Biodiversity loss and the taxonomic bottleneck: emerging biodiversity science

Human domination of the Earth has resulted in dramatic changes to global and local patterns of biodiversity. Biodiversity is critical to human sustainability because it drives the ecosystem services that provide the core of our life-support system. As we, the human species, are the primary factor leading to the decline in biodiversity, we need detailed information about the biodiversity and species composition of specific locations in order to understand how different species contribute to ecosystem services and how humans can sustainably conserve and manage biodiversity. Taxonomy and ecology, two fundamental sciences that generate the knowledge about biodiversity, are associated with a number of limitations that prevent them from providing the information needed to fully understand the relevance of biodiversity in its entirety for human sustainability: (1) biodiversity conservation strategies that tend to be overly focused on research and policy on a global scale with little impact on local biodiversity; (2) the small knowledge base of extant global biodiversity; (3) a lack of much-needed site-specific data on the species composition of communities in human-dominated landscapes, which hinders ecosystem management and biodiversity conservation; (4) biodiversity studies with a lack of taxonomic precision; (5) a lack of taxonomic expertise and trained taxonomists; (6) a taxonomic bottleneck in biodiversity inventory and assessment; and (7) neglect of taxonomic resources and a lack of taxonomic service infrastructure for biodiversity science. These limitations are directly related to contemporary trends in research, conservation strategies, environmental stewardship, environmental education, sustainable development, and local site-specific conservation. Today’s biological knowledge is built on the known global biodiversity, which represents barely 20% of what is currently extant (commonly accepted estimate of 10 million species) on planet Earth. Much remains unexplored and unknown, particularly in hotspots regions of Africa, South Eastern Asia, and South and Central America, including many developing or underdeveloped countries, where localized biodiversity is scarcely studied or described. "Backyard biodiversity", defined as local biodiversity near human habitation, refers to the natural resources and capital for ecosystem services at the grassroots level, which urgently needs to be explored, documented, and conserved as it is the backbone of sustainable economic development in these countries. Beginning with early identification and documentation of local flora and fauna, taxonomy has documented global biodiversity and natural history based on the collection of "backyard biodiversity" specimens worldwide. However, this branch of science suffered a continuous decline in the latter half of the twentieth century, and has now reached a point of potential demise. At present there are very few professional taxonomists and trained local parataxonomists worldwide, while the need for, and demands on, taxonomic services by conservation and resource management communities are rapidly increasing. Systematic collections, the material basis of biodiversity information, have been neglected and abandoned, particularly at institutions of higher learning. Considering the rapid increase in the human population and urbanization, human sustainability requires new conceptual and practical approaches to refocusing and energizing the study of the biodiversity that is the core of natural resources for sustainable development and biotic capital for sustaining our life-support system. In this paper we aim to document and extrapolate the essence of biodiversity, discuss the state and nature of taxonomic demise, the trends of recent biodiversity studies, and suggest reasonable approaches to a biodiversity science to facilitate the expansion of global biodiversity knowledge and to create useful data on backyard biodiversity worldwide towards human sustainability.     

The terrestrial arthropods of Mauritius: a neglected conservation target

Entomology in Mauritius has historically been linked with the agricultural and medical fields but concern should now be directed towards the conservation of native forest insects given that they are key components of the local ecosystem. Despite its young age, small size and remoteness, the island has a well-developed native insect fauna with a high proportion of endemic species. A majority of the insect orders are represented on the island. We document the current state of knowledge for Mauritian arthropods, with particular focus on the Coleoptera. This is the most diverse order locally with 1,032 species. In addition, it is the best catalogued historically, providing a framework for future conservation studies to evaluate the current status of this group. We explore the current threats facing the native insect fauna and highlight the needs for concern on this vital component of local biodiversity. We recognize that the initial step for conserving the native insects will depend largely on the establishment of a local taxonomic knowledge base with international expert input.     

Effectiveness of Protected Areas for biodiversity conservation: Mammal occupancy patterns in the Iguaçu National Park,Brazil

Protected areas – widely recognized as the main strategy for biodiversity conservation – have greatly expanded, covering ∼15% of the Earth; however, we still lack detailed information on biodiversity to evaluate their effectiveness. This is particularly urgent for biodiversity hotspots where protected areas are islands within human modified landscapes. We focus on mammals of the Iguaçu National Park – one of the most important parks in the Atlantic Forest hotspot – to evaluate the effectiveness of protected areas in conserving biodiversity. We monitored 300 km² with 37 cameras traps during five years to assess if (1) species occupancy declined over time, and (2) if species occupancy/detectability are spatially associated with illegal hunting, proximity to tourism infrastructure and distance from the edge, estimating the proportion of the park where these negative effects are detected. Many species that are rare in most Atlantic Forest remnants presented high occupancy within the park, and no decline in occupancy was observed over time. However, the distribution of 11 species was spatially associated primarily with the distance from the edge and proximity to tourism infrastructure, resulting in a decline, across half of the park area, from 13 to 23% in occupancy and from 19 to 35% in detectability (values averaged among species). These negative effects should be even stronger on smaller protected areas, which are the majority in highly altered hotspots. Re-establishing and properly managing buffer zones and restricting tourism to localized areas are essential to ensure the effectiveness of protected areas for biodiversity conservation.     

Stability or breakdown under climate change? A key group of woody bamboos will find suitable areas in its richness center

Bamboos play an important role in forest dynamics, but management strategies are needed to avoid monodominance. Understanding how climate change would influence the geographic distribution of bamboos could provide management tools for habitat conservation, as well as prevent the expansion of this group. We investigated the distribution patterns of Merostachys species that are endemic to the Brazilian Atlantic Forest, under current and future climate scenarios. We obtained occurrence records based on field collection, herbaria data and online databases. We used the Maxent algorithm to model potential distribution. Future scenarios considered the IPCC forecasted climate for 2070. Our models showed that a reduction in suitable areas for Merostachys species will likely occur, but the existence of suitable areas under climate changes in the Brazilian Atlantic Forest indicates climatic stability in some areas of occurrence of these species in their richness center. Since the fact that in places with local dominance of woody bamboos there is a decrease in the diversity of other plant species, the occurrence of Merostachys throughout the suitable areas may represent risks to biodiversity conservation. Investigations of the synergistic effects of climate change and the local dominance of woody bamboos are required. Therefore, management measures may be very important to control the occurrence of woody bamboos in the Brazilian Atlantic Forest, mainly in climatically stable areas.     

Endemic birds of the Atlantic Forest: traits,conservation status,and patterns of biodiversity

The bird fauna of the Brazilian Atlantic Forest is exceptionally diverse and threatened, with high levels of endemism. Available lists of the endemic birds of the Atlantic Forest were generated before recent taxonomic revisions lumped or split species and before the recent increase in species occurrence records. Our objective, therefore, was to compile a new list of the endemic birds of the Atlantic Forest, characterize these species in terms of conservation status and natural history traits, and map remaining vegetation and protected areas. We combined GIS analysis with a literature search to compile a list of endemic species and, based on the phylogeny and distribution of these species, characterized areas in terms of species richness, phylogenetic diversity, and endemism. We identified 223 species of birds endemic to the Atlantic Forest, including 12 species not included in previous lists. In addition, 14 species included in previous lists were not considered endemic, either because they occur outside the Atlantic Forest biome or because they are not considered valid species. The typical Atlantic Forest endemic bird is a small forest‐dependent invertivore. Of the species on our list, 31% are considered threatened or extinct. Only ~ 34% of the spatial analysis units had > 10% forest cover, and protected area coverage was consistently low (< 1%). In addition, we found spatial incongruity among the different measures of biodiversity (species richness, relative phylogenetic diversity, restricted‐range species, and irreplaceability). Each of these measures provides information concerning different aspects of biological diversity. However, regardless of which aspect(s) of biodiversity might be considered most important, preservation of the remaining areas of remnant vegetation and further expansion of protected areas are essential if we are to conserve the many endemic species of birds in the Atlantic Forest.     

Fine-scale sites of global conservation importance in the Atlantic forest of Brazil

The Brazilian Atlantic Forest is a highly threatened biodiversity hotspot that has been the subject of several complementary conservation assessments and priority-setting initiatives in the last 30 years. Results of these initiatives have relied on distinct types of distribution data for biodiversity features and differ in the objectivity and repeatability of their methodologies. Here we refine earlier priority-setting exercises using the key biodiversity areas (KBA) approach. We evaluate how well these KBAs are represented in the existing protected areas system, prioritize among them, and analyze critical aspects of the KBA methodology in the Brazilian Atlantic Forest context, such as its ability to guide specific conservation strategies. Building upon an extensive database with 1,636 species records and 122 previously identified Important Bird Areas, we demonstrate that conservation assessments in highly fragmented landscapes may be benefited by high resolution species data as is required by the KBA process. We identify 538 KBAs for 141 globally threatened vertebrate species. Prioritizing among these KBA, we highlight the 24 most irreplaceable sites for terrestrial vertebrate species conservation in the Atlantic Forest, based on existing data.     

Pervasive defaunation of forest remnants in a tropical biodiversity hotspot

Tropical deforestation and forest fragmentation are among the most important biodiversity conservation issues worldwide, yet local extinctions of millions of animal and plant populations stranded in unprotected forest remnants remain poorly explained. Here, we report unprecedented rates of local extinctions of medium to large-bodied mammals in one of the world's most important tropical biodiversity hotspots. We scrutinized 8,846 person-years of local knowledge to derive patch occupancy data for 18 mammal species within 196 forest patches across a 252,669-km(2) study region of the Brazilian Atlantic Forest. We uncovered a staggering rate of local extinctions in the mammal fauna, with only 767 from a possible 3,528 populations still persisting. On average, forest patches retained 3.9 out of 18 potential species occupancies, and geographic ranges had contracted to 0-14.4% of their former distributions, including five large-bodied species that had been extirpated at a regional scale. Forest fragments were highly accessible to hunters and exposed to edge effects and fires, thereby severely diminishing the predictive power of species-area relationships, with the power model explaining only ～9% of the variation in species richness per patch. Hence, conventional species-area curves provided over-optimistic estimates of species persistence in that most forest fragments had lost species at a much faster rate than predicted by habitat loss alone.     

Accommodating Species Climate-Forced Dispersal and Uncertainties in Spatial Conservation Planning

Spatial conservation prioritization should seek to anticipate climate change impacts on biodiversity and to mitigate these impacts through the development of dynamic conservation plans. Here, we defined spatial priorities for the conservation of amphibians inhabiting the Atlantic Forest Biodiversity Hotspot that overcome the likely impacts of climate change on the distribution of this imperiled fauna. First, we built ecological niche models (ENMs) for 431 amphibian species both for current time and for the mid-point of a 30-year period spanning 2071–2099 (i.e. 2080). For modeling species'' niches, we combined six modeling methods and three different climate models. We also quantified and mapped model uncertainties. Our consensus models forecasted range shifts that culminate with high species richness in central and eastern Atlantic Forest, both for current time and for 2080. Most species had a significant range contraction (up to 72%) and 12% of species were projected to be regionally extinct. Most species would need to disperse because suitable climatic sites will change. Therefore, we identified a network of priority sites for conservation that minimizes the distance a given species would need to disperse because of changes in future habitat suitability (i.e. climate-forced dispersal) as well as uncertainties associated to ENMs. This network also maximized complementary species representation across currently established protected areas. Priority sites already include possible dispersal corridors linking current and future suitable habitats for amphibians. Although we used the a top-ranked Biodiversity Hotspot and amphibians as a case study for illustrating our approach, our study may help developing more effective conservation strategies under climate change, especially when applied at different spatial scales, geographic regions, and taxonomic groups.     

Efficiency of protected areas in Amazon and Atlantic Forest conservation: A spatio-temporal view

The Amazon and Atlantic Forest are considered the world's most biodiverse biomes. Human and climate change impacts are the principal drivers of species loss in both biomes, more severely in the Atlantic Forest. In response to species loss, the main conservation action is the creation of protected areas (PAs). Current knowledge and research on the PA network's conservation efficiency is scarce, and existing studies have mainly considered a past temporal view. In this study, we tested the efficiency of the current PA network to maintain climatically stable areas (CSAs) across the Amazon and Atlantic Forest. To this, we used an ecological niche modeling approach to biome and paleoclimatic simulations. We propose three categories of conservation priority areas for both biomes, considering CSAs, PAs and intact forest remnants. The biomes vary in their respective PA networks' protection efficiency. Regarding protect CSAs, the Amazon PA network is four times more efficient than the Atlantic Forest PA network. New conservation efforts in these two forest biomes require different approaches. We discussed the conservation actions that should be taken in each biome to increase the efficiency of the PA network, considering both the creation and expansion of PAs as well as restoration programs.     

An overview of mammalian conservation at Poço das Antas Biological Reserve, southeastern Brazil

Atlantic Forest mammals are still poorly known and very few localities have been properly surveyed and/or studied. Protected reserves are of paramount importance for the conservation of native flora and fauna. Hereby we provide a survey of mammals captured and/or observed in Poço das Antas Biological Reserve, the largest lowland Atlantic Forest reserve in Rio de Janeiro state, southeastern Brazil. A total of 77 species were recorded, several of them endemics and/or listed as threatened either by IUCN's Red List, by the Brazilian Red List or by the regional Red List of Rio de Janeiro State. Mammals are threatened in several ways in this area: (1) habitat loss and fragmentation, (2) road mortality, (3) fires, (4) poaching, (5) cattle grazing, (6) pollution, (7) exotic species, and (8) feral populations of dogs Canis familiaris and cats Felis catus. Despite all threats, this is an important site for biodiversity conservation and scientific research. Better management and more investment would surely improve its effectiveness in protecting Atlantic Forest mammals.     

The unknown northern green: evaluation of a national forest biodiversity research program

The taxonomic knowledge gap and lack of knowledge on species-level diversity has been a global concern within conservation biology through the recent two decades. As a national response, Finland has funded a Research Program of Poorly Known and Threatened Forest Species from the year 2003. The program is an essential part of the knowledge base applied in Finnish forest policy. The present paper evaluates the outcomes of the program, covering scientific publication, training, taxonomic coverage, increased knowledge on boreal forest biodiversity and awareness rising. The ongoing program has been funded by 6.5 million Euros to date including 59 projects. The program has produced 19 master’s theses and six doctoral theses. Due to their expertise the graduated biologists have been employed in environmental administration or become researchers. The program has produced 163 refereed scientific articles, 104 of which are recognized by the Web of Science; with an average impact factor of 1.81. The results of the program include 15 genera and 348 species new to science, and 60 genera and 1,664 species to Finland’s list of known species. Due to new knowledge gathered in the program 3,000–4,000 species could be included in the most recent National Red List assessment. The publishing of identification books on local language has proved as the most effective way of advancing general species knowledge among the public and end-users. The high number of new species to science from a biodiversity-poor boreal country describes the scale of the huge work still be done in describing the global species-level diversity. The program has achieved its goals in many ways, but the program leaves out a large part of the species that do not occur in forest biotopes. Moreover, the funding has decreased through the years despite the international goal of halting the world’s biodiversity loss has not been met.     

Nearctic earthworm fauna in the southern USA: biodiversity and effects on ecosystem processes

An important aspect of biodiversity is the relative importance of species in the functioning of ecosystems; this is particularly so for the soil biota which regulate organic matter and nutrient dynamics in soil. This paper explores some of the relationships between biodiversity and ecosystem processes, using the example of the nearctic earthworm fauna in the glacial refugium of the southern USA. Competitive exclusion of nearctic earthworm species by exotic species has been postulated but there is little direct evidence of it; habitat alteration is the likely cause of native species decline. Reduced earthworm diversity may or may not strongly affect certain ecosystem processes, but more diverse assemblages may more effectively exploit soil resources and influence a wider array of processes. Nearctic species may be better adapted than exotics to local conditions and thus more strongly influence ecosystem processes. Earthworm communities provide a clear case for the union of functional and taxonomic biodiversity studies, because of the recognized ecological strategies of many species. However, some nearctic taxa may deviate from these strategies. Earthworms utilize course woody debris in forests both as a refuge and a resource, while enhancing the decomposition of wood. Management strategies to maintain or increase biodiversity of soil biota should include residual wood on the forest floor. An important task for ecosystem management is to restore biodiversity in degraded ecosystems; introduction programmes and techniques such as periodic burning may increase the abundance and diversity of native earthworm species. Whole ecosystem conservation and management are probably the most practical ways to conserve biodiversity generally and may be the only ways to maintain soil biodiversity.     

Human impacts,habitat quantity and quality affect the dimensions of diversity and carbon stocks in subtropical forests: A landscape-based approach

Fragmentation is recognized as one of the main factors affecting species and functionality losses in tropical landscapes. In this study, we assess how landscape quality and quantity affect taxonomic and functional diversities and carbon stocks in the Atlantic Forest. We used a large dataset, which comprises 92,754 adult trees of 668 species, distributed over an area of ​​95,733 km2 in the state of Santa Catarina, southern Brazil. In each plot, we quantified the taxonomic diversity (species richness), the functional diversity (functional richness), and the aboveground carbon stock and related it to different landscape metrics (fragment area and total area, number of fragments, total edge area, index of the largest fragment, effective network size and aggregation index) and anthropogenic impacts in three surrounding landscape buffers (radius 1000, 3000 and 5000 m). We built multiple regression models, selecting the best models (Akaike's criterion), to assess the influence of the landscape and anthropogenic index on diversities and carbon stocks. Our study shows that the landscape quantity and quality, and the anthropogenic effects are factors that negatively affect the carbon stock, reinforcing that small-scale exploration, within the fragment itself, is an important factor in reducing diversity and carbon stock. The importance of considering local exploitation has important implications for conservation, and these results bring important insights for conservation, especially for forest fragments in anthropized landscapes, where exploration within the fragments are factors that interfere in the conservation and maintenance of biodiversity and ecosystem functioning.     

Why is biodiversity data-deficiency an ongoing conservation dilemma in Africa?

Recent reports illustrate deficiencies in knowledge about current conditions and long-term trends in population sizes of hundreds of African plants and animals’ species. In this commentary, I discuss the lack of standardized data for assessing and monitoring biodiversity in Africa. I present my own views on the causes for these knowledge and data gaps, their consequences for conservation, and future directions that could improve the current situation.There are many reasons for lack of standardized data including; ongoing conflicts and political instability in many biodiversity-rich countries; absence of regular and policy-driven monitoring programs; weak facilities; and irregular or insufficient funding. Existing biodiversity monitoring initiatives are often short-term, poorly-designed surveys, largely dependent on volunteer researchers or international partners, biased towards large “charismatic” animal species, and published in difficult-to-access outlets. Consequently, up-to-date and rigorous reports about conditions and trends of African biodiversity are limited, and conservation planning, comparative studies and accurate valuation of ecosystem services continue to be difficult.Urgent actions include: 1) commitments and support of local governments to implement effective conservation monitoring programs; 2) establishment of a network of carefully designed long-term and continent-wide monitoring initiatives for endangered species and biodiversity; and 3) involvement of universities, research centers, Non-Governmental Organizations (NGOs) and local communities in such monitoring efforts. Such actions could stimulate further in-depth studies and systematic analysis of the root causes and solutions for the decades-long African biodiversity knowledge gap. Examples of highly needed systematic analysis and documentation in the coming efforts towards filling up the biodiversity data gap in Africa should clearly define biodiversity data-deficiency by taxonomic groups and by countries.     

Synthesis of Knowledge on Marine Biodiversity in European Seas: From Census to Sustainable Management

The recently completed European Census of Marine Life, conducted within the framework of the global Census of Marine Life programme (2000–2010), markedly enhanced our understanding of marine biodiversity in European Seas, its importance within ecological systems, and the implications for human use. Here we undertake a synthesis of present knowledge of biodiversity in European Seas and identify remaining challenges that prevent sustainable management of marine biodiversity in one of the most exploited continents of the globe. Our analysis demonstrates that changes in faunal standing stock with depth depends on the size of the fauna, with macrofaunal abundance only declining with increasing water depth below 1000 m, whilst there was no obvious decrease in meiofauna with increasing depth. Species richness was highly variable for both deep water macro- and meio- fauna along latitudinal and longitudinal gradients. Nematode biodiversity decreased from the Atlantic into the Mediterranean whilst latitudinal related biodiversity patterns were similar for both faunal groups investigated, suggesting that the same environmental drivers were influencing the fauna. While climate change and habitat degradation are the most frequently implicated stressors affecting biodiversity throughout European Seas, quantitative understanding, both at individual and cumulative/synergistic level, of their influences are often lacking. Full identification and quantification of species, in even a single marine habitat, remains a distant goal, as we lack integrated data-sets to quantify these. While the importance of safeguarding marine biodiversity is recognised by policy makers, the lack of advanced understanding of species diversity and of a full survey of any single habitat raises huge challenges in quantifying change, and facilitating/prioritising habitat/ecosystem protection. Our study highlights a pressing requirement for more complete biodiversity surveys to be undertaken within contrasting habitats, together with investigations in biodiversity-ecosystem functioning links and identification of separate and synergistic/cumulative human-induced impacts on biodiversity.     

Structural organization of the social paper wasp (Hymenoptera: Polistinae) assemblage along a latitudinal gradient in the Atlantic Rainforest: correlating fauna partitioning to biodiversity centers

Based on species endemism, three biodiversity centers, called “Ecological Corridors” have been proposed as one of the main conservation strategies for the Atlantic Rain Forest. This study tested whether the organization of the social paper wasp assemblage fits those centers. A standardized protocol was used for sampling the social paper wasp fauna. The structural organization was estimated by Nonmetric Multidimensional Scaling (NMDS) based on the similarity indexes of Sorensen (qualitative data) and Morisita-Horn (quantitative data). Regressive models were applied to the first axes’ site scores of the NMDS, to the latitudinal and altitudinal variations, and to the speciation and immigration probabilities predicted by the neutral theory for a metacommunity. Our results indicated that the social paper wasp assemblage is organized in a continuum, with two distinct biodiversity centers. The organization of the assemblage along the gradient was dependent on latitudinal and altitudinal variations and their interactions, and also on the speciation and immigration probabilities. Several studies have demonstrated that the current biodiversity patterns of the Atlantic Forest might be explained by the past climate and, consequently, by the connection between the Amazon and the Atlantic Forest. In addition, speciation and immigration probabilities strongly influence the compositional and structural variations of the social paper wasp assemblage along the latitudinal gradient.     

The role of a local rediscovery in the evaluation of the conservation status of a plant species: Testing the hypothesis of the biodiversity knowledge gap

Although habitat destruction and the introduction of exotic species are causing the extinction of many native species, the number of extinct species that are then rediscovered is surprising. However, before searching for meaning of rediscoveries, we should distinguish between a false and a true rediscovery to avoid the interpretation of changes in biodiversity knowledge as changes in the efforts to conserve biodiversity. Here, we proposed the hypothesis of the biodiversity knowledge gap and a conceptual scheme to test this hypothesis, discussing how to deal with the rediscovery of a putatively extinct species. In this paper, we dealt with the local rediscovery of the plant Neptunia pubescens Benth. (Fabaceae), hypothesizing that if its local rediscovery is a case of the biodiversity knowledge gap (false rediscovery), its conservation status will change. Furthermore, we provided taxonomic data, geographic coordinates and figures as support for its local rediscovery, as well as some considerations about the implications for the conservation of N. pubescens.