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Data Repo for "Momentum-resolved spin-conserving two-triplon bound state and continuum in a cuprate ladder"

Data repo for the paper "Momentum-resolved spin-conserving two-triplon bound state and continuum in a cuprate ladder"

opencc-zeroMay 2023View details →

Data for: High focus on threatened species and habitats may undermine biodiversity conservation: evidence from the northern Baltic Sea

Conservation policies and environmental impact assessments commonly target threatened species and habitats. Nevertheless, macroecological research provides reasons why also common species should be considered. We investigate the consequences of focusing solely on legally protected species and habitats in a spatial conservation planning context using a comprehensive, benthic marine dataset from the northern Baltic Sea. Using spatial prioritization and surrogacy analysis, we show that the common approach in conservation planning, where legally listed threatened species and habitats are the focus of conservation efforts, could lead to poor outcomes for common species (and therefore biodiversity as a whole), allowing them to decline in the future. If conservation efforts were aimed solely at threatened species, common species would experience a loss of 62% coverage. In contrast, if conservation plans were based only on common species, threatened species would suffer a loss of 1%. Threatened species are rare and their ecological niches distinct, making them poor surrogates for biodiversity. The best results are achieved by unified planning for all species and habitats. The minimal step towards acknowledging common species in conservation planning would be the inclusion of the richness of common species, complemented by information on indicator species or species of high importance for ecosystem functioning. The trade-off between planning for rare and common species should be evaluated, to minimize losses to biodiversity.

Identifying the environmental drivers of corridors and predicting connectivity between seasonal ranges in multiple populations of Alpine ibex (Capra ibex) as tools for conserving migration

# GPS locations of Alpine ibex This dataset contains migratory tracks of Alpine ibex identified using the application Migration Mapper (https://migrationinitiative.org/content/migration-mapper) and used in the work Identifying the environmental drivers of corridors and predicting connectivity between seasonal ranges in multiple populations of Alpine ibex (Capra ibex) as tools for conserving migration # Dataset structure Each row of the dataset represents a GPS location with its coordinates contained in the x (longitude) and y(latitude) columns. Coordinates are given in wgs84 (epsg 4326). The column t1_ informs on the date and time the location was recorded. The id and pop columns provide information about the identity of the animal and the population to which it belongs.

Assessing the conservation status of Chinese freshwater fish using deep learning

The lack of information on the extinction risk of most species is a fundamental challenge in prioritizing conservation strategies and bending the curve of current biodiversity decline. Machine learning methods have shown promising potential to fill this gap, but their applicability remains to be validated at different taxa (especially aquatic species) and spatial scales. We assessed the extinction risk of 1,162 freshwater fish species in China that have not yet been included in the latest IUCN Red List using multiple neural network algorithms based on datasets of species occurrences, biological traits, phylogeny, and relevant environmental layers. The best deep learning models dramatically improved the assessment coverage from 29.9% (496 species) to 93.2–93.9% (1,545–1,557 species) of the whole fauna with an accuracy of 95.4–99.0%. By combining our prediction results with the IUCN Red List, we found that 23.8–26.5% (394–440 species) of Chinese freshwater fishes were identified as possibly threatened species, which is roughly four times the IUCN assessment. Newly assessed species and threatened species were mainly from the orders Cypriniformes (prediction added: 837–846 species; final threatened: 325–350 species), Siluriformes (113–122; 28–37) and Perciformes (74–76; 18–25). The increase in threatened species richness based on predictions was led by the upper reaches of the Pearl and Yangtze. Overall, our findings suggest that deep learning algorithms can provide robust and time-saving assessments of extinction risk for entire freshwater fish fauna on a large national scale, thereby facilitating relevant conservation prioritization.

Fig. 1 in Ex-situ conservation of the critically endangered swamp forest crab Parathelphusa reticulata Ng, 1990 (Decapoda: Brachyura: Gecarcinucidae): observations on its reproduction and biology in captivity

Fig. 1. Captive breeding facility in the Singapore Botanic Gardens. Photograph: Daniel J. J. Ng.

Data from: Conservation of Chinese Theaceae species under future climate and land use changes

Aim: Climate and land use changes are two major pervasive and growing global causes of rapid changes in the distribution patterns of biodiversity, challenging the future effectiveness of protected areas (PAs), which were mainly designed based on a static view of biodiversity. Therefore, evaluating the effectiveness of protected areas for protecting the species threatened by climate and land use change is critical for future biodiversity conservation. Location: China Methods: Here, using distributions of 200 Chinese Theaceae species and ensemble species distribution models, we identified species threatened by future climate and land use change (i.e. species with predicted loss of suitable habitat ≥ 30%) under scenarios incorporating climate change, land use change and dispersal. We then estimate the richness distribution patterns of threatened species and identify priority conservation areas and conservation gaps of the current PA network. Results: Our results suggest that 36.30%-51.85% of Theaceae species will be threatened by future climate and land use conditions, and that although the threatened species are mainly distributed at low latitudes in China under both current and future periods, the mean richness of the threatened species per grid cell will decline by 0.826-3.188 species by the 2070s. Moreover, we found that these priority conservation areas are highly fragmented and that the current PA network only covers 14.21%-20.87% of the 'areas worth exploring' and 6.91%-7.91% of the 'areas worth attention'. Main conclusions: Our findings highlight the necessity of establishing new protected areas and ecological corridors in priority conservation areas to protect the threatened species. Moreover, our findings also highlight the importance of taking into consideration the potential threatened species under future climate and land use conditions when designating priority areas for biodiversity conservation.

Forest conservation maximises açaí palm pollination services and yield in the Brazilian Amazon

<ol> <li>Agricultural expansion is one of the main drivers of global pollinator loss. Paradoxically, this occurs while agriculture is becoming increasingly dependent on biotic pollination, raising concerns about food production. Integrated Crop Pollination (ICP), the use of both wild and managed pollinators in crop fields, can help conserve pollinator diversity while ensuring effective pollination services for growers. However, given the context-dependent nature of this approach, there is an urgent need to evaluate its application across different landscapes and crops.</li> <li>We apply the ICP approach to açaí palm (Euterpe oleracea Mart.) production in the eastern Brazilian Amazon to explore effects of a native stingless bee, Scaptotrigona aff. postica (Apidae: Meliponini), and landscape-level forest conservation on yield and socioeconomic outcomes for açaí fruit growers. We assessed flower visitor assemblages and fruit production on 18 plantations across a landscape forest cover gradient, with bee colonies introduced on nine plantations. Field data were combined with information from semi-structured interviews of growers to estimate yield and profit per hectare under different pollinator management scenarios.</li> <li>Bee colonies and forest cover enhanced flower visitor abundance on palm inflorescences, but abundance increases attributed to managed bees were associated with shifts in flower visitor evenness and diversity (species richness), due to reduced visitation of wild bees near managed colonies.</li> <li>Fruit production on inflorescences was positively related to bee abundance and bee diversity. Consequently, overall pollination performance was lower in plantations with bee colonies. This was repeated at the hectare scale, where yield and profit were associated with surrounding forest cover and not bee colonies.</li> <li> Synthesis and applications. Managed bees can increase pollinator densities and fruit production, but the increased environmental and socioeconomic risks associated with this activity means açaí growers should prioritise forest conservation to safeguard pollination services and improve overall sustainability of açaí production in the eastern Brazilian Amazon.</li> </ol>

opencc-by-4.0Jun 2023View details →

Allele surfing causes maladaptation in a Pacific salmon of conservation concern

How different factors including demography, recombination or genome duplication may impact selection efficacy and the burden of deleterious mutations in different populations is a central question of evolutionary biology and genetics. Here we show that key evolutionary processes, including variation in effective population size through postglacial change in demography and recombination rates have affected the efficacy of selection and impacted the genetic load in Coho salmon (Oncorhynchus kisutch), a widely distributed salmonid species on the west coast of North America. Using whole genome resequencing data from 14 populations at different travelled migratory distances from their southern glacial refugium, we found support for postglacial gene surfing, with reduced Ne at the range recolonization front, thus inducing both a reduction in the efficacy of selection and a surf of deleterious alleles in populations evolving at low Ne. This inference was robust to various proxies of the load. In addition, comparing residual tetrasomic and re-diploidizing regions of the salmon genome, we found support for a prime role of recombination rates in shaping the within-genome variation of the load. Overall, our empirical results are remarkably consistent with expectations under the nearly neutral theory of molecular evolution. We discuss the fundamental and applied implications of these findings for evolutionary and conservation genomics.

Fine-scale intraspecific niche partitioning in a highly mobile, marine megafauna species: implications for ecology and conservation

A species may partition its realized ecological niche along bionomic and/or scenopoetic axes due to intraspecific competition for limited resources. How partitioning manifests depends on resource needs and availability by and for the partitioning groups. Here we demonstrate the utility of analyzing short- and long-term stable carbon and nitrogen isotope ratios from imperiled marine megafauna to elucidate realized niche partitioning in these species. We captured 113 loggerhead (Caretta caretta) sea turtles at a high-use area near Crystal River, Florida, between 2016–2022, comprising 53 subadults, 10 adult males, and 50 adult females. Isotopic analyses indicated that loggerheads partition their realized ecological niche by life stage, along a scenopoetic axis. Most adults likely forage and reside in shallow areas of the study site, with most subadults displaying habitat switching between deeper locations to forage and shallower locations to rest. Some subadults, like adults, also forage and reside in shallow areas, and may display behaviors to avoid intraspecific competition. Analysis of stable isotopes with different turnover rates was critical for this characterization of intraspecific niche partitioning in loggerhead turtles, which has direct implications for ongoing research and conservation efforts for this and other imperiled species.

Data from: Conserving habitat for migratory ungulates: how wide is a migration corridor?

<ol> <li>Conserving migratory ungulates relies on the analysis of GPS collar data and associated maps of migration corridors to inform management and policy actions. Current methods for identifying migratory corridors use complex statistical models designed to account for movement uncertainty rather than estimating the amount of space required by animals to migrate. Further, such methods can complicate conservation efforts by producing highly variable corridor widths and non-contiguous corridors that do not fully connect seasonal ranges.</li> <li>To remedy this, we propose an intuitive line buffer approach for delineating individual migration corridors that is simple to implement and focuses on the functional corridor widths needed by migratory ungulates. </li> <li>By buffering a line that connects successive GPS locations, we can delineate individual migration corridors with consistent widths that are robust to variable parameters (GPS fix-rate, travel speed, tortuosity) and provide contiguous connection between seasonal ranges. Using a combination of expert knowledge, simulation, and 10-min GPS collar data collected from mule deer (Odocoileus hemionus) and pronghorn (Antilocapra americana), we suggest 400 to 600 m are reasonable estimates of functional migration corridor widths for individuals of those species.</li> <li>Our line buffer approach is intended to simplify migration corridor delineation, improve transparency, and encourage a broader discussion of functional corridor widths. These considerations help advance efforts to conserve habitat within migration corridors and prioritize conservation efforts within a single corridor or across multiple corridors.</li> </ol>

opencc-zeroJul 2023View details →

Data for: Population structure of a grassland songbird (Dolichonyx oryzivorus) to inform conservation units

Understanding the patterns and processes driving population structure is crucial for conservation planning. Spatial conservation units (CUs) for one or more species have been defined using similarities in communities, habitats, and resource management concerns. Additionally, CU boundaries can be informed by population genetic structure. Here, we determined the population structure of the Bobolink (Dolichonyx oryzivorus), a migratory grassland bird. Its breeding range spans longitudinally across most of North America in the northern U.S. and southern Canada, and its population has declined by 59% from 1971 to 2014. We sampled blood from Bobolinks at seven breeding sites and used a ddRAD sequencing approach to identify 3236 SNPs for population genetic analyses. Using the Bayesian clustering approach, STRUCTURE, we found low levels of genetic differentiation across the breeding range. F st values ranged from 0.002 to 0.036 among all population pairs, and genetic structure followed an isolation-by-distance model. Despite low levels of genetic differentiation, we found evidence for four genetic groupings— breeding populations in Oregon and British Columbia were distinct from each other as well as from Central and eastern North American breeding populations. Investigating the demographic history of the populations using approximate Bayesian computation, we found evidence that western Bobolink populations are not relict populations but instead were founded during a recent westward range expansion, possibly enabled by agricultural expansion. We identify four genetics-based CUs that may serve as a complementary spatial framework, broader in scale compared to the commonly-used Bird Conservation Regions, for defining and achieving population objectives.

opencc-zeroJul 2023View details →

Data from: A wide megafauna gap undermines China's expanding coastal ecosystem conservation

To fulfill sustainable development goals, many countries are expanding efforts to conserve ecologically and societally critical coastal ecosystems. Although megafauna profoundly impact the functioning of ecosystems, they are neglected as a key component in the conservation scheme for coastal ecosystems in many geographic contexts. Here, we reveal a rich diversity of extant megafauna associated with all major types of coastal ecosystems in China, including 218 species of mammals, birds, reptiles, cephalopods and fishes across terrestrial and marine environments. However, 44% of these species are globally threatened and 78% have not yet been assessed in China for extinction risk. More worrisome, 73% of these megafauna have not been designated as nationally protected species, and <10% of their most important habitats are protected. Filling this wide "megafauna gap" in China, and globally, would be a leading step as humanity strives to thrive with coastal ecosystems.

opencc-by-4.0Jul 2023View details →

Modeling liquid transport in the Earth's mantle as two-phase flow: Effect of an enforced positive porosity on liquid flow and mass conservation

These data files include the raw data for the figures shown in Lee et al. titled as 'Modeling liquid transport in the Earth’s mantle as two-phase flow: Effect of an enforced positive porosity on liquid flow and mass conservation'.

opencc-zeroAug 2023View details →

Supplementary material: for Using anticipation to unveil drivers of local livelihoods in Transfrontier Conservation Areas: a call for more environmental justice

<ol> <li> Calling on the concept of environmental justice in its distributive, procedural, and recognition dimensions, we implemented a collaborative scenario-building approach to explore sustainable livelihood pathways in four sites belonging to two Transfrontier Conservation Areas (TFCAs) in southern Africa. </li> <li>Grounded on participation and transdisciplinarity, as a foundation for decolonised anticipatory action research, we aimed at stimulating knowledge exchange and providing insights on the future of local livelihoods by engaging experts living within these TFCAs. </li> <li>Our results show that wildlife and wildlife-related activities are not seen as the primary drivers of local livelihoods, despite the focus and investments of dominant stakeholders in these sectors. Instead, local governance and land use regulations emerged as key drivers in the four study sites. The state of natural resources, including water, and appropriate farming systems also appeared critical to sustain future livelihoods in TFCAs, together with the recognition of indigenous culture, knowledge, and value systems.</li> <li>Nature conservation, especially in Africa, is rooted in its colonial past and struggles to free or decolonise itself from the habits of this past despite decades of reconsideration. To date, the enduring coloniality of conservation prevents local citizens from truly participating in the planning and designing of the TFCAs they live in, leaving room for limited benefits to local citizens and often limiting indigenous people's capacity to conserve. </li> <li> A practical way forward is to consider environmental justice as a cement between the two pillars of the TFCA concept, i.e.nature conservation and socioeconomic development of local or neighbouring communities, as part of a more broad and urgent need to rethink the relationships between people in, and with, the rest of nature. </li> </ol>

opencc-by-4.0Mar 2023View details →

Repeated mapped tree inventory data in a tree plantation for pedunculate oak (Quercus robur) genetic conservation

We performed replicated, repeated mapped tree inventory measures (x,y, height, diameter, vitality, etc.) to allow analysis of the spatial and temporal structure in 1 ha planted pedunculate oak (Quercus robur) stand established in 2003 to resemble the oak-hornnbeam forests for genetic conservation purposes in Po Valley (Foresta Carpaneta). Two inventories were carried out in 2009 and 2019. The use of replicated, repeated, and mapped tree measures allows the examination of true changes in spatial pattern processes through time in this forest type.

opencc-zeroAug 2023View details →

Raw target enrichment of conserved element sequence data for 24 black coral species

Deep-sea lineages are generally thought to arise from shallow-water ancestors, but this hypothesis is based on a relatively small number of taxonomic groups. Anthozoans, which include corals and sea anemones, are significant contributors to the faunal diversity of the deep sea, but the timing and mechanisms of their invasion into this biome remain elusive. Here, we reconstruct a fully resolved, time-calibrated phylogeny of 83 species in the order Antipatharia (black coral) to investigate their bathymetric evolutionary history. Our reconstruction indicates that extant black coral lineages first diversified in continental slope depths (~250–3,000 m) during the early Silurian (~437 Ma) and subsequently radiated into, and diversified within, both continental shelf (<250 m) and abyssal (>3,000 m) habitats. Ancestral state reconstruction analysis suggests that the appearance of morphological features that enhanced the ability of black corals to acquire nutrients coincided with their invasion of novel depths. Our findings have important conservation implications for anthozoan lineages, as the loss of "source" slope lineages could threaten millions of years of evolutionary history and confound future invasion events, thereby warranting protection.

opencc-zeroAug 2023View details →

Data from: The contributions of flower strips to wild bee conservation in agricultural landscapes can be predicted using pollinator habitat suitability models

Sowing flower strips along field edges is a widely adopted method for conserving pollinating insects in agricultural landscapes. To maximize the effect of flower strips given limited resources, we need spatially explicit tools that can prioritize their placement, and for identifying plant species to include in seed mixtures. We sampled bees and plant species as well as their interactions in a semi-controlled field experiment with roadside/field edge pairs with/without a sown flower strip at 31 sites in Norway and used a regional spatial model of solitary bee species richness to test if the effect of flower strips on bee species richness was predictable from the modelled solitary bee species richness. We found that sites with flower strips were more bee species rich compared to sites without flower strips and that this effect was greatest in areas that the regional solitary bee species richness model had identified to be particularly important for bees. Spatial models revealed that even within small landscapes there were pronounced differences between field edges in the predicted effect of sowing flower strips. Of the plant species that attracted the most bee species, the majority mainly attracted bumblebees and only few species also attracted solitary bees. Considering both the taxonomic diversity of bees and the species richness of bees attracted by plants we suggest that seed mixes containing Hieracium spp. such as Hieracium umbellatum and Pilosella officinarum; Taraxacum spp; Trifolium repens; Lotus corniculatus; Stellaria graminea; and Achillea millefolium would provide resources for diverse bee communities in our region. Spatial prediction models of bee diversity can be used to identify locations where flower strips are likely to have the largest effect and can thereby provide managers with an important tool for prioritizing how funding for agri-environmental schemes such as flower strips should be allocated. Such flower strips should contain plant species that are attractive to both solitary and bumblebees, and do not need to be particularly plant species rich as long as the selected plants complement each other.

opencc-zeroSep 2023View details →

Data for: Beyond Protected Areas: The importance of mixed-use landscapes for the conservation of Sumatran elephants (Elephas maximus sumatranus)

Elephants were once widely distributed across the Indonesian island of Sumatra but now exist in small, isolated populations. Using the best data currently available on elephant occurrence, we mapped suitable habitat for elephants on Sumatra (Elephas maximus sumatranus). We used direct sightings and indirect observations of elephant signs, as well as six remotely-sensed proxies of surface ruggedness, vegetation productivity and structure, and human land use and disturbance, to model habitat suitability in a Google Earth Engine (GEE) environment. We validated the habitat suitability prediction using an independent geolocation dataset collected from global positioning system (GPS) collars fitted on elephants, and also assessed the functional connectivity between known elephant population ranges by deriving a resistance surface for Circuitscape from this prediction. Thirty-two percent (135,646 km2) of Sumatra's land area was predicted to be suitable habitat, with 43 patches of suitable habitat located across Sumatra. Areas with high connectivity were concentrated in the Riau and North Sumatra provinces. Though our analysis highlights the need to improve the quality of data collected on Sumatran elephants, it suggests that more suitable habitat remains on Sumatra than is used by known populations. Targeted habitat conservation, especially of the suitable habitat in and by the Lamno, Balai Raja, Tesso Tenggara, Tesso Utara, Bukit Tigapuluh, Seblat, Padang Sugihan, and Bukit Barisan Selatan ranges, may improve the long-term viability of the critically endangered species.

opencc-by-4.0May 2022View details →

Supplementary data and material, Global strategy for the conservation and use of eggplants.

Supplementary data and material from Solberg, S., van Zonneveld, M., Rakha, M. T. , Taher, D. I. , Prohens, J., Jarret, R. van Dooijeweert, W., and Peter Giovannini. 2022. Global strategy for the conservation and use of eggplants. Global Crop Diversity Trust. Bonn, Germany.