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Supplementary material 3 from: Neves MO, Cabral H, Pedrozo M, Ferreira VL, Moura M, Santana DJ (2020) Dataset of occurrences and ecological traits of amphibians from Upper Paraguay River Basin, central South America. Nature Conservation 41: 71-89. https://doi.org/10.3897/natureconservation.41.54265
References from the citations contained in Suppl. material 2
Supplementary material 2 from: Neves MO, Cabral H, Pedrozo M, Ferreira VL, Moura M, Santana DJ (2020) Dataset of occurrences and ecological traits of amphibians from Upper Paraguay River Basin, central South America. Nature Conservation 41: 71-89. https://doi.org/10.3897/natureconservation.41.54265
Table S2
Supplementary material 1 from: Neves MO, Cabral H, Pedrozo M, Ferreira VL, Moura M, Santana DJ (2020) Dataset of occurrences and ecological traits of amphibians from Upper Paraguay River Basin, central South America. Nature Conservation 41: 71-89. https://doi.org/10.3897/natureconservation.41.54265
Table S1
Supplementary material 1 from: Hawkes PG (2020) A new species in the Tetramorium solidum-group (Hymenoptera, Formicidae, Myrmicinae) from the Richtersveld National Park, South Africa, with an assessment of threats and conservation status. ZooKeys 965: 55-71. https://doi.org/10.3897/zookeys.965.52735
File S1
Figure 2 from: Hawkes PG (2020) A new species in the Tetramorium solidum-group (Hymenoptera, Formicidae, Myrmicinae) from the Richtersveld National Park, South Africa, with an assessment of threats and conservation status. ZooKeys 965: 55-71. https://doi.org/10.3897/zookeys.965.52735
Figure 2 Dorsal view of mesosoma and petiole segments ATetramorium nama sp. nov. holotype worker, CASENT0818990 BT. grandinode, CASENT0818846. (Photos by Peter Hawkes, from www.AntWeb.org)
Figure 1 from: Hawkes PG (2020) A new species in the Tetramorium solidum-group (Hymenoptera, Formicidae, Myrmicinae) from the Richtersveld National Park, South Africa, with an assessment of threats and conservation status. ZooKeys 965: 55-71. https://doi.org/10.3897/zookeys.965.52735
Figure 1 Tetramorium nama sp. nov. A–C holotype worker, CASENT0818990: A full-face view B lateral view C dorsal view D map of Africa (inset, with South Africa shaded dark grey) and detail of South Africa (main image), showing known distribution of Tetramorium nama sp. nov. (black dot), with a white outline indicating the Richtersveld National Park. (Photos by Bradley Reynolds, from www.AntWeb.org)
Figure 3 from: Hawkes PG (2020) A new species in the Tetramorium solidum-group (Hymenoptera, Formicidae, Myrmicinae) from the Richtersveld National Park, South Africa, with an assessment of threats and conservation status. ZooKeys 965: 55-71. https://doi.org/10.3897/zookeys.965.52735
Figure 3 A riverine fringe habitat in which Tetramorium nama sp. nov. was collected, showing living vegetation dominated by Euclea pseudebenus as well as numerous cut Prosopis glandulosa (freshly cut and piles of dry branches) B alluvial terrace gravel and C alluvial fan habitats (in which T. pogonion and T. rufescens were collected) between the river and the rocky mountains to the southwest: the alluvial fan lies between the gravel terrace and the mountains.
Supplementary material 1 from: Shorb CM, Freymiller LA, Hernandez DL (2020) Differential responses of prairie rodents to edge effects from recreational trails. Nature Conservation 41: 113-140. https://doi.org/10.3897/natureconservation.41.52100
Tables S1, S2
Supplementary material 2 from: Huang J, Guo Z, Tang S, Ren W, Chu G, Wang L, Zhao L, Yu R, Xu Y, Ding Y, Zang R (2020) Floristic composition and plant diversity in distribution areas of native species congeneric with Betula halophila in Xinjiang, northwest China. Nature Conservation 42: 1-17. https://doi.org/10.3897/natureconservation.42.54735
Figure S2. The distribution frequency of Betula species varies with the environment gradients
Dataset for: "BACPHLIP: Predicting bacteriophage lifestyle from conserved protein domains"
<p>This is the dataset used in the manuscript titled "BACPHLIP: Predicting bacteriophage lifestyle from conserved protein domains". The dataset is necessary to run the code that can be found at <a href="https://github.com/adamhockenberry/dca-weighting">https://github.com/adamhockenberry/bacphlip-model-dev</a> and outside of the context of the code this data will likely not be super well-annotated or helpful. The code within that repository, however, should provide sufficient information about the structure and usage of this dataset. </p>
Data from: Habitat suitability and connectivity modeling reveal priority areas for Indiana bat (Myotis sodalis) conservation in a complex habitat mosaic
Context <p>Conservation for the Indiana bat (<i>Myotis sodalis), </i>a federally endangered species in the United States of America, is typically focused on local maternity sites; however, the species is a regional migrant, interacting with the environment at multiple spatial scales. Hierarchical levels of management may be necessary, but we have limited knowledge of landscape-level ecology, distribution, and connectivity of suitable areas in complex landscapes.</p> Objectives <p>We sought to 1) identify factors influencing <i>M. sodalis </i>maternity colony distribution in a mosaic landscape, 2) map suitable maternity habitat, and 3) quantify connectivity importance of patches.</p> Methods <p>Using 3 decades of occurrence data, we tested <i>a priori</i>,<i> </i>hypothesis-driven<i> </i>habitat suitability models. We mapped suitable areas and quantified connectivity importance of habitat patches with probabilistic habitat availability metrics.</p> Results <p>Factors improving landscape-scale suitability included limited agriculture, more forest cover, forest edge, proximity to medium-sized water bodies, lower elevations, and limited urban development. Areas closer to hibernacula and rivers were suitable. Binary maps showed that thirty percent of the study area was suitable for <i>M. sodalis</i> and 29% was important for connectivity. Most suitable patches were important for intra-patch connectivity and far fewer contributed to inter-patch connectivity.</p> Conclusions <p>While simple models may be effective for small, homogenous landscapes, complex models are needed to explain habitat suitability in large, mixed landscapes. Suitability modeling identified factors that made sites attractive as maternity areas. Connectivity analysis improved our understanding of important areas for bats, identified suitable patches that may be isolated from the habitat network, and prioritized areas to target restoration.</p>
Water stress and insect herbivory interactively reduce crop yield while the insect pollination benefit is conserved
<p>Climate change is predicted to hamper crop production due to precipitation deficits and warmer temperatures inducing both water stress and increasing herbivory due to more abundant insect pests. Consequently, crop yields will be impacted simultaneously by abiotic and biotic stressors. Extensive yield losses due to such climate change stressors might, however, be mitigated by ecosystem services such as insect pollination. We examined the single and combined effects of water stress, insect herbivory and insect pollination on faba bean yield components and above- and belowground plant biomass under realistic field conditions. We used rainout shelters to simulate a scenario in line with climate change projections, with adequate water supply at sowing followed by a long period without precipitation. This induced a gradually increasing water stress, culminating around crop flowering and yield formation. We found that gradually increasing water stress combined with insect herbivory by aphids interactively shaped yield in faba beans. Individually, aphid herbivory reduced yield by 79 % and water stress reduced yield by 52 %. However, the combined effect of water stress and aphid herbivory reduced yield less (84 %) than the sum of the individual stressor effects. In contrast, insect pollination increased yield by 68 % independently of water availability and insect herbivory. Our results suggest that yield losses can be greatly reduced when both water stress and insect herbivory are reduced simultaneously. In contrast, reducing only one stressor has negligible benefits on yield as long as the crop is suffering from the other stressor. We call for further exploration of interactions among ecosystem services and biotic and abiotic stressors that simulate realistic conditions under climate change.</p>
Supplement (interactive Excel tool) to MAGIC Deliverable 6.4 'Intervention directed towards environmental protection: Biodiversity conservation on agricultural land'
<p>Interactive Excel data sheets to analyse potential interventions (i.e. changes in land use type and intensity) in the Dutch dairy production system towards conserving biodiversity. The tool uses the Dutch dairy sector as a case study and represents the current land use by dairy farmers in the Netherlands. The measures applied result in different landscapes that satisfy different biodiversity targets. At the same time, the tool measures the (negative) impact on food production.</p> <p>This interactive Excel tool is a supplement to: Kok A., Ripoll Bosch R., de Olde E.M., Muscat A., de Boer I.J.M. (2020), 'Intervention directed towards environmental protection: Biodiversity conservation on agricultural land', MAGIC (H2020–GA 689669) Project Deliverable 6.4, 24 February 2020, available online: <a href="https://magic-nexus.eu/documents/d64-intervention-directed-towards-environmental-protection">https://magic-nexus.eu/documents/d64-intervention-directed-towards-environmental-protection</a>.</p> <p> </p>
Metabolic rates and growth data for: Do small precocial birds enter torpor to conserve energy during development?
<p>Precocial birds hatch feathered and mobile, but when they become fully endothermic soon after hatching, their heat loss is high and they may become energy-depleted. These chicks could benefit from using energy-conserving torpor, which is characterised by controlled reductions of metabolism and body temperature (T<sub>b</sub>). We investigated at what age the precocial king quail <i>Cortunix chinensis</i> can defend a high T<sub>b</sub> under a mild thermal challenge and whether they can express torpor soon after achieving endothermy to overcome energetic and thermal challenges. Measurements of surface temperature (T<sub>s</sub>) using an infrared thermometer showed that king quail chicks are partially endothermic at 2-10 days, but can defend high T<sub>b</sub> at a body mass of ~13 g. Two chicks expressed shallow nocturnal torpor at 14 and 17 days for 4 to 5 hours with a reduction of metabolism by > 40% and another approached torpor threshold. Although chicks were able to rewarm endogenously from the first torpor bout, metabolism and T<sub>s</sub> decreased again by the end of the night, but they rewarmed passively when removed from the chamber. The total metabolic rate increased with body mass. All chicks measured showed a greater reduction of nocturnal metabolism than previously reported in quails. Our data show that shallow torpor can be expressed during the early postnatal phase of quails, when thermoregulatory efficiency is still developing, but heat loss is high. We suggest that torpor may be a common strategy for overcoming challenging conditions during the development in small precocial and not only altricial birds.</p>
Global biogeographic synthesis and priority conservation regions of the relict tree family Juglandaceae
<p><span><b>Abstract</b></span></p> <p><span><b>Aim:</b> To establish a complete database of Juglandaceae at a spatiotemporal scale and develop a phylogeographic framework with which to elucidate the distributional patterns, diversity patterns, origins, evolution, and conservation priority regions of this family.</span></p> <p><span><b>Location:</b> Worldwide</span></p> <p><span><span><b>Methods: </b>Data on the distribution of all the extant and fossil species of Juglandaceae were collected, followed by analyses of its latitudinal distribution, elevational distribution, and species and generic diversity. Furthermore, based on all genera and 87% of the species, we reconstructed phylogenetic relationships, estimated divergence times, calculated phylogenetic diversity and inferred ancestral distributions.</span></span></p> <p><span><b>Results: </b>Extant Juglandaceae (10 genera and 60 species) are mainly distributed in eastern Asia and North America (principally between 20°N and 40°N). Tropical Juglandaceae mainly inhabit mountainous areas higher than 1000 m, especially in the New World. Southwest China and northern Vietnam are characterized by high species, generic, and phylogenetic diversity. The United States of America has only high species diversity. The area of origin of Juglandaceae was North America and Europe in the early Eocene, and its widespread dispersal mainly occurred between 13 and 26 Ma.</span></p> <p><span><b>Main conclusions: </b>The members of Juglandaceae inhabit areas with temperate climatic conditions. The diversification centre has shifted intercontinentally from North America and Europe to Southwest China and northern Vietnam, which are identified as conservation priority regions. The high-latitude cooling during the Oligocene followed by a long-term stable warmer climate in the early and middle Miocene drove the southward translocation of the family.</span></p>
Improving conservation strategies of raptors through landscape ecology analysis. the case of the endemic Cuban black hawk
<p><span>1. Raptor species conservation should consider a landscape perspective in order to include habitat requirements associated to large home ranges around nesting sites. Landscape analysis can help to better understand raptor habitat requirements and the degree of tolerance to habitat changes at different scales.</span></p> <p><span>2. We used a landscape ecology perspective to determine the nesting habitat selection of endemic and endangered Cuban Black Hawk, and using ecological niche modelling we obtained the potential distribution of nests to evaluate the effectiveness of protected areas (PAs) for raptor conservation. </span></p> <p><span>3. Nesting habitat selection was related to breeding success at a landscape scale using data from 27 different nesting sites during 2012-2013 breeding seasons. The potential nesting areas distribution was compared with current officially PAs design in the central region of Cuba.</span></p> <p><span>4. All nests were located in mangrove swamp. Pairs chose nesting sites with low soil-vegetation moisture and low soil reflectance. At the landscape level, they selected low shape complexity of patches and few patches of coastal vegetation around nesting sites which contained similar mangrove patch size and shape. The potential distribution of nests increased close to the coastline. The model predicted a suitable narrow area of 556 km<sup>2</sup>, and the most favourable nesting area represented 2% of this total. A 33% of nests were located within officially natural protected areas while 27% were close to or inside highly threatened areas. A 16% of high to medium suitable nesting habitat overlaps with urban areas. Currently, PAs contain 23% of the nesting area distribution.</span></p> <p>5. Our study shows landscape ecology and nest-site selection approach is crucial to evaluate the persistence of Cuban Black Hawk, as environmental variables and human activity can be related to its productivity. This approach can be applied in conservation strategies of island raptors.</p>
Hibiscus nextRAD-seq conservation genomics
<p>The Neches River Rose Mallow (<i>Hibiscus dasycalyx</i>) is a rare wildflower endemic to Texas that is federally protected in the US. While previous work suggests that <i>H. dasycalyx</i> may be hybridizing with its widespread congeners, the Halberd-leaved Rose Mallow (<i>H. laevis</i>) and the Wolly Rose Mallow (<i>H. moscheutos</i>), this has not been studied in detail. We evaluated the relative threats to <i>H. dasycalyx</i> posed by hybridization with <i>H. laevis</i> and <i>H. moscheutos</i> by 1) examining their relatedness to one another via modern phylogenomic methods, 2) examining the species' ecological (dis)similarities to one another using ecological niche modeling, and 3) looking for genomic evidence of hybridization among the three species. Our results suggest that <i>H. dasycalyx</i> is very closely related and ecologically similar to <i>H. laevis</i>, and suggest that <i>H. laevis</i> is interbreeding with <i>H. dasycalyx</i> in the wild. Conversely, <i>H. moscheutos</i> appears to be more distantly related to <i>H. dasycalyx</i> and more ecologically dissimilar, and the two are most likely not hybridizing. For these reasons, we believe that <i>H. laevis</i> poses a greater threat to <i>H. dasycalyx</i> than <i>H. moscheutos</i>. We offer some hypotheses as to why <i>H. dasycalyx</i> and <i>H. laevis</i> are coming into secondary contact where hybridization can occur.</p>
Supplementary material 1 from: Liu J, Jiang R, Zhang G (2020) Number and distribution of large old ginkgos in east China: Implications for regional conservation. Nature Conservation 42: 71-87. https://doi.org/10.3897/natureconservation.42.59284
The large old ginkgos in Jiangsu Province, east China
Figure 9 from: França RC, Morais M, França FGR, Rödder D, Solé M (2020) Snakes of the Pernambuco Endemism Center, Brazil: diversity, natural history and conservation. ZooKeys 1002: 115-158. https://doi.org/10.3897/zookeys.1002.50997
Figure 9 Geographic distribution records for snakes of the Pernambuco Endemism Center (PEC). AApostolepis longicaudata and A. cearensisBAtractus caete, A. maculatus and A. potschiCBoiruna sertaneja and Caaeteboia sp. DDipsas mikanii and D. neuwiediED. sazimai and D. variegataFEchinanthera cephalomaculata and E. cephalostriataGErythrolamprus almadensis, E. taeniogaster, E. miliaris, and E. aesculapiiHE. poecilogyrus, E. viridis and E. reginae. IHelicops angulatus and H. leopardinus.
Figure 5 from: França RC, Morais M, França FGR, Rödder D, Solé M (2020) Snakes of the Pernambuco Endemism Center, Brazil: diversity, natural history and conservation. ZooKeys 1002: 115-158. https://doi.org/10.3897/zookeys.1002.50997
Figure 5 Snake species from the Pernambuco Endemism Center. AErythrolamprus taeniogasterBErythrolamprus viridisCHelicops angulatusDHelicops leopardinusEHydrodynastes gigasFImantodes cenchoaGLeptodeira annulataHLygophis dilepisIOxyrhopus guibeiJOxyrhopus petolariusKOxyrhopus trigeminusLPhilodryas nattereriMPhilodryas olfersiiNPhilodryas patagoniensisOPhimophis guerini. Photograph credits: Frederico França (A, C, F, H, I, K, M, N, O), Vanessa Nascimento (B, D), Ivan L. Sampaio (E), Willianilson Pessoa (G), Rafaela França (J, L).
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.