Find research datasets worth reusing

opencc-zeroOct 2020View details →

Supplementary material 2 from: Smart AS, Tingley R, Phillips BL (2020) Estimating the benefit of quarantine: eradicating invasive cane toads from islands. NeoBiota 60: 117-136. https://doi.org/10.3897/neobiota.60.34941

Figure S1. Estimated density of cane toads on each island using density calculated per km of shoreline, and per km2 of landmass

opencc-by-4.0Oct 2020View details →

pjhop/DNAmCrosshyb: hg38 and hg19 bisulfite-converted genomes (R .rds files)

Bisulfite-converted genomes as used in the DNAmCrosshyb R package (<a href="http://github.com/pjhop/DNAmCrosshyb">github.com/pjhop/DNAmCrosshyb</a>). Data is saved per chromosome in the ‘DNAString’ format as implemented in the Biostrings BioConductor package. The data is saved in the R rds file format and can be read using the ‘readRDS()’ function. Scripts used to generate these data can be found at <a href="https://github.com/pjhop/DNAmCrosshyb/blob/master/data-raw/bisulfite_convert_hg19.R">https://github.com/pjhop/DNAmCrosshyb/blob/master/data-raw/bisulfite_convert_hg19.R</a> and <a href="https://github.com/pjhop/DNAmCrosshyb/blob/master/data-raw/bisulfite_convert_hg38.R">https://github.com/pjhop/DNAmCrosshyb/blob/master/data-raw/bisulfite_convert_hg38.R</a> . See <a href="https://github.com/pjhop/DNAmCrosshyb">https://github.com/pjhop/DNAmCrosshyb</a> for examples on how to map Illumina 450k/EPIC array probes to the bisulfite-converted genomes.

opencc-zeroOct 2020View details →

Supplementary material 1 from: Brundu G, Pauchard A, Pyšek P, Pergl J, Bindewald AM, Brunori A, Canavan S, Campagnaro T, Celesti-Grapow L, Dechoum M de S, Dufour-Dror J-M, Essl F, Flory SL, Genovesi P, Guarino F, Guangzhe L, Hulme PE, Jäger H, Kettle CJ, Krumm F, Langdon B, Lapin K, Lozano V, Le Roux JJ, Novoa A, Nuñez MA, Porté AJ, Silva JS, Schaffner U, Sitzia T, Tanner R, Tshidada N, Vítková M, Westergren M, Wilson JRU, Richardson DM (2020) Global guidelines for the sustainable use of non-native trees to prevent tree invasions and mitigate their negative impacts. NeoBiota 61: 65-116. https://doi.org/10.3897/neobiota.61.58380

Global guidelines for the sustainable use of non-native trees to prevent tree invasions and mitigate their negative impacts (GG-NNTs) Background information (Annex to the GG-NNTs)

opencc-by-4.0Oct 2020View details →

Mask R-CNN for characterization of yardang landforms

This includes the source code and datasets for the automated characterization of yardang landforms using Mask R-CNN. Codes and datasets used in the manuscript will be submitted to the Journal of Geophysical Research: Earth Surface are included. The readability of codes and other documents will be updated soon.

Supplementary material 1 from: Vagmaker N, Pereira-Ribeiro J, Colombo Ferreguetti Á, Boazi A, Gama-Matos R, Bergallo HG, Duarte Rocha CF (2020) Structure of the leaf litter frog community in an area of Atlantic Forest in southeastern Brazil. Zoologia 37: 1-10. https://doi.org/10.3897/zoologia.37.e38877

Table S1. Voucher for anuran species collected at the Duas Bocas Biological Reserve, Espírito Santo, and deposited in the amphibian collection of the Museu Nacional do Rio de Janeiro, Rio de Janeiro, Brazil.

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Data and R Markdown files for: Estimating the capacity of Chamaecrista fasciculata for adaptation to change in precipitation

Adaptation through natural selection may be the only means by which small and fragmented plant populations will persist through present day environmental change. A population's additive genetic variance for fitness (VA(W)) represents its immediate capacity to adapt to the environment in which it exists. We evaluated this property for a population of the annual legume Chamaecrista fasciculata through a quantitative genetic experiment in the tallgrass prairie region of the Midwest USA, where changing climate is predicted to include more variability in rainfall. To reduce incident rainfall, relative to controls receiving ambient rain, we deployed rain exclusion shelters. We found significant VA(W) in both treatments. We also detected a significant genotype-by-treatment interaction for fitness which suggests that the genetic basis of the response to natural selection will differ depending on precipitation. For the trait specific leaf area, we detected maladaptive phenotypic plasticity and an interaction between genotype and environment. Selection for thicker leaves was detected with increased precipitation. These results indicate capacity of this population of C. fasciculata to adapt in situ to environmental change.

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R code, spatial and tabular data to fully reproduce STEPS simulations of population change for common brushtail possum, grassland melomys and northern brown bandicoot in northern Australia

<ol> <li> The development of effective fire management for biodiversity conservation is a global challenge. The highly dynamic nature of fire, the difficulty in replicating 'real-world' fire experiments, and the need to understand population changes at large spatiotemporal scales make computer simulations particularly useful for identifying optimal fire management regimes for biodiversity conservation. </li> <li> We aimed to develop a flexible modelling approach with which to investigate how the spatiotemporal application of fire (i.e. management scenarios) influences savanna biodiversity. We used existing data from a landscape-scale fire experiment to develop population simulations for the common brushtail possum (Trichosurus vulpecula), grassland melomys (Melomys burtoni) and northern brown bandicoot (Isoodon macrourus) across the Kapalga area of Kakadu National Park in northern Australia. We simulated how populations were expected to change between 1995 and 2015 in response to the fire patterns observed at Kapalga over this period, and under a hypothetical management scenario of extensive prescribed burning. </li> <li> Our models predicted a substantial decline in all three species in response to the observed fire regime at Kapalga, suggesting that the fire patterns observed at Kapalga, with the associated mechanisms and interactions with other ecological processes, were not conducive with the persistence of native mammal populations. </li> <li> Our prescribed burning scenario had little effect on the predicted population trajectory of the common brushtail possum and grassland melomys, but markedly improved the population trajectory of the northern brown bandicoot. These inconsistencies highlight the need for a nuanced approach to fire management across northern Australian savannas, that is tailored to local conditions and management objectives. </li> <li> Synthesis and applications. The modelling approach outlined here, provides a basis for identifying fire patterns that are beneficial for conserving biodiversity, thereby increasing our capacity to establish clear targets for prescribed fire management. Importantly, this approach is flexible and can be easily adapted to other taxa and fire-prone ecosystems. </li> </ol>

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Data and R Code for publication: Should dispersers be fast learners? Modelling the role of cognition in dispersal

Both cognitive abilities and dispersal tendencies can vary strongly between individuals. Since cognitive abilities may help dealing with unknown circumstances it is conceivable that dispersers may rely more heavily on learning abilities than residents. However, cognitive abilities are costly and leaving a familiar place might result in losing the advantage of having learned to deal with local conditions. Thus, individuals which invested in learning to cope with local conditions may be more reluctant to leave their natal place. In order to disentangle the complex relationship between dispersal and learning abilities we implemented individual-based simulations. By allowing for developmental plasticity, individuals could either develop a "resident" or "dispersal" cognitive phenotype. In line with our expectations, the correlation between learning abilities and dispersal could take any direction, depending how much time individuals had to recoup their investment in cognition. Both, longevity and the timing of dispersal within lifecycles determine the time individuals have to recoup that investment and thus crucially influence this correlation. We therefore suggest that species' life-history will strongly impact the expected cognitive abilities of dispersers, relative to their resident conspecifics, and that cognitive abilities might be an integral part of dispersal syndromes.

Supplementary material 11 from: Tomaskinova J, Dicks L, Collier M, Geneletti D, Grace M, Longato D, Sadula R, Stoev P, Sapundzhieva A, Balzan MV (2020) Capacity-building and networking events for nature-based solutions and re-naturing in Malta. Research Ideas and Outcomes 6: e60893. https://doi.org/10.3897/rio.6.e60893

Identifying priority knowledge needs for implementing nature-based solutions-results from Malta and other Mediterranean islands

Supplementary material 9 from: Tomaskinova J, Dicks L, Collier M, Geneletti D, Grace M, Longato D, Sadula R, Stoev P, Sapundzhieva A, Balzan MV (2020) Capacity-building and networking events for nature-based solutions and re-naturing in Malta. Research Ideas and Outcomes 6: e60893. https://doi.org/10.3897/rio.6.e60893

Management and restoration of Mediterranean wetlands to provide ecosystem services and other benefits

Supplementary material 12 from: Tomaskinova J, Dicks L, Collier M, Geneletti D, Grace M, Longato D, Sadula R, Stoev P, Sapundzhieva A, Balzan MV (2020) Capacity-building and networking events for nature-based solutions and re-naturing in Malta. Research Ideas and Outcomes 6: e60893. https://doi.org/10.3897/rio.6.e60893

Non-material ecosystem benefits of protected areas as a bridge to future challenges in sustainable development

opennotspecifiedDec 2020View details →

FIGURE 8. Melanosuchus niger UFAC R-203 in On a new Melanosuchus species (Alligatoroidea: Caimaninae) from Solimões Formation (Eocene-Pliocene), Northern Brazil, and evolution of Caimaninae

FIGURE 8. Melanosuchus niger UFAC R-203 in anterolateral view. (A) Original specimen; (B) Schematic draw elucidating the presence and positioning of the rostral ridges. Anatomical abbreviations: l, lacrimal; EN, external nares; ITF, infratemporal fenestra; J, jugal; pmx, premaxilla; mx, maxilla; n, nasal; nc, narial crest; O, orbit; rd1, rostral ridge 1; rd2, rostral ridge 2. Scale bar = 20mm.

F I G U R E 7 in Ecology and morphology of mouse lemurs (Microcebus spp.) in a hotspot of microendemism in northeastern Madagascar, with the description of a new species

F I G U R E 7 Outer morphology of Microcebus jonahi. (a) Drawing of an adult individual; (b) Habitus of adult female (paratype individual BD1); (c–e) Close‐ups of adult male (holotype B34). Illustration copyright by Stephen D. Nash/IUCN SSC Primate Specialist Group; used with permission. Photos by D. Schüssler

F I G U R E 6 in Ecology and morphology of mouse lemurs (Microcebus spp.) in a hotspot of microendemism in northeastern Madagascar, with the description of a new species

F I G U R E 6 Reproductive records for adult males (a) and females (b) of Microcebus spp. in northeastern Madagascar and presence of juvenile individuals (c) in the population

F I G U R E 5 in Ecology and morphology of mouse lemurs (Microcebus spp.) in a hotspot of microendemism in northeastern Madagascar, with the description of a new species

F I G U R E 5 Linear discriminant analysis including all morphometric parameters (except third toe length). All five linages can be distinguished statistically (Wilk's lambda = 0.005; F = 10.338; p <.001) with a misclassification rate of 12.8%. dia, Mantadia NP; vala, Ambavala

F I G U R E 4 in Ecology and morphology of mouse lemurs (Microcebus spp.) in a hotspot of microendemism in northeastern Madagascar, with the description of a new species

F I G U R E 4 Principal component analysis including all morphometric parameters (except third toe length) showing PC1/PC2 (left) and PC3/PC4 (right). Small (M. mittermeieri and M. lehilahytsara) and large (M. sp. #3 and M. macarthurii) lineages differ along PC1, with some differentiation of M. mittermeieri and M. lehilahytsara along both PC1 and PC2, whereas M. sp. #3 and M. macarthurii split along PC3. Clusters corresponding to the five lineages were significantly different from each other (PERMANOVA: F = 36.88; df = 77; p <.001). dia, Mantadia NP; PERMANOVA, permutational multivariate analysis of variances; vala, Ambavala

F I G U R E 2 in Ecology and morphology of mouse lemurs (Microcebus spp.) in a hotspot of microendemism in northeastern Madagascar, with the description of a new species

F I G U R E 2 Maximum likelihood tree illustrating the phylogenetic relationships between Microcebus spp. in northeastern Madagascar as inferred by RAxML (based on nuclear sequence data). Sampling locations are indicated at the tips of the branches. Illustration adapted from Poelstra et al. (2020). NP, National Park; SNR, Special Nature Reserve; SR, Special Reserve

F I G U R E 1 in Ecology and morphology of mouse lemurs (Microcebus spp.) in a hotspot of microendemism in northeastern Madagascar, with the description of a new species

F I G U R E 1 Map depicting the study region with confirmed species occurrences (Hotaling et al., 2016; Kappeler et al., 2005; Louis et al., 2006; Radespiel et al., 2008, 2012; Weisrock et al., 2010). New sampling locations for this study are indicated with "*" and forest cover in 2017/2018 was derived from Vieilledent et al. (2018) and Schüssler et al. (2020). NP, National Park; SNR, Special Nature Reserve; SR, Special Reserve

F I G U R E 3 in Ecology and morphology of mouse lemurs (Microcebus spp.) in a hotspot of microendemism in northeastern Madagascar, with the description of a new species

F I G U R E 3 Selected morphometric measurements of Microcebus spp. in northeastern Madagascar. Comparison based on one‐way ANOVA (p <.001 for all parameters) and grouping (letters above values) according to Tukey post hoc tests. Plots for all parameters in Figure S1. ANOVA, analysis of variance; leh, M. lehilahytsara (at Mantadia NP); mac, M. macarthurii (at Anjiahely); mit, M. mittermeieri (at Anjiahely); sim, M. simmonsi (at Ambodiriana); sp.3, M. sp. #3 (at Ambavala and Antanambe)

FIGURE 2. J–R in Taxonomy of the Oriental leafhopper genus Parabolopona (Hemiptera: Cicadellidae: Deltocephalinae: Drabescini) with a new species from China

FIGURE 2. J–R Male genitalia of Parabolopona yunnanensis sp. nov.; J, Genital capsule, left lateral view; K, Valve, subgenital plate, style, connective and aedeagus, dorsal view; L, Valve, subgenital plate and style, dorsal view; M, Right style, dorsal view; N, Right style, ventral view; O–P, Connective, ventral and lateral view; Q–R, Aedeagus, lateral and posterior view, respectively.