Environmental and topographic drivers of amphibian phylogenetic diversity and endemism in the Iberian Peninsula.

Understanding the ecological and evolutionary processes driving biodiversity patterns and allowing their persistence is of utmost importance. Many hypotheses have been proposed to explain spatial diversity patterns, including water-energy availability, habitat heterogeneity, and historical climatic refugia. The main goal of this study is to identify if general spatial drivers of species diversity patterns of phylogenetic diversity (PD) and phylogenetic endemism (PE) at the global scale are also predictive of PD and PE at regional scales, using Iberian amphibians as a case study.

Protecting Biodiversity (in All Its Complexity): New Models and Methods.

We are facing a biodiversity crisis at the same time as we are acquiring an unprecedented view of the world's biodiversity. Vast new datasets (e.g.

Phylolink: phylogenetically-based profiling, visualisations and metrics for biodiversity.

Summary: Phylolink is a research collaboration toolkit through which biodiversity can be explored from a phylogenetic perspective. It is an update of PhyloJiVE that has been integrated into the framework of the Atlas of Living Australia, including its spatial portal. Phylolink connects phylogenetic tree nodes with species occurrence records, environmental data, and species trait information.

Pleistocene climatic changes drive diversification across a tropical savanna.

Spatial responses of species to past climate change depend on both intrinsic traits (climatic niche breadth, dispersal rates) and the scale of climatic fluctuations across the landscape. New capabilities in generating and analysing population genomic data, along with spatial modelling, have unleashed our capacity to infer how past climate changes have shaped populations, and by extension, complex communities. Combining these approaches, we uncover lineage diversity across four codistributed lizards from the Australian Monsoonal Tropics and explore how varying climatic tolerances interact with regional climate history to generate common vs.

Phylogenetically informed spatial planning is required to conserve the mammalian tree of life.

In the face of the current extinction crisis and severely limited conservation resources, safeguarding the tree of life is increasingly recognized as a high priority. We conducted a first systematic global assessment of the conservation of phylogenetic diversity (PD) that uses realistic area targets and highlights the key areas for conservation of the mammalian tree of life. Our approach offers a substantially more effective conservation solution than one focused on species.

Trans-biome diversity in Australian grass-specialist lizards (Diplodactylidae: Strophurus).

Comparisons of biodiversity patterns within lineages that occur across major climate gradients and biomes, can provide insights into the relative roles that lineage history, landscape and climatic variation, and environmental change have played in shaping regional biotas. In Australia, while there has been extensive research into the origins and patterns of diversity in the Australian Arid Zone (AAZ), how diversity is distributed across this biome and the Australian Monsoonal Tropics (AMT) to the north, has been less studied. We compared the timing and patterns of diversification across this broad aridity gradient in a clade of lizards (Strophurus: phasmid geckos) that only occur in association with a unique Australian radiation of sclerophyllous grasses (Triodia: spinifex).

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.

Basking behavior predicts the evolution of heat tolerance in Australian rainforest lizards.

There is pressing urgency to understand how tropical ectotherms can behaviorally and physiologically respond to climate warming. We examine how basking behavior and thermal environment interact to influence evolutionary variation in thermal physiology of multiple species of lygosomine rainforest skinks from the Wet Tropics of northeastern Queensland, Australia (AWT). These tropical lizards are behaviorally specialized to exploit canopy or sun, and are distributed across marked thermal clines in the AWT.

A guide to phylogenetic metrics for conservation, community ecology and macroecology.

The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub-disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub-disciplines hampers potential meta-analyses, syntheses, and generalizations of existing results.

Multilocus phylogeography reveals nested endemism in a gecko across the monsoonal tropics of Australia.

Multilocus phylogeography can uncover taxonomically unrecognized lineage diversity across complex biomes. The Australian monsoonal tropics include vast, ecologically intact savanna-woodland plains interspersed with ancient sandstone uplands. Although recognized in general for its high species richness and endemism, the biodiversity of the region remains underexplored due to its remoteness.

Assessing biodiversity and endemism using phylogenetic methods across multiple taxonomic groups.

Identifying geographical areas with the greatest representation of the tree of life is an important goal for the management and conservation of biodiversity. While there are methods available for using a single phylogenetic tree to assess spatial patterns of biodiversity, there has been limited exploration of how separate phylogenies from multiple taxonomic groups can be used jointly to map diversity and endemism. Here, we demonstrate how to apply different phylogenetic approaches to assess biodiversity across multiple taxonomic groups.

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.

Phylodiversity to inform conservation policy: An Australian example.

Phylodiversity measures summarise the phylogenetic diversity patterns of groups of organisms. By using branches of the tree of life, rather than its tips (e.g.

Phylogenetic diversity meets conservation policy: small areas are key to preserving eucalypt lineages.

Evolutionary and genetic knowledge is increasingly being valued in conservation theory, but is rarely considered in conservation planning and policy. Here, we integrate phylogenetic diversity (PD) with spatial reserve prioritization to evaluate how well the existing reserve system in Victoria, Australia captures the evolutionary lineages of eucalypts, which dominate forest canopies across the state. Forty-three per cent of remaining native woody vegetation in Victoria is located in protected areas (mostly national parks) representing 48% of the extant PD found in the state.

Mistaking geography for biology: inferring processes from species distributions.

Over the past few decades, there has been a rapid proliferation of statistical methods that infer evolutionary and ecological processes from data on species distributions. These methods have led to considerable new insights, but they often fail to account for the effects of historical biogeography on present-day species distributions. Because the geography of speciation can lead to patterns of spatial and temporal autocorrelation in the distributions of species within a clade, this can result in misleading inferences about the importance of deterministic processes in generating spatial patterns of biodiversity.

Prediction of phylogeographic endemism in an environmentally complex biome.

Phylogeographic endemism, the degree to which the history of recently evolved lineages is spatially restricted, reflects fundamental evolutionary processes such as cryptic divergence, adaptation and biological responses to environmental heterogeneity. Attempts to explain the extraordinary diversity of the tropics, which often includes deep phylogeographic structure, frequently invoke interactions of climate variability across space, time and topography. To evaluate historical versus contemporary drivers of phylogeographic endemism in a tropical system, we analyse the effects of current and past climatic variation on the genetic diversity of 25 vertebrates in the Brazilian Atlantic rainforest.

Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis.

Background: Recently, various evolution-related journals adopted policies to encourage or require archiving of phylogenetic trees and associated data. Such attention to practices that promote sharing of data reflects rapidly improving information technology, and rapidly expanding potential to use this technology to aggregate and link data from previously published research. Nevertheless, little is known about current practices, or best practices, for publishing trees and associated data so as to promote re-use.

Integrating species traits with extrinsic threats: closing the gap between predicting and preventing species declines.

In studies of extinction risk, it is often insufficient to conclude that species with narrow ranges or small clutch sizes require prioritized protection. To improve conservation outcomes, we also need to know which threats interact with these traits to endanger some species but not others. In this study, we integrated the spatial patterns of key threats to Australian amphibians with species' ecological/life-history traits to both predict declining species and identify their likely threats.

A genetic basis for the phenotypic differentiation between siscowet and lean lake trout (Salvelinus namaycush).

In Lake Superior there are three principal forms of lake trout (Salvelinus namaycush): lean, siscowet and humper. Wild lean and siscowet differ in the shape and relative size of the head, size of the fins, location and size of the eyes, caudal peduncle shape and lipid content of the musculature. To investigate the basis for these phenotypic differences, lean and siscowet lake trout, derived from gametes of wild populations in Lake Superior, were reared communally under identical environmental conditions for 2.

Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history.

We present a new, broadly applicable measure of the spatial restriction of phylogenetic diversity, termed phylogenetic endemism (PE). PE combines the widely used phylogenetic diversity and weighted endemism measures to identify areas where substantial components of phylogenetic diversity are restricted. Such areas are likely to be of considerable importance for conservation.