Biodiversity Conservation Research Research Articles

The Use of R and R Packages in Biodiversity Conservation Research

R is one of the most powerful programming languages for conducting data analysis, modeling, and visualization. Although it is widely utilized in biodiversity conservation research, the comprehensive trends in R and R package usage and patterns in the field still remain unexplored. We conducted a comprehensive analysis of R and R package usage frequencies spanning fifteen years, from 2008 to 2022, encompassing over 24,100 research articles published in eight top biodiversity conservation journals. Within this extensive dataset, 10,220 articles (42.3% of the total) explicitly utilized R for data analysis. The use ratio of R demonstrated a consistent linear growth, escalating from 11.1% in 2008 to an impressive 70.6% in 2022. The ten top utilized R packages were vegan, lme4, MuMIn, nlme, mgcv, raster, MASS, ggplot2, car, and dismo. The frequency of R package utilization varied among journals, underscoring the distinct emphases each journal places on specific focuses of biodiversity conservation research. This analysis highlights the pivotal role of R, with its powerful statistical and data visualization capabilities, in empowering researchers to conduct in-depth analyses and gain comprehensive insights into various dimensions of biodiversity conservation science.

Global distribution modelling of a conspicuous Gondwanian soil protist reveals latitudinal dispersal limitation and range contraction in response to climate warming

AbstractAimThe diversity and distribution of soil microorganisms and their potential for long‐distance dispersal (LDD) are poorly documented, making the threats posed by climate change difficult to assess. If microorganisms do not disperse globally, regional endemism may develop and extinction may occur due to environmental changes. Here, we addressed this question using the testate amoeba Apodera vas, a morphologically conspicuous model soil microorganism in microbial biogeography, commonly found in peatlands and forests mainly of former Gondwana. We first documented its distribution. We next assessed whether its distribution could be explained by dispersal (i.e. matching its climatic niche) or vicariance (i.e. palaeogeography), based on the magnitude of potential range expansions or contractions in response to past and on‐going climatic changes. Last, we wanted to assess the likelihood of cryptic diversity and its potential threat from climate and land‐use changes (e.g. due to limited LDD).LocationDocumented records: Southern Hemisphere and intertropical zone; modelling: Global.MethodsWe first built an updated global distribution map of A. vas using 401 validated georeferenced records. We next used these data to develop a climatic niche model to predict its past (LGM, i.e. 21 ± 3 ka BP; PMIP3 IPSL‐CM5A‐LR), present and future (IPSL‐CMP6A‐LR predictions for 2071–2100, SSP3 and 5) potential distributions in responses to climate, by relating the species occurrences to climatic and topographic predictors. We then used these predictions to test our hypotheses (dispersal/vicariance, cryptic diversity, future threat from LDD limitation).ResultsOur models show that favourable climatic conditions for A. vas currently exist in the British Isles, an especially well‐studied region for testate amoebae where this species has never been found. This demonstrates a lack of interhemispheric LDD, congruent with the palaeogeography (vicariance) hypothesis. Longitudinal LDD is, however, confirmed by the presence of A. vas in isolated and geologically young peri‐Antarctic islands. Potential distribution maps for past, current and future climates show favourable climatic conditions existing on parts of all southern continents, with shifts to higher land from LGM to current in the tropics and a strong range contraction from current to future (global warming IPSL‐CM6A‐LR scenario for 2071–2100, SSP3.70 and SSP5.85) with favourable conditions developing on the Antarctic Peninsula.Main ConclusionsThis study illustrates the value of climate niche models for research on microbial diversity and biogeography, along with exploring the role played by historical factors and dispersal limitation in shaping microbial biogeography. We assess the discrepancy between latitudinal and longitudinal LDD for A. vas, which is possibly due to contrast in wind patterns and/or likelihood of transport by birds. Our models also suggest that climate change may lead to regional extinction of terrestrial microscopic organisms, thus illustrating the pertinence of including microorganisms in biodiversity conservation research and actions.

Distribution patterns and drivers of nonendemic and endemic glires species in China.

Spatial patterns and determinants of species richness in complex geographical regions are important subjects of current biogeography and biodiversity conservation research. Glires are small herbivorous mammal species with limited migratory ability that may serve as an indicator of biodiversity and ecosystems. Herein, we aimed to evaluate how multiple ecological hypotheses could explain the species richness patterns of glires in China. Initially, we constructed a mapping grid cell operating units of 80 × 80 km2 which covered China's land mass and mapped the distribution ranges of the 237 glires species that had recorded. The glires taxa were separated into three response variables based on their distribution: (a) all species, (b) nonendemic species, and (c) endemic species. The species richness patterns of the response variables were evaluated using four predictor sets: (a) hydrothermal characteristics, (b) climatic seasonality, (c) habitat heterogeneity, and (d) human factors. We performed regression tree analysis, multiple linear regression analysis, and variation partitioning analyses to determine the effects of predictors on spatial species patterns. The results showed that the distribution pattern of species richness was the highest in the Hengduan Mountains and surrounding areas in southwest China. However, only a few endemic species adapted to high-latitude environments. It was found that there are differences about the determinants between nonendemic and endemic species. Habitat heterogeneity was the most influential determinant for the distribution patterns of nonendemic species richness. Climatic seasonality was the best predictor to determine the richness distribution pattern of endemic species, whereas this was least affected by human factors. Furthermore, it should be noted that hydrothermal characteristics were not strong predictors of richness patterns for all or nonendemic species, which may be due to the fact that there are also more species in some areas with less precipitation or energy. Therefore, glires are likely to persist in areas with characteristics of high habitat heterogeneity and stable climate.

Integrative Conservation: A new journal from the conservation frontline

<i>Integrative Conservation</i>: A new journal from the conservation frontline

Global progress in climate change and biodiversity conservation research

Climate change is always an immense challenge for conservation biologists in the development and implementation of effective conservation strategies. The expected loss of biodiversity due to climate change weakens the delivery of ecosystem functioning and services, which can lead to a global environmental crisis. This study aims to conduct a comprehensive review of literature on recent progress in climate change and biodiversity conservation research and identifies the leading countries, institutions and researchers in this research area. We also aim to explore the current research trends, and existing scientific knowledge as well as to provide perspectives on the topic. A scientometric analysis approach included co-occurrence analysis of countries, institutions, and authors for research productivity and academic development; co-occurrence of keywords for identification of research hotspots; co-citation analysis for prominent articles and journals; and keyword burst for detection of global research trends, was applied by using CiteSpace based on 1965 articles retrieved from the Web of Science Core Collection for the period 2000–2021. We found an increasing research production over time on climate change and biodiversity conservation research. Although climate change and biodiversity conservation research have been studied across the globe (particularly in developed countries such as the USA) and institutions (such as the University of Queensland, Australia), several more countries, regions and institutions are underrepresented across the globe. The current research hot topics we found are mainly “management”, “impact”, “diversity” and “land use”, whereas the research trends are “richness”, “scenario”, “perception” and “REDD”. Thus, further research is needed to cover the huge knowledge gap related to humans, climate change, biodiversity, and ecosystem functioning across the globe (particularly in unexplored countries and regions) through several interdisciplinary approaches and collaborations.

Application of genomics technology in biodiversity conservation research

Application of genomics technology in biodiversity conservation research

Current and Forthcoming Approaches for Benchmarking Genetic and Genomic Diversity

The current attrition of biodiversity extends beyond loss of species and unique populations to steady loss of a vast genomic diversity that remains largely undescribed. Yet the accelerating development of new techniques allows us to survey entire genomes ever faster and cheaper, to obtain robust samples from a diversity of sources including degraded DNA and residual DNA in the environment, and to address conservation efforts in new and innovative ways. Here we review recent studies that highlight the importance of carefully considering where to prioritize collection of genetic samples (e.g., organisms in rapidly changing landscapes or along edges of geographic ranges) and what samples to collect and archive (e.g., from individuals of little-known subspecies or populations, even of species not currently considered endangered). Those decisions will provide the sample infrastructure to detect the disappearance of certain genotypes or gene complexes, increases in inbreeding levels, and loss of genomic diversity as environmental conditions change. Obtaining samples from currently endangered, protected, and rare species can be particularly difficult, thus we also focus on studies that use new, non-invasive ways of obtaining genomic samples and analyzing them in these cases where other sampling options are highly constrained. Finally, biological collections archiving such samples face an inherent contradiction: their main goal is to preserve biological material in good shape so it can be used for scientific research for centuries to come, yet the technologies that can make use of such materials are advancing faster than collections can change their standardized practices. Thus, we also discuss current and potential new practices in biological collections that might bolster their usefulness for future biodiversity conservation research.

Fieldwork during pandemic: Backyard bird survey and making student’s biological field practice works

Abstract. Winarni NL, Anugra BG, Anisafitri S, Kaunain NN, Pradana DH. 2021. Fieldwork during pandemic: Backyard bird survey and making student’s biological field practice works. Biodiversitas 22: 1887-1894. The COVID-19 pandemic situations had forced universities to shutdown face-to-face lectures and change it to online teaching. This change had brought significant challenges to biological courses which need field practice in their syllabus and therefore field practice should be adjusted and innovative. During November-December 2020, we compared students' field practice from the Ornithology class to urban bird survey to evaluate whether the data collected by students can contribute to citizen science as well as to enhance field practice during online courses. We used point count methods to survey bird communities in urban environment in Jakarta and its satellite cities. We found that the students tended to observe the most abundant birds such as the cave swiftlet and Eurasian tree sparrow and missed unfamiliar species which were smaller-sized birds that use aerial and upper canopy. It was suggested that the data from field practice can also support citizen science when prioritized to common, abundance species. In addition, best practices for field practice were provided, emphasizing the independent field practice incorporating technology in which the results were communicated to the students. Hence, strengthening field practice for biological courses is important to support biodiversity conservation research and activities.

Impact Indicators for Biodiversity Conservation Research: Measuring Influence within and beyond Academia

ABSTRACT Measuring, reporting, and forecasting research impact beyond academia has become increasingly important to demonstrate and understand real-world benefits. This is arguably most important in crisis disciplines such as medicine, environmental sustainability and biodiversity conservation, where application of new knowledge is urgently needed to improve health and environmental outcomes. Increasing focus on impact has prompted the development of theoretical guidance and practical tools tailored to a range of disciplines, but commensurate development of tools for conservation is still needed. In the present article, we review available tools for evaluating research impact applicable to conservation research. From these, and via a survey of conservation professionals, we compiled and ranked a list of 96 impact indicators useful for conservation science. Our indicators apply to a logic chain of inputs, processes, outputs, outcomes, and impacts. We suggest the list can act as a clear guide to realize and measure potential impacts from conservation research within and beyond academia.

Data Infrastructure and Local Stakeholder Engagement with Biodiversity Conservation Research

Data Infrastructure and Local Stakeholder Engagement with Biodiversity Conservation Research

From a variety of ethics to the integrity and congruence of research on biodiversity conservation.

This article aims to find the elements that are required for a common ethical approach that is suitable for the different perspectives adopted in integrative biodiversity conservation research. A general reflection on the integrity of research is a priority worldwide, with a common aim to promote good research practice. Beyond the relationship between researcher and research subject, the integrity of research is considered in a broader perspective which entails scientific integrity towards society. In research involving a variety of disciplines and a diversity of legal and ethical frameworks, there is a need of harmony between different sets of values. The notion of congruence (or more pragmatically, alignment) reflects the consistency of ethics in research within the biodiversity conservation's community of researchers. It also bears on the coherence of values shared between the scientific community and society. We examine the notion of research integrity in a broad sense. This examination is to be conducted in relation to the goal of protecting ecological integrity, which is at the core of biodiversity conservation. The notion of integrity constraints should be investigated further to develop a pragmatic response to the need for integrity and congruence in research for biodiversity conservation.

"Forestry and Biodiversity Conservation Research in the Indian Himalayan Region: Emerging Concepts"

Forest ecosystems play a crucial role in sustaining life on the planet earth. In traditional thinking forests were seen mainly as a source of timber and minor forest products to generate income. However, the first Earth Summit held in 1992 at Rio De Janeiro emphasized the value of forests largely for the environmental benefits. It is encouraging to note that our understanding over the years, has broadened considerably to value and recognize the equally important role of forests as providers of economic, social and cultural benefits. Globally forests are now regarded as the major repository of nature to be conserved and managed for posterity, and not to be regarded solely as an important source of revenue. In the Indian context, forests are a prominent feature of the Indian landscape, covering almost a quarter (23.8%) of the geographical area of the country [1]. These forests are integral to the environment, economy, culture and history of the country. While providing multiple tangible benefits such as timber, fuel-wood, pulp-wood, fodder, fibre, medicines and other valuable non-wood products, forests also regulate the hydrological cycle, protect aquifers, conserve biodiversity, enhance carbon sequestration as a spin-off effect of forest conservation, and promote ecotourism. The release of Millennium Ecosystem Assessment was an important milestone, highlighting the dependence of humans on ecosystems, and stressed the need to better describe, quantify and value the ecosystem goods and service. Accordingly recent decades have witnessed several advancement and challenges in forestry research and management. This paper highlights the need to bring about a paradigm shift in the traditional thinking and approach in forestry research in respect of the Indian Himalayan Region (IHR) and evolve research programmes that are sensitive to stakeholder needs in addition to being forest friendly and in tune with the fast changing global thinking on the subject, especially in Rio+20 scenario.

A blueprint towards accounting for the management of ecosystems

PurposeThe purpose of this paper is to propose a new ecological-issues-centered accounting research agenda, at the crossroads of accounting research and conservation science.Design/methodology/approachBased on a case study of the Natural Capital Project, the research examines the efforts and challenges of conservation practitioners regarding the use of evaluative information systems for conservation (EISC) in complex social and ecological contexts. It discusses why and how, to address these challenges, EISC promoters would benefit from theoretical and empirical insights coming from accounting research.FindingsThe paper suggests that the use of new information systems centered on organized collective action for biodiversity conservation should be regarded as a new type of accounting for the management of ecosystems, complementary to organization-centered biodiversity accounting and to ecosystem accounting at the national scale. A research agenda inspired by critical accounting should be developed for EISC design and use by: critically analyzing the organizational models currently underlying the use of new calculative practices for ecosystems; and developing new analytical and practical avenues on the basis of more explicit and powerful theories adapted to collective action for conservation perimeters.Originality/valueThe paper shows the importance of combining three domains of research and practice that are usually disconnected: the design and use of innovative information systems in biodiversity conservation research and practice; accounting research; and theories and conceptual models of collective action to resolve ecological challenges.

Measuring the impact of a journal

The Ecological Management & Restoration (EMR) journal's long journey to become listed on the Web of Science (previously referred to as ISI listing) – and thus be included in the Science Citation Index Expanded (SCIE) – has now been rewarded. In short, EMR now has an Impact Factor. In the 2016 Journal Citation Report, EMR received a score of 1.139 – which places the journal 115/153 in the Ecology category. Papers from EMR are now being cited widely. For example, the Scopus 2016 database listed 130 EMR papers that were cited in nearly 90 different SCIE journals and publications. This is not bad for a newcomer and is a clear baseline from which the journal can build. There are several issues with the listing process that explain the long time this has taken. One of the main reasons is that a journal needs a minimum qualifying level of citations in papers published in already listed journals to get to the bottom rung of the ladder. This is hard enough for any new journal but is doubly hard for an intentionally applied science journal with a largely management-oriented readership – given that most of the journals already in SCIE are primarily directed to a research readership and may be less likely to cite applied science papers. It is significant, then, that this Impact Factor was attained despite ESA's decision to retain the journal's current scope and format, only making very minimal concessions to improve EMR’s conformity to a science journal format. That is, EMR is, and will remain, primarily a management-oriented journal linking science and practice. But having an Impact Factor means that EMR may now be a more attractive first-choice publication outlet for researchers working in universities – while also retaining a strong representation from management authors and a strong management readership. It is this readership, after all, that is one of the reasons many established researchers send particular (applied) papers to EMR as their first-choice publication outlet. In his interview in this issue, Andrew Bennett – who has been a dedicated executive member of the EMR board since its inception in the year 2000 – reflects on the importance of communicating science to end-users. He is not alone in his view that the motivation behind the work of many scientists working in the nature conservation area is to make the world a better place, requiring researchers to communicate their work not only to other researchers but also to managers. Bennett raises more novel ways being considered by the Australian Research Council (which funds research) to measure the degree a project engages with industry partners and others who may use the research findings. The interview is a good read also because it provides us with some insights into the author's own career, his background, his drive to consider questions at larger and larger scales and his hopes for the future of biodiversity conservation research and practice in Australia. Bennett speaks of the importance of not only spatial scale but also temporal scale. We need longer-term efforts and longer-term research and practice. This is echoed by David Lamb's comment piece in this issue which eloquently challenges both science and practice institutions to take stronger steps to protect long-term data- or old data that can act as a baseline for building upon in the future. Linda Broadhurst and colleagues also take a big picture temporal view in their article on designing protocols for revegetation that can double as experimentation into genetic adaptation in the context of changing climates. The remaining offerings of long and short technical and research reports in this issue epitomize the management relevance of EMR papers. Each of these grapples with measuring the effects of solution-based restoration or management. Of the longer articles, this includes Ben Carr and colleagues’ review of the use of Conservation Action Planning to improve, in particular, the management of private conservation reserves in Australia including on Indigenous lands; Peter Kyne and Pierre Feutry focus on mitigating recreational overfishing; Joseph Stapleton and colleagues focus on trialling the introduction of coarse woody debris to reduce mammalian browsing in revegetation; Chris Gillies and colleagues focus on oyster reef restoration, and Konrad Uebel and colleagues and Steve Sinclair and colleagues focus on the observations of natural recovery of vegetation communities after a range of interventions. Indeed, it is the quality of the applied science papers that will retain and build EMR's Impact Factor, although our applied focus will always limit citations in pure research publications. We know that EMR counts in terms of end-user impact and recommend that it be continued to be considered as such by researchers and the bodies who fund them, rather than now judging EMR by its SCIE Impact Factor alone.

Taxonomic bias and international biodiversity conservation research

While greater research on threatened species alone cannot ensure their protection, understanding taxonomic bias may be helpful to address knowledge gaps in order to identify research directions and inform policy. Using data for over 10 000 animal species listed on the International Union for Conservation of Nature Red List, we investigated taxonomic and geographic biodiversity conservation research trends worldwide. We found extreme bias in conservation research effort on threatened vertebrates compared with lesser-studied invertebrates in both terrestrial and aquatic habitats at a global scale. Based on an analysis of common threats affecting vertebrates and invertebrates, we suggest a path forward for narrowing the research gap between threatened vertebrates and invertebrates.

Biodiversity conservation research challenges in the 21st century: A review of publishing trends in 2000 and 2011

The Strategic Plan for Biodiversity 2011–2020 recognizes the increasing importance of scientific knowledge to support conservation policies and decision making. In this study, we assessed the tendency of such knowledge in the first decade of the 21st century. We carried out a systematic review of publications in biodiversity conservation, considering the following aspects: type of research, main topic of study, object of study (i.e. biodiversity organizational level, taxonomic groups and ecosystems), pressures and drivers of change, as well as geographical distribution. In total, 966 publications were analyzed within the three journals with higher academic reach in the field under study: Biodiversity & Conservation, Biological Conservation, and Conservation Biology. Our results show that there are several biases in scientific knowledge associated with the object of study, and analyzed drivers of changes, as well as geographical distribution. However, research trends are not uniform along the first decade of 21st century, as there are some differences between 2000 and 2011 regarding the main topic of the study, the spatial scale and geographical region, and the analyzed ecosystems. We finally discuss the implications of current knowledge trends in biodiversity conservation for achieving the targets delineated by the Strategic Plan for Biodiversity 2011–2020.

Outstanding challenges for urban conservation research and action

Researchers, advocates and policymakers have proposed urban conservation as an emerging, integrative discipline that can contribute to sustainable cities by delivering co-benefits to human and non-human components of biodiversity. Given the recent growth in biodiversity-friendly designs and management schemes, there is an urgent need for a synthesis of this fragmented research base to inform planners and decision-makers. We conducted a systematic multidisciplinary literature review (787 papers) and found that the importance of urban areas for general conservation is not convincingly supported by empirical research. Only few studies demonstrated that cities can directly contribute to conservation efforts, by hosting viable populations of rare or endangered species, or by providing green corridors for the passage of natural populations. From a social perspective, while several studies demonstrated that green infrastructure could provide services for people (notably cultural services), only few studies explored the role of species diversity per se. Our review also shows strong geographical, location and taxonomic biases in urban biodiversity conservation research that make generalisations difficult. It is a disturbing paradox that while research in urban biodiversity conservation is rising exponentially, the main motivations for conserving urban biodiversity remain largely untested and unproven. We thus propose a framework for promoting integrative urban conservation research to bridge those gaps. Together, these findings warn against expanding cities under green planning and call for enhancing biodiversity experience by improving the quality of existing green spaces throughout the entire urban matrix. We provide a set of recommendations for practitioners and decision-makers to continue action.

Inter‐specific interactions linking predation and scavenging in terrestrial vertebrate assemblages

Predation and scavenging have been classically understood as independent processes, with predator-prey interactions and scavenger-carrion relationships occurring separately. However, the mere recognition that most predators also scavenge at variable rates, which has been traditionally ignored in food-web and community ecology, leads to a number of emergent interaction routes linking predation and scavenging. The general goal of this review is to draw attention to the main inter-specific interactions connecting predators (particularly, large mammalian carnivores), their live prey (mainly ungulates), vultures and carrion production in terrestrial assemblages of vertebrates. Overall, we report an intricate network of both direct (competition, facilitation) and indirect (hyperpredation, hypopredation) processes, and provide a conceptual framework for the future development of this promising topic in ecological, evolutionary and biodiversity conservation research. The classic view that scavenging does not affect the population dynamics of consumed organisms is questioned, as multiple indirect top-down effects emerge when considering carrion and its facultative consumption by predators as fundamental and dynamic components of food webs. Stimulating although challenging research opportunities arise from the study of the interactions among living and detrital or non-living resource pools in food webs.

Application of MALDI‐MS analysis of Rainforest chemodiversity: a keystone for biodiversity conservation and sustainable use

Brazil hosts the largest proportion of global biodiversity and has demonstrated its commitment in conservation and sustainable use being a key negotiator of the Nagoya Protocol. The “Convention on Biological Diversity” (CBD) calls for actions to reduce extinction rates, something that according with different theories is of fundamental importance for the survival of life on Earth. Contrary to its position in the CBD meetings, Brazil approved a new Forest Code that will result in escalating deforestation, increasing the urgency to demonstrate the value of native species. Extractive-based activities of forest inhabitants are basically economical prospective activities upon the forest richness whose act harmfully against the environment. For centuries, such activity resulted in low profits, triggering a perverse logic that profit increase is necessarily linked to extraction increase. In the last decades, new strategies, as for instance the Sustainable Development Reserve Mamiraua, are showing that forest preservation can also be profitable. Considering the new paradigm of green economy, which now surrounds all this tensioned discussion, we are bringing to the eyesight of policy-makers results on biodiversity conservation research: combining floristic and chemodiversity surveys, using fast high throughput mass spectrometry screening (HT-MSS), to screen forest leaves for economically valued natural products. Matrix-assisted laser desorption/ionization (MALDI) ionizationbased machines are well known by their ability to furnish fast data and can be an important tool for HT-MSS. One of the aims of a long-term ongoing BIOTA/FAPESP research project at the Serra do Mar State Park is to understand ecophysiological traits of leaves, and MALDI-MS was an alternative to identify alkaloids as one of the nitrogen sink. Regarding the following main points: (1) analysis of plant attributed nitrogen fixation and (2) profitable policies for biodiversity conservation, we suggest the screening for alkaloids to be carried out using the leaves of the trees that are top ranked in population density lists within the forest sociology. In order to reach these aims, a set larger than 500 samples was screened for the occurrence of alkaloids and botanical identification. Classical chemical procedures were also applied to validate the results (Dragendorff, Mayer and Wagner assays). In this letter, we provide the first HT MALDI-MS and MALDI-MS/MS forest screening method to provide added value to local specimens of plants. Ionic liquid was used to get around known ionization problems of small molecules (< 1200Da) by avoiding isobaric ions formation by the matrix. Although, LC-ESI-MS is the common technique to screen small molecules, it is highly time consuming, since in six days, only 50 samples can be analyzed. Therefore, our strategy is based on the ability of MALDI to quickly screen a very large number of samples using an ionic liquid as matrix. Using this approach, we can screen up to 200 samples within a 3 h time-frame.

Biodiversity Conservation Research, Training, and Policy in São Paulo

The BIOTA-FAPESP program is linking a decade of research on biodiversity into public policy in the state of São Paulo.