannah habitat during the Plio/Pleistocene and the associated increase in aridity.

Lineage range estimation method reveals fine-scale endemism linked to Pleistocene stability in Australian rainforest herpetofauna.

Areas of suitable habitat for species and communities have arisen, shifted, and disappeared with Pleistocene climate cycles, and through this shifting landscape, current biodiversity has found paths to the present. Evolutionary refugia, areas of relative habitat stability in this shifting landscape, support persistence of lineages through time, and are thus crucial to the accumulation and maintenance of biodiversity. Areas of endemism are indicative of refugial areas where diversity has persisted, and endemism of intraspecific lineages in particular is strongly associated with late-Pleistocene habitat stability.

Aridification drove repeated episodes of diversification between Australian biomes: evidence from a multi-locus phylogeny of Australian toadlets (Uperoleia: Myobatrachidae).

Australia is a large and complex landmass that comprises diverse biomes ranging from tropical rainforests to harsh deserts. While Australian biotic diversity has evolved in response to landscape and climate changes, evidence of Miocene or later biome shifts are few. The Australo-Papuan endemic frog genus Uperoleia is widely distributed across mesic, monsoonal tropic and arid regions of Australia.

A new frog species (Myobatrachidae: Uperoleia) from the Northern Deserts region of Australia, with a redescription of U. trachyderma.

The frog genus Uperoleia (Myobatrachidae) is species rich, with the greatest diversity in the northern monsoonal region of Australia. Due in part to their small body size, conservative morphology and distribution in diverse habitats, the genus is likely to harbor cryptic species. A recent study (Catullo et al.