Terrestrial ecologists ignore aquatic literature: Asymmetry in citation breadth in ecological publications and implications for generality and progress in ecology

The search for generality in ecology should include assessing the influence of studies done in one system on those done in other systems. Assuming generality is reflected in citation patterns, we analyzed frequencies of terrestrial, marine, and freshwater citations in papers categorized as terrestrial, marine and freshwater in high-impact “general” ecological journals. Citation frequencies were strikingly asymmetric. Aquatic researchers cited terrestrial papers ~ 10 times more often than the reverse, implying uneven cross-fertilization of information between aquatic and terrestrial ecologists. Comparisons between citation frequencies in the early 1980s and the early 2000s for two of the seven journals yielded similar results. Summing across all journals, 60% of all research papers (n = 5824) published in these journals in 2002–2006 were terrestrial vs. 9% freshwater and 8% marine. Since total numbers of terrestrial and aquatic ecologists are more similar than these proportions suggest, the representation of publications by habitat in “general” ecological journals appears disproportional and unrepresentative of the ecological science community at large. Such asymmetries are a concern because (1) aquatic and terrestrial systems can be tightly integrated, (2) pressure for across-system understanding to meet the challenge of climate change is increasing, (3) citation asymmetry implies barriers to among-system flow of understanding, thus (4) impeding scientific and societal progress. Changing this imbalance likely depends on a bottom-up approach originating from the ecological community, through pressure on societies, journals, editors and reviewers.     

Small scale application and assessment of a Index of Biotic Integrity for a large boreal river

Modifications and use of Karr’s Index of Biotic Integrity (IBI) for assessing the effects of anthropogenic impacts to aquatic ecosystems have typically occurred using data collected at the macro scale. However, some non-point sources of habitat degradation occur at small scales. One possible source of perturbation to fish habitat in boreal rivers is the application of rip rap shoreline armouring in human use areas. In this study we assess the use of IBI in a small scale setting and discuss the potential impact of rip rap shoreline armouring. We captured small and juvenile fishes weekly during 2002–2003 from 12 sample sites within the littoral zone of a human use area using a modified beach seine. Principal component analysis (PCA) was performed on the data to examine the relationship between species composition and IBI scores. We also performed PCA on the IBI metrics to assess our modifications. The IBI method produced higher scores for armoured sites than for unarmoured sites. We found a strong rank order correlation (Spearman’s ρ > 0.93; p < 0.001) between the modified IBI scores and the first principal component, suggesting that Karr’s original empirically-based IBI is strongly linked to species composition. We found a high degree of redundancy between the metrics of the IBI that validate our modifications. These results suggest that IBI can be a suitable method for assessing non-point impacts from within a small study area. Our results also indicate that fish habitat from rip rap armoured sites within the test area had consistently higher IBI scores that unarmoured sites.     

Status assessment in acid-sensitive and non-acid-sensitive Maryland coastal planin streams using an integrated biological,chemical, physical,and land-use approach

This study was designed to: (1) evaluate the ecological status of acid-sensitive and non acid-sensitive Maryland coastal plain streams using biological (Index of biotic Integrity [IBI] for fish), chemical and physical habitat conditions; (2) determine if a low IBI for coastal plain stream fish can be related to stream sensitivity from acidic inputs and (3) correlate land use activities and watershed size in the coastal plain streams with biological, chemical and physical conditions. IBI values obtained using 12 community metrics for Maryland coastal plain stream fish demonstrated that there were no significant differences in these values when acid-sensitive and non-acid-sensitive streams were compared. However, other complementary data in acid-sensitive streams such as absence of the acid-sensitive species, blacknose dace and higher numbers and biomass of tolerant species suggested that these streams may be impacted. IBI values were also found to be negatively correlated with various trace metals in acid-sensitive streams but not in non-acid-sensitive areas. Chemical conditions such as trace metals and nutrients were associated with land use activities. Highest concentrations of trace metals (chromium, nickel, and cadmium) were found in streams with the highest percentage of low residential housing. Nitrate concentrations were significantly higher in streams found in agricultural areas than in forested areas. Agriculturally dominated streams with highest nitrate concentrations (> 10 mg l^-1) also contained the highest percentage of livestock feeding operations. The mean IBI score for streams draining agricultural land was higher than the mean value for forested streams when all streams were compared. However, when several streams that were only marginally forested (< 50%) were removed from the analysis, the IBI scores did not differ significantly by land use. Two physical habitat indices exhibited a strong associated with each other. Each habitat index also correlated with IBI values.     

Assessment of an index of biological integrity (IBI) to quantify the quality of two tributaries of river Chenab,Sialkot, Pakistan

Nullah Aik and Nullah Palkhu, two tributaries of river Chenab, were investigated for the assessment of fish habitat degradation as indicator of stream health. Fish abundance data were collected from 18 sites from September 2004 to April 2006 to develop multimetric indices for fish assemblage integrity and to detect the intensity of habitat degradation. A total of 12 metrics were calculated on the basis of taxonomic richness, habitat preference, trophic guild, stress tolerance and origin of species to develop stepped and continuous index of biological integrity (IBI) criteria. Cluster analysis (CA) classified sites based on species composition into three groups, viz., reference, moderately impaired and impaired groups. Non-metric multidimensional scaling (NMDS) was applied to identify underlying ecological gradient to highlight the habitat degradation. NMDS segregated two sites as less impaired, five sites as moderately impaired and eleven sites as impaired groups. Axes 1 and 2 explained a total variation of 53.3%. First axis explained the level of habitat impairment, whereas axis 2 indicated species richness along longitudinal gradient of streams. Sites located upstream of Nullah Aik showed higher IBI scores which dropped to its lowest in downstream sites near Sialkot city. Lowest values of IBI of sites in close proximity of city indicated the role of anthropogenic activities in catchment areas. The results indicated that variability in water chemistry can be related as a function of stream sites impairments (i.e., unimpaired, moderately impaired, and severely impaired). Water quality parameters showed strong correlation with IBI scores. Significantly negative correlation of IBI scores with COD, TDS, turbidity, Fe, Cr, Zn and positive correlation with DO and pH was found. The results can be used for restoration and future management of small streams passing through urban areas of Pakistan. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Handling editor: J. A. Cambray     

Automated location invariant animal detection in camera trap images using publicly available data sources

1. A time‐consuming challenge faced by camera trap practitioners is the extraction of meaningful data from images to inform ecological management. An increasingly popular solution is automated image classification software. However, most solutions are not sufficiently robust to be deployed on a large scale due to lack of location invariance when transferring models between sites. This prevents optimal use of ecological data resulting in significant expenditure of time and resources to annotate and retrain deep learning models.
2. We present a method ecologists can use to develop optimized location invariant camera trap object detectors by (a) evaluating publicly available image datasets characterized by high intradataset variability in training deep learning models for camera trap object detection and (b) using small subsets of camera trap images to optimize models for high accuracy domain‐specific applications.
3. We collected and annotated three datasets of images of striped hyena, rhinoceros, and pigs, from the image‐sharing websites FlickR and iNaturalist (FiN), to train three object detection models. We compared the performance of these models to that of three models trained on the Wildlife Conservation Society and Camera CATalogue datasets, when tested on out‐of‐sample Snapshot Serengeti datasets. We then increased FiN model robustness by infusing small subsets of camera trap images into training.
4. In all experiments, the mean Average Precision (mAP) of the FiN trained models was significantly higher (82.33%–88.59%) than that achieved by the models trained only on camera trap datasets (38.5%–66.74%). Infusion further improved mAP by 1.78%–32.08%.
5. Ecologists can use FiN images for training deep learning object detection solutions for camera trap image processing to develop location invariant, robust, out‐of‐the‐box software. Models can be further optimized by infusion of 5%–10% camera trap images into training data. This would allow AI technologies to be deployed on a large scale in ecological applications. Datasets and code related to this study are open source and available on this repository: https://doi.org/10.5061/dryad.1c59zw3tx.

     

Suburban scenario development based on multiple landscape assessments

Housing suburbanisation led in the past decades to problems caused by deconcentration of population and intensive area-consumption. Major social, economic and ecological functions for a sustainable spatial decision support in the suburban landscape are described and functionalised by indicators and modelled using GIS with the aim to minimise the problems related to the suburbanisation. The indicators chosen include human-ecological functions, accessibility and infrastructure development and the regulation and regeneration of population and biocoenosis. Out of a balanced list of 11 indicators (one is used twice) the regulation of traffic noise immissions, the landscape accessibility to the nearest freeway and the habitat network integration of sites are modelled, assessed and discussed detailed. The indicator modelling operationalises a wide range of methods including the analysis of travel costs, distance functions, visibility analysis and landscape metrics on the basis of public available data (biotope types, digital elevation model and road data). The methods are applied to a suburban agricultural landscape northeast of Leipzig in Saxony/Germany (66 km²). Three scenarios developed for the aggregation of multiple considerations are demonstrated with maps — based on the status quo of the “(mono)-functional landscape”, the “multi functional landscape” and the “sustainable landscape”. The scenarios aggregate an increasing number of indicators to form a comprehensive assessment. The result maps clearly show the suitable areas for private housing that fulfil e.g. silence, recreational functions while simultaneously ensuring nature protection. The paper emphasises the integrative prospects of landscape functions for monitoring, indicator assessment and the integration to land use decision-making in the context of spatial planning.     

Environmental diagnosis: Integrating biodiversity conservation in management of Natura 2000 forest spaces

The conservation of biodiversity in Europe is defined by Directive 92/43/EEC – commonly known as the Habitats Directive – relating to the conservation of natural habitats and of wild flora and fauna. This Directive established the creation of an ecological network of European protected areas – the Natura 2000 network – , and also recognised the need to manage these areas to maintain their “favourable conservation status”.This paper proposes a methodology which enables the conservation of biodiversity to be integrated into the management of Natura 2000 forest spaces. The methodology comprises an “environmental diagnosis” in three phases. The first phase evaluates the current conservation status of habitats using the following criteria: vital functions; floristic richness; forest structure; area occupied by the habitat; and recovery capacity. The second phase assesses the fragility of the space to determine the degree of vulnerability of habitats. This involves evaluating the fire hazard, erosion hazard, and the fragility of the vegetation. The last phase combines the two previous ones to generate management areas (optimum, intermediate or unfavourable) and to prioritise management actions.This methodology was applied in a protected forest area in the Natura 2000 network, located in Avila (Spain). Different management areas were generated for biodiversity conservation, and each habitat was associated to one of them. Finally, actions were prioritised and designed to raise the habitats to a “favourable conservation status”.     

The use of fish in ecological assessments

Abstract Fish provide powerful tools for assessing aquatic environments. Three attributes are especially significant: the sensitivity of fish to most forms of human disturbance, their usefulness at all levels of biological organization and the favourable benefit-to-cost ratio offish assessment programmes. Fish can be used as indicators over wide temporal and spatial ranges. Because they cover all trophic levels of consumer ecology, fish can effectively integrate the whole range of ecological processes in waterways. Fish have been used in many different roles for assessing river health and monitoring responses to remedial management. Three of these applications appear to have particular value for management of Australian rivers: (i) automated systems monitoring fish ventilation can provide sensitive, broad-spectrum and continuous sensing of water quality to protect receiving waters or water-supply intakes; (ii) programmes collecting routine data on commercial or recreational fisheries can be designed and analysed so as to isolate confounding effects due to fishery-specific factors and, hence, used to detect and monitor environmental change on large scales; (iii) the Index of Biotic Integrity (IBI) can be modified to suit Australian conditions and fish communities to meet the important need for a predictive model of aquatic environmental quality. The IBI is a quantitative biological tool with a strong ecological foundation that integrates attributes from several levels of ecosystem organization. Examples of the use of IBI elsewhere suggest its robustness, flexibility and sensitivity can cope effectively with the low diversity of the Australian fish fauna and the dominance of ecological generalists. A provisional structure is suggested for a test of the IBI in four riverine regions of New South Wales.     

Improving biological indicators to better assess the condition of streams

Biological indicators of stream condition are in use by water resource managers worldwide. The State of Maryland and many other organizations that use Indices of Biotic Integrity (IBIs) must determine when and how to refine their IBIs so that better stream condition information is provided. With completion of the second statewide round in 2004, the Maryland Biological Stream Survey (MBSS) had collected data from 2500 stream sites, more than doubling the number of sites that were available for the original IBI development. This larger dataset provided an opportunity for the MBSS to address the following shortcomings in the original IBIs: (1) substantial disturbance apparent in some reference sites, (2) fish IBIs could not be applied to very small streams, (3) natural variability within IBIs (based on regions) resulted in some stream types (e.g., coldwater and blackwater streams) receiving lower IBI scores and (4) one IBI was not able to discriminate degradation as desired (i.e., Coastal Plain fish IBI). Therefore, development of new fish and benthic macroinvertebrate IBIs was undertaken to achieve the goals of: (1) increased confidence that the reference conditions are minimally disturbed, (2) including more natural variation (such as stream size) across the geographic regions and stream types of Maryland and (3) increased sensitivity of IBIs by using more classes (strata) and different metric combinations. New fish IBIs were developed for four geographical and stream type strata: Coastal Plain, Eastern Piedmont, warmwater Highlands and coldwater Highlands streams; new benthic macroinvertebrate IBIs were developed for three geographical strata: Coastal Plain, Eastern Piedmont and Highlands streams. The addition of one new fish IBI and one new benthic macroinvertebrate IBI partitioned natural variability into more homogeneous strata. At the same time, smaller streams (i.e., those draining catchments <300 ac), which constituted a greater proportion of streams (25%) sampled in Round Two (2000–2004) than Round One (1995–1997), because of the finer map scale, were included in the reference conditions used to develop the new IBIs. The resulting new IBIs have high classification efficiencies of 83–96% and are well balanced between Type I and Type II errors. By scoring coldwater streams, smaller streams and to some extent blackwater streams higher, the new IBIs improve on the original IBIs. Overall, the new IBIs provide better assessments of stream condition to support sound management decisions, without requiring substantial changes by cooperating stream assessment programs.     

Remotely-sensed indicators for monitoring the general condition of “natural habitat” in watersheds: an application for Delaware’s Nanticoke River watershed

Over the past two decades there has been increasing interest in developing indicators to monitor environmental change. Remote sensing techniques have been primarily used to generate information on land use/land cover changes. The US Fish and Wildlife Service has used this technology to monitor wetland trends and recently developed a set of remotely-sensed indicators to characterize and assess trends in the integrity of natural habitat in watersheds. The indices largely focus on the extent of “natural” cover throughout a given watershed, with an emphasis on locations important to fish, wildlife, and water quality. Six indices address natural habitat extent and four deal with human-caused disturbance. A composite index of natural habitat integrity combining the habitat extent and habitat disturbance indices may be formulated to provide an overall numeric value for a watershed or subbasin. These indices facilitate comparison between watersheds (and subbasins) and assesssment of trends useful for environmental monitoring. This paper describes the indices and presents an example of their application for characterizing and assessing conditions of subbasins within Delaware’s Nanticoke River watershed.     

Developing a wetland IBI with statewide application after multiple testing iterations

An index of biotic integrity (IBI) is a frequently used approach for assessing the ecological integrity of streams with fish and macroinvertebrates the faunal assemblages most commonly used as indicator taxa. The IBI approach has been much less commonly applied to wetlands, despite the legal, policy and scientific need to assess wetland condition and develop ecological performance goals for wetland creation, restoration and enhancement. While some IBIs are sophisticated systems with statewide application that have undergone one or more testing iterations, many published IBIs are derived from single data sets of a single class of aquatic resource with limited geographic application. The State of Ohio initiated development of a wetland IBI using vascular plants in 1996. Sampling methods were investigated and ultimately a plot-based method was adopted. Potential attributes and different human disturbance gradients were evaluated in several studies. Ultimately, IBIs for emergent, forest and shrub dominated wetlands were developed. Data from the Vegetation IBI-emergent (VIBI-E) is presented to illustrate this process. Subsequent testing and refinement is a critical step in the development of a robust IBI with more than local application. Throughout its initial development (R² = 0.863, p < 0.001), first major testing iteration (R² = 82.2%, p < 0.001), second test iteration (R² = 75.0%, p < 0.001) and third test iteration (R² = 82.1%, p < 0.001), the VIBI-E has remained significantly correlated with the disturbance gradient. Eight of the original 10 metrics proposed continued to have significant and interpretable relationships with the disturbance gradient, with 4 metrics remaining completely unchanged, and 4 undergoing relatively minor modifications, and 2 being replaced. The VIBI-E and its component metrics were also evaluated against a new disturbance gradient (Landscape Development Index or LDI), derived from land use percentages within a 1 km radius of the wetlands, that was not used during VIBI-E development. The VIBI-E score and 9 of 10 metrics were significantly correlated with the LDI disturbance gradient providing separate confirmation of the VIBI. The Vegetation IBI-E consistently and reliably assessed wetland condition across the whole range of wetland types throughout Ohio's ecological regions.     

长江中游浅水湖泊生物完整性时空变化

介绍了采用 Karr提出、经 Fausch等修订后的生物完整性指数 (IBI)进行水环境质量评价的原理和概念 ,并根据长江中游鱼类种类组成特征、可获得数据的类型和资料的性质 ,初步建立了适合长江中游浅水湖泊的 IBI体系。同时 ,以基本保持了长江中游浅水湖泊自然属性的五湖 1978年的调查数据为参照 ,选择长江中游不同类型的浅水湖泊进行了生物完整性时空变化的比较研究。结果表明 :以洪湖为例进行纵向比较 ,在 196 4、1981、1993年和 1998年等 4个不同的年代 ,其生物完整性呈逐步下降的趋势 ;以 2 0世纪 90年代初期的资料进行横向比较 ,三湖连江水库和保安湖的生物完整性表现为一般 ,洪湖为差 ,东湖则很差。上述湖泊所呈现的生物完整性的时空变化趋势与其它相关研究所反映的湖泊水环境质量互为补充验证 ,可以为湖泊管理、持续发展和利用以及水环境保护提供更为充分的科学依据     

Ecological engineering: A field whose time has come

Ecological engineering is defined as “the design of sustainable ecosystems that integrate human society with its natural environment for the benefit of both.” It involves the restoration of ecosystems that have been substantially disturbed by human activities such as environmental pollution or land disturbance; and the development of new sustainable ecosystems that have both human and ecological value. While there was some early discussion of ecological engineering in the 1960s, its development was spawned later by several factors, including loss of confidence in the view that all pollution problems can be solved through technological means and the realization that with technological means, pollutants are just being moved from one form to another. Conventional approaches require massive amounts of resources to solve these problems, and that in turn perpetuates carbon and nitrogen cycle problems, for example. The development of ecological engineering was given strong impetus in the last decade with a textbook, the journal Ecological Engineering and two professional ecological engineering societies. Five principles about ecological engineering are: (1) It is based on the self-designing capacity of ecosystems; (2) It can be the acid test of ecological theories; (3) It relies on system approaches; (4) It conserves non-renewable energy sources; and (5) It supports biological conservation. Ecology as a science is not routinely integrated into engineering curricula, even in environmental engineering programs, while shortcoming, ecologists, environmental scientists, and managers miss important training in their profession—problem solving. These two problems could be solved in the integrated field of ecological engineering.     

Assessment of environmental conditions of Nan-Shih stream in Taiwan

Restoration is a complex endeavor requiring the understanding of the degrading environment before applying any improvement measure. Environmental and ecological data in Nan-Shih stream were investigated in this study to assess its stream condition. Based on the data collected, the Index of Biotic Integrity (IBI index) which takes fish species as the major target, the Family-level Biotic Index (FBI) aquatic insects Hilsenhoff index and the Genus Index (GI) of algae were thus analyzed to quantify Nan-Shih stream's ecological system. The indices above were then applied on Index of Stream Condition (ISC index) to describe the overall river condition. Modified sub-indices, including the hydrology, physical form, streamside zone, water quality, and aquatic life, were made and used to provide baseline assessment information. ISC value is 33.89 evaluated as marginal level, in which hydrology sub-index score was the lowest indicating impact of artificial structures affecting flow significantly. The recommendations of the river corridor restoration and the habitat improvement were thus proposed as a reference for river management.     

Proteome analysis: I. Gene products are where the biological action is

Two-dimensional electrophoresis has rapidly become the method of choice for resolving complex mixtures of proteins. Since the technique was pioneered in 1975, 2-D gel methods have undergone a series of enhancements to optimize resolution and reproducibility. Recent improvements in the sensitivity of mass spectrometry have allowed the direct identification of polypeptides from 2-D gels by a procedure termed “mass profiling”. In combination, these two techniques have made possible the characterization of the complete collection of gene products, or proteome, of an organism. Proteomes are increasingly being documented as interactive informational databases available on the World Wide Web (WWW). This availability of organismic global protein patterns will no doubt be an invaluable resource aiding the discovery of diagnostic and therapeutic disease markers.     

Modification of an index of biotic integrity based on fish assemblages to characterize rivers of the Seine Basin,France

The Index of Biotic Integrity (IBI) is a measure of fish assemblage health that has been used to assess catchment and stream quality throughout North America. It reflects human perturbations on natural environmental structures and processes. While preserving the ecological foundation of the original North American metrics, we have modified and adapted the IBI to the mainstem Seine River and its major tributaries in France. This successful modification of the IBI to a considerably different fish fauna on a different continent further supports its wider use outside the midwestern United States. Using data collected in 1967, 1981, and 1988–1989 from a total of 46 sites, we show spatial and temporal variation in the Seine as indicated by IBI scores. Statistically significant relationships were found between IBI and catchment area but insignificant relationships existed between IBI and an independent Water Quality Index (WQI) based on water chemistry. Comparisons between the IBI and the WQI indicate that the former is a more sensitive and robust measure of water body quality. Our results demonstrate that the IBI, combined with a statistically designed national monitoring program, would offer a reliable means of assessing spatial patterns and temporal trends in water body improvement or degradation in France. The more primitive fish families in the Basin were affected first by perturbations. These families include all the diadromous species found in the Seine and suggest serious disruption of their life histories.     

Impact of habitat diversity on the sampling effort required for the assessment of river fish communities and IBI

The spatial variation in the fish communities of four small Belgian rivers with variable habitat diversity was investigated by electric fishing to define the minimum sampling distance required for optimal fish stock assessment and determination of the Index of Biotic Integrity. This study shows that the standardised sampling distance of 100 m was not always sufficient to collect most species present. The required minimum sampling distance seems to be correlated with habitat diversity. In homogeneous streams, a mean sample distance of 282, 452 and 572 m is necessary to capture 80, 90 and 95% of all species present, respectively. In heterogeneous streams, these sample distances decrease to 217, 380 and 503 m. Hence, at least 300 m should be sampled to catch most species present with a single-pass sampling method. However, our results show that a 100 m sampling distance as presently used in the Flemish monitoring programs is sufficient to accurately describe the ecological quality since differences in IBI evaluation between adjacent stretches could at least for some rivers be explained by differences in habitat heterogeneity.     

Hong Kong’s worst “red tide”—causative factors reflected in a phytoplankton study at Port Shelter station in 1998

From March through April 1998, a massive “red tide” occurred in coastal waters of south China, including Hong Kong. The “red tide” rapidly killed various species of caged fish and affected coral fishes, killing a few of them, and caused great economic loss and ecological damage. Samples collected from a permanent station located in Port Shelter revealed a new dinoflagellate species, Karenia digitata which was suspected to be the causative species of this “red tide”. Species composition and abundance analysis revealed that an algal bloom persisted in Port Shelter during this entire period. Diatoms and dinoflagellates were the two main groups which dominated the phytoplankton and, in general, when there was an increase in the density of diatoms there was a decline in the density of dinoflagellates, and vice versa. The suspected “red tide” causative species together with other dinoflagellate species started to bloom in late February and reached their highest density on 18 March, when fish kills were first reported at Crooked Island, a semi-enclosed bay to the northeast of Hong Kong. During a 16-week period, dinoflagellate species dominated three times, and coincided with low wind speeds. Constant salinity and a continuing increase in sea surface water temperature suggested warm water intrusion into Hong Kong’s coastal waters during this “red tide” bloom period. Various nutrient elements, e.g. NH₄-N, total Kjeldahl nitrogen (TKN), and PO₄-P were high at the beginning of the bloom but experienced a sharp decrease thereafter. It is suggested that this early 1998 massive “red tide” in Hong Kong waters might have been triggered by a synchronous appearance of optimal climatic, nutritional and hydrographic conditions.