Error in statistical tests of error in statistical tests

BACKGROUND: A recent paper found that terminal digits of statistical values in Nature deviated significantly from an equiprobable distribution, indicating errors or inconsistencies in rounding. This finding, as well as the discovery that a large percentage of p values were inconsistent with reported test statistics, led to a great deal of concern in the popular press and scientific community. The findings ultimately led to new guidelines for all Nature Research Journals. METHODS: We checked the statistical analysis behind the original paper's tests of equiprobability. RESULTS: The original paper tested equiprobability with the Kolmogorov-Smirnov test outside its regime of validity. Correct tests find no statistically significant deviations from equiprobability for the statistical values in Nature. CONCLUSION: Statistical tests should be used correctly

Mapping Oil and Gas Development Potential in the US Intermountain West and Estimating Impacts to Species

Many studies have quantified the indirect effect of hydrocarbon-based economies on climate change and biodiversity, concluding that a significant proportion of species will be threatened with extinction. However, few studies have measured the direct effect of new energy production infrastructure on species persistence. in the western US and translate the build-out scenarios into estimated impacts on sage-grouse. We project that future oil and gas development will cause a 7–19 percent decline from 2007 sage-grouse lek population counts and impact 3.7 million ha of sagebrush shrublands and 1.1 million ha of grasslands in the study area.Maps of where oil and gas development is anticipated in the US Intermountain West can be used by decision-makers intent on minimizing impacts to sage-grouse. This analysis also provides a general framework for using predictive models and build-out scenarios to anticipate impacts to species. These predictive models and build-out scenarios allow tradeoffs to be considered between species conservation and energy development prior to implementation

Win-Win for Wind and Wildlife: A Vision to Facilitate Sustainable Development

Wind energy offers the potential to reduce carbon emissions while increasing energy independence and bolstering economic development. However, wind energy has a larger land footprint per Gigawatt (GW) than most other forms of energy production, making appropriate siting and mitigation particularly important. Species that require large unfragmented habitats and those known to avoid vertical structures are particularly at risk from wind development. Developing energy on disturbed lands rather than placing new developments within large and intact habitats would reduce cumulative impacts to wildlife. The U.S. Department of Energy estimates that it will take 241 GW of terrestrial based wind development on approximately 5 million hectares to reach 20% electricity production for the U.S. by 2030. We estimate there are ∼7,700 GW of potential wind energy available across the U.S., with ∼3,500 GW on disturbed lands. In addition, a disturbance-focused development strategy would avert the development of ∼2.3 million hectares of undisturbed lands while generating the same amount of energy as development based solely on maximizing wind potential. Wind subsidies targeted at favoring low-impact developments and creating avoidance and mitigation requirements that raise the costs for projects impacting sensitive lands could improve public value for both wind energy and biodiversity conservation

DNA repair and resistence to UV-B radiation in western spotted frogs

assessed DNA repair and resistance to solar radiation in eggs of members of the western spotted frog complex (Rana pretiosa and R. luteiventris), species whose populations are suffering severe range reductions and declines. Specifically, we measured the activity of photoreactivating enzyme (photolyase) in oocytes of spotted frogs. In some species, photoreactivation is the most important mechanism for repair of UV-damaged DNA. Using field experiments, we also compared the hatching success of spotted frog embr yos at natural oviposition sites at three elevations, where some embr yos were subjected to ambient levels of UV-B radiation and others were shielded from UV-B radiation. Compared with other amphibians, photolyase activities in spotted frogs were relatively high. At all sites, hatching success was unaffected by UV-B. Our data support the interpretation that amphibian embr yos with relatively high levels of photolyase are more resistant to UV-B radiation than those with lower levels of photolyase. At the embr yonic stage, UV-B radiation does not presently seem to be contributing to the population declines of spotted frogs.Peer reviewe

Natural climate solutions

Our thanks for inputs by L. Almond, A. Baccini, A. Bowman, S. CookPatton, J. Evans, K. Holl, R. Lalasz, A. Nassikas, M. Spalding, M. Wolosin, and expert elicitation respondents. Our thanks for datasets developed by the Hansen lab and the NESCent grasslands working group (C. Lehmann, D. Griffith, T. M. Anderson, D. J. Beerling, W. Bond, E. Denton, E. Edwards, E. Forrestel, D. Fox, W. Hoffmann, R. Hyde, T. Kluyver, L. Mucina, B. Passey, S. Pau, J. Ratnam, N. Salamin, B. Santini, K. Simpson, M. Smith, B. Spriggs, C. Still, C. Strömberg, and C. P. Osborne). This study was made possible by funding from the Doris Duke Charitable Foundation. Woodbury was supported in part by USDA-NIFA Project 2011-67003-30205 Data deposition: A global spatial dataset of reforestation opportunities has been deposited on Zenodo (https://zenodo.org/record/883444). This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1710465114/-/DCSupplemental.Peer reviewedPublisher PD

Optimizing land use decision-making to sustain Brazilian agricultural profits, biodiversity and ecosystem services

AbstractDesigning landscapes that can meet human needs, while maintaining functioning ecosystems, is essential for long-term sustainability. To achieve this goal, we must better understand the trade-offs and thresholds in the provision of ecosystem services and economic returns. To this end, we integrate spatially explicit economic and biophysical models to jointly optimize agricultural profit (sugarcane production and cattle ranching), biodiversity (bird and mammal species), and freshwater quality (nitrogen, phosphorus, and sediment retention) in the Brazilian Cerrado. We generate efficiency frontiers to evaluate the economic and environmental trade-offs and map efficient combinations of agricultural land and natural habitat under varying service importance. To assess the potential impact of the Brazilian Forest Code (FC), a federal policy that aims to promote biodiversity and ecosystem services on private lands, we compare the frontiers with optimizations that mimic the habitat requirements in the region. We find significant opportunities to improve both economic and environmental outcomes relative to the current landscape. Substantial trade-offs between biodiversity and water quality exist when land use planning targets a single service, but these trade-offs can be minimized through multi-objective planning. We also detect non-linear profit-ecosystem services relationships that result in land use thresholds that coincide with the FC requirements. Further, we demonstrate that landscape-level planning can greatly improve the performance of the FC relative to traditional farm-level planning. These findings suggest that through joint planning for economic and environmental goals at a landscape-scale, Brazil's agricultural sector can expand production and meet regulatory requirements, while maintaining biodiversity and ecosystem service provision

Prioritizing global land protection for population persistence can double the efficiency of habitat protection for reducing mammal extinction risk

Halting the alarming rate of species extinction, driven primarily by habitat destruction, motivated the international community to adopt the Global Biodiversity Framework (2022) and its targets aimed at reversing habitat and species loss. Because of urgency and resource constraints, a key challenge is meeting targets effectively and efficiently. Here we conduct a global prioritization linking 70,492 unique population maps and life history characteristics for 861 threatened terrestrial mammal species. Incorporating individual population data to identify priority areas for conservation nearly doubled the likely long-term persistence of species for the same amount of land compared with a typical approach based on species distributions alone. We map and rank global mammal persistence priority areas and assess how well the current protected area (PA) system captures these important regions. Our results offer a clearer, quantifiable link between conservation actions and global extinction risk than previously possible at a global scale

Homogeneity and persistence of transgene expression by omitting antibiotic selection in cell line isolation

Nonuniform, mosaic expression patterns of transgenes are often linked to transcriptional silencing, triggered by epigenetic modifications of the exogenous DNA. Such phenotypes are common phenomena in genetically engineered cells and organisms. They are widely attributed to features of transgenic transcription units distinct from endogenous genes, rendering them particularly susceptible to epigenetic downregulation. Contrary to this assumption we show that the method used for the isolation of stably transfected cells has the most profound impact on transgene expression patterns. Standard antibiotic selection was directly compared to cell sorting for the establishment of stable cells. Only the latter procedure could warrant a high degree of uniformity and stability in gene expression. Marker genes useful for the essential cell sorting step encode mostly fluorescent proteins. However, by combining this approach with site-specific recombination, it can be applied to isolate stable cell lines with the desired expression characteristics for any gene of interest

Setting robust biodiversity goals

The new global biodiversity framework (GBF) being developed under the Convention on Biological Diversity must drive action to reverse the ongoing decline of the Earth’s biodiversity. Explicit, measurable goals that specify the outcomes we want to achieve are needed to set the course for this action. However, the current draft goals and targets fail to set out these clear outcomes. We argue that distinct outcome goals for species, ecosystems, and genetic diversity are essential, and should specify net outcomes required for each. Net outcome goals such as ‘no net loss’ do, however, have a controversial history, and loose specification can lead to perverse outcomes. We outline seven general principles to underpin net outcome goal-setting that minimise risk of such perverse outcomes. Finally, we recommend inclusion of statements of impact in action targets that support biodiversity goals, and we illustrate the importance of this with examples from the draft GBF action targets. These modifications would help reveal the specific contribution each would make to achieving the outcome goals, and provide clarity on whether the successful achievement of action targets would be adequate to achieve the outcome goals and, in turn, the 2050 vision: living in harmony with nature

Evidence for acquisition of virulence effectors in pathogenic chytrids

Background The decline in amphibian populations across the world is frequently linked to the infection of the chytrid fungus Batrachochytrium dendrobatidis (Bd). This is particularly perplexing because Bd was only recently discovered in 1999 and no chytrid fungus had previously been identified as a vertebrate pathogen. Results In this study, we show that two large families of known virulence effector genes, crinkler (CRN) proteins and serine peptidases, were acquired by Bd from oomycete pathogens and bacteria, respectively. These two families have been duplicated after their acquisition by Bd. Additional selection analyses indicate that both families evolved under strong positive selection, suggesting that they are involved in the adaptation of Bd to its hosts. Conclusions We propose that the acquisition of virulence effectors, in combination with habitat disruption and climate change, may have driven the Bd epidemics and the decline in amphibian populations. This finding provides a starting point for biochemical investigations of chytridiomycosis