The Importance and Benefits of Species

Evolutionary history and systematics of European blind mole rats (Rodentia: Spalacidae: Nannospalax): Multilocus phylogeny and species delimitation in a puzzling group

Species delimitation is a powerful approach to assist taxonomic decisions in challenging taxa where species boundaries are hard to establish. European taxa of the blind mole rats (genus Nannospalax) display small morphological differences and complex chromosomal evolution at a shallow evolutionary divergence level. Previous analyses led to the recognition of 25 'forms' in their distribution area. We provide a comprehensive framework to improve knowledge on the evolutionary history and revise the taxonomy of European blind mole rats based on samples from all but three of the 25 forms. We sequenced two nuclear-encoded genetic regions and the whole mitochondrial cytochrome b gene for phylogenetic tree reconstructions using concatenation and coalescence-based species-tree estimations. The phylogenetic analyses confirmed that Aegean N. insularis belongs to N. superspecies xanthodon, and that it represents the second known species of this superspecies in Europe. Mainland taxa reached Europe from Asia Minor in two colonisation events corresponding to two superspecies-level taxa: N. superspecies monticola (taxon established herewith) reached Europe c. 2.1 million years ago (Mya) and was followed by N. superspecies leucodon (re-defined herewith) c. 1.5 Mya. Species delimitation allowed the clarification of the taxonomic contents of the above superspecies. N. superspecies monticola contains three species geographically confined to the western periphery of the distribution of blind mole rats, whereas N. superspecies leucodon is more speciose with six species and several additional subspecies. The observed geographic pattern hints at a robust peripatric speciation process and rapid chromosomal evolution. The present treatment is thus regarded as the minimum taxonomic content of each lineage, which can be further refined based on other sources of information such as karyological traits, crossbreeding experiments, etc. The species delimitation models also allowed the recognition of a hitherto unnamed blind mole rat taxon from Albania, described here as a new subspecies.

Zoonoses in a changing world

Animals are continuously exposed to pathogens but rarely get infected, because pathogens must overcome barriers to establish successful infections. Ongoing planetary changes affect factors relevant for such infections, such as pathogen pressure and pathogen exposure. The replacement of wildlife with domestic animals shrinks the original host reservoirs, whereas expanding agricultural frontiers lead to increased contact between natural and altered ecosystems, increasing pathogen exposure and reducing the area where the original hosts can live. Climate change alters species' distributions and phenology, pathogens included, resulting in exposure to pathogens that have colonized or recolonized new areas. Globalization leads to unwilling movement of and exposure to pathogens. Because people and domestic animals are overdominant planetwide, there is increased selective pressure for pathogens to infect them. Nature conservation measures can slow down but not fully prevent spillovers. Additional and enhanced surveillance methods in potential spillover hotspots should improve early detection and allow swifter responses to emerging outbreaks.

Conserving avian evolutionary history can effectively safeguard future benefits for people

Phylogenetic diversity (PD)-the evolutionary history of a set of species-is conceptually linked to the maintenance of yet-to-be-discovered benefits from biodiversity or "option value." We used global phylogenetic and utilization data for birds to test the PD option value link, under the assumption that the performance of sets of PD-maximizing species at capturing known benefits is analogous to selecting the same species at a point in human history before these benefits were realized. PD performed better than random at capturing utilized bird species across 60% of tests, with performance linked to the phylogenetic dispersion and prevalence of each utilization category. Prioritizing threatened species for conservation by the PD they encapsulate performs comparably to prioritizing by their functional distinctiveness. However, species selected by each metric show low overlap, indicating that we should conserve both components of biodiversity to effectively conserve a variety of uses. Our findings provide empirical support for the link between evolutionary history and benefits for future generations.

Calling time on alien plantscapes

Both urban and rural environments around the globe have become dominated by alien plant species to the extent that plantscapes from one region or country have become difficult to distinguish from many others. This process of plant community homogenisation comes at a cost to cultural identity and undermines people's sense of place. Although invasive alien plant species have received considerable attention in recent decades, issues with non-invasive alien plant species have largely been ignored, and yet they contribute significantly to biotic homogeneity and impose an ever accumulating invasion debt: a debt that increases in proportion with their population sizes. By contrast, an abundance of native species in the places where people live is important for strengthening commitment to biodiversity conservation. Is there therefore sufficient evidence of harm from increasing numbers of non-invasive alien plants to justify local and central governments introducing measures to substantially reduce the proportion of non-invasive aliens in both urban and rural environments?

Ecosystem Services at the Farm Level-Overview, Synergies, Trade-Offs, and Stakeholder Analysis

The current geological epoch is characterized by anthropogenic activity that greatly impacts on natural ecosystems and their integrity. The complex networks of ecosystem services (ESs) are often ignored because the provision of natural resources, such as food and industrial crops, is mistakenly viewed as an independent process separate from ecosystems and ignoring the impacts on ecosystems. Recently, research has intensified on how to evaluate and manage ES to minimize environmental impacts, but it remains unclear how to balance anthropogenic activity and ecosystem integrity. This paper reviews the main ESs at farm level including provisioning, regulating, habitat, and cultural services. For these ESs, synergies are outlined and evaluated along with the respective practices (e.g., cover- and intercropping) and ES suppliers (e.g., pollinators and biocontrol agents). Further, several farm-level ES trade-offs are discussed along with a proposal for their evaluation. Finally, a framework for stakeholder approaches specific to farm-level ES is put forward, along with an outlook on how existing precision agriculture technologies can be adapted for improved assessment of ES bundles. This is believed to provide a useful framework for both decision makers and stakeholders to facilitate the development of more sustainable and resilient farming systems.

An Ethical Overview of the CRISPR-Based Elimination of Anopheles gambiae to Combat Malaria

Approximately a quarter of a billion people around the world suffer from malaria each year. Most cases are located in sub-Saharan Africa where Anopheles gambiae mosquitoes are the principal vectors of this public health problem. With the use of CRISPR-based gene drives, the population of mosquitoes can be modified, eventually causing their extinction. First, we discuss the moral status of the organism and argue that using genetically modified mosquitoes to combat malaria should not be abandoned based on some moral value of A. gambiae. Secondly, we argue that environmental impact studies should be performed to obtain an accurate account of the possible effects of a potential eradication of the organism. However, the risks from the purposeful extinction of A. gambiae should not overtake the benefits of eradicating malaria and risk assessments should be used to determine acceptable risks. Thirdly, we argue that the eventual release of the genetically modified mosquitoes will depend on transparency, community involvement, and cooperation between different nations.

The Checklist of Sicilian Macrofungi: Second Edition

Approximately 30 years after the publication of the first Sicilian checklist of macrofungi, a new updated version is presented here. The census of macromycetes was carried out through periodic observations in different agricultural and forest ecosystems, in urban areas, in public and private gardens, and in botanical gardens. The 1919 infraspecific taxa included in 508 genera belonging to 152 families were collected in the Sicilian territory. Ectomycorrhizal fungi are the most represented ecological category, followed by saprotrophs on wood, saprotrophs on litter, and terricolous saprotrophs. The interest in this rich group of organisms is evidenced by the nutritional and therapeutic value of a high percentage of species. The actions linked to the National Recovery and Resilience Plan and The Network for the Study of Mycological Diversity will further increase the number of macrofungi for Sicily in the future.

A classification framework for interspecific trade-offs in aquatic ecology

In some cases, wildlife management objectives directed at multiple species can conflict with one another, creating species trade-offs. For managers to effectively identify trade-offs and avoid their undesirable outcomes, they must understand the agents involved and their corresponding interactions. A literature review of interspecific trade-offs within freshwater and marine ecosystems was conducted to illustrate the scope of potential interspecific trade-offs that may occur. We identified common pitfalls that lead to failed recognition of interspecific trade-offs, including, single-species management and limited consideration of the spatial and temporal scale of ecosystems and their management regimes. We devised a classification framework of common interspecific trade-offs within aquatic systems. The classification can help managers determine whether the conflict is species based through direct relationships (i.e., predator-prey, competition, other antagonistic relationships) or indirect relationships involving intermediate species (i.e., conflict-generating species) or whether the conflict is driven by opposing management objectives for species that would otherwise not interact (i.e., nontarget management effects). Once the nature and scope of trade-offs are understood, existing decision-making tools, such as structured decision-making and real-options analysis, can be incorporated to improve the management of aquatic ecosystems. Article Impact Statement: A synthesis of interspecific trade-offs in aquatic ecosystems supports their identification and resolution.

Airborne environmental DNA metabarcoding detects more diversity, with less sampling effort, than a traditional plant community survey

Background

Airborne environmental DNA (eDNA) research is an emerging field that focuses on the detection of species from their genetic remnants in the air. The majority of studies into airborne eDNA of plants has until now either focused on single species detection, specifically only pollen, or human health impacts, with no previous studies surveying an entire plant community through metabarcoding. We therefore conducted an airborne eDNA metabarcoding survey and compared the results to a traditional plant community survey.

Results

Over the course of a year, we conducted two traditional transect-based visual plant surveys alongside an airborne eDNA sampling campaign on a short-grass rangeland. We found that airborne eDNA detected more species than the traditional surveying method, although the types of species detected varied based on the method used. Airborne eDNA detected more grasses and forbs with less showy flowers, while the traditional method detected fewer grasses but also detected rarer forbs with large showy flowers. Additionally, we found the airborne eDNA metabarcoding survey required less sampling effort in terms of the time needed to conduct a survey and was able to detect more invasive species than the traditional method.

Conclusions

Overall, we have demonstrated that airborne eDNA can act as a sensitive and efficient plant community surveying method. Airborne eDNA surveillance has the potential to revolutionize the way plant communities are monitored in general, track changes in plant communities due to climate change and disturbances, and assist with the monitoring of invasive and endangered species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01947-x.

Comparative Study of Semen Parameters and Hormone Profile in Small-Spotted Catshark (Scyliorhinus canicula): Aquarium-Housed vs. Wild-Captured

Simple Summary

Comprehensive knowledge of chondrichthyan reproductive biology is crucial for the development of reproductive technologies. For that reason, a male reproductive evaluation was performed on the basis of a comparison of samples collected from wild-captured and aquarium-housed small-spotted catshark (Scyliorhinus canicula). Semen quality, sperm morphometry, and reproductive hormones were assessed. The results demonstrate good in vitro semen quality in aquarium-housed sharks, although there was lower plasma testosterone.

Abstract

Several chondrichthyan species are threatened, and we must increase our knowledge of their reproductive biology in order to establish assisted reproductive protocols for ex situ or in situ endangered species. The small-spotted catshark (Scyliorhinus canicula) is one of the most abundant shark species of the Mediterranean coast and is easy to maintain in aquaria; therefore, it is considered an ideal reproductive model. This study aimed to compare S. canicula male reproductive function in aquarium-housed (n = 7) and wild-captured animals, recently dead (n = 17). Aquarium-housed animals had lower semen volume (p = 0.005) and total sperm number (p = 0.006) than wild-captured animals, but similar sperm concentrations. In terms of sperm parameters, aquarium-housed sharks showed higher total sperm motility (p = 0.004), but no differences were observed regarding sperm viability, mitochondrial membrane potential, or membrane integrity. A morphometric study pointed to a significantly longer head (p = 0.005) and acrosome (p = 0.001) in wild-captured animals. The results of the spermatozoa morphological study of S. canicula were consistent with previous results obtained in other chondrichthyan species. With regard to sex hormones, testosterone levels were significantly lower in aquarium-housed animals (p ≤ 0.001), while similar levels of 17β-estradiol and progesterone were found. In short, the present study provides evidence of good in vitro semen quality in S. canicula housed in an aquarium, underlining their excellent potential for application in reproductive technologies for this and other chondrichthyan species.

Linking Taxonomic, Phylogenetic and Functional Plant Diversity with Ecosystem Services of Cliffs and Screes in Greece

Sparsely vegetated habitats of cliffs and screes act as refugia for many regional and local endemic specialized plant taxa most of which have evolved precisely for that type of habitat. The interplay between taxonomic, phylogenetic, and functional plant diversity on rock and scree habitats of extreme environmental conditions, enlightens the relations of plant communities and ecosystems and facilitates management planning for the conservation of biodiversity and ecosystem services. The identification of biodiversity patterns and hotspots (taxonomic, phylogenetic, and functional) contributes to the integration of the ecosystem services (ES) approach for the mapping and assessment of ecosystems and their services (MAES) implementation in Greece and the creation of thematic maps based on the MAES reporting format. The overlap among the protected areas’ network revealed that almost all areas of cliffs and screes of medium, high, and very high taxonomic and phylogenetic plant endemism are included in the Natura 2000 area network. The results of this study provide the baseline information for ES assessments at sparsely vegetated land of cliffs and screes. Our results contribute to the implementation of certain indicators of the national set of MAES indicators in Greece such as (a) floristic diversity and (b) microrefugia of endemic diversity and support of decision-making.

Valuation and Appreciation of Biodiversity: The “Maintenance of Options” Provided by the Variety of Life

“Nature’s contributions to people” (NCP) is an important expansion beyond the standard ecosystem services framework, particularly as a pathway to better address global/regional biodiversity values. NCP18, “maintenance of options,” refers broadly to the capacity of ecosystems, habitats, species, or genotypes to keep options open to support a good quality of life. “Biodiversity,” interpreted as living variation, is an important, but under-appreciated, aspect of “maintenance of options.” IPBES refers to “the “option values of biodiversity,” that is, the value of maintaining living variation in order to provide possible future uses and benefits.” IPBES assessments include biodiversity option value, and use phylogenetic diversity (PD) as an indicator of change in status of NCP18. At the same time, IPBES notes the need for greater appreciation of option values of biodiversity. Popular ecosystem services framings forget the long history of consideration of these global benefits of biotic diversity to humanity, and their normative links. Popular ecological definitions mean that many current valuations of “biodiversity” neglect the benefits of biodiversity-as-variety. Economic valuations of “biodiversity” typically have focused on ecosystem aspects, not variety; related ecosystems framings value “biodiversity” with a focus on those critical elements relating to functioning of ecosystems. Greater appreciation of biodiversity option value and NCP18 may depend on clearer messaging from academia, better highlighting of the link between biodiversity and intergenerational justice, and greater communication of stories of past surprising discoveries of benefits from species that highlight biodiversity as an ongoing source of future benefits. An important pathway for better appreciation of insurance and investment benefits of variety is to understand and communicate the reasons why we value these benefits from variety. Biodiversity-as-variety is valued because we care about the welfare of future generations.

Kindergarten Children’s Perception about the Ecological Roles of Living Organisms

Young children will inherit the biosphere; therefore, it is crucial that they recognize the importance of all living organisms based on their intrinsic value and ecosystem function, not only on their “cuteness”. However, children’s knowledge about the interdependence among organisms has been little investigated. We interviewed 56 kindergarten children (5–6 years old) in Norway. The aim of the study was to investigate their perception of the importance for nature of six organisms, representing different trophic levels of food webs (producers, consumers, decomposers) and providing different ecosystem services (production, decomposition, and pollination). There was no difference in ranking between sexes or between ordinary and farm-based kindergartens. Bumblebees and earthworms were perceived as the most important organisms, followed by squirrel, trees, and wolf. None of the children recognized the ecological role of mushrooms. Our results show that, although upon completing kindergarten many children had gained an early understanding of the role of different organisms in nature, they missed the importance of plants and fungi. Kindergarten children’s “fungi blindness” might reflect a neglect of the public for this extremely important, diverse, and dominating taxon. We should therefore put more emphasis in raising awareness about the interdependence among trophic levels in food webs.

DNA barcodes and new primers for nature's pest controllers: the social wasps

Globally, biodiversity is declining because of anthropogenic pressures, and this could lead to extinction of some species before they are discovered. The loss of insect taxa is of prime concern, given recent reports of significant declines in the populations of many taxa across the globe. Efforts to document biodiversity have met with several challenges, amongst which are the difficulties in using morphological features to discriminate species, especially in insects. DNA barcoding is a rapid and reliable method for species identification and discovery but choosing appropriate primers to amplify the barcode region without co-amplifying contaminants remains a key challenge. We developed and tested a set of primers for PCR amplification of the DNA barcode region of the COI gene in polistine wasps. We tested their efficacy in 36 species of vespid wasps, and the solitary wasp Zethus miniatus Saussure. Samples were obtained from Africa, Americas, Asia, and Europe. The polistine-specific primers successfully amplified the barcode region for all polistines tested, without amplifying any Wolbachia present; they also worked with many species from the other Vespidae wasp subfamilies. The new primers are valuable for the discovery and accurate documentation of polistine wasps in the four continents.

Toward Unifying Global Hotspots of Wild and Domesticated Biodiversity

Global biodiversity hotspots are areas containing high levels of species richness, endemism and threat. Similarly, regions of agriculturally relevant diversity have been identified where many domesticated plants and animals originated, and co-occurred with their wild ancestors and relatives. The agro-biodiversity in these regions has, likewise, often been considered threatened. Biodiversity and agro-biodiversity hotspots partly overlap, but their geographic intricacies have rarely been investigated together. Here we review the history of these two concepts and explore their geographic relationship by analysing global distribution and human use data for all plants, and for major crops and associated wild relatives. We highlight a geographic continuum between agro-biodiversity hotspots that contain high richness in species that are intensively used and well known by humanity (i.e., major crops and most viewed species on Wikipedia) and biodiversity hotspots encompassing species that are less heavily used and documented (i.e., crop wild relatives and species lacking information on Wikipedia). Our contribution highlights the key considerations needed for further developing a unifying concept of agro-biodiversity hotspots that encompasses multiple facets of diversity (including genetic and phylogenetic) and the linkage with overall biodiversity. This integration will ultimately enhance our understanding of the geography of human-plant interactions and help guide the preservation of nature and its contributions to people.

Assessing ecological function in the context of species recovery

Species interactions matter to conservation. Setting an ambitious recovery target for a species requires considering the size, density, and demographic structure of its populations such that they fulfill the interactions, roles, and functions of the species in the ecosystems in which they are embedded. A recently proposed framework for an International Union for Conservation of Nature Green List of Species formalizes this requirement by defining a fully recovered species in terms of representation, viability, and functionality. Defining and quantifying ecological function from the viewpoint of species recovery is challenging in concept and application, but also an opportunity to insert ecological theory into conservation practice. We propose 2 complementary approaches to assessing a species' ecological functions: confirmation (listing interactions of the species, identifying ecological processes and other species involved in these interactions, and quantifying the extent to which the species contributes to the identified ecological process) and elimination (inferring functionality by ruling out symptoms of reduced functionality, analogous to the red-list approach that focuses on symptoms of reduced viability). Despite the challenges, incorporation of functionality into species recovery planning is possible in most cases and it is essential to a conservation vision that goes beyond preventing extinctions and aims to restore a species to levels beyond what is required for its viability. This vision focuses on conservation and recovery at the species level and sees species as embedded in ecosystems, influencing and being influenced by the processes in those ecosystems. Thus, it connects and integrates conservation at the species and ecosystem levels.

Sampling bias in reptile occurrence data for the Kruger National Park

o effectively conserve and manage species, it is important to (1) understand how they are spatially distributed across the globe at both broad and fine spatial resolutions and (2) elucidate the determinants of these distributions. However, information pertaining to the distributions of many species remains poor as occurrence data are often scarce or collected with varying motivations, making the resulting patterns susceptible to sampling bias. Exacerbating an already limited quantity of occurrence data with an assortment of biases hinders their effectiveness for research, thus making it important to identify and understand the biases present within species occurrence data sets. We quantitatively assessed occurrence records of 126 reptile species occurring in the Kruger National Park (KNP), South Africa, to quantify the severity of sampling bias within this data set. We collated a data set of 7118 occurrence records from museum, literature and citizen science sources and analysed these at a biologically relevant spatial resolution of 1 km × 1 km. As a result of logistical challenges associated with sampling in KNP, approximately 92% of KNP is data deficient for reptile occurrences at the 1 km × 1 km resolution. Additionally, the spatial coverage of available occurrences varied at species and family levels, and the majority of occurrence records were strongly associated with publicly accessible human infrastructure. Furthermore, we found that sampled areas within KNP were not necessarily ecologically representative of KNP as a whole, suggesting that areas of unique environmental space remain to be sampled. Our findings highlight the need for substantially greater sampling effort for reptiles across KNP and emphasise the need to carefully consider the sampling biases within existing data should these be used for conservation management decision-making. Modelling species distributions could potentially serve as a short-term solution, but a concomitant increase in surveys across the park is needed.Conservation implications: The sampling biases present within KNP reptile occurrence data inhibit the inference of fine-scale species distributions within and across the park, which limits the usage of these data towards meaningfully informing conservation management decisions as applicable to reptile species in KNP.

Large carnivores and zoos as catalysts for engaging the public in the protection of biodiversity

Addressing the biodiversity crisis requires renewed collaborative approaches. Large carnivores are ambassador species, and as such they can aid the protection of a wide range of species, including evolutionarily distinct and threatened ones, while being popular for conservation marketing. However, conflicts between carnivores and people present a considerable challenge to biodiversity conservation. Our cross disciplinary essay brings together original research to discuss key issues in the conservation of large carnivores as keystone species for biodiversity rich, healthy ecosystems. Our findings suggest the need to promote coexistence through challenging ‘wilderness’ myths; to consider coexistence/conflict as a continuum; to include varied interest groups in decision making; to address fear through positive mediated experiences, and to explore further partnerships with zoos. As wide-reaching institutions visited by over 700 million people/year worldwide, zoos combine knowledge, emotion and social context creating ideal conditions for the development of care towards nature, pro-environmental behaviors and long-term connections between visitors and carnivores. Based on current research, we provide evidence that large carnivores and zoos are both powerful catalysts for public engagement with biodiversity conservation, recognizing barriers and suggesting future ways to collaborate to address biodiversity loss.

Expansion and loss events characterized the occurrence of MIF-like genes in bivalves

Macrophage migration inhibitory factor (MIF) dynamically connects innate and adaptive immune systems in vertebrate animals, allowing highly orchestrated systemic responses to various insults. The occurrence of MIF-like genes in non-vertebrate organisms suggests its origin from an ancestral metazoan gene, whose function is still a matter of debate. In the present work, by analyzing available genomic and transcriptomic data from bivalve mollusks, we identified 137 MIF-like sequences, which were classified into three types, based on phylogeny and conservation of key residues: MIF, D-DT, and the lineage-specific type MDL. Comparative genomics revealed syntenic conservation of homologous genes at the family level, the loss of D-DT in the Ostreidae family as well as the expansion of MIF-like genes in the Mytilidae family, possibly underpinning the neofunctionalization of duplicated gene copies. In M. galloprovincialis, MIF and one D-DT were mostly expressed in haemocytes and mantle rim of untreated animals, while D-DT paralogs often showed very limited expression, suggesting an accessory role or their persistence as relict genes.

The role of flagship species in the economic valuation of wildfire impacts: An application to two Mediterranean protected areas

Disturbance events play an important role in ecosystem services management and species biodiversity. In this sense, species biodiversity may constitute a large proportion of the total ecosystem value, mainly in natural protected areas. The present research proposes a methodology for the economic valuation of flagship species; the value of charismatic species was estimated using two complementary approaches based on recovery programs and contingent valuation method (CVM). While recovery programs approach is related to government expenditure, CVM is associated with survey results according to the society's willingness to pay. There are significant differences between both approaches as flagship species are highly valued by the society. In this sense, a difference of 43.75% on the species value can be found depending on the scenario of CVM (all respondents or only affirmative respondents). Our research was done on the integration of economic tools and wildfire severity of two burned areas in order to evaluate the effects caused in their habitat and, as a consequence, in the food chain. The results obtained from both the studied areas emphasized the importance of wildfire impacts on flagship species (209,619.08-445,495.88 € from Doñana wildfire and 634.68-5792.98 € from Segura wildfire) which are often omitted in valuation reports. The use of Geographic Information Systems helps to identify flagship species impacts per unit area (74.89-159.17 €/ha from Doñana wildfire and 0.76-6.98 €/ha from Segura wildfire) and to prioritize restoration activities on the most susceptible areas. This methodology could be extrapolated to any territory and spatial resolution based on the revision of the questionnaires regarding flagship species. The availability of cartography of flagship species´ susceptibility could play a critical role in budget optimization and the decision-making process on restoration planning.

Applying ecosystem services for pre-market environmental risk assessments of regulated stressors

Ecosystem services (ES) are the benefits that people obtain from ecosystems. Investigating the environment through an ES framework has gained wide acceptance in the international scientific community and is applied by policymakers to protect biodiversity and safeguard the sustainability of ecosystems. This approach can enhance the ecological and societal relevance of pre‐market/prospective environmental risk assessments (ERAs) of regulated stressors by: (1) informing the derivation of operational protection goals; (2) enabling the integration of environmental and human health risk assessments; (3) facilitating horizontal integration of policies and regulations; (4) leading to more comprehensive and consistent environmental protection; (5) articulating the utility of, and trade‐offs involved in, environmental decisions; and (6) enhancing the transparency of risk assessment results and the decisions based upon them. Realisation of these advantages will require challenges that impede acceptance of an ES approach to be overcome. Particularly, there is concern that, if biodiversity only matters to the extent that it benefits humans, the intrinsic value of nature is ignored. Moreover, our understanding of linkages among ecological components and the processes that ultimately deliver ES is incomplete, valuing ES is complex, and there is no standard ES lexicon and limited familiarity with the approach. To help overcome these challenges, we encourage: (1) further research to establish biodiversity–ES relationships; (2) the development of approaches that (i) quantitatively translate responses to chemical stressors by organisms and groups of organisms to ES delivery across different spatial and temporal scales, (ii) measure cultural ES and ease their integration into ES valuations, and (iii) appropriately value changes in ES delivery so that trade‐offs among different management options can be assessed; (3) the establishment of a standard ES lexicon; and (4) building capacity in ES science and how to apply ES to ERAs. These development needs should not prevent movement towards implementation of an ES approach in ERAs, as the advantages we perceive of using this approach render it more than worthwhile to tackle those challenges. Society and the environment stand to benefit from this shift in how we conduct the ERA of regulated stressors.

Community-wide scan identifies fish species associated with coral reef services across the Indo-Pacific

Determining whether many functionally complementary species or only a subset of key species are necessary to maintain ecosystem functioning and services is a critical question in community ecology and biodiversity conservation. Identifying such key species remains challenging, especially in the tropics where many species co-occur and can potentially support the same or different processes. Here, we developed a new community-wide scan (CWS) approach, analogous to the genome-wide scan, to identify fish species that significantly contribute, beyond the socio-environmental and species richness effects, to the biomass and coral cover on Indo-Pacific reefs. We found that only a limited set of species (51 out of approx. 400, approx. 13%), belonging to various functional groups and evolutionary lineages, are strongly and positively associated with fish biomass and live coral cover. Many of these species have not previously been identified as functionally important, and thus may be involved in unknown, yet important, biological mechanisms that help sustain healthy and productive coral reefs. CWS has the potential to reveal species that are key to ecosystem functioning and services and to guide management strategies as well as new experiments to decipher underlying causal ecological processes.

Gymnosperms on the EDGE

Driven by limited resources and a sense of urgency, the prioritization of species for conservation has been a persistent concern in conservation science. Gymnosperms (comprising ginkgo, conifers, cycads, and gnetophytes) are one of the most threatened groups of living organisms, with 40% of the species at high risk of extinction, about twice as many as the most recent estimates for all plants (i.e. 21.4%). This high proportion of species facing extinction highlights the urgent action required to secure their future through an objective prioritization approach. The Evolutionary Distinct and Globally Endangered (EDGE) method rapidly ranks species based on their evolutionary distinctiveness and the extinction risks they face. EDGE is applied to gymnosperms using a phylogenetic tree comprising DNA sequence data for 85% of gymnosperm species (923 out of 1090 species), to which the 167 missing species were added, and IUCN Red List assessments available for 92% of species. The effect of different extinction probability transformations and the handling of IUCN data deficient species on the resulting rankings is investigated. Although top entries in our ranking comprise species that were expected to score well (e.g. Wollemia nobilis, Ginkgo biloba), many were unexpected (e.g. Araucaria araucana). These results highlight the necessity of using approaches that integrate evolutionary information in conservation science.

Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building

Background

Advancements in portable scientific instruments provide promising avenues to expedite field work in order to understand the diverse array of organisms that inhabit our planet. Here, we tested the feasibility for in situ molecular analyses of endemic fauna using a portable laboratory fitting within a single backpack in one of the world's most imperiled biodiversity hotspots, the Ecuadorian Chocó rainforest. We used portable equipment, including the MinION nanopore sequencer (Oxford Nanopore Technologies) and the miniPCR (miniPCR), to perform DNA extraction, polymerase chain reaction amplification, and real-time DNA barcoding of reptile specimens in the field.

Findings

We demonstrate that nanopore sequencing can be implemented in a remote tropical forest to quickly and accurately identify species using DNA barcoding, as we generated consensus sequences for species resolution with an accuracy of >99% in less than 24 hours after collecting specimens. The flexibility of our mobile laboratory further allowed us to generate sequence information at the Universidad Tecnológica Indoamérica in Quito for rare, endangered, and undescribed species. This includes the recently rediscovered Jambato toad, which was thought to be extinct for 28 years. Sequences generated on the MinION required as few as 30 reads to achieve high accuracy relative to Sanger sequencing, and with further multiplexing of samples, nanopore sequencing can become a cost-effective approach for rapid and portable DNA barcoding.

Conclusions

Overall, we establish how mobile laboratories and nanopore sequencing can help to accelerate species identification in remote areas to aid in conservation efforts and be applied to research facilities in developing countries. This opens up possibilities for biodiversity studies by promoting local research capacity building, teaching nonspecialists and students about the environment, tackling wildlife crime, and promoting conservation via research-focused ecotourism.

Unexpected high vulnerability of functions in wilderness areas: evidence from coral reef fishes

High species richness is thought to support the delivery of multiple ecosystem functions and services under changing environments. Yet, some species might perform unique functional roles while others are redundant. Thus, the benefits of high species richness in maintaining ecosystem functioning are uncertain if functions have little redundancy, potentially leading to high vulnerability of functions. We studied the natural propensity of assemblages to be functionally buffered against loss prior to fishing activities, using functional trait combinations, in coral reef fish assemblages across unfished wilderness areas of the Indo-Pacific: Chagos Archipelago, New Caledonia and French Polynesia. Fish functional diversity in these wilderness areas is highly vulnerable to fishing, explained by species- and abundance-based redundancy packed into a small combination of traits, leaving most other trait combinations (60%) sensitive to fishing, with no redundancy. Functional vulnerability peaks for mobile and sedentary top predators, and large species in general. Functional vulnerability decreases for certain functional entities in New Caledonia, where overall functional redundancy was higher. Uncovering these baseline patterns of functional vulnerability can offer early warning signals of the damaging effects from fishing, and may serve as baselines to guide precautionary and even proactive conservation actions.

Protected area coverage of threatened vertebrates and ecoregions in Peru: Comparison of communal, private and state reserves

Protected areas (PAs) are a conservation mainstay and arguably the most effective conservation strategy for species protection. As a 'megadiverse' country, Peru is a priority for conservation actions. Peruvian legislation allows for the creation of state PAs and private/communal PAs. Using publicly available species distribution and protected area data sets we evaluated the coverage of Threatened terrestrial vertebrate species distributions and ecoregions provided by both kinds of PA in Peru. Peru's state PA system covers 217,879 km² and private/communal PAs cover 16,588 km². Of the 462 species of Threatened and Data Deficient species we evaluated, 75% had distributions that overlapped with at least one PA but only 53% had ≥10% of their distributions within PAs, with inclusion much reduced at higher coverage targets. Of the species we evaluated, 118 species are only found in national PAs and 29 species only found in private/communal PAs. Of the 17 terrestrial ecoregions found in Peru all are represented in PAs; the national PA system included coverage of 16 and private/communal PAs protect 13. One ecoregion is only protected in private/communal PAs, whereas four are only covered in national PAs. Our results show the important role private/communal PAs can play in the protection of ecological diversity.

Litter Accumulation and Nutrient Content of Roadside Plant Communities in Sichuan Basin, China

It is widely recognized that feedbacks exist between plant litter and plant community species composition, but this relationship is difficult to interpret over heterogeneous conditions typical of modified environments such as roadways. Given the need to expedite natural recovery of disturbed areas through restoration interventions, we characterized litter accumulation and nutrient content (i.e., organic carbon, total N, and P) and quantified their association with key plant species. Plant species cover and litter characteristics were sampled at 18 successional forest plant communities along major roadways in Sichuan Basin, western China. Variation in litter across communities was assessed with principal component analysis (PCA) and species with the highest correlation to PCA axes were determined with Pearson’s r coefficients. Plant communities with the longest time since road construction (i.e., 70 years) were distinctly different in litter total N and organic carbon compared to plant communities with a shorter disturbance history. We encountered 59 plant species across sampling plots, but only four rare species (i.e., frequency < 5) were strongly correlated with litter characteristics (p < 0.01); none of which were the most abundant where they occurred. These results highlight the importance of site-specific factors (i.e., geographic location, disturbance age) regulating plant litter across heavily disturbed landscapes and how litter characteristics and rare plant species are correlated.

Taxonomic bias in biodiversity data and societal preferences

Studying and protecting each and every living species on Earth is a major challenge of the 21^st century. Yet, most species remain unknown or unstudied, while others attract most of the public, scientific and government attention. Although known to be detrimental, this taxonomic bias continues to be pervasive in the scientific literature, but is still poorly studied and understood. Here, we used 626 million occurrences from the Global Biodiversity Information Facility (GBIF), the biggest biodiversity data portal, to characterize the taxonomic bias in biodiversity data. We also investigated how societal preferences and taxonomic research relate to biodiversity data gathering. For each species belonging to 24 taxonomic classes, we used the number of publications from Web of Science and the number of web pages from Bing searches to approximate research activity and societal preferences. Our results show that societal preferences, rather than research activity, strongly correlate with taxonomic bias, which lead us to assert that scientists should advertise less charismatic species and develop societal initiatives (e.g. citizen science) that specifically target neglected organisms. Ensuring that biodiversity is representatively sampled while this is still possible is an urgent prerequisite for achieving efficient conservation plans and a global understanding of our surrounding environment.

Quantification of heat shock protein 70 and acetylcholinesterase over a time course suggests environmental adaptation in a foundational molluscan species

Waterways in urban areas often act as repositories for sewage, industrial waste, and environmental contaminants. In response, inhabitants of these watersheds undergo physiological adaptations specific to their respective environments. Effects of these stressors can be assayed by quantification of various well-documented biomarkers in sentinel species such as the Atlantic Ribbed mussel, Geukensia demissa, a native to the Bronx River Estuary, Bronx, NY, USA. Heat shock protein 70 (Hsp70) is a universally expressed biomarker for an array of environmental stressors including toxins and low dissolved oxygen. To better understand the mechanisms by which organisms tolerate their contaminated environments, we monitored the constitutive and heat shock-induced levels of two proteins: Hsp70 and acetylcholinesterase (AChE) in natural populations of G. demissa from differentially impacted sites: the Bronx River and Greenwich Cove estuaries. We show that G. demissa from the Bronx River exhibits a higher level of constitutive Hsp70, and launches a more rapid and robust heat shock response than does its Greenwich Cove counterpart. In addition, AChE levels are recovered more quickly in Bronx River mussels. Based on response pattern investigations from heat stress as well as constitutive expression, we suggest that the Hsp70/AChE chaperone/client relationship exemplifies the unique adaptive mechanisms utilized by organisms in order to tolerate environmentally impacted habitats. Results from this study offer important insights from an ecological perspective into the molecular and cellular basis of stress response and provide valuable information regarding adaptation to the increased demands of challenging environments.

Meeting the Aichi targets: Pushing for zero extinction conservation

Effective protection of the ~19 000 IUCN-listed threatened species has never been more pressing. Ensuring the survival of the most vulnerable and irreplaceable taxa and places, such as those identified by the Alliance for Zero Extinction (AZE) species and their associated sites (AZEs&s), is an excellent opportunity to achieve the Aichi 2020 Targets T11 (protected areas) and T12 (preventing species extinctions). AZE taxa have small, single-site populations that are especially vulnerable to human-induced extinctions, particularly for the many amphibians. We show that AZEs&s can be protected feasibly and cost-effectively, but action is urgent. We argue that the Alliance, whose initial main aim was to identify AZEs&s, must be followed up by a second-generation initiative that directs and co-ordinates AZE conservation activities on the ground. The prominent role of zoos, conservation NGOs, and governmental institutions provides a combination of all-encompassing knowhow that can, if properly steered, maximize the long-term survival of AZEs&s.

Scientific Opinion addressing the state of the science on risk assessment of plant protection products for in-soil organisms

Following a request from EFSA, the Panel on Plant Protection Products and their Residues developed an opinion on the science behind the risk assessment of plant protection products for in-soil organisms. The current risk assessment scheme is reviewed, taking into account new regulatory frameworks and scientific developments. Proposals are made for specific protection goals for in-soil organisms being key drivers for relevant ecosystem services in agricultural landscapes such as nutrient cycling, soil structure, pest control and biodiversity. Considering the time-scales and biological processes related to the dispersal of the majority of in-soil organisms compared to terrestrial non-target arthropods living above soil, the Panel proposes that in-soil environmental risk assessments are made at in- and off-field scale considering field boundary levels. A new testing strategy which takes into account the relevant exposure routes for in-soil organisms and the potential direct and indirect effects is proposed. In order to address species recovery and long-term impacts of PPPs, the use of population models is also proposed.

Estimating economic losses to tourism in Africa from the illegal killing of elephants

Recent surveys suggest tens of thousands of elephants are being poached annually across Africa, putting the two species at risk across much of their range. Although the financial motivations for ivory poaching are clear, the economic benefits of elephant conservation are poorly understood. We use Bayesian statistical modelling of tourist visits to protected areas, to quantify the lost economic benefits that poached elephants would have delivered to African countries via tourism. Our results show these figures are substantial (∼USD $25 million annually), and that the lost benefits exceed the anti-poaching costs necessary to stop elephant declines across the continent's savannah areas, although not currently in the forests of central Africa. Furthermore, elephant conservation in savannah protected areas has net positive economic returns comparable to investments in sectors such as education and infrastructure. Even from a tourism perspective alone, increased elephant conservation is therefore a wise investment by governments in these regions.

An ongoing elephant poaching crisis is threatening not only elephant populations but also the local economies that rely on nature-based tourism. Here, Naidoo and colleagues use an economic model to estimate the financial contribution of elephants to tourism and the possible consequences of their loss.

Integrating data-deficient species in analyses of evolutionary history loss

There is an increasing interest in measuring loss of phylogenetic diversity and evolutionary distinctiveness which together depict the evolutionary history of conservation interest. Those losses are assessed through the evolutionary relationships between species and species threat status or extinction probabilities. Yet, available information is not always sufficient to quantify the threat status of species that are then classified as data deficient. Data‐deficient species are a crucial issue as they cause incomplete assessments of the loss of phylogenetic diversity and evolutionary distinctiveness. We aimed to explore the potential bias caused by data‐deficient species in estimating four widely used indices: HEDGE, EDGE, PDloss, and Expected PDloss. Second, we tested four different widely applicable and multitaxa imputation methods and their potential to minimize the bias for those four indices. Two methods are based on a best‐ vs. worst‐case extinction scenarios, one is based on the frequency distribution of threat status within a taxonomic group and one is based on correlates of extinction risks. We showed that data‐deficient species led to important bias in predictions of evolutionary history loss (especially high underestimation when they were removed). This issue was particularly important when data‐deficient species tended to be clustered in the tree of life. The imputation method based on correlates of extinction risks, especially geographic range size, had the best performance and enabled us to improve risk assessments. Solving threat status of DD species can fundamentally change our understanding of loss of phylogenetic diversity. We found that this loss could be substantially higher than previously found in amphibians, squamate reptiles, and carnivores. We also identified species that are of high priority for the conservation of evolutionary distinctiveness.

Loss and conservation of evolutionary history in the Mediterranean Basin

BACKGROUND

Phylogenetic diversity and evolutionary distinctiveness are highly valuable components of biodiversity, but they are rarely considered in conservation practices. Focusing on a biodiversity hotspot, the Mediterranean Basin, we aimed to identify those areas where evolutionary history is highly threatened and range-restricted in the region. Using null models, we first compared the spatial distributions of three indices: two measured threatened evolutionary history-Expected PDloss and Heightened Evolutionary distinctiveness and Global Endangerment-and one measured endemic evolutionary history-Biogeographically Evolutionary Distinctiveness. We focused on three vertebrate groups with high proportions of endemic, threatened species: amphibians, squamates and terrestrial mammals. Second, we estimated the spatial overlap of hotspots of threatened and endemic evolutionary history within the network of protected areas under several conservation scenarios.

RESULTS

Areas that concentrate evolutionary history of conservation interest greatly differed among taxa and indices, although a large proportion of hotspots were identified in the Maghreb, in the East of the Mediterranean Basin as well as in islands. We found that, in a minimum conservation scenario, there was a significant proportion of hotspots for amphibians and squamates that were protected but not for terrestrial mammals. However, in a strong conservation scenario, only few hotspots overlapped with protected areas and they were significantly less protected than in a model where hotspots were chosen randomly.

CONCLUSIONS

Some sites concentrate highly threatened and range-restricted evolutionary history of the Mediterranean basin and their conservation could be much improved. These sites are relevant for conservation studies aimed at designing new conservation actions to preserve evolutionary history and the option values it represents.

Free mate choice enhances conservation breeding in the endangered giant panda

Conservation breeding programmes have become an increasingly important tool to save endangered species, yet despite the allocation of significant resources, efforts to create self-sustaining populations have met with limited success. The iconic giant panda (Ailuropoda melanoleuca) embodies the struggles associated with ex situ species conservation. Here we show that behavioural mate preferences in giant pandas predict reproductive outcomes. Giant pandas paired with preferred partners have significantly higher copulation and birth rates. Reproductive rates increase further when both partners show mutual preference for one another. If managers were to incorporate mate preferences more fully into breeding management, the production of giant panda offspring for China's reintroduction programme might be greatly expedited. When extended to the increasing numbers of species dependent on ex situ conservation breeding to avoid extinction, our findings highlight that mate preference and other aspects of informed behavioural management could make the difference between success and failure of these programmes.

Ex situ conservation breeding programmes for endangered species are expensive, and not always guaranteed to succeed. Here, Martin-Wintle et al. show that when captive giant pandas are given the opportunity to choose their preferred mate, copulation and birth rates increase significantly.