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A new species of Philoria (Anura: Limnodynastidae) from the uplands of the Gondwana Rainforests World Heritage Area of eastern Australia
Abstract
The six species of mountain frogs (Philoria: Limnodynastidae: Anura) are endemic to south-eastern Australia. Five species occur in headwater systems in mountainous north-eastern New South Wales (NSW) and south-eastern Queensland (Qld), centred on the Gondwana Rainforests of Australia World Heritage Area. A previous molecular genetic analysis identified divergent genetic lineages in the central and western McPherson Ranges region of Qld and NSW, but sampling was inadequate to test the species status of these lineages. With more comprehensive geographic sampling and examination of the nuclear genome using SNP analysis, we show that an undescribed species, P. knowlesi sp. nov., occurs in the central and western McPherson Ranges (Levers Plateau and Mount Barney complex). The new species is not phylogenetically closely related to P. loveridgei in the nuclear data but is related to one of two divergent lineages within P. loveridgei in the mtDNA data. We postulate that the discordance between the nuclear and mtDNA outcomes is due to ancient introgression of the mtDNA genome from P. loveridgei into the new species. Male advertisement calls and multivariate morphological analyses do not reliably distinguish P. knowlesi sp. nov. from any of the Philoria species in northeast NSW and southeast Qld. The genetic comparisons also enable us to define further the distributions of P. loveridgei and P. kundagungan. Samples from the Lamington Plateau, Springbrook Plateau, Wollumbin (Mt Warning National Park), and the Nightcap Range, are all P. loveridgei, and its distribution is now defined as the eastern McPherson Ranges and Tweed caldera. Philoria kundagungan is distributed from the Mistake Mountains in south-eastern Qld to the Tooloom Scrub on the Koreelah Range, southwest of Woodenbong, in NSW, with two subpopulations identified by SNP analysis. We therefore assessed the IUCN threat category of P. loveridgei and P. kundagungan and undertook new assessments for each of its two subpopulations and for the new taxon P. knowlesi sp. nov., using IUCN Red List criteria. Philoria loveridgei, P. kundagungan (entire range and northern subpopulation separately) and P. knowlesi sp. nov. each meet criteria for “Endangered” (EN B2(a)(b)[i, iii]). The southern subpopulation of P. kundagungan, in the Koreelah Range, meets criteria for “Critically Endangered” (CE B2(a)(b)[i, iii]). These taxa are all highly threatened due to the small number of known locations, the restricted nature of their breeding habitat, and direct and indirect threats from climate change, and the potential impact of the amphibian disease chytridiomycosis. Feral pigs are an emerging threat, with significant impacts now observed in Philoria breeding habitat in the Mistake Mountains.
... All are range-restricted species, have montane distributions, are listed as endangered by the International Union for Conservation of Nature and are considered at risk from climate change [1]. All six species occur on mountaintops in northern New South Wales and southeastern Queensland and occupy seepages or the boggy margins of headwater streams or drainage lines, mostly in upland rainforest [18][19][20]. They lay their eggs in small chambers excavated in mud, leaf litter or under rocks, and metamorphosis requires the constant moisture these microhabitats provide [18,21]. ...
... Adults are rarely encountered outside of their underground breeding chambers, and detection relies upon the advertisement call of males (from within burrows). Due to these traits and the remoteness of their habitats, all species are poorly studied [18,19,21]. Knowledge of their ecology is urgently required to develop effective conservation strategies to mitigate the effects of climate change. ...
... Further, we demonstrate that using bioacoustics is a reliable method for examining the vocal behaviour in amphibians. Given that the vocalisations of P. kundagungan are indistinguishable from those of P. loveridgei, P. pughi, P. richmondensis and P. knowlesi [18,19], our algorithm and method could be utilised in multispecies calling ...
Amphibians are the most endangered class of vertebrate on Earth. Knowledge of their ecology is crucial to their conservation; however, many species have received scant attention from researchers, particularly in regions that are difficult to access or when traditional monitoring methods are impractical. In recent years, technological advancements in environmental audio collection techniques and signal detection algorithms (i.e., call recognition) have created a new set of tools for examining the ecology of amphibians. This study utilises these recent technological advancements to examine the calling phenology of a poorly known Australian mountain frog (Philoria kundagungan). Audio recordings and meteorological data were collected from six localities across the species range, with recordings made every hour for ten minutes between July 2016 and March 2018. We developed an audio recognition algorithm that detected over 1.8 million P. kundagungan calls in 8760 h of audio recordings with a true positive rate of 95%. Our results suggest that calling activity was driven by substrate temperature and precipitation, which has potential consequences for the species as the climate warms and seasonal precipitation patterns shift under climate change. With this detailed knowledge of P. kundagungan calling phenology, this difficult-to-find species will now be more reliably detected, removing a barrier that has hindered efforts to study and conserve this species.
... Indirect or 'second order' effects include starvation, increased predation and habitat modifications that may affect breeding, movement and population viability (Davis et al., 2019;Hradsky et al., 2017). Exposure to periodic, low-severity fires over long evolutionary periods allows organisms to develop adaptations to fire that are behavioural (Pausas & Parr, 2018), biological and morphological (Keeley et al., 2011;Mahony, Gould, et al., 2022;Mahony, Hines, et al., 2022). Yet, even fire-tolerant species may be overwhelmed by fires that have undergone rapid shifts in schedules, intensity and extent because of climate change. ...
... The impact of fire varies between amphibian species and is dependent on habitat associations and the presence/absence of specific traits. Rain forest obligates are less adapted to fire compared with species occupying dry forest, as fire is not a common feature of rain forests and thus unlikely to have been a driving factor in their evolutionary histories (Mahony, Hines, et al., 2022). This is apparent by the lower upper thermal limits of Australian frogs from cool temperate rain forests (between 28 and 29°C) compared with those from dry forests (up to 36°C;Brattstrom, 1970). ...
... darlingtoni, M. iteratus and P. pughi). Negative fire-related impacts were not just limited to rain forest-dwelling amphibians but also to species that have evolved and adapted to fire-prone vegetation communities Mahony, Hines, et al., 2022), highlighting the scale and severity of the fires. We discuss the impacts of wildfires on two ecological scales: the metacommunity scale and the species scale. ...
Aim
Changes to the extent and severity of wildfires driven by anthropogenic climate change are predicted to have compounding negative consequences for ecological communities. While there is evidence that severe weather events like drought impact amphibian communities, the effects of wildfire on such communities are not well understood. The impact of wildfire on amphibian communities and species is likely to vary, owing to the diversity of their life‐history traits. However, no previous research has identified commonalities among the amphibians at most risk from wildfire, limiting conservation initiatives in the aftermath of severe wildfire. We aimed to investigate the impacts of the unprecedented 2019–2020 black summer bushfires on Australian forest amphibian communities.
Location
Eastern coast of New South Wales, Australia.
Methods
We conducted visual encounter surveys and passive acoustic monitoring across 411 sites within two regions, one in northeast and one in southeast New South Wales. We used fire severity and extent mapping in two multispecies occupancy models to assess the impacts of fire on 35 forest amphibian species.
Results
We demonstrate a negative influence of severe fire extent on metacommunity occupancy and species richness in the south with weaker effects in the north—reflective of the less severe fires that occurred in this region. Both threatened and common species were impacted by severe wildfire extent. Occupancy of burrowing species and rain forest specialists had mostly negative relationships with severe wildfire extent, while arboreal amphibians had neutral relationships.
Main Conclusion
Metacommunity monitoring and adaptive conservation strategies are needed to account for common species after severe climatic events. Ecological, morphological and life‐history variation drives the susceptibility of amphibians to wildfires. We document the first evidence of climate change‐driven wildfires impacting temperate forest amphibian communities across a broad geographic area, which raises serious concern for the persistence of amphibians under an increasingly fire‐prone climate.
... The Gondwanan rainforests of northern New South Wales and southern Queensland support several species of endemic, rangerestricted amphibians that contribute to the outstanding universal values of the World Heritage area. Notable among these are six of seven species in the genus Philoria (Limnodynastidae), being P. knowlesi, P. kundagungan, P. loveridgei, P. pughi, P. richmondensis, and P. sphagnicolus (Knowles et al., 2004;Mahony et al., 2022). ...
... These species are all allopatric, occurring as scattered mountaintop endemics restricted to headwater drainage lines, seepages, and small bogs in rainforest and adjoining mesic vegetation (Knowles et al., 2004, Mahony et al., 2022. Males construct and call from nests in saturated soil. ...
Deepening droughts and unprecedented wildfires are at the leading edge of climate change. Such events pose an emerging threat to species maladapted to these perturbations, with the potential for steeper declines than may be inferred from the gradual erosion of their climatic niche. This study focused on two species of amphibians-Philoria kundagungan and Philoria richmondensis (Limnodynastidae)-from the Gondwanan rainforests of eastern Australia that were extensively affected by the "Black Summer" megafires of 2019/2020 and the severe drought associated with them. We sought to assess the impact of these perturbations by quantifying the extent of habitat affected by fire, assessing patterns of occurrence and abundance of calling males post-fire, and comparing post-fire occurrence and abundance with that observed pre-fire. Some 30% of potentially suitable habitat for P. kundagungan was fire affected, and 12% for P. richmondensis. Field surveys revealed persistence in some burnt rainforest; however, both species were detected at a higher proportion of unburnt sites. There was a clear negative effect of fire on the probability of site occupancy, abundance and the probability of persistence for P. kundagungan. For P. richmondensis, effects of fire were less evident due to the limited penetration of fire into core habitat; however, occupancy rates and abundance of calling males were depressed during the severe drought that prevailed just prior to the fires, with the reappearance of calling males linked to the degree of rehydration of breeding habitat post-fire. Our results highlight the possibility that severe negative impacts of climate change for montane rainforest endemics may be felt much sooner than commonly anticipated under a scenario of gradual (decadal-scale) changes in mean climatic conditions. Instead, the increased rate of severe stochastic events places these narrow range species at a heightened risk of extinction in the near-term.
... Among the amphibian species found within the GRAWHA are six of the seven described species of Mountain frog (Philoria). These allopatric species occur as scattered mountaintop endemics 42 and primarily occupy headwater streams and seepages within rainforest or adjoining wet sclerophyll vegetation communities 43,44 . Males call from nest burrows constructed in saturated soil, often associated with boggy stream margins. ...
... All species distribution models were performed in RStudio (version 1.4; Rstudio Team 2020) using the Biomod2 package 51 . All Philoria species are allopatric and genetic data shows they have speciated based on millions of years of isolation 43,44 , as such 43 , climatically suitable areas for P. kundagungan and P. richmondensis predicted within the known range of a neighbouring Philoria species were removed. Changes in the area of climatically suitable habitat between current and future climates were analysed in ArcMap 10.4.1 using the calculate geometry tool. ...
Montane ecosystems cover approximately 20% of the Earth's terrestrial surface and are centres of endemism. Globally, anthropogenic climate change is driving population declines and local extinctions across multiple montane taxa, including amphibians. We applied the maximum entropy approach to predict the impacts of climate change on the distribution of two poorly known amphibian species (Philoria kundagungan and Philoria richmondensis) endemic to the subtropical uplands of the Gondwana Rainforests of Australia, World Heritage Area (GRAWHA). Firstly, under current climate conditions and also future (2055) low and high warming scenarios. We validated current distribution models against models developed using presence-absence field data. Our models were highly concordant with known distributions and predicted the current distribution of P. kundagungan to contract by 64% under the low warming scenario and by 91% under the high warming scenario and that P. richmondensis would contract by 50% and 85%, respectively. With large areas of habitat already impacted by wildfires, conservation efforts for both these species need to be initiated urgently. We propose several options, including establishing ex-situ insurance populations increasing the long-term viability of both species in the wild through conservation translocations.
We present the latest version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which contains many sophisticated
methods and tools for phylogenomics and phylomedicine. In this major upgrade, MEGA has been optimized for use on 64-bit computing
systems for analyzing bigger datasets. Researchers can now explore and analyze tens of thousands of sequences in MEGA. The
new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict
gene duplication events in gene family trees. The 64-bit MEGA is made available in two interfaces: graphical and command line.
The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OSX. The command
line MEGA is available as native applications for Windows, Linux, and Mac OSX. They are intended for use in high-throughput
and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
Extreme wildfires have recently caused disastrous impacts in Australia and other regions of the world, including events with strong convective processes in their plumes (i.e., strong pyroconvection). Dangerous wildfire events such as these could potentially be influenced by anthropogenic climate change, however, there are large knowledge gaps on how these events might change in the future. The McArthur Forest Fire Danger Index (FFDI) is used to represent near-surface weather conditions and the Continuous Haines index (CH) is used here to represent lower to mid-tropospheric vertical atmospheric stability and humidity measures relevant to dangerous wildfires and pyroconvective processes. Projected changes in extreme measures of CH and FFDI are examined using a multi-method approach, including an ensemble of global climate models together with two ensembles of regional climate models. The projections show a clear trend towards more dangerous near-surface fire weather conditions for Australia based on the FFDI, as well as increased pyroconvection risk factors for some regions of southern Australia based on the CH. These results have implications for fields such as disaster risk reduction, climate adaptation, ecology, policy and planning, noting that improved knowledge on how climate change can influence extreme wildfires can help reduce future impacts of these events.
Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) (Drummond et al., 2002; Mau et al., 1999; Rannala and Yang, 1996) flourishes as a popular approach to uncover the evolutionary relationships among taxa, such as genes, genomes, individuals or species. MCMC approaches generate samples of model parameter values - including the phylogenetic tree -drawn from their posterior distribution given molecular sequence data and a selection of evolutionary models. Visualising, tabulating and marginalising these samples is critical for approximating the posterior quantities of interest that one reports as the outcome of a Bayesian phylogenetic analysis. To facilitate this task, we have developed the Tracer (version 1.7) software package to process MCMC trace files containing parameter samples and to interactively explore the high-dimensional posterior distribution. Tracer works automatically with sample output from BEAST (Drummond et al., 2012), BEAST2 (Bouckaert et al., 2014), LAMARC (Kuhner, 2006), Migrate (Beerli, 2006), MrBayes (Ronquist et al., 2012), RevBayes (Höhna et al., 2016) and possibly other MCMC programs from other domains.
In animals and plants, symbiotic bacteria can play an important role in disease resistance of host and are the focus of much current research. Globally, amphibian population declines and extinctions have occurred due to chytridiomycosis, a skin disease caused by the pathogen Batrachochytrium dendrobatidis (Bd). Currently amphibian skin bacteria are increasingly recognized as important symbiont communities with a relevant role in the defense against pathogens, as some bacteria can inhibit the growth of B. dendrobatidis. This study aims to document the B. dendrobatidis infection status of wild populations of a terrestrial cryptic frog (Philoria loveridgei), and to determine whether infection status is correlated with changes in the skin microbial communities. Skin samples of P. loveridgei were collected along an altitudinal range within the species distribution in subtropical rainforests in southeast Australia. Sampling was conducted in two years during two breeding seasons with the first classified as a "La Niña" year. We used Taqman real-time PCR to determine B. dendrobatidis infection status and 16S amplicon sequencing techniques to describe the skin community structure. We found B. dendrobatidis-positive frogs only in the second sampling year with low infection intensities, and no correlation between B. dendrobatidis infection status and altitude, frog sex or size. Skin bacterial diversity was significantly higher in P. loveridgei frogs sampled in the 1st year than in the 2nd year. In addition, 7.4% of the total OTUs were significantly more abundant in the 1st year compared to the 2nd year. We identified 67 bacterial OTUs with a significant positive correlation between infection intensity and an OTU's relative abundance. Forty-five percent of these OTUs belonged to the family Enterobacteriaceae. Overall, temporal variation was strongly associated with changes in B. dendrobatidis infection status and bacterial community structure of wild populations of P. loveridgei.
Though vast technological advances have been made and genetic software packages are growing in number, it is not a trivial task to analyse SNP data. We announce a new R package, dartR, enabling the analysis of single nucleotide polymorphism data for population genomic and phylogenomic applications. DartR provides user-friendly functions for data quality control and marker selection, and permits rigorous evaluations of conformation to Hardy-Weinberg equilibrium, gametic-phase disequilibrium, and neutrality. The package reports standard descriptive statistics, permits exploration of patterns in the data through principal components analysis, and conducts standard F-statistics, as well as basic phylogenetic analyses, population assignment, isolation by distance and exports data to a variety of commonly used downstream applications (e.g. newHybrids, fastSTRUCTURE, phylogeny applications) outside of the R environment.
The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches.
Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested datasets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.
Vocalizations of anuran amphibians have received much attention in studies of behavioral ecology and physiology, but also provide informative characters for identifying and delimiting species. We here review the terminology and variation of frog calls from a perspective of integrative taxonomy, and provide hands-on protocols for recording, analyzing, comparing, interpreting and describing these sounds. Our focus is on advertisement calls, which serve as premating isolation mechanisms and, therefore, convey important taxonomic information. We provide recommendations for terminology of frog vocalizations, with call, note and pulse being the fundamental subunits to be used in descriptions and comparisons. However, due to the complexity and diversity of these signals, an unequivocal application of the terms call and note can be challenging. We therefore provide two coherent concepts that either follow a note-centered approach (defining uninterrupted units of sound as notes, and their entirety as call) or a call-centered approach (defining uninterrupted units as call whenever they are separated by long silent intervals) in terminology. Based on surveys of literature, we show that numerous call traits can be highly variable within and between individuals of one species. Despite idiosyncrasies of species and higher taxa, the duration of calls or notes, pulse rate within notes, and number of pulses per note appear to be more static within individuals and somewhat less affected by temperature. Therefore, these variables might often be preferable as taxonomic characters over call rate or note rate, which are heavily influenced by various factors. Dominant frequency is also comparatively static and only weakly affected by temperature, but depends strongly on body size. As with other taxonomic characters, strong call divergence is typically indicative of species-level differences, whereas call similarities of two populations are no evidence for them being conspecific. Taxonomic conclusions can especially be drawn when the general advertisement call structure of two candidate species is radically different and qualitative call differences are thus observed. On the other hand, quantitative differences in call traits might substantially vary within and among conspecific populations, and require careful evaluation and analysis. We provide guidelines for the taxonomic interpretation of advertisement call differences in sympatric and allopatric situations, and emphasize the need for an integrative use of multiple datasets (bioacoustics, morphology, genetics), particularly for allopatric scenarios. We show that small-sized frogs often emit calls with frequency components in the ultrasound spectrum, although it is unlikely that these high frequencies are of biological relevance for the majority of them, and we illustrate that detection of upper harmonics depends also on recording distance because higher frequencies are attenuated more strongly. Bioacoustics remains a prime approach in integrative taxonomy of anurans if uncertainty due to possible intraspecific variation and technical artifacts is adequately considered and acknowledged.
The water-holding frog, Cyclorana platycephala, occurs in the Australian arid and semi-arid zones but not in the central Australian deserts. Recent inspection of morphological variation in adults and larvae suggests that the taxon comprises three regional populations: eastern, northern and western that may each represent separate species. To assess the systematic status of these populations, we documented phylogenetic relationships using mitochondrial and nuclear DNA markers, divergence in adult and larval morphology and male advertisement call. Our molecular genetic data demonstrates that the western population of C. platycephala is not the sister taxon of eastern and northern representatives of this nominate species, as the latter two are more closely related to another morphologically distinct species, C. verrucosa. Discriminant Function Analysis of 14 morphological traits in adults and 15 in larvae showed a high degree of morphological differentiation of western versus eastern/northern C. platycephala. Calls of eastern and western populations differed in duration, pulse rate, frequency and especially in amplitude modulation pattern across the call duration. We describe the western population as a new species, whose range is contained entirely within Western Australia. In addition, we redescribe Cyclorana platycephala, quantify morphological and genetic differences between the eastern and northern populations, and conclude that these data support recognition of a single species, Cyclorana platycephala, for populations found in New South Wales, the Barkly Tablelands and south-eastern Northern Territory, Queensland and South Australia.
The influence of climatic changes occurring since the late Miocene on Australia’s eastern mesic ecosystems has received significant attention over the past 20 years. In particular, the impact of the dramatic shift from
widespread rainforest habitat to a much drier landscape in which closed forest refugia were dissected by open
woodland/savannah ecosystems has long been a focal point in Australian ecology and biogeography. Several
specific regions along the eastern coast have been identified previously as potentially representing major
biogeographical disjunctions for closed forest taxa. Initially, evidence stemmed from recognition of common zones where avian species/subspecies distributions and/or floral communities were consistently separated, but the body of work has since grown significantly with the rise of molecular phylogeographic tools and there is now a significant literature base that discusses the drivers, processes and effects of these hypothesised major biogeographical junctions (termed barriers). Here, we review the literature concerning eight major barriers argued to have influenced closed forest taxa; namely, the Laura Basin, Black Mountain Corridor, Burdekin Gap, Saint Lawrence Gap, Brisbane Valley Barrier, Hunter Valley Barrier, Southern Transition Zone and East Gippsland Barrier. We synthesise reported phylogeographical patterns and the inferred timing of influence with current climatic, vegetation and geological characteristics for each barrier to provide insights into regional evolution and seek to elicit common trends. All eight putative biogeographical barriers are characterised currently by lowland zones of drier, warmer, more open woodland and savannah habitat, with adjacent closed forest habitats isolated to upland cool, wet refugia. Molecular divergence estimates suggest two pulses of divergence, one in the early Miocene (~20–15 Mya) and a later one from the Pliocene–Pleistocene (~6–0.04 Mya). We conclude with a prospectus for future research on the eastern Australian closed forests and highlight critical issues for ongoing studies of biogeographical barriers worldwide.
This article presents W-IQ-TREE, an intuitive and user-friendly web interface and server for IQ-TREE, an efficient phylogenetic
software for maximum likelihood analysis. W-IQ-TREE supports multiple sequence types (DNA, protein, codon, binary and morphology)
in common alignment formats and a wide range of evolutionary models including mixture and partition models. W-IQ-TREE performs
fast model selection, partition scheme finding, efficient tree reconstruction, ultrafast bootstrapping, branch tests, and
tree topology tests. All computations are conducted on a dedicated computer cluster and the users receive the results via
URL or email. W-IQ-TREE is available at http://iqtree.cibiv.univie.ac.at. It is free and open to all users and there is no login requirement.
Single nucleotide polymorphisms (SNPs) are useful markers for phylogenetic studies owing in part to their ubiquity throughout the genome and ease of collection. Restriction site associated DNA sequencing (RADseq) methods are becoming increasingly popular for SNP data collection, but an assessment of the best practices for using these data in phylogenetics is lacking. We use computer simulations, and new double digest RADseq (ddRADseq) data for the lizard family Phrynosomatidae, to investigate the accuracy of RAD loci for phylogenetic inference. We compare the two primary ways RAD loci are used during phylogenetic analysis, including the analysis of full sequences (i.e., SNPs together with invariant sites), or the analysis of SNPs on their own after excluding invariant sites. We find that using full sequences rather than just SNPs is preferable from the perspectives of branch length and topological accuracy, but not of computational time. We introduce two new acquisition bias corrections for dealing with alignments composed exclusively of SNPs, a conditional likelihood method and a reconstituted DNA approach. The conditional likelihood method conditions on the presence of variable characters only (the number of invariant sites that are unsampled but known to exist is not considered), while the reconstituted DNA approach requires the user to specify the exact number of unsampled invariant sites prior to the analysis. Under simulation, branch length biases increase with the amount of missing data for both acquisition bias correction methods, but branch length accuracy is much improved in the reconstituted DNA approach compared to the conditional likelihood approach. Phylogenetic analyses of the empirical data using concatenation or a coalescent-based species tree approach provide strong support for many of the accepted relationships among phrynosomatid lizards, suggesting that RAD loci contain useful phylogenetic signal across a range of divergence times despite the presence of missing data. Phylogenetic analysis of RAD loci requires careful attention to model assumptions, especially if downstream analyses depend on branch lengths.
© The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.
Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast
programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus,
there is need for additional approaches that employ different search strategies to find ML trees and that are at the same
time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation
method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found
higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use
the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein
alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3–97.1%. IQ-TREE
is freely available at http://www.cibiv.at/software/iqtree.
Motivation:
Increasing attention has been devoted to estimation of species-level phylogenetic relationships under the coalescent model. However, existing methods either use summary statistics (gene trees) to carry out estimation, ignoring an important source of variability in the estimates, or involve computationally intensive Bayesian Markov chain Monte Carlo algorithms that do not scale well to whole-genome datasets.
Results:
We develop a method to infer relationships among quartets of taxa under the coalescent model using techniques from algebraic statistics. Uncertainty in the estimated relationships is quantified using the nonparametric bootstrap. The performance of our method is assessed with simulated data. We then describe how our method could be used for species tree inference in larger taxon samples, and demonstrate its utility using datasets for Sistrurus rattlesnakes and for soybeans.
Availability and implementation:
The method to infer the phylogenetic relationship among quartets is implemented in the software SVDquartets, available at www.stat.osu.edu/∼lkubatko/software/SVDquartets.
The potential for anthropogenic climate change to impact upon native vegetation has emphasised the need for monitoring and for dynamic management regimes. Potential impacts are numerous, but will likely include the upslope movement of species’ ranges and increasing in situ turnover (compositional change) within plant assemblages. By assessing the potential impacts of climate change on subtropical rainforest communities in south-east Queensland through the establishment of an altitudinal transect, we aimed to establish the baseline composition of the vegetation and to develop two hypotheses against which climate change scenarios can be tested. The study identified existing high levels of turnover across tree assemblages from low to mid elevations absent at higher elevations and we predict: (1) subtropical rainforest communities which currently sit at the level of the cloud base (800–900 m) will experience increasing floristic turnover, and (2) novel vegetation communities will emerge as species move upslope in response to a changing climate. Monitoring floristic turnover as a surrogate for shifting climatic habitats may be confounded both by a lack of knowledge regarding the underlying turnover rates of rainforest communities and by the disparity in temporal scales of tree community turnover and accelerating anthropogenic climate change. The identification of ‘break points’ in the relationship between current vegetation communities and gradients of precipitation and temperature will allow better direction of monitoring efforts.
Including the impacts of climate change in decision making and planning
processes is a challenge facing many regional governments including the
New South Wales (NSW) and Australian Capital Territory (ACT) governments
in Australia. NARCliM (NSW/ACT Regional Climate Modelling project) is a
regional climate modelling project that aims to provide a comprehensive
and consistent set of climate projections that can be used by all
relevant government departments when considering climate change. To
maximise end user engagement and ensure outputs are relevant to the
planning process, a series of stakeholder workshops were run to define
key aspects of the model experiment including spatial resolution, time
slices, and output variables. As with all such experiments, practical
considerations limit the number of ensembles members that can be
simulated such that choices must be made concerning which Global Climate
Models (GCMs) to downscale from, and which Regional Climate Models
(RCMs) to downscale with. Here a methodology for making these choices is
proposed that aims to sample the uncertainty in both GCMs and RCMs, as
well as spanning the range of future climate projections present in the
full GCM ensemble. The created ensemble provides a more robust view of
future regional climate changes.
Anthropogenic climate change is a key threat to global biodiversity. To inform strategic actions aimed at conserving biodiversity as climate changes, conservation planners need early warning of the risks faced by different species. The IUCN Red List criteria for threatened species are widely acknowledged as useful risk assessment tools for informing conservation under constraints imposed by limited data. However, doubts have been expressed about the ability of the criteria to detect risks imposed by potentially slow-acting threats such as climate change, particularly because criteria addressing rates of population decline are assessed over time scales as short as 10 years. We used spatially explicit stochastic population models and dynamic species distribution models projected to future climates to determine how long before extinction a species would become eligible for listing as threatened based on the IUCN Red List criteria. We focused on a short-lived frog species (Assa darlingtoni) chosen specifically to represent potential weaknesses in the criteria to allow detailed consideration of the analytical issues and to develop an approach for wider application. The criteria were more sensitive to climate change than previously anticipated; lead times between initial listing in a threatened category and predicted extinction varied from 40 to 80 years, depending on data availability. We attributed this sensitivity primarily to the ensemble properties of the criteria that assess contrasting symptoms of extinction risk. Nevertheless, we recommend the robustness of the criteria warrants further investigation across species with contrasting life histories and patterns of decline. The adequacy of these lead times for early warning depends on practicalities of environmental policy and management, bureaucratic or political inertia, and the anticipated species response times to management actions.
A water balance study of a small subtropical rainforest catchment (10 ha, 1000
m altitude) was conducted at Gambubal State Forest, near the headwaters of the
Condamine River, 200 km south-west of Brisbane, south-eastern Queensland. Mean
annual rainfall of the site is approximately 1125 mm, but is variable and
often less than 900 mm. Tree transpiration rates are low and depletion of the
large soil moisture reserves enables extraction for lengthy periods of time,
permitting survival during extended dry seasons (May–November). Fog
deposition to the forest provides the equivalent of an additional 40%
of rainfall to the site as measured using a conventional rain gauge. A
frequently wet canopy results in reduced transpiration rates and direct foliar
absorption of moisture alleviates water deficits of the upper crown leaves and
branches during the dry season. These features of this vegetation type may
enable long-term survival at what could be considered to be a marginal
rainforest site.
We are currently facing the likelihood of severe climate change before the close of the century. In the face of such a global driver of species loss, we urgently need to identify refugia that will shelter species from the worst impacts of climate change. This will be a critical component of successful conservation and management of our biodiversity. Despite this, little is known about how best to identify refugia in the landscape, and the practical strategies needed to identify, protect and expand refugia are just beginning to be developed. Identifying refugia that will protect most species, or large numbers of species, remains a complex and daunting endeavour due to the large variations in climatic and biotic requirements of species.
A first step to identifying refugia for biodiversity across Australia is to locate the areas which show the least change into the future (i.e. the most environmentally stable), particularly along axes of temperature and precipitation. The second and crucial step is to identify the areas that will retain most of their biodiversity and provide opportunities for additional species to relocate to into the future. Using these approaches in this project, we take the first steps to identify refugial areas across the Australian continent under contemporary climate change scenarios. We find that the southern and eastern parts of the continent contain refugia that many species will retreat to over the next 75 years, but that the current reserve system may be inadequate to allow species to shift to and persist in these areas. Disturbingly, we also find that there is a large portion of the Australian vertebrate community for which adequate natural refugia do not appear to exist. Fine-scaled regional analyses will be required to clarify these broad findings, and we examine a number of case studies demonstrating how these regional analyses might best proceed.
Lessons learnt across the multiple techniques employed in this study include:
1. High elevation areas are important refugia.
2. Tasmania and the east coast of mainland Australia contain most of the key areas for refugia into the future.
3. Results are dependent on which objectives, techniques, taxonomic groups and climate scenarios are used.
Analyses of allozyme and mitochondrial nucleotide sequence variation in Philoria from northeastern NSW and southeastern Queensland revealed that there are more species than the three that are currently recognized. In addition to the three species presently recognized P. kundagungan, P. loveridgei, and P. sphagnicolus, another two species P. pughi n.sp. and P. richmondensis n.sp. were recognized under the evolutionary species concept. All species are allopatric. Each of the five species had two or more fixed genetic differences with all other species. Additionally, each species possessed two or more unique allozyme characters (apomorphies). Each species had strongly supported reciprocally monophyletic mitochondrial haplotypes in comparison with each of the other species. Multivariate morphometric analysis was able to distinguish P. sphagnicolus from the remaining four northern taxa but was unsuccessful in reliably distinguishing the two new species. Mating call analysis identified two distinct call groups: P. sphagnicolus and the remaining species, the latter showing little discrimination between species. The distribution of Philoria in NSW and Queensland shows a strong association with high rainfall rainforest at mid to high altitudes (above 600 m elevation). The habitat of all species is remarkably similar, all are found predominantly in the headwaters of rainforest streams or soaks on the forest floor. All species lay their eggs in nests in the ground, where the larvae remain throughout their entire development until they emerge post metamorphosis. It was confirmed that nests where the embryos were at an early stage of development were of two types: foaming egg masses, and nests containing a non-foaming jelly substance. All species are limited in their distribution. In particular P. richmondensis is in need of special conservation consideration, as it is known from only three localities within a very small range. A number of populations in southeastern Queensland and northern NSW await molecular analysis to be identified with certainty. KNOWLES, ROSS, MICHAEL MAHONY, JAN ARMSTRONG & STEPHEN DONNELLAN, 2004. Systematics of sphagnum frogs of the genus Philoria (Anura: Myobatrachidae) in eastern Australia, with the description of two new species.
We present STRUCTURE HARVESTER (available at http://taylor0.biology.ucla.edu/structureHarvester/), a web-based program for collating results generated by the program STRUCTURE. The program provides a fast way to assess
and visualize likelihood values across multiple values of K and hundreds of iterations for easier detection of the number of genetic groups that best fit the data. In addition, STRUCTURE
HARVESTER will reformat data for use in downstream programs, such as CLUMPP.
KeywordsStructure–Population structure–Population genetics–Evanno method–Visualization–Clustering
Global climate change (GCC) is expected to lead to massive loss of global biodiversity in the alpine regions of mountain ranges.
Studies on the potential effects of GCC on low mountain areas remain sparse, however, despite the high conservation value
of these areas as biodiversity refugia. We chose a species distribution modeling approach to assess potential GCC impacts
on the future distributions of montane freshwater invertebrates under two different greenhouse gas scenarios and three averaged
general circulation models. For this, ensemble models consisting of six algorithms [generalized linear model (GLM), generalized
boosted model (GBM), generalized additive model (GAM), classification tree analysis (CTA), artificial neural networks (ANN),
and multivariate adaptive regression splines (MARS)] were applied to project areas of 23 cold-stenothermic aquatic insects
from montane regions of Central Europe. We found an average loss of 70–80% of the potential distribution for the study species
until 2080, depending on the underlying Intergovernmental Panel on Climate Change scenario. Species distribution ranges below
1000m above sea level were found to decrease by up to~96% according to the severest greenhouse gas emission scenario. While
the Alps remain the single main refugium under the A2a greenhouse gas emission scenario, the more moderate climate scenario
B2a shows fragmented potential persistence of montane insects in some low mountain ranges. The results show that montane freshwater
assemblages in low mountain ranges are particularly threatened by ongoing GCC. As vertical dispersal is limited by elevational
restriction, low mountain ranges may act as summit traps under GCC. We thus propose that GCC will lead to the extinction of
several species and unique genetic lineages of postglacial relict species, resulting in a significant decline in Central European
fauna.
KeywordsBIOMOD–Climate change–Low mountain ranges–Montane aquatic insects–Species distribution models
Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data.Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.Contact:
peter@biomatters.com
Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
1. The study of geographic variation and the racial affinities between populations is of central importance to systematics and evolutionary theory. When using phenotypic variation to measure the similarity between the populations of a species one should analyse the variation in several characters simultaneously. This is a statistical procedure and is known as multivariate analysis. Multivariate analysis of phenotypic variation, unlike some other methods, has the advantage of not being dependent on living specimens.
2. To obtain an adequate sample at each locality, and an adequate distribution of localities within a given geographic area, can be a major problem. The pooling of data from adjacent localities is discussed.
3. There are several sources of phenotypic variation within a species, e.g. sexual and ontogenetic variation. Failure to eliminate the non‐geographic sources of variation can confuse the assessment of the similarity between populations.
4. Correlation between characters can reflect similar genetic control and/or similar patterns of geographic variation, the biological interpretation being influenced by whether the data come from one locality or many.
5. The influences of environmental induction and genetic control cannot easily be separated. Also, some characters may not be entirely homologous throughout the range of the species.
6. Most studies rely on far too few characters of a too restricted type to give an ‘overall’ assessment of the phenotypic similarity. This is one of the most neglected aspects of the study of geographic variation.
7. The various forms of clinal and categorical variation, the precise nature and position of sharp transition (hybrid) zones, the relationship between non‐adjacent as well as adjacent populations and the phenotypic divergence between island populations, etc., all come under the heading of geographic variation. The ideal technique should be able to elucidate all types of geographic variation but some techniques can only be used effectively with a few of them. Moreover, techniques may be limited in their application because they require the data to conform to certain models, e.g. normal distribution.
8. The degree of phenotypic similarity between populations can be measured by a wide range of similarity coefficients. Comparison between even a small series of populations produces a large set (or matrix) of similarity coefficients that is difficult to interpret. However, the relationships between populations can be summarized in several ways and these may be loosely grouped into four categories; (i) network diagrams, (ii) contours and isometric plots, (iii) hierarchical clusters, and (iv) ordination methods. These methods are explained and their advantages and limitations discussed.
9. The hierarchical (dendritic) model of cluster analysis is unsuitable for analysing all but a few types of geographic variation.
10. There are several types of ordination technique. They all aim to summarize the variation of many characters in a reduced number of axes. One can either emphasize the biological interpretation of each separate axis, or treat the analysis as a classifying technique and assess the grouping of the populations in the space defined by the axes. Considerable care is needed in interpreting the results of both of these approaches.
If correctly applied, ordination techniques generally can be used to analyse all the forms of geographical variation and are therefore recommended. Contrary to current practice they can be used with a large number of characters. The advantages and limitations of the various ordination techniques are discussed.
11. Contours and their three‐dimensional isometric plots can be used to portray geographic variations in the information obtained from a multivariate analysis. However, contours and isometric plots are limited in their applicability and the amount of information they can convey.
12. The sophistication of some multivariate methods should not be allowed to cloak the scientific inadequacies of a study. The use of more than one technique and variety in the choice of pertinent parameters may be of value in indicating the reliability of the results.
The identification of genetically homogeneous groups of individuals is a long standing issue in population genetics. A recent Bayesian algorithm implemented in the software STRUCTURE allows the identification of such groups. However, the ability of this algorithm to detect the true number of clusters (K) in a sample of individuals when patterns of dispersal among populations are not homogeneous has not been tested. The goal of this study is to carry out such tests, using various dispersal scenarios from data generated with an individual-based model. We found that in most cases the estimated 'log probability of data' does not provide a correct estimation of the number of clusters, K. However, using an ad hoc statistic DeltaK based on the rate of change in the log probability of data between successive K values, we found that STRUCTURE accurately detects the uppermost hierarchical level of structure for the scenarios we tested. As might be expected, the results are sensitive to the type of genetic marker used (AFLP vs. microsatellite), the number of loci scored, the number of populations sampled, and the number of individuals typed in each sample.
In the last several decades, habitat loss, overexploitation, invasive organisms, disease, pollution and, more recently, climate change have led to catastrophic declines in amphibian biodiversity. Montane amphibian species, particularly those with narrow distributions and specific habitat requirements are likely to be at particular risk under future climate change scenarios. Despite this, fundamental ecological data are lacking for most of these species. Philoria kundagungan is a poorly known representative of a range-restricted genus of montane amphibians from eastern Australia. Using an occupancy framework, we conducted repeated call playback surveys at 32 sites across the mountainous regions of south-east Queensland and north-eastern New South Wales, Australia, to investigate: (1) the current extent of this species’ geographic range, and (2) environmental predictors of this species’ presence. We found that P. kundagungan has a highly restricted and fragmented distribution, being limited to ~11 km2 of potentially suitable habitat, and that its presence is strongly associated with high elevation (>800 m). Our survey protocol resulted in a high probability of detection (>70%) at occupied sites from relatively few visits. From these baseline data, future studies will have the ability to determine changes in this species’ geographic range and occupancy rate in response to the ever-increasing threats faced by P. kundagungan, thereby supporting more effective conservation strategies and policy decisions.
Population declines and range contractions among Australian frogs that commenced in the early 1980s continue in some species that were once widespread. The generality of this pattern has been difficult to discern, especially for those species that are encountered rarely because they have restricted periods of calling activity with poorly defined habitat preferences, and are not common. Several lines of evidence indicate that Litoria littlejohni is such a species. This frog was once known from mid-eastern New South Wales to eastern Victoria, and evidence from wildlife atlas databases and targeted searches indicate that it has declined in large portions of its former range, leaving several populations that are isolated, in some cases restricted in distribution, and of small size. We investigated the relationships among populations using mitochondrial ND4 nucleotide sequences and single nucleotide polymorphisms (SNPs) from the nuclear genome. We found that northern and southern populations form two highly divergent genetic groups whose distributions abut at the southern margin of the Sydney Basin Bioregion and these genetic groups also show divergence in morphology and male advertisement calls. Here we describe the populations to the south of the Sydney Basin Bioregion as a new species and provide information on its distribution and ecology. In light of the apparent isolation and small size of known populations of the new species and the consequent restriction of the range of L. littlejohni, we assessed the conservation status of both species.
Understanding the evolutionary history of diversifying lineages and the delineation of evolutionarily significant units and species remain major challenges for evolutionary biology. Low cost representational sampling of the genome for single nucleotide polymorphisms (SNPs) shows great potential at the temporal scales that are typically the focus of species delimitation and phylogeography. We apply these markers to a case study of a freshwater turtle, Emydura macquarii, whose systematics has so far defied resolution, to bring to light a dynamic system of substantive allopatric lineages diverging on independent evolutionary trajectories, but held back in the process of speciation by low level and episodic exchange of alleles across drainage divides on various timescales. In the context of low‐level episodic gene flow, speciation is often reticulate, rather than a bifurcating process. We argue that species delimitation needs to take into account the pattern of ancestry and descent of diverging lineages in allopatry together with the recent and contemporary processes of dispersal and gene flow that retard and obscure that divergence. Underpinned by a strong focus on lineage diagnosabilty, this combined approach provides a means for addressing the challenges of incompletely isolated populations with uncommon, but recurrent gene flow in studies of species delimitation, a situation likely to be frequently encountered. Taxonomic decisions in cases of allopatry often require subjective judgements. Our strategy, which adds an additional level of objectivity before that subjectivity is applied, reduces the risk of taxonomic inflation that can accompany lineage approaches to species delimitation.
This article is protected by copyright. All rights reserved.
Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.
We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.
Descriptions and diagnoses are alternative choices in all Codes of Nomenclature because Linnaeus relied on diagnoses, not descriptions, to name ca. 13400 animals, plants, and fungi. A diagnosis names characters
in which a new taxon differs from the most similar known taxon; a description mixes taxonomically informative and uninformative
features, usually without indicating which is which. The first formal diagnoses of new taxa that included DNA-based characters
came out in 2001, and by November 2015, at least 98 names of species of mites, acoels, lichens, angiosperms, annelids, alveolates,
arachnids, centipedes, turtles, fishes, butterflies, mollusks, nematodes, and pathogenic fungi have been published based on
diagnostic mitochondrial, plastid, or nuclear DNA substitutions, indels, or rarely genetic distances, with or without additional
morphological features. Authors have found diverse ways to specify the diagnostic traits (all published studies are here tabulated).
While descriptions try to 'cover' within-species variation, a goal rarely accomplished because of (i) the stochastic nature
of specimen availability (thousands of species are known from single collections) and (ii) the subjective circumscription
of species, the purpose of diagnoses was and is speedy identification. Linnaeus tried to achieve this by citing images, geographic
occurrence, and previous literature. The renewed attention to sharp diagnosis now coincides with worldwide barcoding efforts,
may speed up formal naming, and matches the increasing reliance on DNA for both classification and identification. I argue
for DNA-based diagnoses of new species becoming a recommendation in all Codes, not just the bacterial code.
Historically, the quantitative study of sound has been wedded to the development of sound-measurement technology. Researchers have routinely seized on and resourcefully adapted various technological tools, whether intended for sound analysis or not. Sabine (1900), for example, developed acoustical reverberation theory in an empty theater at Harvard University, using an organ pipe, a chronograph, and his own hearing to measure reverberant sound duration. Similarly, Brand (1934) characterized the time-varying frequency of birdsong by recording vocalizations on motion-picture film and measuring spatial line-density on the soundtrack. Successive milestones in sound-measurement technology — notably the microphone, the oscilloscope, and later the sound spectrograph — helped researchers to visualize and measure sounds but not to model them directly. Modeling of acoustic communication was instead typically performed indirectly via statistical analysis, comparison, and classification of individual measured sound features.
The identification of the genetic structure of populations from multilocus genotype data has become a central component of modern population-genetic data analysis. Application of model-based clustering programs often entails a number of steps, in which the user considers different modeling assumptions, compares results across different pre-determined values of the number of assumed clusters (a parameter typically denoted K), examines multiple independent runs for each fixed value of K, and distinguishes among runs belonging to substantially distinct clustering solutions. Here, we present Clumpak (Cluster Markov Packager Across K), a method that automates the post-processing of results of model-based population structure analyses. For analyzing multiple independent runs at a single K value, Clumpak identifies sets of highly similar runs, separating distinct groups of runs that represent distinct modes in the space of possible solutions. This procedure, which generates a consensus solution for each distinct mode, is performed by the use of a Markov clustering algorithm that relies on a similarity matrix between replicate runs, as computed by the software Clumpp. Next, Clumpak identifies an optimal alignment of inferred clusters across different values of K, extending a similar approach implemented for a fixed K in Clumpp, and simplifying the comparison of clustering results across different K values. Clumpak incorporates additional features, such as implementations of methods for choosing K and comparing solutions obtained by different programs, models, or data subsets. Clumpak, available at http://clumpak.tau.ac.il, simplifies the use of model-based analyses of population structure in population genetics and molecular ecology. This article is protected by copyright. All rights reserved.
This article is protected by copyright. All rights reserved.
Amphibians are the most threatened vertebrate taxon of modern times. Baseline data and affordable methods to monitor populations are absent for many Australian frog species. Furthermore, some species are visually cryptic, and detection often relies upon male advertisement calls. Imperfect detection rates impede our ability to assess the status of populations over time. Understanding the factors that influence calling is essential to inform the timing of survey effort and increase survey efficiency. Automated recording systems offer considerable potential to determine calling phenology and establish the relationship between calling and abiotic factors. The mountain frogs (Philoria Myobatrachidae) of the Gondwana rainforests are considered susceptible to climate change impacts, such as shifts in the timing of calling. In order to describe the calling phenology of Philoria richmondensis, commercially available automated recording systems were deployed at five locations, and over 5000 h of sound recordings were captured and analysed. Peak calling activity occurred during morning and evening periods in the austral spring. Ambient temperature was found to significantly contribute to the probability of a call occurring, with the highest frequency of calls recorded occurring between 15°C and 16°C, and there was a negative relationship between precipitation and calling activity. The results allow future surveys to be better targeted and provide a benchmark with which to detect changes in calling phenology over time.
— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.
In the last 20 years, we have observed an exponential growth of the DNA sequence data and simular increase in the volume of DNA polymorphism data generated by numerous molecular marker technologies. Most of the investment, and therefore progress, concentrated on human genome and genomes of selected model species. Diversity Arrays Technology (DArT), developed over a decade ago, was among the first "democratizing" genotyping technologies, as its performance was primarily driven by the level of DNA sequence variation in the species rather than by the level of financial investment. DArT also proved more robust to genome size and ploidy-level differences among approximately 60 organisms for which DArT was developed to date compared to other high-throughput genotyping technologies. The success of DArT in a number of organisms, including a wide range of "orphan crops," can be attributed to the simplicity of underlying concepts: DArT combines genome complexity reduction methods enriching for genic regions with a highly parallel assay readout on a number of "open-access" microarray platforms. The quantitative nature of the assay enabled a number of applications in which allelic frequencies can be estimated from DArT arrays. A typical DArT assay tests for polymorphism tens of thousands of genomic loci with the final number of markers reported (hundreds to thousands) reflecting the level of DNA sequence variation in the tested loci. Detailed DArT methods, protocols, and a range of their application examples as well as DArT's evolution path are presented.
The subduction of oceanic plateaux, which contain extraordinarily thick basaltic crust and are the marine counterparts of continental flood-basalt provinces, is an important factor in many current models of plate motion and provides a potential mechanism for triggering plate reorganization. To evaluate such models, it is essential to decipher the history of the collision between the largest and thickest of the world's oceanic plateaux, the Ontong Java plateau, and the Australian plate, but this has been hindered by poor constraints for the arrival of the plateau at the Melanesian trench. Here we present (40)Ar-(39)Ar geochronological data on hotspot volcanoes in eastern Australian that reveal a strong link between collision of the Greenland-sized Ontong Java plateau with the Melanesian arc and motion of the Australian plate. The new ages define a short-lived period of reduced northward plate motion between 26 and 23 Myr ago, coincident with an eastward offset in the contemporaneous tracks of seamount chains in the Tasman Sea east of Australia. These features record a brief westward deflection of the Australian plate as the plateau entered and choked the Melanesian trench 26 Myr ago. From 23 Myr ago, Australia returned to a rapid northerly trajectory at roughly the same time that southwest-directed subduction began along the Trobriand trough. The timing and brevity of this collisional event correlate well with offsets in hotspot seamount tracks on the Pacific plate, including the archetypal Hawaiian chain, and thus provide strong evidence that immense oceanic plateaux, like the Ontong Java, can contribute to initiating rapid change in plate boundaries and motions on a global scale.
In the present paper, a normalization technique to scale data that exhibit an allometric growth is presented and the way it has to be used is described. It is shown how the method has been derived from the theoretical equations of allometric growth. Consequently, the method completely removes all the information related to size, not only scaling all individuals to the same size, but also adjusting their shape to that they would have in the new size according to allometry. In the particular case of isometry when the measures are of identical dimension, this normalization coincides with ratios (one of the most popular methods but only valid in this particular case). This procedure is a theoretical generalization of the technique used by Thorpe (1975, Biol. J. Linn. Soc.7, 27-43; 1976, Biol. Rev.51, 407-452) which was recorded as one of the most efficient methods in the empirical evaluation done by Reist (1985, Can. J. Zool.63, 1429-1439).
Conservation planning has tended to focus more on pattern (representation) than process (persistence) and, for the former, has emphasized species and ecosystem or community diversity over genetic diversity. Here I consider how best to incorporate knowledge of evolutionary processes and the distribution of genetic diversity into conservation planning and priority setting for populations within species and for biogeographic areas within regions. Separation of genetic diversity into two dimensions, one concerned with adaptive variation and the other with neutral divergence caused by isolation, highlights different evolutionary processes and suggests alternative strategies for conservation. Planning for both species and areas should emphasize protection of historically isolated lineages (Evolutionarily Significant Units) because these cannot be recovered. By contrast, adaptive features may best be protected by maintaining the context for selection, heterogeneous landscapes, and viable populations, rather than protecting specific phenotypes. A useful strategy may be to (1) identify areas that are important to represent species and (vicariant) genetic diversity and (2) maximize within these areas the protection of contiguous environmental gradients across which selection and migration can interact to maintain population viability and (adaptive) genetic diversity. These concepts are illustrated with recent results from analysis of a rainforest fauna from northeast Australia.
In 2002, we developed and released a rapid multiple sequence alignment program MAFFT that was designed to handle a huge (up to approximately 5,000 sequences) and long data (approximately 2,000 aa or approximately 5,000 nt) in a reasonable time on a standard desktop PC. As for the accuracy, however, the previous versions (v.4 and lower) of MAFFT were outperformed by ProbCons and TCoffee v.2, both of which were released in 2004, in several benchmark tests. Here we report a recent extension of MAFFT that aims to improve the accuracy with as little cost of calculation time as possible. The extended version of MAFFT (v.5) has new iterative refinement options, G-INS-i and L-INS-i (collectively denoted as [GL]-INS-i in this report). These options use a new objective function combining the weighted sum-of-pairs (WSP) score and a score similar to COFFEE derived from all pairwise alignments. We discuss the improvement in accuracy brought by this extension, mainly using two benchmark tests released very recently, BAliBASE v.3 (for protein alignments) and BRAliBASE (for RNA alignments). According to BAliBASE v.3, the overall average accuracy of L-INS-i was higher than those of other methods successively released in 2004, although the difference among the most accurate methods (ProbCons, TCoffee v.2 and new options of MAFFT) was small. The advantage in accuracy of [GL]-INS-i became greater for the alignments consisting of approximately 50-100 sequences. By utilizing this feature of MAFFT, we also examined another possible approach to improve the accuracy by incorporating homolog information collected from database. The [GL]-INS-i options are applicable to aligning up to approximately 200 sequences, although not applicable to thousands of sequences because of time and space complexities.
Tadpoles and Frogs of Australia
- M Anstis
Anstis, M. (2013) Tadpoles and Frogs of Australia. New Holland Publishers, Sydney, 831pp.
Distribution, ecology, disease and physiology of mountain-top endemic frogs in the face of climate change: A study on Philoria sp
- M Familiar López
Familiar López, M. (2016) Distribution, ecology, disease and physiology of mountain-top endemic frogs in the face of climate
change: A study on Philoria sp. PhD Dissertation, Griffith University, Brisbane. Available from: https://research-repository.
griffith.edu.au/handle/10072/368164?show=full (accessed 8 February 2022)
Post-fire impact assessment for priority frogs: northern Philoria. NESP Threatened Species Recovery Hub
- G Heard
- L Bolitho
- D Newell
- H Hines
- H Mccall
- J Smith
- B Scheele
Heard, G., Bolitho, L., Newell, D., Hines, H., McCall, H., Smith, J. & Scheele, B. (2021) Post-fire impact assessment for priority frogs: northern Philoria. NESP Threatened Species Recovery Hub Project 8.1.3 report, Brisbane. Available from;
A new species of Kyarranus (Anura: Leptodactylidae) from Queensland
- G J Ingram
- C J Corben
Ingram, G.J. & Corben, C.J. (1975) A new species of Kyarranus (Anura: Leptodactylidae) from Queensland, Australia. Memoirs
of the Queensland Museum, 17, 335-339.
Guidelines for application of IUCN Red List criteria at regional and national levels
- Iucn
IUCN (2012) Guidelines for application of IUCN Red List criteria at regional and national levels. Version 4.0. Available
from: https://www.iucn.org/content/guidelines-application-iucn-red-list-criteria-regional-and-national-levels-version-40
(acessed 8 February 2022)
Monitoring the effects of climate change: A survey and report on the status of endemic high altitude frogs in the Gondwana Rainforests of Australia World Heritage Area. Grant report Gondwana WHA (DECCW-720-2010). Unpublished Report for the NSW Office of Environment and Heritge
- M J Mahony
- D Ross
- D Newell
- R Willacy
- J-M Hero
- Familiar-Lopez
- G Lollback
Mahony, M.J., Ross, D., Newell, D., Willacy, R., Hero, J-M., Familiar-Lopez, & Lollback, G. (2013) Monitoring the effects of
climate change: A survey and report on the status of endemic high altitude frogs in the Gondwana Rainforests of Australia
World Heritage Area. Grant report Gondwana WHA (DECCW-720-2010). Unpublished Report for the NSW Office of
Environment and Heritge, Sydney. pp. 1-97.