Article impact statement: Biodiversity of unexplored and unmapped environments cannot be conserved until they have been described, mapped, and analyzed.
Exhaustive biodiversity data, covering all the taxa in an environment, would be fundamental to understand how global changes influence organisms living at different trophic levels, and to evaluate ...impacts on interspecific interactions. Molecular approaches such as DNA metabarcoding are boosting our ability to perform biodiversity inventories. Nevertheless, even though a few studies have recently attempted exhaustive reconstructions of communities, holistic assessments remain rare. The majority of metabarcoding studies published in the last years used just one or two markers and analysed a limited number of taxonomic groups. Here, we provide an overview of emerging approaches that can allow all‐taxa biological inventories. Exhaustive biodiversity assessments can be attempted by combining a large number of specific primers, by exploiting the power of universal primers, or by combining specific and universal primers to obtain good information on key taxa while limiting the overlooked biodiversity. Multiplexes of primers, shotgun sequencing and capture enrichment may provide a better coverage of biodiversity compared to standard metabarcoding, but still require major methodological advances. Here, we identify the strengths and limitations of different approaches, and suggest new development lines that might improve broad scale biodiversity analyses in the near future. More holistic reconstructions of ecological communities can greatly increase the value of metabarcoding studies, improving understanding of the consequences of ongoing environmental changes on the multiple components of biodiversity.
Climate change is determining a generalized phenological advancement, and amphibians are among the taxa showing the strongest phenological responsiveness to warming temperatures. Amphibians are ...strongly influenced by climate change, but we do not have a clear picture of how climate influences important parameters of amphibian populations, such as abundance, survival, breeding success and morphology. Furthermore, the relative impact of temperature and precipitation change remains underappreciated. We used Bayesian meta-analysis and meta-regression to quantify the impact of temperature and precipitation change on amphibian phenology, abundance, individual features and performance. We obtained effect sizes from studies performed in five continents. Temperature increase was the major driver of phenological advancement, while the impact of precipitation on phenology was weak. Conversely, population dynamics was mostly determined by precipitation: negative trends were associated with drying regimes. The impact of precipitation on abundance was particularly strong in tropical areas, while the importance of temperature was feeble. Both temperature and precipitation influenced parameters representing breeding performance, morphology, developmental rate and survival, but the response was highly heterogeneous among species. For instance, warming temperature increased body size in some species, and decreased size in others. Similarly, rainy periods increased survival of some species and reduced the survival of others. Our study showed contrasting impacts of temperature and precipitation changes on amphibian populations. Both climatic parameters strongly influenced amphibian performance, but temperature was the major determinant of the phenological changes, while precipitation had the major role on population dynamics, with alarming declines associated with drying trends.
Coronary artery anomalies (CAAs) are a group of congenital conditions characterized by abnormal origin or course of any of the 3 main epicardial coronary arteries. Although CAAs have been identified ...as a common underlying condition in young athletes with sudden cardiac death, the widespread use of invasive and noninvasive coronary imaging has led to increased recognition of CAAs among adults. CAAS are often discovered as an incidental finding during the diagnostic workup for ischemic heart disease. The clinical correlates and prognostic implication of CAAs remain poorly understood in this context, and guideline-recommended therapeutic choices are supported by a low level of scientific evidence. Several studies have examined whether assessment of CAA-related myocardial ischemia can improve risk stratification in these patients, suggesting that multimodality imaging and functional tests may be key in the management of CAAs. The aim of this review is to outline definitions, classification, and epidemiology of the most relevant CAAs, highlighting recent advances and the potential impact of multimodality evaluation, and to discuss current therapeutic opportunities.
When different proposals exist (or can reasonably be formulated) for the size of the unit cell (in terms of number of atoms) and space group of crystalline compounds, a strategy for exploring with ...simulation methods the various cases and for investigating their relative stability must be defined. The optimization schemes of periodic quantum mechanical codes work in fact at fixed space group and number of atoms per unit cell, so that only the fractional coordinates of the atoms and the lattice parameters are optimized. A strategy is here presented, based on four standard tools, used synergistically and in sequence: (1) the optimization of inner coordinates and unit cell parameters; (2) the calculation of the vibrational frequencies not only at Γ, but also at a set of k→ points (in the example presented here they are eight, generated by a shrinking factor 2), looking for possible negative wavenumbers. The latter correspond to maxima, rather than minima, along the coordinate described by the corresponding normal mode; (3) the exploration of the total energy along the mode with negative wavenumber, looking for the minimum of the curve; (4) the identification of the new space group corresponding to the reduced symmetry resulting from the previous step. The strategy is illustrated with reference to the KMnF3 perovskite compound, for which many space groups are proposed in the literature, ranging from cubic Pm3¯m to tetragonal P4mbmorI4mcm and orthorhombic (Pnma and Cmcm) down to monoclinic (P21/m). The corresponding primitive cells contain 5, 10, and 20 atoms in the various cases, and the point symmetry reduces from 48 to 4 operators. In nature, the KMnF3 phase transitions also include the magnetic phases. For simplicity, here we limit the analysis to the ones that take place between ferromagnetic phases, as they are sufficiently rich for illustrating the proposed strategy. As the total energy differences involved can be as small as, say, 10–50 μHartree, a high numerical accuracy at each one of the steps mentioned above is required. The present calculations, performed with the CRYSTAL code, by using an all electron basis set and the Hartree‐Fock and B3LYP functionals, document such an accuracy. The energy difference between the tetragonal I4mcm and cubic Pm3¯m phases is 225 μHartree, with a volume reduction of 0.58 Å3; the differences between the orthorhombic and tetragonal phases are an order of magnitude smaller, being 23 μHartree and 0.06 Å3 for total energy and cell volume, respectively.
A strategy for following the space group reduction from cubic to tetragonal, down to orthorhombic, common to many perovskites, is proposed and applied to KMnF3. This reduction, that requires to consider increasing unit cells (containing 5, 10, and 20 atoms, respectively) and reduced point symmetries (from 48 to 16 to 4 point operators) cannot simply result from a global (lattice parameters and fractional atomic coordinates) optimization, but requires additional tools (including the calculation of the vibrational frequencies at a set of k→ points in reciprocal space and scanning the resulting modes with imaginary wavenumbers) and high numerical accuracy.
Environmental DNA (eDNA) and metabarcoding are boosting our ability to acquire data on species distribution in a variety of ecosystems. Nevertheless, as most of sampling approaches, eDNA is not ...perfect. It can fail to detect species that are actually present, and even false positives are possible: a species may be apparently detected in areas where it is actually absent. Controlling false positives remains a main challenge for eDNA analyses: in this issue of Molecular Ecology Resources, Lahoz‐Monfort et al. () test the performance of multiple statistical modelling approaches to estimate the rate of detection and false positives from eDNA data. Here, we discuss the importance of controlling for false detection from early steps of eDNA analyses (laboratory, bioinformatics), to improve the quality of results and allow an efficient use of the site occupancy‐detection modelling (SODM) framework for limiting false presences in eDNA analysis.
The recently emerged 2019 Novel Coronavirus (SARS‐CoV‐2) and associated COVID‐19 disease cause serious or even fatal respiratory tract infection and yet no approved therapeutics or effective ...treatment is currently available to effectively combat the outbreak. This urgent situation is pressing the world to respond with the development of novel vaccine or a small molecule therapeutics for SARS‐CoV‐2. Along these efforts, the structure of SARS‐CoV‐2 main protease (Mpro) has been rapidly resolved and made publicly available to facilitate global efforts to develop novel drug candidates. Recently, our group has developed a novel deep learning platform – Deep Docking (DD) which provides fast prediction of docking scores of Glide (or any other docking program) and, hence, enables structure‐based virtual screening of billions of purchasable molecules in a short time. In the current study we applied DD to all 1.3 billion compounds from ZINC15 library to identify top 1,000 potential ligands for SARS‐CoV‐2 Mpro protein. The compounds are made publicly available for further characterization and development by scientific community.
The COVID-19 pandemic zoonosis has determined extensive lockdowns worldwide that provide an unprecedented opportunity to understand how large-scale shifts of human activities can impact wildlife. We ...addressed the impacts of the COVID-19 lockdown on wildlife in Italy, the first European country that performed a countrywide lockdown, and identified potentially beneficial and negative consequences for wildlife conservation and management. We combined a qualitative analysis of social media information with field data from multiple taxa, data from citizen science projects, and questionnaires addressed to managers of protected areas. Both social media information and field data suggest that a reduction of human disturbance allowed wildlife to exploit new habitats and increase daily activity. The field data confirmed some positive effects on wildlife conservation, such as an increase in species richness in temporarily less-disturbed habitats, a higher breeding success of an aerial insectivorous bird, and reduction of road-killing of both amphibians and reptiles. Despite some positive effects, our data also highlighted several negative impacts of the COVID-19 crisis on wildlife. The lower human disturbance linked to lockdown was in fact beneficial for invasive alien species. Results from questionnaires addressed to managers of protected areas highlighted that the COVID-19 lockdown interrupted actions for the control of invasive alien species, and hampered conservation activities targeting threatened taxa. Furthermore, the reduction of enforcement could cause a surge of illegal killing of wildlife. The COVID-19 crisis, besides having deep socio-economic impacts, might profoundly affect wildlife conservation, with potentially long-lasting effects.
•Lockdowns following COVID-19 provide an unprecedented opportunity for conservation studies.•We combined multiple tools to understand Italian lockdown's effects on wildlife.•Wildlife exploited new habitats and increased daily activity and breeding success.•Also some invasive alien species took advantage from the lockdown.•Negative effects occurred on conservation actions and alien species eradications.
Abstract
Invasive predators can exert strong selection on native populations. If selection is strong enough, populations could lose the phenotypic variation caused by adaptation to heterogeneous ...environments. We compare frog tadpoles prior to and 14 years following invasion by crayfish. Prior to the invasion, populations differed in their intrinsic developmental rate, with tadpoles from cold areas reaching metamorphosis sooner than those from warm areas. Following the invasion, tadpoles from invaded populations develop faster than those from non-invaded populations. This ontogenetic shift overwhelmed the intraspecific variation between populations in a few generations, to the point where invaded populations develop at a similar rate regardless of climate. Rapid development can have costs, as fast-developing froglets have a smaller body size and poorer jumping performance, but compensatory growth counteracts some costs of development acceleration. Strong selection by invasive species can disrupt local adaptations by dampening intraspecific phenotypic variation, with complex consequences on lifetime fitness.
The continuous decline of biodiversity is determined by the complex and joint effects of multiple environmental drivers. Still, a large part of past global change studies reporting and explaining ...biodiversity trends have focused on a single driver. Therefore, we are often unable to attribute biodiversity changes to different drivers, since a multivariable design is required to disentangle joint effects and interactions. In this work, we used a meta‐regression within a Bayesian framework to analyze 843 time series of population abundance from 17 European amphibian and reptile species over the last 45 years. We investigated the relative effects of climate change, alien species, habitat availability, and habitat change in driving trends of population abundance over time, and evaluated how the importance of these factors differs across species. A large number of populations (54%) declined, but differences between species were strong, with some species showing positive trends. Populations declined more often in areas with a high number of alien species, and in areas where climate change has caused loss of suitability. Habitat features showed small variation over the last 25 years, with an average loss of suitable habitat of 0.1%/year per population. Still, a strong interaction between habitat availability and the richness of alien species indicated that the negative impact of alien species was particularly strong for populations living in landscapes with less suitable habitat. Furthermore, when excluding the two commonest species, habitat loss was the main correlate of negative population trends for the remaining species. By analyzing trends for multiple species across a broad spatial scale, we identify alien species, climate change, and habitat changes as the major drivers of European amphibian and reptile decline.
Through meta‐analysis, we assessed the relative importance of multiple global change drivers in determining long‐term changes in population abundance of European amphibians and reptiles. Population trends are driven by the combined effects of alien species, climate change, habitat features, and habitat changes, with complex joint and interactive effects among factors. Even though we identified general patterns in the response to some environmental drivers, it is important to consider that the same factors can act differently among taxonomic groups; for instance, habitat change showed a contrasting effect across species and its crucial role was only evident for a subset of them.
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