Monitoring Changes In Biodiversity Research Articles

DNA barcodes for Great Salt Lake brine flies establish a baseline for monitoring changes in biodiversity

ABSTRACT Great Salt Lake (GSL) is the center of a valuable wetland ecosystem in the Great Basin of North America. The lake is an important site for millions of migratory birds that feed on 2 principal invertebrates, brine shrimp and brine flies (Diptera: Ephydridae). Despite their ecological and economic importance, no genetic studies have been published for either resident GSL invertebrate. The family Ephydridae (shore flies and brine flies) is one of the largest in the order Diptera, with nearly 2000 described species. Members of this family are prominent in a variety of aquatic environments and are particularly interesting because of their adaptation to several marginal habitats, including hot springs, oil ponds, highly saline lakes, and inland alkaline pools and marshes. This report provides cytochrome c oxidase I (COI) DNA barcodes for 5 species of GSL shore flies, distributed among 5 genera and 3 subfamilies. The phylogenetic content of these DNA sequences is explored by comparing a molecular phylogeny to those based on morphological features. Over the past decade, urbanization and inflow diversion have reduced the surface area of GSL by nearly 50%, with unknown consequences for the ecosystem. This study establishes a genetic framework to assess changes in GSL invertebrate diversity important in monitoring the effects of anthropogenic and climate pressures on this important natural resource.

A framework for near-real time monitoring of diversity patterns based on indirect remote sensing, with an application in the Brazilian Atlantic rainforest.

Monitoring biodiversity change is key to effective conservation policy. While it is difficult to establish in situ biodiversity monitoring programs at broad geographical scales, remote sensing advances allow for near-real time Earth observations that may help with this goal. We combine periodical and freely available remote sensing information describing temperature and precipitation with curated biological information from several groups of animals and plants in the Brazilian Atlantic rainforest to design an indirect remote sensing framework that monitors potential loss and gain of biodiversity in near-real time. Using data from biological collections and information from repeated field inventories, we demonstrate that this framework has the potential to accurately predict trends of biodiversity change for both taxonomic and phylogenetic diversity. The framework identifies areas of potential diversity loss more accurately than areas of species gain, and performs best when applied to broadly distributed groups of animals and plants.

Monitoring rocky reef biodiversity by underwater geo-referenced photoquadrats

Digital images are an excellent tool for divers to sample hard-bottom subtidal habitats as bottom time is limited and high-definition images can be collected quickly and accurately. The present paper describes a sampling protocol for benthic rocky reef communities using geo-referenced photoquadrats and tests the method over several rocky reefs of Atlantic Patagonia. This method was tested in two localities, separated by 100 km in a semi-enclosed gulf, covering a total of 5800 m of 11 rocky reefs using track roaming transects. The protocol is non-destructive, relatively low-cost and can adequately assess changes in marine habitats as rocky reefs. The implementation of artificial intelligence analysis using human expert training may reduce analysis time and increase the amount of data collected. The present study recommends this sampling methodology for programs aimed at monitoring changes in biodiversity.

The Importance of Surface Orientation in Biodiversity Monitoring Protocols: The Case of Patagonian Rocky Reefs

Temperate rocky reefs in Atlantic Patagonia are productive areas that support a high diversity of invertebrates, algae, and fishes. Complex surface structures on rocky reefs offer a range of microhabitats, which in turn, lead to a broad variety of co-existing species. Despite their ecological importance and the ecosystem services they provide, Patagonian rocky reef habitats have received limited attention. Until now studies have not discerned nor consequently described the assemblages found on each of the different surface orientations, namely horizontal, vertical, overhang and cavefloor. During this study we developed a protocol for sampling different surface orientations on subtidal rocky reefs using georeferenced high-resolution photoquadrats. We described and compared the epibenthic assemblage of surface orientations on 7 rocky reefs within 1–25 m depth in a northern Patagonia gulf. A total of 70 taxa were identified (12 macroalgae, 44 invertebrates, 10 tunicates, and 4 fishes), which doubles the number of species previously reported for the area. Each surface orientation presented a different assemblage structure while species richness was higher on vertical surfaces. The overhang surfaces had the most distinct assemblage conformed by cnidarians, tunicates, sponges and the absence of algae. The average overall species richness increased with depth due to the increase of sponge and tunicate species. Our results highlight the need of including several surface orientations in rocky reef biodiversity monitoring. This study offers a protocol for large-scale programs aimed at monitoring changes in biodiversity, which is broadly accessible and will provide accurate information. With robust yet simple, non-destructive and relatively low-cost practices this protocol can adequately assess changes in marine habitats, which provide important ecosystem services.

Rapid Least Concern: towards automating Red List assessments.

BackgroundThe IUCN Red List of Threatened SpeciesTM (hereafter the Red List) is an important global resource for conservation that supports conservation planning, safeguarding critical habitat and monitoring biodiversity change (Rodrigues et al. 2006). However, a major shortcoming of the Red List is that most of the world's described species have not yet been assessed and published on the Red List (Bachman et al. 2019Eisenhauer et al. 2019). Conservation efforts can be better supported if the Red List is expanded to achieve greater coverage of mega-diverse groups of organisms such as plants, fungi and invertebrates. There is, therefore, an urgent need to speed up the Red List assessment and documentation workflow.One reason for this lack of species coverage is that a manual and relatively time-consuming procedure is usually employed to assess and document species. A recent update of Red List documentation standards (IUCN 2013) reduced the data requirements for publishing non-threatened or 'Least Concern' species on the Red List. The majority of the required fields for Least Concern plant species can be found in existing open-access data sources or can be easily calculated. There is an opportunity to consolidate these data and analyses into a simple application to fast-track the publication of Least Concern assessments for plants. There could be as many as 250,000 species of plants (60%) likely to be categorised as Least Concern (Bachman et al. 2019), for which automatically generated assessments could considerably reduce the outlay of time and valuable resources for Red Listing, allowing attention and resources to be dedicated to the assessment of those species most likely to be threatened.New informationWe present a web application, Rapid Least Concern, that addresses the challenge of accelerating the generation and documentation of Least Concern Red List assessments. Rapid Least Concern utilises open-source datasets, such as the Global Biodiversity Information Facility (GBIF) and Plants of the World Online (POWO) through a simple web interface. Initially, the application is intended for use on plants, but it could be extended to other groups, depending on the availability of equivalent datasets for these groups.Rapid Least Concern users can assess a single species or upload a list of species that are assessed in a batch operation. The batch operation can either utilise georeferenced occurrence data from GBIF or occurrence data provided by the user. The output includes a series of CSV files and a point map file that meet the minimum data requirements for a Least Concern Red List assessment (IUCN 2013). The CSV files are compliant with the IUCN Red List SIS Connect system that transfers the data files to the IUCN database and, pending quality control checks and review, publication on the Red List.We outline the knowledge gap this application aims to fill and describe how the application works. We demonstrate a use-case for Rapid Least Concern as part of an ongoing initiative to complete a global Red List assessment of all native species for the United Kingdom Overseas Territory of Bermuda.

Hybridization between two high Arctic cetaceans confirmed by genomic analysis

In 1990, a skull from a morphologically unusual Monodontid was found in West Greenland and collected for the Natural History Museum of Denmark, University of Copenhagen. From its intermediate morphology, the skull was hypothesized to be a beluga/narwhal hybrid. If confirmed, the specimen would, to our knowledge, represent the sole evidence of hybridization between the only two toothed whale species endemic to the Arctic. Here we present genome-wide DNA sequence data from the specimen and investigate its origin using a genomic reference panel of eight belugas and eight narwhals. Our analyses reveal that the specimen is a male, first-generation hybrid between a female narwhal and a male beluga. We use stable carbon and nitrogen isotope analysis to investigate the dietary niche of the hybrid and find a higher δ13C value than in both belugas and narwhals, suggesting a foraging strategy unlike either parental species. These results further our understanding of the interaction between belugas and narwhals, and underscore the importance of natural history collections in monitoring changes in biodiversity. In addition, our study exemplifies how recent major advances in population genomic analyses using genotype likelihoods can provide key biological and ecological insights from low-coverage data (down to 0.05x).

Brazilian Network on Plant-Pollinator Interactions: an update on the initiative of a standard for plant-pollinator interactions data

The Brazilian Plant-Pollinator Interactions Network*1 (REBIPP) aims to develop scientific and teaching activities in plant-pollinator interaction. The main goals of the network are to: generate a diagnosis of plant-pollinator interactions in Brazil; integrate knowledge in pollination of natural, agricultural, urban and restored areas; identify knowledge gaps; support public policy guidelines aimed at the conservation of biodiversity and ecosystem services for pollination and food production; and encourage collaborative studies among REBIPP participants. To achieve these goals the group has resumed and built on previous works in data standard definition done under the auspices of the IABIN-PTN (Etienne Américo et al. 2007) and FAO (Saraiva et al. 2010) projects (Saraiva et al. 2017). The ultimate goal is to standardize the ways data on plant-pollinator interactions are digitized, to facilitate data sharing and aggregation. A database will be built with standardized data from Brazilian researchers members of the network to be used by the national community, and to allow sharing data with data aggregators. To achieve those goals three task groups of specialists with similar interests and background (e.g botanists, zoologists, pollination biologists) have been created. Each group is working on the definition of the terms to describe plants, pollinators and their interactions. The glossary created explains their meaning, trying to map the suggested terms into Darwin Core (DwC) terms, and following the TDWG Standards Documentation Standard*2 in definition. Reaching a consensus on terms and their meaning among members of each group is challenging, since researchers have different views and concerns about which data are important to be included into a standard. That reflects the variety of research questions that underlie different projects and the data they collect. Thus, we ended up having a long list of terms, many of them useful only in very specialized research protocols and experiments, sometimes rarely collected or measured. Nevertheless we opted to maintain a very comprehensive set of terms, so that a large number of researchers feel that the standard meets their needs and that the databases based on it are a suitable place to store their data, thus encouraging the adoption of the data standard. An update of the work will soon be available at REBIPP website and will be open for comments and contributions. This proposal of a data standard is also being discussed within the TDWG Biological Interaction Data Interest Group*3 in order to propose an international standard for species interaction data. The importance of interaction data for guiding conservation practices and ecosystem services provision management has led to the proposal of defining Essential Biodiversity Variables (EBVs) related to biological interactions. Essential Biodiversity Variables (Pereira et al. 2013) were developed to identify key measurements that are required to monitoring biodiversity change. EBVs act as intermediate abstract layer between primary observations (raw data) and indicators (Niemeijer 2002). Five EBV classes have been defined in an initial stage: genetic composition, species populations, species traits, community composition, ecosystem function and ecosystem structure. Each EBV class defines a list of candidate EBVs for biodiversity change monitoring (Fig. 1). Consequently, digitalization of such data and making them available online are essential. Differences in sampling protocols may affect data scalability across space and time, hence imposing barriers to the full use of primary data and EBVs calculation (Henry et al. 2008). Thus, common protocols and methods should be adopted as the most straightforward approach to promote integration of collected data and to allow calculation of EBVs (Jürgens et al. 2011). Recently a Workshop was held by GLOBIS B*4 (GLOBal Infrastructures for Supporting Biodiversity research) to discuss Species Interactions EBVs (February, 26-28, Bari, Italy). Plant-pollinator interactions deserved a lot of attention and REBIPP's work was presented there. As an outcome we expect to define specific EBVs for interactions, and use plant-pollinators as an example, considering pairwise interactions as well as interaction network related variables. The terms in the plant-pollinator data standard under discussion at REBIPP will provide information not only on EBV related with interactions, but also on other four EBV classes: species populations, species traits, community composition, ecosystem function and ecosystem structure. As we said, some EBVs for specific ecosystem functions (e.g. pollination) lay beyond interactions network structures. The EBV 'Species interactions' (EBV class 'Community composition') should incorporate other aspects such as frequency (Vázquez et al. 2005), duration and empirical estimates of interaction strengths (Berlow et al. 2004). Overall, we think the proposed plant-pollinator interaction data standard which is currently being developed by REBIPP will contribute to data aggregation, filling many data gaps and can also provide indicators for long-term monitoring, being an essential source of data for EBVs.

Using soundscapes to detect variable degrees of human influence on tropical forests in Papua New Guinea.

There is global concern about tropical forest degradation, in part, because of the associated loss of biodiversity. Communities and indigenous people play a fundamental role in tropical forest management and are often efficient at preventing forest degradation. However, monitoring changes in biodiversity due to degradation, especially at a scale appropriate to local tropical forest management, is plagued by difficulties, including the need for expert training, inconsistencies across observers, and lack of baseline or reference data. We used a new biodiversity remote-sensing technology, the recording of soundscapes, to test whether the acoustic saturation of a tropical forest in Papua New Guinea decreases as land-use intensity by the communities that manage the forest increases. We sampled soundscapes continuously for 24 hours at 34 sites in different land-use zones of 3 communities. Land-use zones where forest cover was fully retained had significantly higher soundscape saturation during peak acoustic activity times (i.e., dawn and dusk chorus) compared with land-use types with fragmented forest cover. We conclude that, in Papua New Guinea, the relatively simple measure of soundscape saturation may provide a cheap, objective, reproducible, and effective tool for monitoring tropical forest deviation from an intact state, particularly if it is used to detect the presence of intact dawn and dusk choruses.

Hard times for Italian coastal dunes: insights from a diachronic analysis based on random plots

Multi-year temporal studies are invaluable tools for monitoring changes in biodiversity through time. However, their applications in coastal ecosystems are still scarce. We investigated temporal trends in coastal dunes analyzing a set of 858 randomly-sampled georeferenced releves performed between 2002 and 2015 along Central Italy’s sandy coastlines. Specifically, we explored changes in species richness and cover of targeted sandy habitats, we investigated trends in the cover of selected psammophilous native species and we assessed patterns of invasion by means of regression techniques. We observed a significant decrease in species richness and cover of the dune grasslands habitat. The species-level analysis confirmed a negative trend for two characteristic species of dune grasslands, Cutandia maritima and Medicago littoralis, while revealing a similar decline for Crucianella maritima and for Ammophila arenaria subsp. australis, key species of mobile dunes. The most striking trends emerged analyzing patterns in the cover of an invasive alien species, Carpobrotus sp., which showed a concerning increase in shifting dunes. In conclusion, our analyses reveal concerning changes involving dune grasslands, and at the same time hint at “early warnings” of degradation processes traceable in shifting dunes.

Acoustic Ecology of European Bats: Species Identification, Study of Their Habitats and Foraging Behavior

Barataud, M. 2016. Acoustic Ecology of European Bats: Species Identification, Study of Their Habitats and Foraging Behavior. University of Chicago Press, Chicago, Illinois, 352 pp. (cloth). ISBN: 987-2-85653-771-8. $55. Acoustic surveys are useful for monitoring biodiversity change, particularly with bats as indicators since they constantly produce sound to detect and categorize objects (Schnitzler et al. 2003). European bat acoustics is the theme of this compilation of 8 chapters which examines the complexity of acoustic ecology, species identification, and how acoustic studies can help better understand the relationship between bats and the environment. Insights on biological sonar, basic concepts of acoustics, and parameter assessment of the use of ultrasound detectors are presented, enabling the reader to understand the fundamentals and acquire a working knowledge of the field. Comprising 352 pages, it includes a list of European bat species with potential acoustical identification of 84% of the species known, an outstanding illustrated glossary, and a list of abbreviations used in the text. The book includes a valuable CD with information that can be use in the laboratory to enable comparison with bat sounds recorded in the field. Two introductory chapters … Laboratorio de Bioconservacion y Manejo, Posgrado en Ciencias Quimicobiologicas, Departamento de Zoologia, Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, Mexico City, Mexico; e-mail: artibeus2{at}aol.com;

Reducing costs in biodiversity monitoring: Shortcuts for plant diversity in meadows as a case study

Monitoring changes in biodiversity requires credible measures of species richness and diversity. Since biodiversity monitoring programmes are challenging and expensive, conservation scientists are increasingly applying proxies; unfortunately, the evidence supporting these methods is still scarce. Here, we explore the cost-effectiveness of shortcuts for the estimation of plant species richness and diversity in meadows. We used regression methods and multimodel inference techniques to calibrate a number of models linking the relative abundance of 5, 4 or 3 plant species (indicators) with the richness and diversity of whole assemblages. The species selected as indicators are common in the study area, with a large regional distribution and frequency of occurrence. Then, with a new dataset, we validated the use of shortcuts with high goodness-of-fit (R2>70%). Mean relative bias varied between +12.5% and −6.1%, which we considered acceptable. Finally, by using computer intensive Monte Carlo simulation techniques to quantify the effect of changes on both (i) number of researchers and technicians in field teams and (ii) number of species to be assessed, we evaluated the cost-effectiveness (time and money) of biodiversity monitoring by comparing full inventories vs. shortcuts. We found that cost-savings can reach 90% (with a shortcut of 5 species) or even higher (93%, with 4 species), which imply that sampling effort could be multiplied ca. 12 times (5 species) or even more (ca. 15 times, 4 species), without increasing costs. It was concluded that calibration and validation of shortcuts can help improve the cost-effectiveness of biodiversity monitoring in managed meadows.

Indices for monitoring biodiversity change: Are some more effective than others?

Abstract Statistically rigorous methods for summarizing and reporting trends in the intactness of biodiversity are a key element of effective biodiversity monitoring programs. There are four major approaches for translating complex monitoring data into easily communicated summary statistics: (1) traditional diversity indices such as species richness and Simpson's diversity, (2) species intactness indices based on occurrence, (3) species intactness indices based on abundance, and (4) multivariate community indices. We use simulated data to evaluate the effectiveness of 13 indices from these four categories based on statistical robustness, sensitivity to errors and noise in the data, ecological relevance, and ease of communication. We show that indices that calculate species intactness using equations like Buckland's arithmetic mean index are the most effective for use in large-scale biodiversity intactness monitoring programs. Traditional diversity indices are unsuitable for monitoring of biodiversity intactness, and multivariate indices can be highly sensitive to errors and noise in the data. Finally, we provide guidelines for the application of these indices in biodiversity intactness monitoring.

Community participatory landscape classification and biodiversity assessment and monitoring of grazing lands in northern Kenya

In this study, we asked the Ariaal herders of northern Kenya to answer “why, what and how” they classified landscape, and assessed and monitored the biodiversity of 10 km 2 of grazing land. To answer the “why question” the herders classified grazing resources into 39 landscape patches grouped into six landscape types and classified soil as ‘warm’, ‘intermediate’ or ‘cold’ for the purpose of land use. For the “what question” the herders used soil conditions and vegetation characteristics to assess biodiversity. Plant species were described as ‘increasers’, ‘decreasers’ or ‘stable’. The decreaser species were mostly grasses and forbs preferred for cattle and sheep grazing and the increasers were mostly woody species preferred by goats. The herders evaluated biodiversity in terms of key forage species and used absence or presence of the preferred species from individual landscapes for monitoring change in biodiversity. For the “how question” the herders used anthropogenic indicators concerned with livestock management for assessing landscape potential and suitability for grazing. The anthropogenic indicators were related to soils and biodiversity. The herders used plant species grazing preferences to determine the links between livestock production and biodiversity. By addressing these three questions, the study shows the value of incorporating the indigenous knowledge of herders into classification of landscape and assessment and monitoring of biodiversity in the grazing lands. We conclude that herder knowledge of biodiversity is related to the use as opposed to exclusive conservation practices. This type of knowledge is extremely valuable to conservation agencies for establishing a baseline for monitoring changes in biodiversity in the future.

Monitoring change in aquatic invertebrate biodiversity : sample size, faunal elements and analytical methods.

Replication is usually regarded as an integral part of biological sampling, yet the cost of extensive within-wetland replication prohibits its use in broad-scale monitoring of trends in aquatic invertebrate biodiversity. In this paper, we report results of testing an alternative protocol, whereby only two samples are collected from a wetland per monitoring event and then analysed using ordination to detect any changes in invertebrate biodiversity over time. Simulated data suggested ordination of combined data from the two samples would detect 20% species turnover and be a cost-effective method of monitoring changes in biodiversity, whereas power analyses showed about 10 samples were required to detect 20% change in species richness using ANOVA. Errors will be higher if years with extreme climatic events (e.g. drought), which often have dramatic short-term effects on invertebrate communities, are included in analyses. We also suggest that protocols for monitoring aquatic invertebrate biodiversity should include microinvertebrates. Almost half the species collected from the wetlands in this study were microinvertebrates and their biodiversity was poorly predicted by macroinvertebrate data.