Modelling habitat preference,abundance and species richness of alien macrocrustaceans in surface waters in Flanders (Belgium) using decision trees

The introduction and the spread of alien invasive species are a worldwide phenomenon causing global ecological and economic damages. Among the invaders, alien macrocrustaceans are known to be very successful invertebrates that colonise new habitats rapidly. Data from different fresh and brackish waters gathered by the Flemish Environment Agency (VMM) were used to build data-driven models predicting habitat preference, abundance and species richness of alien macro-Crustacea present in surface waters in Flanders. Different techniques such as regression and classification trees in combination with several optimisation methods (e.g. pruning) were used to construct the models. The performance of the models was moderate, because a balance between performance, ecological relevance and complexity was strived for. When using a three-fold cross validation it was found that the variation between the folds was limited, which is an indication of the robustness and the good reliability of the constructed models. Based on a sensitivity analysis the importance of conductivity, Kjeldahl nitrogen and shipping were stressed as well as graphically illustrated. Alien macrocrustaceans were predicted as present under brackish water conditions as well as in fresh waters with intensive ship traffic and low levels of organic pollution. The alien species richness was higher in rivers with intensive ship traffic and increased with increasing conductivity. Especially in brackish waters, alien macrocrustaceans reached high abundances. In fresh water, the abundance of alien species was generally lower. An integrated model that combined our habitat suitability model with a water quality model was used to predict the future distribution of alien macrocrustaceans. The predictions indicated that the prevalence and the species richness of alien macrocrustaceans are likely to increase with improving chemical water quality, whereas their abundance will probably decrease slightly. From our analysis, it is clear that models are a useful tool and that decision makers should focus on vulnerable areas such as brackish water areas and areas with intensive ship traffic in order to prevent the further introduction and spread of alien species.     

Influence of livestock,habitat type,and density of roe deer (<Emphasis Type="Italic">Capreolus capreolus</Emphasis>) on parasitic larvae abundance and infection seroprevalence in wild populations of roe deer from central Iberian Peninsula

Livestock farming is a common human activity that not only modifies natural habitat but also may lead to interactions with other wild animal species. We studied whether health status of roe deer (Capreolus capreolus) is influenced by density, livestock, and type of habitat. We analyzed 208 samples (120 fecal and 88 sera) from roe deer populations of central Iberian Peninsula to evaluate both presence and abundance of parasitic oocysts, eggs, and/or larvae, especially of gastrointestinal and bronchopulmonary parasites, as well as the prevalence of five infectious diseases (infectious bovine rhinotracheitis (IBR), pestivirosis (BVD/BD), paratuberculosis (PTB), bluetongue (BT), and brucellosis). Fecal samples were collected in transects in pine and oak forests and endoparasites were detected by means of coprological techniques. Serum samples were obtained from hunted individuals and the serological testing for the infectious pathogens was performed by ELISA and Rose Bengal tests. Livestock and habitat type were associated both with the presence and the number of bronchopulmonary nematode L1-larvae per gram of feces (lpg), which was higher in areas with livestock and in pine forests. However, roe deer density neither influenced parasite presence nor lpg values. Regarding infectious pathogens, only seropositive samples for PTB and pestivirus were obtained indicating a possible transmission between domestic and wild ungulates in the study area. The low prevalence found is consistent with other studies in the Iberian Peninsula suggesting that roe deer have little contact with the infectious agents studied. Our results highlight that both habitat type and livestock significantly mediate abundance of parasitic larvae in roe deer, being higher under competition scenarios and in habitats of lower quality, a valuable aspect to be considered in future management and conservation strategies.     

Genomic data sampling and its effect on classification performance assessment

Background  

Supervised classification is fundamental in bioinformatics. Machine learning models, such as neural networks, have been applied to discover genes and expression patterns. This process is achieved by implementing training and test phases. In the training phase, a set of cases and their respective labels are used to build a classifier. During testing, the classifier is used to predict new cases. One approach to assessing its predictive quality is to estimate its accuracy during the test phase. Key limitations appear when dealing with small-data samples. This paper investigates the effect of data sampling techniques on the assessment of neural network classifiers.     

A field course survey of three English river systems

A hydrobiological field course for undergraduates in the Department of Biology, University of Salford has proved useful in investigating river pollution, and parts of the course may be suitable for upper school studies. The course compares the Lancashire rivers Lune, Ribble and Irwell, but could be adapted for still waters.

The water quality was assessed by simple chemical methods and the bacteriological quality by multiple tube and membrane filtration techniques. These assessments were then related to the benthic inverte-brates in the rivers—dipteran larvae, oligochaete worms, leeches, molluscs, stoneflies and mayflies. The Irwell was found to be grossly polluted, the Ribble mildly polluted and the Lune relatively unpolluted.     

Is it better to combine predictions?

We have compared the accuracy of the individual protein secondary structure prediction methods: PHD, DSC, NNSSP and Predator against the accuracy obtained by combing the predictions of the methods. A range of ways of combing predictions were tested: voting, biased voting, linear discrimination, neural networks and decision trees. The combined methods that involve 'learning' (the non-voting methods) were trained using a set of 496 non-homologous domains; this dataset was biased as some of the secondary structure prediction methods had used them for training. We used two independent test sets to compare predictions: the first consisted of 17 non-homologous domains from CASP3 (Third Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction); the second set consisted of 405 domains that were selected in the same way as the training set, and were non-homologous to each other and the training set. On both test datasets the most accurate individual method was NNSSP, then PHD, DSC and the least accurate was Predator; however, it was not possible to conclusively show a significant difference between the individual methods. Comparing the accuracy of the single methods with that obtained by combing predictions it was found that it was better to use a combination of predictions. On both test datasets it was possible to obtain a approximately 3% improvement in accuracy by combing predictions. In most cases the combined methods were statistically significantly better (at P = 0.05 on the CASP3 test set, and P = 0.01 on the EBI test set). On the CASP3 test dataset there was no significant difference in accuracy between any of the combined method of prediction: on the EBI test dataset, linear discrimination and neural networks significantly outperformed voting techniques. We conclude that it is better to combine predictions.     

DEMOGRAPHIC SOURCE-SINK DYNAMICS RESTRICT LOCAL ADAPTATION IN ELLIOTT'S BLUEBERRY (VACCINIUM ELLIOTTII)

In heterogeneous landscapes, divergent selection can favor the evolution of locally adapted ecotypes, especially when interhabitat gene flow is minimal. However, if habitats differ in size or quality, source-sink dynamics can shape evolutionary trajectories. Upland and bottomland forests of the southeastern USA differ in water table depth, light availability, edaphic conditions, and plant community. We conducted a multiyear reciprocal transplant experiment to test whether Elliott's blueberry ( Vaccinium elliottii ) is locally adapted to these contrasting environments. Additionally, we exposed seedlings and cuttings to prolonged drought and flooding in the greenhouse to assess fitness responses to abiotic stress. Contrary to predictions of local adaptation, V. elliottii families exhibited significantly higher survivorship and growth in upland than in bottomland forests and under drought than flooded conditions, regardless of habitat of origin. Neutral population differentiation was minimal, suggesting widespread interhabitat migration. Population density, reproductive output, and genetic diversity were all significantly greater in uplands than in bottomlands. These disparities likely result in asymmetric gene flow from uplands to bottomlands. Thus, adaptation to a marginal habitat can be constrained by small populations, limited fitness, and immigration from a benign habitat. Our study highlights the importance of demography and genetic diversity in the evolution of local (mal)adaptation.     

Time-series effective habitat area (EHA) modeling using cost-benefit raster based technique

For successful characterization of ecological processes and prioritization of habitat networks it is necessary to describe and quantify landscape structure and connectivity. However, at landscape scale, it is highly impractical to measure and map all elements of biodiversity, and therefore, biodiversity surrogates are commonly used to represent biodiversity values. Land cover and vegetation are most often used as a biodiversity surrogate. The study investigated how land use change affects the status of the biodiversity surrogates in terms of the loss or gain of habitat (areal extent), loss of habitat condition (degradation) and habitat fragmentation. Effective habitat area (EHA) and raster based cost–benefit analysis (CBA) modeling techniques were used for the assessment of the impact of land use change scenarios on wildlife habitat as biodiversity surrogates. The modeling was carried out on time-series land cover data from 1972 to 2009 for the Liverpool Range of New South Wales (NSW). The model estimated the future condition of vegetation in each and every grid-cell in the region as a function of current condition, existing land cover, and the threatening processes. The results indicated a continuous pattern of clearing in the region, while the habitat conditions were mostly static throughout the study period. There was a decline in EHA after 1993, by 3%. Clearing was identified as the main cause of such decline during the change period.     

Isolation of faecal coliform bacteria from the American alligator (Alligator mississippiensis)

Aims: To determine whether American alligators (Alligator mississippiensis) are an unrecognized poikilothermic source of faecal coliform and/or potential pathogenic bacteria in South Carolina’s coastal waters. Methods and Results: Bacteria from the cloaca of American alligators, as well as bacteria from surface water samples from their aquatic habitat, were isolated and identified. The predominant enteric bacteria identified from alligator samples using biochemical tests included Aeromonas hydrophila, Citrobacter braakii, Edwardsiella tarda, Escherichia coli, Enterobacter cloacae, Plesiomonas shigelloides and putative Salmonella, and these were similar to bacteria isolated from the surface waters in which the alligators inhabited. Based on most‐probable‐number enumeration estimates from captive alligator faeces, faecal coliform bacteria numbered 8·0 × 10⁹ g^?1 (wet weight) of alligator faecal material, a much higher concentration than many other documented endothermic animal sources. Conclusions: A prevalence of enteric bacteria, both faecal coliforms and potential pathogens, was observed in American alligators. The high faecal coliform bacterial density of alligator faeces may suggest that alligators are a potential source of bacterial contamination in South Carolina coastal waters. Significance and Impact of the Study: These findings help to increase our understanding of faecal coliform and potential pathogenic bacteria from poikilothermic reptilian sources, as there is the potential for these sources to raise bacterial water quality levels above regulatory thresholds.     

CHARACTERIZATION OF BEAKED WHALE (ZIPHIIDAE) AND SPERM WHALE (PHYSETER MACROCEPHALUS) SUMMER HABITAT IN SHELF-EDGE AND DEEPER WATERS OFF THE NORTHEAST U. S.

Sperm whales ( Physeter macrocephalus ) and beaked whales ( Mesoplodon spp. and Ziphius cavirostris ) are deep-diving cetaceans that frequent shelf-edge and Gulf Stream waters off the northeast U. S. coast. Sighting data collected during seven summer (1990, 1991, 1993, and 1995–1998) shipboard surveys were analyzed using a geographic information system to determine habitat use based on bathymetric and oceanographic features. Although sighting rates were lower for beaked whales, both taxa occupied similar habitats. Beaked whales were concentrated at the colder shelf edge, whereas sperm whales were associated with warmer off-shelf water. Mean sighting rates for both taxa were higher in canyon features, but only beaked whale sighting rates were significantly different between canyon and non-canyon habitat (Wilcoxon signed rank test P = 0.007). Within the shared habitat, the two taxa were separated at fine-scale based on oceanographic features.     

Gopher Tortoise Response to Habitat Management by Prescribed Burning

ABSTRACT As quality of forested habitat declines from altered fire regimes, gopher tortoises (Gopherus polyphemus) often move into ruderal areas to the detriment of the animal and land manager. We evaluated effects of a dormant-and-growing-season prescribed fire on habitat and gopher tortoise use of degraded longleaf pine (Pinus palustris) forests surrounding military training areas. We burned 4 of 8 sites in winter 2001–2002 and again in April 2003. Changes in vegetation measured during 2001–2004 indicated that burn treatments did not increase herbaceous vegetation. Similarly, movement patterns, burrow usage, and home range of tortoises radiotracked from 2002–2004 did not differ between treatments. Woody cover initially was reduced in the forests postburn, and we found more new burrows in burned forest sites. Once shrub cover was reduced, tortoises started using forested habitat that had become overgrown. However, shrub reduction may be temporary, as woody stem densities increased postburn. Thus, the one-time use of fire to manage tortoise habitat may not rapidly restore the open canopy, sparse woody midstory, and abundant herbaceous vegetation that this species requires. Repeated prescribed fires or additional management techniques may be needed for complete restoration.     

Fathead minnows (Pimephales promelas) learn to recognize chemical stimuli from high-risk habitats by the presence of alarm substance

We exposed fathead minnows (Pimephales promelas) to water fromone of two distinct habitat types (an open water site or a vegetatedcover site in the same stream) that we mixed with either alarmsubstance or a distilled water control. Upon subsequent exposuresto the habitat waters alone, minnows showed a fright responseto the habitat water that they received in conjunction withalarm substance but not to the other habitat water. These resultsindicate that minnows can learn to recognize high-risk habitatsbased on the association of habitat specific chemical cues withalarm substance. The ability to recognize these habitats couldpotentially lower the minnows' risk of predation. These resultsprovide evidence of a long-term benefit to receivers of a chemicalalarm signal.     

Improvements of the Biological Diatom Index (BDI): Description and efficiency of the new version (BDI-2006)

The Biological Diatom Index (BDI) is a standardized method routinely used in France for the surveillance of watercourse quality. This index is based on a list of 209 key species showing different pollution sensitivities. The pollution sensitivity, or “ecological profile”, is determined through the species presence probability values along a seven quality classes gradient. In a sample, the presence and abundance of species from this list are used to calculate the BDI score. Recently, water managers pointed out several weaknesses of this index: (a) the BDI fails to correctly assess water quality in acidobiontic and brackish conditions, and (b) pollution sensitivity and tolerance of several key species used to calculate the index need to be improved.This paper presents and discusses the new version of the BDI, called BDI-2006. 2802 samples were used to create this new index (samples collected on all French river types during the last thirty years), where 1063 diatom species were identified. For each sample, the community was described with species relative abundance, and relevant physico-chemical parameters were collected: pH, conductivity, dissolved oxygen, biological oxygen demand, ammonium, orthophosphates and nitrates.Eight hundreds and thirty eight key species were finally kept, including species typical of acidic and brackish waters, tropical taxa and abnormal forms of many widespread taxa (as evidence of toxicological impacts).The physico-chemical and the biological datasets were explored with classical analysis (Principal Component Analysis) and neural networks (Self-Organizing Maps), combined to draw the new key species ecological profiles. Comparing to the initial version of the BDI, several species profiles (Nitzschia paleacea for example) were clearly enhanced.This new version was adopted by the French standardisation authority (AFNOR) in October 2007.     

Diatoms of Dindifelou fall (upper Basin of the Gambia River,Senegal): floristic inventory

The Dindifelou fall, located in south‐eastern Senegal, receives its water from discharging springs located in Dande plate‐land. These waters form, at the foot of the cliff, a pond that drains into the Thiokoye, a tributary of the Gambia River. The water quality of the pond and the stream is very good based on physicochemical analyses. Around the pond region, a microclimate characterized by a higher humidity and a lower temperature compared with the surrounding area is present. Diatoms study is carried out in different habitat types associated with this fall. The samples were taken by scraping the surface of rocks and rinsing fern leaves with sparkling water. Dande plate‐land is made of Upper Proterozoic sandstones whose gravity accumulations litter the bottom of the pond and the stream. This study allowed us to inventory 61 species and varieties of diatoms belonging to 28 genera. The most represented genera are Achnanthidium (ten species), Eunotia and Pinnularia (eight species each). Twelve species and varieties are reported for the first time in Senegambia including five of the genera Achnanthidium. The microflora is dominated by Achnantidium minutissimum and Achnanthidium catenatum, followed by Ulnaria ulna and various species of the genera Eunotia and Brachysira. Aerial habitats are more diversified here than the epilithic samples.     

一种自优化RBF神经网络的叶绿素a浓度时序预测模型

藻类水华发生过程具有复杂性、非线性、时变性等特点,其准确预测一直是一个国际性难题.以天津市于桥水库为研究对象,根据2000年1月至2003年12月常规监测的水生生态数据(采样周期为10 d),提出了一种结合时序方法的可自优化RBF神经网络智能预测模型,对判断藻类水华的重要指标叶绿素a浓度进行预测.研究了训练样本量及RBF神经网络扩展速度SPREAD值的可自优化性能,以及该模型用于于桥水库叶绿素a浓度的短期变化趋势预测的可行性.结果表明,预测性能指标随SPREAD值及样本量不同发生变化,该预测模型能自动寻到最优SPREAD值,并发现至少需要约两年的训练样本量才能达到较好预测效果.当样本量为105,SPREAD值为10时,预测效果最好,精度较高,预测值与实测值的相关系数R达到0.982.该方法对水库的藻类水华预警有一定的参考价值.     

基于PCA和SOM模型的龙感湖水质时空动态研究

为评估湖泊渔业模式转型阶段水环境的时空动态,选择长江中下游典型湖泊龙感湖为研究地点,于2017—2018年对该湖的黄梅水域和宿松水域进行周年季度水质监测,通过主成分分析(PCA)和自组织特征映射人工神经网络(SOM)模型定量分析了水体理化参数的时空变化特征,采用综合营养状态指数法(TLI)对水体富营养化状况进行了评价。PCA分析结果表明,龙感湖宿松水域和黄梅水域的水质差异较小,季节动态明显。全湖氨氮夏季平均浓度高达0.64 mg/L;总氮夏季平均浓度为2.30 mg/L,冬季平均浓度为1.04 mg/L;叶绿素a夏季平均含量达95.28μg/L,秋季平均浓度为28.30μg/L; pH夏季最高,达9.27;总磷冬季最高,平均为0.22 mg/L; TLI指数表明龙感湖除秋季属于轻度富营养水体外,其他3个季节均属于中度富营养状态。SOM模型结果具有可视化强的优点,能够更清晰和直观地反映龙感湖水质的时空分布动态。围栏拆除和禁渔等管理措施有助于湖泊渔业环境修复和资源恢复,建议对渔业模式转型后的湖泊生态系统变化进行长期跟踪监测评估。     

Variation between European eel <Emphasis Type="Italic">Anguilla anguilla</Emphasis> (L.) stocks in five marshes of the Thames Estuary (United Kingdom)

The European eel (Anguilla anguilla, L.) was historically widely distributed throughout the United Kingdom, in coastal waters, lakes, rivers and wetlands. Recruitment has declined in recent decades and the species is now listed as ‘Critically Endangered’ on the International Union for Conservation of Nature and Natural Resources (IUCN) Red List. Management of suitable wetland habitats may contribute to species recovery; however, little is known about the stocks in these areas. In this study, yellow (adult stage?>?300 mm) eels were sampled in ditches in five marshes bordering the Thames Estuary in England, UK. Ecological variables, including ditch characteristics, invertebrate abundance and water quality parameters were measured. Habitat features were also observed and recorded, including access, land use and water management regimes. Eels were found in all marshes, but at varying catch-per-unit-effort (CPUE). There were no significant correlations between CPUE and the ecological variables, except ditch width. However, a significant difference in CPUE was found between two of the marshes, which may be explained by variations in local habitat management. Mean lengths showed a high proportion of females and mean body condition of four of the marshes was also found to be greater than in three rivers in the same region. These findings suggest that the marshes are potentially favourable eel habitats and that factors influencing habitat quality, such as land use and water management, may affect eel abundance, production of females and body condition. Effective management of such wetlands may therefore contribute to the conservation of European eel.     

The impact of conifer plantation forestry on the Chydoridae (Cladocera) communities of peatland lakes

Conifer plantation forestry is recognised as a potential source of diffuse pollution to surface waters and represents a risk to their ecological status. In this study, the water chemistry and Chydoridae (Cladocera) communities of 26 small blanket bog lakes were investigated to assess the impact of plantation forestry. The study was conducted over a 12-month period in 2009?C2010 by comparing lakes with three distinct catchment land uses: (i) unplanted blanket bog only present in the catchment, (ii) mature conifer plantation forests only present in the catchment and (iii) catchments containing mature conifer plantation forests with recently clearfelled areas. All three catchment land uses were replicated across two geologies: sandstone and granite. Lakes with afforested catchments had very high concentrations of plant nutrients (P and N), total dissolved organic carbon (TDOC) and heavy metals (Al and Fe), the highest concentrations being recorded from the clearfelled lakes. Similarly, the chydorid communities differed between lakes of contrasting catchment land use. The dominance of Alonopsis elongata in the unplanted blanket bog lakes shifted to dominance by the smaller bodied Chydorus sphaericus, along with Alonella nana, Alonella excisa and Alonella exigua, in the plantation forestry-effected lakes, consistent with a shift in lake trophy. Our findings have shown that plantation forestry can have a profound impact on the water quality of small peatland lakes, especially at the clearfell stage. The response of the chydorid communities is consistent with plantation forestry exerting a trophic, rather than an acidic or toxic, effect on lake ecosystems.     

A test of the cosmopolitan distribution of fresh-water protozoans

Summary The cosmopolitan distribution and invasion of fresh-water protozoans were examined on Abaco Island, Bahamas by comparing: (1) samples from surface waters; (2) containers of sterile water exposed to colonization; and (3) cultured soil samples. The distributional pattern of protozoans in the various surface waters was not uniform; the number of species found varied widely (from 1–32 sp.). Out of 74 species from surface waters and 119 species from the soil cultures, 20 species were common to both studies. Other species common only to soil samples may act as a reservoir group which furnishes colonizing species should a suitable aquatic habitat be present. Very few species (range of 0–6 per container) were collected from jars of exposed sterile water. The variation in numbers and kinds of species found in surface waters may be due to variations in water quality or variation of invaders, while differences in number of species found in the containers may indicate some variation in air-borne invasion rate since water quality was essentially the same.     

Non detection of enterovirus in the bivalve Anadara tuberculosa (Bivalvia:Arcidae) caused by chemical contamination in the Pacific of Costa Rica

Anadara tuberculosa is one of the most abundant mollusks of commercial importance in Costa Rica. Its habitat water is a potential source of fecal and chemical contamination to humans. We wanted to asses enterovirus, mainly poliovirus and hepatitis A virus and chemicals such as sulphates and nitrates in meat and body fluids. Thirteen samples were taken from four sites in Nicoya Gulf, three sites in the Sierpe-Térraba mangrove (Pacific of Costa Rica) and from five fish markets in San José, the capital of Costa Rica. Samples were tested for 1) fecal coliforms (Most Probable Number/100 ml), 2) isolation of enterovirus in cell culture (Hep-2, FrhK-4), 3) cell cytotoxicity in Vero cells and 4) the ability to inactivate 10 ID50% of poliovirus in cell culture. The Most Probable Number/100 ml in surrounding water was higher than the accepted standard for recreational waters, although the number of fecal coliforms in meats and body fluids was lower than in the external water. No cytopathogenic agents were isolated, but we found nitrate and sulphate concentrations that exceeded maxima for human consumption and recreation. The intrinsic cytotoxicity of the samples was at a 1/8 dilution, but some samples were cytotoxic at dilutions of 1/128. Body fluids were more cytotoxic than meats, but a positive correlation between cytotoxicity and chemical contamination was not determined: apparently other pollutants not identified in this study were responsible. Fluid and meat capacity to inactivate 10 ID50% of poliovirus in cell culture was demonstrated. Samples that were toxic for cell cultures also showed a higher percentage of poliovirus inactivation. Monitoring chemical pollution in these waters is highly recommended.