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Datasets related to the paper 'Identifying priority areas for restoring mountain ungulates in the Caucasus ecoregion'
<p>Three datasets are contained here:</p> <p>1. The final habitat suitability map for bezoar goats <span class="st">(Capra aegagrus aegagrus)</span> for the Caucasus ecoregion (in TIFF format)</p> <p>2. The table of occurence location used for generating this map (in CSV format)</p> <p>3. The habitat patches derived from the habitat suitability map and their priority ranking according to three conservation scenarios (in SHP format)</p>
Comparative Study of the Restorative effects of Forest and Urban Videos during Covid-19 Lockdown: Intrinsic and Benchmark Value
<p>Article: "Comparative Study of the Restorative effects of Forest and Urban Videos during Covid-19 Lockdown: Intrinsic and Benchmark Value"</p> <p>Video S1: forest environment </p> <p>Video S2: urban environment</p>
Data from: Exotic species drive patterns of plant species diversity in 93 restored tallgrass prairies
<p>A primary goal of restoration ecology is to understand the factors that generate variability in species diversity and composition among restorations. Plant communities may assemble deterministically towards a common community type, or they may assemble stochastically, ending differently because of weather conditions during establishment, soil legacy effects, or exotic species propagule pressure. To test these alternative hypotheses, we sampled plant communities and soil at 93 randomly selected restored prairies distributed throughout Iowa, USA. Five remnant sites were sampled as a reference. We tested our hypotheses using multiple regressions and investigated the strength of direct and indirect effects on species diversity and richness using structural equation models. The prairie restorations were highly variable in their age, size, diversity, soil characteristics, and how they were managed post-seeding. The strongest predictor of plant species richness and diversity was the degree of invasion, as measured by the abundance of exotic species. Restorations planted with species-rich seed mixes had reduced exotic species abundance, which led indirectly to higher species richness of restorations. Sites with higher organic matter and a more linear shape had a direct positive effect on exotic abundance, which in turn decreased diversity. We found little support for deterministic assembly, and diversity did not increase with the age of planting. Our results indicate that restored prairie communities tend to assemble into states of high or low diversity, driven by invasion from exotic plant species. Management of exotic species is essential for maximizing species diversity in temperate grassland restorations.</p>
Morphoecological characteristics of grasses used to restore degraded semi-arid African rangelands
<p class="CxSpFirst">Progressive loss of productivity and plant diversity has been a major concern for land managers of global arid and semi-arid rangelands. This is often attributed to heavy grazing by large livestock herds and wildlife leading to land degradation threatening millions of livelihoods that rely on rangeland resources. Consequently, combating land degradation has increasingly become important global agenda. Active restoration technologies such as indigenous grass reseeding has been identified as a viable ecological solution for restoring degraded rangeland landscapes and providing forage for sustainable livestock production. Grass species indigenous to African rangelands <i>Cenchrus ciliaris</i> L. (African foxtail grass), <i>Eragrostis superba</i> Peyr. (Maasai love grass), <i>Enteropogon macrostachyus</i> (Hochst. Ex A. Rich.) Monro ex Benth. (Bush rye grass), <i>Chloris roxburghiana </i>Schult. (Horsetail grass) and <i>Chloris gayana </i>Kunth. cv Boma (Rhodes grass) were established in an African semi-arid rangeland landscape under natural conditions to compare their morphoecological characteristics and suitability for ecological restoration. Seed viability, seedling emergence, biomass dry matter yields, plant densities, basal cover, seed production, tiller densities and plant height were determined. <i>Chloris gayana </i>cv Boma and <i>E. superba </i>produced significantly higher<i> </i>dry matter biomass yields and seed production. High biomass and seed production demonstrate their suitability to support livestock production and replenish depleted soil seed banks, respectively.<i> Enteropogon macrostachyus </i>and <i>C. ciliaris </i>displayed significantly higher values for plant densities, tiller densities and basal cover, also used to measure establishment and ecological restoration success. <i>Chloris roxburghiana </i>ranked lowest in all the measured morphoecological characteristics. This could be a strong indicator of ecological site-specific characteristic of <i>C. roxburghiana</i>. Active restoration of degraded African semi-arid rangelands and forage provision for herbivores using indigenous grass reseeding can best be achieved through careful selection of grass species to take advantage on their specific multiple morphoecological characteristics. Furthermore, selection of the grass species to use should primarily be informed by the intended use of the rangeland.</p>
Coastal Habitat Restoration Survey
<p>Online expert elicitation survey of the membership of Coastal and Estuarine Research Federation (CERF) and International Coral Reef Society (ICRS). This dataset includes responses to a series of questions exploring scientist and practitioner experience restoring particular coastal habitats (coral reefs, oyster reefs, mangroves, salt marsh, and seagrasses), as well as perceptions of the purpose of restoration, site selection practices, the types of metrics used to evaluate restoration success, and the potential challenges to successful restoration.</p>
Data from: Genetic diversity of the rain tree (Albizia saman) in Colombian seasonally dry tropical forest for informing conservation and restoration interventions
<p><i>Albizia saman</i> is a multipurpose tree species of seasonally dry tropical forests (SDTFs) of Mesoamerica and northern South America typically cultivated in silvopastoral and other agroforestry systems around the world, a trend that is bound to increase in light of multimillion hectare commitments for forest and landscape restoration. The effective conservation and sustainable use of <i>A. saman</i> requires detailed knowledge of its genetic diversity across its native distribution range of which surprisingly little is known to date. We assessed the genetic diversity and structure of <i>A.saman</i> across twelve representative locations of SDTF in Colombia, and how they may have been shaped by past climatic changes and human influence. We found four different genetic groups which may be the result of differentiation due to isolation of populations in pre-glacial times. The current distribution and mixture of genetic groups across STDF fragments we observed might be the result of range expansion of SDTFs during the last glacial period followed by range contraction during the Holocene and human-influenced movement of germplasm associated with cattle ranching. Despite the fragmented state of the presumed natural <i>A. saman</i> stands we sampled we did not find any signs of inbreeding, suggesting that gene flow is not jeopardized in humanized landscapes. However, further research is needed to assess potential deleterious effects of fragmentation on progeny. Climate change is not expected to seriously threaten the <i>in situ</i> persistence of <i>A. saman</i> populations and might present opportunities for future range expansion. However, the sourcing of germplasm for tree planting activities needs to be aligned with the genetic affinity of reference populations across the distribution of Colombian SDTFs. We identify priority source populations for i<i>n situ</i> conservation based on their high genetic diversity, lack or limited signs of admixture and/or genetic uniqueness.</p>
FIGURE 10 in Restoration of two Carabidae (Coleoptera) species from the Sistema Ibérico Ranges (North-Central Iberian Peninsula): Nebria (Nebria) urbionensis Arribas 1991 and Zabrus (Iberozabrus) cameranus Arribas, 1994, bonae species
FIGURE 10. Three Nebria specimens (coll OA) from Sierra de Béjar labelled as collected by J.P. Zaballos in El Calvitero (2400 m) all the same day (28-8-83): A) latero-dorsal view photography; B) dorsal view photography. The middle specimen is a N. (N.) vuillefroyi, but is mounted and labelled in a totally different material that the other two specimens (true N. pazi). This is probably a mislabeled specimen, similar to any others that reach Ledoux & Roux and give birth to the erroneous reference of N. (N.) vuillefroyi in Béjar. Only N. (N.) pazi has been collected in the high summits of Béjar and Gredos.
FIGURE 9 in Restoration of two Carabidae (Coleoptera) species from the Sistema Ibérico Ranges (North-Central Iberian Peninsula): Nebria (Nebria) urbionensis Arribas 1991 and Zabrus (Iberozabrus) cameranus Arribas, 1994, bonae species
FIGURE 9. Phylogenetic Tree showing the position of the Zabrus (Iberozabrus) cameranus (403 bp.) sequenced in this study and 30 Zabrus sequences, with Amara aenea as outgroup, downloaded from GenBank (numbers in the tree are the GenBank ones). Phylogenetic analyses were performed with maximum-Likelihood (ML) in RAxML v.7.4.2 (Stamatakis, 2006) as implemented in RAxML-GUI v.1.3 (Silvestro & Michalak, 2012). The ML tree was inferred with the GTR+G model of sequence evolution and 100 random addition replicates. Nodal support was assessed with 1,000 bootstrap replicates. Only bootstrap values superior to 70 are indicated. Zabrus (I.) cameranus is supported by a bootstrap value of 78 % as outgroup of the Z. (I.) laurae and Z. (I.) seidlitzi clade.
FIGURE 8 in Restoration of two Carabidae (Coleoptera) species from the Sistema Ibérico Ranges (North-Central Iberian Peninsula): Nebria (Nebria) urbionensis Arribas 1991 and Zabrus (Iberozabrus) cameranus Arribas, 1994, bonae species
FIGURE 8. Canonical Discriminant Analysis (CDA) plot of the biometrical characteristics of the three Zabrus species studied: Z. (I.) cameranus from Sierra de Cameros, Z. (I.) laurae from Sierra de Ayllón, and Z. (I.) seidlitzi seidlitzi from Sierra de Guadarrama. See text for explanation of the results. An "X" inside each polygon represents the centroid; that is, a hypothetical middle individual of each sample.
FIGURE 7 in Restoration of two Carabidae (Coleoptera) species from the Sistema Ibérico Ranges (North-Central Iberian Peninsula): Nebria (Nebria) urbionensis Arribas 1991 and Zabrus (Iberozabrus) cameranus Arribas, 1994, bonae species
FIGURE 7. Internal female genitalia (A, B and C) and detail of the distal section of the villosus duct (B and C): A) Zabrus (Iberozabrus) seidlitzi seidlitzi, from Ortuño et al. (2003); B) Zabrus (Iberozabrus) laurae from Pico Tres Provincias; C) Zabrus (Iberozabrus) cameranus from Ortigosa de Cameros (paratype).
FIGURE 4 in Restoration of two Carabidae (Coleoptera) species from the Sistema Ibérico Ranges (North-Central Iberian Peninsula): Nebria (Nebria) urbionensis Arribas 1991 and Zabrus (Iberozabrus) cameranus Arribas, 1994, bonae species
FIGURE 4. Male genitalia of Nebria (Nebria) vuillefroyi from Collado de Valdemartín (A–D) and Nebria (Nebria) urbionensis from Pico de Urbión (E–H): A, E) median lobe in left lateral view (evaginated internal sac); B, F) apex of the median lobe in dorsal view; C, G) left paramere in left lateral view; D, H) right paramere in right lateral view.
FIGURE 6 in Restoration of two Carabidae (Coleoptera) species from the Sistema Ibérico Ranges (North-Central Iberian Peninsula): Nebria (Nebria) urbionensis Arribas 1991 and Zabrus (Iberozabrus) cameranus Arribas, 1994, bonae species
FIGURE 6. Canonical Discriminant Analysis (CDA) plot of the biometrical characteristics of the three Nebria samples studied: N. (N.) vuillefroyi from Sierra de Guadarrama and from Sierra de Ayllón, and N. (N.) urbionensis from Sierra de Urbión. See text for explanation of the results. An "X" inside each polygon represents the centroid; that is, a hypothetical middle individual of each sample.
FIGURE 5 in Restoration of two Carabidae (Coleoptera) species from the Sistema Ibérico Ranges (North-Central Iberian Peninsula): Nebria (Nebria) urbionensis Arribas 1991 and Zabrus (Iberozabrus) cameranus Arribas, 1994, bonae species
FIGURE 5. Female genitalia of Nebria (Nebria) vuillefroyi (A: from La Gelecha-La Flecha; C: from Collado Valdemartín; D: from Arroyo Seco) and Nebria (Nebria) urbionensis (B and E: from Pico de Urbión). A–B) External and internal genitalia (scale bar: 0.5 mm); C–E) detail of the helmintoid sclerite (scale bar: 0.2 mm).
FIGURE 3 in Restoration of two Carabidae (Coleoptera) species from the Sistema Ibérico Ranges (North-Central Iberian Peninsula): Nebria (Nebria) urbionensis Arribas 1991 and Zabrus (Iberozabrus) cameranus Arribas, 1994, bonae species
FIGURE 3. Schematic habitus (omitting legs and antennae) in dorsal view: A) Nebria (Nebria) vuillefroyi from Collado de Valdemartín, and B) Nebria (Nebria) urbionensis from Pico de Urbión.
FIGURE 2. A in Restoration of two Carabidae (Coleoptera) species from the Sistema Ibérico Ranges (North-Central Iberian Peninsula): Nebria (Nebria) urbionensis Arribas 1991 and Zabrus (Iberozabrus) cameranus Arribas, 1994, bonae species
FIGURE 2. A) Nebria outline with the studied measurements (see text). B) Pronotum of Nebria, illustrating DMS [length of the medial discal sulcus of pronotum]. C) Pronotum of Zabrus illustrating AAW [length of the anterior angles protruding from the level of the pronotum flange] and PAW [width of the lateral flat flange at the posterior angles].
FIGURE 1. A in Restoration of two Carabidae (Coleoptera) species from the Sistema Ibérico Ranges (North-Central Iberian Peninsula): Nebria (Nebria) urbionensis Arribas 1991 and Zabrus (Iberozabrus) cameranus Arribas, 1994, bonae species
FIGURE 1. A) Relief map of the northern half of the Iberian Peninsula showing main orographic elements. B) Distribution of Nebria (Nebria) vuillefroyi and Nebria (Nebria) urbionensis. C) Distribution of Zabrus (Iberozabrus) seidlitzi, Zabrus (Iberozabrus) laurae and Zabrus (Iberozabrus) cameranus. Each point corresponds to a UTM coordinate of 10 x 10 km.
Data from: Trait-environment interactions affect plant establishment success during restoration
<p>Establishment and persistence are central to community assembly and are determined by how traits interact with the environment to determine performance ('trait-environment interactions'). Community assembly studies have rarely considered such trait-environment interactions, however, which can lead to incorrect inferences about how traits affect assembly. We evaluated how functional traits, environmental conditions, and trait-environment interactions structure plant establishment, as a measure of performance. Within 12 prairie restorations created by sowing 70 species, we quantified environmental conditions and counted individuals of each seeded species to quantify first year establishment. Three trait-environment interactions structured establishment. Leaf nitrogen interacted with herbivore pressure, as low leaf nitrogen species established relatively better under higher herbivory than species with high leaf nitrogen. Soil moisture interacted with root mass fraction (RMF), with low RMF species establishing better with low soil moisture and higher RMF species better on wetter soils. Specific leaf area (SLA) interacted with light availability, as low SLA species established better under high light conditions and high SLA species under low light conditions. Our work illustrates how community assembly can be better described by trait-environment interactions than correlating traits or environment with performance. This knowledge can assist species selection to maximize restoration success.Establishment and persistence are central to community assembly and are determined by how traits interact with the environment to determine performance ('trait-environment interactions'). Community assembly studies have rarely considered such trait-environment interactions, however, which can lead to incorrect inferences about how traits affect assembly. We evaluated how functional traits, environmental conditions, and trait-environment interactions structure plant establishment, as a measure of performance. Within 12 prairie restorations created by sowing 70 species, we quantified environmental conditions and counted individuals of each seeded species to quantify first year establishment. Three trait-environment interactions structured establishment. Leaf nitrogen interacted with herbivore pressure, as low leaf nitrogen species established relatively better under higher herbivory than species with high leaf nitrogen. Soil moisture interacted with root mass fraction (RMF), with low RMF species establishing better with low soil moisture and higher RMF species better on wetter soils. Specific leaf area (SLA) interacted with light availability, as low SLA species established better under high light conditions and high SLA species under low light conditions. Our work illustrates how community assembly can be better described by trait-environment interactions than correlating traits or environment with performance. This knowledge can assist species selection to maximize restoration success.</p>
Data from: Changes in soil microbial communities in post mine ecological restoration: implications for monitoring using high throughput DNA sequencing
<p>The ecological restoration of ecosystem services and biodiversity is a key intervention used to reverse the impacts of anthropogenic activities such as mining. Assessment of the performance of restoration against completion criteria relies on biodiversity monitoring. However, monitoring usually overlooks soil microbial communities (SMC), despite increased awareness of their pivotal role in many ecological functions. Recent advances in cost, scalability and technology has led to DNA sequencing being considered as a cost-effective biological monitoring tool, particularly for otherwise difficult to survey groups such as microbes. However, such approaches for monitoring complex restoration sites such as post-mined landscapes have not yet been tested. Here we examine bacterial and fungal communities across chronosequences of mine site restoration at three locations in Western Australia to determine if there are consistent changes in SMC diversity, community composition and functional capacity. Although we detected directional changes in community composition indicative of microbial recovery, these were inconsistent between locations and microbial taxa (bacteria or fungi). Assessing functional diversity provided greater understanding of changes in site conditions and microbial recovery than could be determined through assessment of community composition alone. These results demonstrate that <span>high-throughput amplicon sequencing of environmental DNA (eDNA)</span> is an effective approach for monitoring the complex changes in SMC following restoration. Future monitoring of mine site restoration using eDNA should consider archiving samples to provide improved understanding of changes in communities over time. Expansion to include other biological groups (e.g. soil fauna) and substrates would also provide a more holistic understanding of biodiversity recovery. </p>
Data from: Habitat restoration benefits wild bees: a meta-analysis
1.Pollinator conservation is of increasing interest in light of managed honeybee (Apis mellifera) declines, and declines in some species of wild bees. Much work has gone into understanding the effects of habitat enhancements in agricultural systems on wild bee abundance, richness, and pollination services. However, the effects of ecological restoration targeting "natural" ecological endpoints (e.g., restoring former agricultural fields to historic vegetation types or improving degraded natural lands) on wild bees have received relatively little attention, despite their potential importance for countering habitat loss. 2.We conducted a meta-analysis to evaluate the effects of ecological restoration on wild bee abundance and richness, focusing on unmanaged bee communities in lands restored and managed to increase habitat availability and quality. Specifically, we assessed bee abundance and/or richness across studies comparing restored vs. unrestored treatments and studies investigating effects of specific habitat restoration techniques, such as burning, grazing, invasive plant removal and seeding. 3.We analysed 28 studies that met our selection criteria: these represented 11 habitat types and 7 restoration techniques. Nearly all restorations associated with these studies were performed without explicit consideration of habitat needs for bees or other pollinators. The majority of restorations targeted plant community goals, which could potentially have ancillary benefits for bees. 4.Restoration had overall positive effects on wild bee abundance and richness across multiple habitat types. Specific restoration actions, tested independently, also tended to have positive effects on wild bee richness and abundance. 5.Synthesis and applications. We found strong evidence that ecological restoration advances wild bee conservation. This is important given that habitat loss is recognized as a leading factor in pollinator decline. Pollinator responses to land management are rarely evaluated in non-agricultural settings and so support for wild bees may be an underappreciated benefit of botanically focused management. Future restoration projects that explicitly consider the needs of wild bees could be more effective at providing nesting, foraging and other habitat resources. We encourage land managers to design and evaluate restoration projects with the habitat needs of wild bee species in mind.
Data from: Corridors restore animal-mediated pollination in fragmented tropical forest landscapes
Tropical biodiversity and associated ecosystem functions have become heavily eroded through habitat loss. Animal-mediated pollination is required in >94% of higher tropical plant species and 75% of the world´s leading food crops, but it remains unclear if corridors avert deforestation-driven pollination breakdown in fragmented tropical landscapes. Here, we used manipulative resource experiments and field observations to show that corridors functionally connect neotropical forest fragments for forest-associated hummingbirds and increase pollen transfer. Further, corridors boosted forest-associated pollinator availability in fragments by 14.3 times compared to unconnected equivalents, increasing overall pollination success. Plants in patches without corridors showed pollination rates equal to bagged control flowers, indicating pollination failure in isolated fragments. This indicates, for the first time, that corridors benefit tropical forest ecosystems beyond boosting local species richness, by functionally connecting mutualistic network partners. We conclude that small-scale adjustments to landscape configuration safeguard native pollinators and associated pollination services in tropical forest landscapes.
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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.