Funding begets biodiversity

Monitoring biodiversity loss in rapidly changing Afrotropical ecosystems: an emerging imperative for governance and research

Africa is experiencing extensive biodiversity loss due to rapid changes in the environment, where natural resources constitute the main instrument for socioeconomic development and a mainstay source of livelihoods for an increasing population. Lack of data and information deficiency on biodiversity, but also budget constraints and insufficient financial and technical capacity, impede sound policy design and effective implementation of conservation and management measures. The problem is further exacerbated by the lack of harmonized indicators and databases to assess conservation needs and monitor biodiversity losses. We review challenges with biodiversity data (availability, quality, usability and database access) as a key limiting factor that impacts funding and governance. We also evaluate the drivers of both ecosystems change and biodiversity loss as a central piece of knowledge to develop and implement effective policies. While the continent focuses more on the latter, we argue that the two are complementary in shaping restoration and management solutions. We thus underscore the importance of establishing monitoring programmes focusing on biodiversity-ecosystem linkages in order to inform evidence-based decisions in ecosystem conservation and restoration in Africa. This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'.

Analysis of intrinsic evolutionary factors leading to microendemic distributions in New Caledonian leaf beetles

Microendemicity, or the condition of some species having local ranges, is a relatively common pattern in nature. However, the factors that lead to this pattern are still largely unknown. Most studies addressing this issue tend to focus on extrinsic factors associated with microendemic distributions, such as environmental conditions, hypothesising a posteriori about underlying potential speciation mechanisms, linked or not to these conditions. Here, we use a multi-faceted approach mostly focusing on intrinsic factors instead, namely diversification dynamics and speciation modes in two endemic sibling genera of leaf beetles with microendemic distributions, Taophila and Tricholapita, in a microendemicity hotspot, New Caledonia. Results suggest that the diversification rate in this lineage slowed down through most of the Neogene and consistently with a protracted speciation model possibly combined with several ecological and environmental factors potentially adding rate-slowing effects through time. In turn, species accumulated following successive allopatric speciation cycles, possibly powered by marked geological and climatic changes in the region in the last 25 million years, with daughter species ranges uncorrelated with the time of speciation. In this case, microendemicity seems to reflect a mature state for the system, rather than a temporary condition for recent species, as suggested for many microendemic organisms.

Multiple forms of hotspots of tetrapod biodiversity and the challenges of open-access data scarcity

The uneven spatial distribution of biodiversity is a defining feature of nature. In fact, the implementation of conservation actions both locally and globally has progressively been guided by the identification of biodiversity 'hotspots' (areas with exceptional biodiversity). However, different regions of the world differ drastically in the availability of fine-scale data on the diversity and distribution of species, thus limiting the potential to assess their local environmental priorities. Within South America-a megadiverse continent-Uruguay represents a peculiar area where multiple tropical and non-tropical eco-regions converge, creating highly heterogeneous ecosystems, but where the systematic quantification of biodiversity remains largely anecdotal. To investigate the constraints posed by the limited access to biodiversity data, we employ the most comprehensive database for tetrapod vertebrates in Uruguay (spanning 664 species) assembled to date, to identify hotspots of species-richness, endemism and threatened species for the first time. Our results reveal negligible spatial congruence among biodiversity hotspots, and that tetrapod sampling has historically concentrated in only a few areas. Collectively, our study provides a detailed account of the areas where urgent biodiversity monitoring efforts are needed to develop more accurate knowledge on biodiversity patterns, offering government and environmental bodies a critical scientific resource for future planning.

Gaps in terrestrial soundscape research: It's time to focus on tropical wildlife

There has been a body of research examining the sounds produced in landscapes. These sounds are commonly defined as soundscapes, however, the term is often used in different contexts. To understand the various meanings attributed to soundscapes, we identified how soundscapes are represented in the scientific literature and identified current knowledge gaps in soundscape research focusing on terrestrial environments. We conducted a quantitative review of published papers with the keyword soundscape available at Web of Science and Scopus databases. A total of 1309 abstracts and a subset of about 5% (N = 68) complete papers and reviews published from 1985 to 2017 were read and analysed, identifying types of sound, types of environment and focal species studied, as well as study regions and climates. By identifying the current focus of research, we also identified gaps and research opportunities. Research was biased towards temperate regions, terrestrial environments, and the impacts on humans in urban areas. Although most of the world's biodiversity is concentrated in tropical wilderness areas, these regions had fewer studies attributed to them. Given the importance of tropical landscapes for biodiversity conservation, we strongly suggest that more research should be undertaken in the tropics, with a particular focus on wildlife in these regions. Furthermore, soundscape research (methods and tools) should increasingly target the anthropogenic impacts on wildlife, including behavioural and physiological changes, alongside the current focus on human-sound interactions and the approach used by bioacoustics methods.

Effects of publication bias on conservation planning

Conservation planners need reliable information on spatial patterns of biodiversity. However, existing data sets are skewed because some ecosystems, taxa, and locations are underrepresented. We determined how many articles have been published in recent decades on the biodiversity of different countries and their constituent provinces. We searched the Web of Science catalogues Science Citation Index (SCI) and Social Science Citation Index (SSCI) for biodiversity-related articles published from 1993 to 2016 that included country and province names. We combined data on research publication frequency with other provincial-scale factors hypothesized to affect the likelihood of research activity (i.e., economic development, human presence, infrastructure, and remoteness). Areas that appeared understudied relative to the biodiversity expected based on site climate likely have been inaccessible to researchers for reasons, notably armed conflict. Geographic publication bias is of most concern in the most remote areas of sub-Saharan Africa and South America. Our provincial-scale model may help compensate for publication biases in conservation planning by revealing the spatial extent of research needs and the low cost of redoing this analysis annually.

Parasitological research in the molecular age

New technological methods, such as rapidly developing molecular approaches, often provide new tools for scientific advances. However, these new tools are often not utilized equally across different research areas, possibly leading to disparities in progress between these areas. Here, we use empirical evidence from the scientific literature to test for potential discrepancies in the use of genetic tools to study parasitic vs non-parasitic organisms across three distinguishable molecular periods, the allozyme, nucleotide and genomics periods. Publications on parasites constitute only a fraction (<5%) of the total research output across all molecular periods and are dominated by medically relevant parasites (especially protists), particularly during the early phase of each period. Our analysis suggests an increasing complexity of topics and research questions being addressed with the development of more sophisticated molecular tools, with the research focus between the periods shifting from predominantly species discovery to broader theory-focused questions. We conclude that both new and older molecular methods offer powerful tools for research on parasites, including their diverse roles in ecosystems and their relevance as human pathogens. While older methods, such as barcoding approaches, will continue to feature in the molecular toolbox of parasitologists for years to come, we encourage parasitologists to be more responsive to new approaches that provide the tools to address broader questions.

Spatial and topical imbalances in biodiversity research

The rapid erosion of biodiversity is among the biggest challenges human society is facing. Concurrently, major efforts are in place to quantify changes in biodiversity, to understand the consequences for ecosystem functioning and human wellbeing, and to develop sustainable management strategies. Based on comprehensive bibliometric analyses covering 134,321 publications, we report systematic spatial biases in biodiversity-related research. Research is dominated by wealthy countries, while major research deficits occur in regions with disproportionately high biodiversity as well as a high share of threatened species. Similarly, core scientists, who were assessed through their publication impact, work primarily in North America and Europe. Though they mainly exchange and collaborate across locations of these two continents, the connectivity among them has increased with time. Finally, biodiversity-related research has primarily focused on terrestrial systems, plants, and the species level, and is frequently conducted in Europe and Asia by researchers affiliated with European and North American institutions. The distinct spatial imbalances in biodiversity research, as demonstrated here, must be filled, research capacity built, particularly in the Global South, and spatially-explicit biodiversity data bases improved, curated and shared.

Using landscape habitat associations to prioritize areas of conservation action for terrestrial birds

Predicting species distributions has long been a valuable tool to plan and focus efforts for biodiversity conservation, particularly because such an approach allows researchers and managers to evaluate species distribution changes in response to various threats. Utilizing data from a long-term monitoring program and land cover data sets, we modeled the probability of occupancy and colonization for 38 bird Species of Greatest Conservation Need (SGCN) in the robust design occupancy modeling framework, and used results from the best models to predict occupancy and colonization on the Iowa landscape. Bird surveys were conducted at 292 properties from April to October, 2006-2014. We calculated landscape habitat characteristics at multiple spatial scales surrounding each of our surveyed properties to be used in our models and then used kriging in ArcGIS to create predictive maps of species distributions. We validated models with data from 2013 using the area under the receiver operating characteristic curve (AUC). Probability of occupancy ranged from 0.001 (SE < 0.001) to 0.995 (SE = 0.004) for all species and probability of colonization ranged from 0.001 (SE < 0.001) to 0.999 (SE < 0.001) for all species. AUC values for predictive models ranged from 0.525-0.924 for all species, with 17 species having predictive models considered useful (AUC > 0.70). The most important predictor for occupancy of grassland birds was percentage of the landscape in grassland habitat, and the most important predictor for woodland birds was percentage of the landscape in woodland habitat. This emphasizes the need for managers to restore specific habitats on the landscape. In an era during which funding continues to decrease for conservation agencies, our approach aids in determining where to focus limited resources to best conserve bird species of conservation concern.

Data gaps in anthropogenically driven local-scale species richness change studies across the Earth's terrestrial biomes

There have been numerous attempts to synthesize the results of local‐scale biodiversity change studies, yet several geographic data gaps exist. These data gaps have hindered ecologist's ability to make strong conclusions about how local‐scale species richness is changing around the globe. Research on four of the major drivers of global change is unevenly distributed across the Earth's biomes. Here, we use a dataset of 638 anthropogenically driven species richness change studies to identify where data gaps exist across the Earth's terrestrial biomes based on land area, future change in drivers, and the impact of drivers on biodiversity, and make recommendations for where future studies should focus their efforts. Across all drivers of change, the temperate broadleaf and mixed forests and the tropical moist broadleaf forests are the best studied. The biome–driver combinations we have identified as most critical in terms of where local‐scale species richness change studies are lacking include the following: land‐use change studies in tropical and temperate coniferous forests, species invasion and nutrient addition studies in the boreal forest, and warming studies in the boreal forest and tropics. Gaining more information on the local‐scale effects of the specific human drivers of change in these biomes will allow for better predictions of how human activity impacts species richness around the globe.

Global priorities for an effective information basis of biodiversity distributions

Gaps in digital accessible information (DAI) on species distributions hamper prospects of safeguarding biodiversity and ecosystem services, and addressing central ecological and evolutionary questions. Achieving international targets on biodiversity knowledge requires that information gaps be identified and actions prioritized. Integrating 157 million point records and distribution maps for 21,170 terrestrial vertebrate species, we find that outside a few well-sampled regions, DAI on point occurrences provides very limited and spatially biased inventories of species. Surprisingly, many large, emerging economies are even more under-represented in global DAI than species-rich, developing countries in the tropics. Multi-model inference reveals that completeness is mainly limited by distance to researchers, locally available research funding and participation in data-sharing networks, rather than transportation infrastructure, or size and funding of Western data contributors as often assumed. Our results highlight the urgent need for integrating non-Western data sources and intensifying cooperation to more effectively address societal biodiversity information needs.

Benefits to poorly studied taxa of conservation of bird and mammal diversity on islands

Protected area delineation and conservation action are urgently needed on marine islands, but the potential biodiversity benefits of these activities can be difficult to assess due to lack of species diversity information for lesser known taxa. We used linear mixed effects modeling and simple spatial analyses to investigate whether conservation activities based on the diversity of well-known insular taxa (birds and mammals) are likely to also capture the diversity of lesser known taxa (reptiles, amphibians, vascular land plants, ants, land snails, butterflies, and tenebrionid beetles). We assembled total, threatened, and endemic diversity data for both well-known and lesser known taxa and combined these with physical island biogeography characteristics for 1190 islands from 109 archipelagos. Among physical island biogeography factors, island area was the best indicator of diversity of both well-known and little-known taxa. Among taxonomic factors, total mammal species richness was the best indicator of total diversity of lesser known taxa, and the combination of threatened mammal and threatened bird diversity was the best indicator of lesser known endemic richness. The results of other intertaxon diversity comparisons were highly variable, however. Based on our results, we suggest that protecting islands above a certain minimum threshold area may be the most efficient use of conservation resources. For example, using our island database, if the threshold were set at 10 km(2) and the smallest 10% of islands greater than this threshold were protected, 119 islands would be protected. The islands would range in size from 10 to 29 km(2) and would include 268 lesser known species endemic to a single island, along with 11 bird and mammal species endemic to a single island. Our results suggest that for islands of equivalent size, prioritization based on total or threatened bird and mammal diversity may also capture opportunities to protect lesser known species endemic to islands.

Biogeographical and taxonomic biases in tropical forest fragmentation research

Despite several decades of research on the effects of fragmentation and habitat change on biodiversity, there remain strong biases in the geographical regions and taxonomic species studied. The knowledge gaps resulting from these biases are of particular concern if the forests most threatened with modification are also those for which the effects of such change are most poorly understood. To quantify the nature and magnitude of such biases, we conducted a systematic review of the published literature on forest fragmentation in the tropics for the period 1980-2012. Studies included focused on any type of response of single species, communities, or assemblages of any taxonomic group to tropical forest fragmentation and on fragmentation-related changes to forests. Of the 853 studies we found in the SCOPUS database, 64% were conducted in the Neotropics, 13% in Asia, 10% in the Afrotropics, and 5% in Australasia. Thus, although the Afrotropics is subject to the highest rates of deforestation globally, it was the most disproportionately poorly studied biome. Significant taxonomic biases were identified. Of the taxonomic groups considered, herpetofauna was the least studied in the tropics, particularly in Africa. Research examining patterns of species distribution was by far the most common type (72%), and work focused on ecological processes (28%) was rare in all biomes, but particularly in the Afrotropics and for fauna. We suggest research efforts be directed toward less-studied biogeographic regions, particularly where the threat of forest fragmentation continues to be high. Increased research investment in the Afrotropics will be important to build knowledge of threats and inform responses in a region where almost no efforts to restore its fragmented landscapes have yet begun and forest protection is arguably most tenuous.

Red List assessments of East African chameleons: a case study of why we need experts

The IUCN Red List of Threatened Species uses geographical distribution as a key criterion in assessing the conservation status of species. Accurate knowledge of a species’ distribution is therefore essential to ensure the correct categorization is applied. Here we compare the geographical distribution of 35 species of chameleons endemic to East Africa, using data from the Global Biodiversity Information Facility (GBIF) and data compiled by a taxonomic expert. Data screening showed 99.9% of GBIF records used outdated taxonomy and 20% had no locality coordinates. Conversely the expert dataset used 100% up-to-date taxonomy and only seven records (3%) had no coordinates. Both datasets were used to generate range maps for each species, which were then used in preliminary Red List categorization. There was disparity in the categories of 10 species, with eight being assigned a lower threat category based on GBIF data compared with expert data, and the other two assigned a higher category. Our results suggest that before conducting desktop assessments of the threatened status of species, aggregated museum locality data should be vetted against current taxonomy and localities should be verified. We conclude that available online databases are not an adequate substitute for taxonomic experts in assessing the threatened status of species and that Red List assessments may be compromised unless this extra step of verification is carried out.

A novel method to handle the effect of uneven sampling effort in biodiversity databases

How reliable are results on spatial distribution of biodiversity based on databases? Many studies have evidenced the uncertainty related to this kind of analysis due to sampling effort bias and the need for its quantification. Despite that a number of methods are available for that, little is known about their statistical limitations and discrimination capability, which could seriously constrain their use. We assess for the first time the discrimination capacity of two widely used methods and a proposed new one (FIDEGAM), all based on species accumulation curves, under different scenarios of sampling exhaustiveness using Receiver Operating Characteristic (ROC) analyses. Additionally, we examine to what extent the output of each method represents the sampling completeness in a simulated scenario where the true species richness is known. Finally, we apply FIDEGAM to a real situation and explore the spatial patterns of plant diversity in a National Park. FIDEGAM showed an excellent discrimination capability to distinguish between well and poorly sampled areas regardless of sampling exhaustiveness, whereas the other methods failed. Accordingly, FIDEGAM values were strongly correlated with the true percentage of species detected in a simulated scenario, whereas sampling completeness estimated with other methods showed no relationship due to null discrimination capability. Quantifying sampling effort is necessary to account for the uncertainty in biodiversity analyses, however, not all proposed methods are equally reliable. Our comparative analysis demonstrated that FIDEGAM was the most accurate discriminator method in all scenarios of sampling exhaustiveness, and therefore, it can be efficiently applied to most databases in order to enhance the reliability of biodiversity analyses.

Global models of ant diversity suggest regions where new discoveries are most likely are under disproportionate deforestation threat

Most of the described and probably undescribed species on Earth are insects. Global models of species diversity rarely focus on insects and none attempt to address unknown, undescribed diversity. We assembled a database representing about 13,000 records for ant generic distribution from over 350 regions that cover much of the globe. Based on two models of diversity and endemicity, we identified regions where our knowledge of ant diversity is most limited, regions we have called "hotspots of discovery." A priori, such regions might be expected to be remote and untouched. Instead, we found that the hotspots of discovery are also the regions in which biodiversity is the most threatened by habitat destruction. Our results not only highlight the immediate need for conservation of the remaining natural habitats in these regions, but also the extent to which, by focusing on well-known groups such as vertebrates, we may fail to conserve the far greater diversity of the smaller species yet to be found.