How good are Bayesian belief networks for environmental management? A test with data from an agricultural river catchment

相似文献   

Parasite diversity as an indicator of environmental change? An example from tropical grouper (Epinephelus fuscoguttatus) mariculture in Indonesia

Fish parasites are used to monitor long-term change in finfish grouper mariculture in Indonesia. A total of 210 Epinephelus fuscoguttatus were sampled in six consecutive years between 2003/04 and 2008/09 and examined for parasites. The fish were obtained from floating net cages of a commercially run mariculture facility that opened in 2001. The fauna was species rich, consisting of ten ecto- and 18 endoparasite species. The ectoparasite diversity and composition was relatively stable, with the monogeneans Pseudorhabdosynochus spp. (83-100% prevalence, Berger-Parker Index of 0·82-0·97) being the predominant taxon. Tetraphyllidean larvae Scolex pleuronectis and the nematodes Terranova sp. and Raphidascaris sp. 1 were highly abundant in 2003/04-2005/06 (max. prevalence S. pleuronectis 40%, Terranova sp. 57%, Raphidascaris sp. 1 100%), and drastically reduced until 2008/09. These parasites together with the prevalence of Trichodina spp., ecto-/endoparasite ratio and endoparasite diversity illustrate a significant change in holding conditions over the years. This can be either referred to a definite change in management methods such as feed use and fish treatment, or a possible transition of a relatively undisturbed marine environment into a more affected habitat. By visualizing all parameters within a single diagram, we demonstrate that fish parasites are useful bioindicators to monitor long-term change in Indonesian grouper mariculture. This also indicates that groupers can be used to monitor environmental change in the wild. Further taxonomic and systematic efforts in less sampled regions significantly contributes to this new application, supporting fish culture and environmental impact monitoring also in other tropical marine habitats.     

How many novel eukaryotic 'kingdoms'? Pitfalls and limitations of environmental DNA surveys

Background  

Over the past few years, the use of molecular techniques to detect cultivation-independent, eukaryotic diversity has proven to be a powerful approach. Based on small-subunit ribosomal RNA (SSU rRNA) gene analyses, these studies have revealed the existence of an unexpected variety of new phylotypes. Some of them represent novel diversity in known eukaryotic groups, mainly stramenopiles and alveolates. Others do not seem to be related to any molecularly described lineage, and have been proposed to represent novel eukaryotic kingdoms. In order to review the evolutionary importance of this novel high-level eukaryotic diversity critically, and to test the potential technical and analytical pitfalls and limitations of eukaryotic environmental DNA surveys (EES), we analysed 484 environmental SSU rRNA gene sequences, including 81 new sequences from sediments of the small river, the Seymaz (Geneva, Switzerland).     

Biodiversity of palm fungi in the tropics: are global fungal diversity estimates realistic?

Two questions are addressed: 'How many species of fungi can occur on a single host palm?' and 'What are the implications of this for global estimates of fungal diversity?' Fungal diversity estimates found in the literature are reviewed. Data on the numbers of fungi occurring on the above-ground tissues of six individual palms in the genus Licuala in Australia and Brunei Darussalam (Borneo) are provided. A total of 189 species of fungi were isolated and/or collected from the six palms. In addition, 53 'morphospecies' of mycelia sterilia were isolated, giving a total of 242 taxa from the 2672 isolates/collections made. The three palms in Australia (sampled once) yielded 100 species (each palm supporting an average of 54.7 taxa), while the three palms in Brunei Darussalam (sampled three times) yielded 172 species in total (approximately 111.3 taxa each). The magnitude of global fungal diversity, estimated at 1.5 million species, is discussed. Our results indicate that 33 to 1 would be a more accurate estimate (than 5.7 to 1) of the ratio of host specific fungal to palm species in the tropics. We therefore propose that global estimates of fungal diversity, based on temperate studies, require revision upwards.     

How good are carabid beetles (Coleoptera,Carabidae) as indicators of invertebrate abundance and order richness?

Ground invertebrates were sampled by pitfall trapping on Brentmoor Heath, Surrey, UK during the summers of 2009 and 2010 to determine whether the abundance and species richness of carabids on bare ground patches are representative of invertebrate abundance and order richness on the same patches. Four patch sizes were investigated as well as the adjacent mown and unmown areas, and a range of environmental parameters were measured at each patch. Results show that increasing abundance and richness of carabids can give a broad indication of whether invertebrate abundance and order richness are increasing. Invertebrates in general are sensitive to a greater number of environmental variables and complex interactions than carabids are, due to the vast array of biological requirements of the large range of invertebrate species. All else being equal, smaller patches appear to benefit both carabid abundance and invertebrate abundance. Converse to the results of carabid species richness, larger patches appear to benefit invertebrate order richness. This study highlights the importance of testing the effect of habitat management strategies on a range of taxa rather than assuming the results for a bioindicator will suffice for management decisions. Whilst bioindicators may give a broad indication of effects on similar taxa, the precise nature of those effects will be determined by a number of species- and site-specific variables.     

What are definitions of life good for? Transdisciplinary and other definitions in astrobiology

The attempt to define life has gained new momentum in the wake of novel fields such as synthetic biology, astrobiology, and artificial life. In a series of articles, Cleland, Chyba, and Machery claim that definitions of life seek to provide necessary and sufficient conditions for applying the concept of life—something that such definitions cannot, and should not do. We argue that this criticism is largely unwarranted. Cleland, Chyba, and Machery approach definitions of life as classifying devices, thereby neglecting their other epistemic roles. We identify within the discussions of the nature and origin of life three other types of definitions: theoretical, transdisciplinary, and diagnostic definitions. The primary aim of these definitions is not to distinguish life from nonlife, although they can also be used for classificatory purposes. We focus on the definitions of life within the budding field of astrobiology, paying particular attention to transdisciplinary definitions, and diagnostic definitions in the search for biosignatures from other planets.     

Low environmental selenium availability as an additional determinant for goiter in East Java, Indonesia?

Iodine deficiency, which is most visibly indicated by goiter, is highly prevalent in Indonesia. Since 1994, Indonesia has a decree that all salt used for human, livestock, and industry must be iodized. However, despite the increased distribution of iodized salt, pockets with significantly higher prevalence of goiter still remain. This situation may be consequence of selenium (Se) deficiency. This study aimed to assess the Se level in the environment of goiter prevalent areas. Five hundred eleven school children participated in this study. Goiter was measured using both ultrasound and palpation. Ninety-nine eggs were collected from free-living chicken in 11 villages, and the Se contents of egg yolk and egg white were determined by neutron activation analysis. In the villages studied, Se concentration in egg yolk ranged from 0.15 to 1.52 Μg/g and in egg white from 0.18 to 2.97 Μg/g. The prevalence of goiter measured by palpation ranged from 18.4% to 70% and by ultrasound from 0% to 100%. Because of the inconsistency of goiter rate measured by palpation and ultrasonography, the question remains whether low availability of Se in the environment might be an additional contributing factor for goiter.     

How Indicative are Changes in Major Metabolites for Freezing Tolerance of Wheat?

Relative growth rate of winter wheat at low temperature (day/night, 4/2 °C) was about 0.02 g g^?1 fresh weight day^?1. There was a substantial increase in dry matter content of shoots and roots, especially during the first week of low temperature exposure, which for the greater part could be attributed to an accumulation of soluble sugars and starch. The freezing tolerance (LT₅₀) of the leaf tissue gradually increased with 6 °C during the 6 weeks exposure, whereas freezing tolerance of roots was hardly affected. Upon low temperature exposure there was an increase in the content of water-soluble non-protein thiols (mainly glutathione), soluble sugars, starch, amino acids and total nitrogen in both shoots and roots. The most substantial increases in the content of thiols, sugars and amino acids already occurred within hours or a few days after the onset of the exposure. The nitrate content in shoots showed a rapid and strong decrease during low temperature exposure, however, in roots its content remained unaffected. It is proposed that the observed rapid increases in the content of various metabolites at low temperature are primarily due to an altered balance in their synthesis and their consumption in growth. There was no direct relation between increases in the content of the various metabolites and the degree of freezing tolerance of the tissue.     

Conservation of Borneo biodiversity: do small lowland parks have a role,or are big inland sanctuaries sufficient? Brunei as an example

Borneo, the World’s fourth largest island, represents a continental mass sandwiched between volcanic arcs. Patterns of tree species richness, here proposed as proxy for overall biodiversity, and endemism within the island are described and interpreted with special reference to Dipterocarpaceae. Most of Borneo’s surface is sedimentary shales, mostly inland, and sandstones, mostly coastal, deposited in past epicontinental seas. The shales mainly support the regional West Malesian (Sundaland) tree flora, while the Neogene coastal hills, especially in the north-west, support the richest communities which are also richest in endemics. The forests of these hills, which include the richest tree communities in the Old World and are therefore of global significance, are accessible and critically endangered. Priorities for their future management are outlined.     

How Robust Is the Mechanism of Folding-Upon-Binding for an Intrinsically Disordered Protein?

The mechanism of interaction of an intrinsically disordered protein (IDP) with its physiological partner is characterized by a disorder-to-order transition in which a recognition and a binding step take place. Even if the mechanism is quite complex, IDPs tend to bind their partner in a cooperative manner such that it is generally possible to detect experimentally only the disordered unbound state and the structured complex. The interaction between the disordered C-terminal domain of the measles virus nucleoprotein (N_TAIL) and the X domain (XD) of the viral phosphoprotein allows us to detect and quantify the two distinct steps of the overall reaction. Here, we analyze the robustness of the folding of N_TAIL upon binding to XD by measuring the effect on both the folding and binding steps of N_TAIL when the structure of XD is modified. Because it has been shown that wild-type XD is structurally heterogeneous, populating an on-pathway intermediate under native conditions, we investigated the binding to 11 different site-directed variants of N_TAIL of one particular variant of XD (I504A XD) that populates only the native state. Data reveal that the recognition and the folding steps are both affected by the structure of XD, indicating a highly malleable pathway. The experimental results are briefly discussed in the light of previous experiments on other IDPs.     

Study of Pinna nobilis growth from inner record: How biased are posterior adductor muscle scars estimates?

Previous studies have shown that the external growth records of the posterior adductor muscle scar (PAMS) of the bivalve Pinna nobilis are incomplete and do not produce accurate age estimations. We have developed a new methodology to study age and growth using the inner record of the PAMS, which avoids the necessity of costly in situ shell measurements or isotopic studies. Using the inner record we identified the positions of PAMS previously obscured by nacre and estimated the number of missing records in adult specimens with strong abrasion of the calcite layer in the anterior portion of the shell. The study of the PAMS and inner record of two shells that were 6 years old when collected showed that only 2 and 3 PAMS were observed, while 6 inner records could be counted, thus confirming our working methodology. Growth parameters of a P. nobilis population located in Moraira, Spain (western Mediterranean) were estimated with the new methodology and compared to those obtained using PAMS data and in situ measurements. For the comparisons, we applied different models considering the data alternatively as length-at-age (LA) and tag-recapture (TR). Among every method we tested to fit the Von Bertalanffy growth model, we observed that LA data from inner record fitted to the model using non-linear mixed effects and the estimation of missing records using the calcite width was the most appropriate. The equation obtained with this method, L = 57.3*(1 − e^{−0.16(t−0.02)}), is very similar to that calculated previously from in situ measurements for the same population.     

How important are large vs. small forest remnants for the conservation of the woodland flora in an urban context?

Aim To test whether, in an urban area, small forest fragments are more important than large ones, the present study aimed at firstly exploring the relationship between plant functional groups or individual species and urban woodlot characteristics such as patch area and isolation, and secondly investigating whether equal‐sized combinations of islands tend to differ in species richness. Location The city of Brussels. Methods We considered the relationship between size, species richness and plant functional groups among one very large (1666 ha) and 11 rather small (2–123 ha) woodlots. Results The largest woodlot harboured species missing in the smaller ones. The species‐area relationship plotted for these wooded patches fitted the semilog model very well. Twenty‐three species had a significantly higher frequency in the main forest. Only six species had a significantly higher frequency in smaller woodlots. The occurrence of species groups with high conservation value (e.g. ancient forest species, rare species) was higher in large patches. However, a SLOSS analysis showed that habitat subdivision appeared to be associated with increased species counts. A marginally nonsignificant effect of distance to the main forest became significant when matrix species were removed from the patch samples. Conclusions Although overall the data showed a higher conservation value for large woods, some plant functional groups (e.g. woodland species vs. ancient forest species) responded differently to fragmentation. This illustrates that, for conservation strategies, studies considering the biotic characteristics of remnants should focus on the species number of particular plant functional groups, especially those with high conservation value. Furthermore, matrix species should be removed from the analysis in order not to mask underlying patch size and distance effects.     

How reliable are harvesting data for analyses of spatio‐temporal population dynamics?

Harvest data are commonly used as proxy for count data, especially in studies of long‐term temporal and spatial patterns of population fluctuations. However, usually the concurrence of the conclusions based on different types of data is impossible to verify due to the lack of count data. Here, we use annual (1964–2004) harvest and population census data for capercaillie, black grouse and hazel grouse from 14 game management districts covering Finland, and demonstrate some mismatch in the information that these data sets provide. Overall, linear regressions of annual harvest against population count give a reasonable fit, but the slopes are less than 1 in every species. Harvest bags have been proportionally larger in north and eastern Finland than in southwestern Finland, with marked species‐specific differences. Considering population variation, the CV% in the census data (30–50%) is consistently smaller than it is in the harvest data (60–70%). Most importantly, conclusions on the spatio‐temporal patterns of the population dynamics are different if based on harvest rather than count data. In capercaillie, synchrony decreases faster with distance according to the harvest data, while in black grouse and hazel grouse the census data show the steeper decline. In addition, the autocorrelation coefficients in the census time series are higher in capercaillie and black grouse than in harvest data, but in hazel grouse the opposite is true. Finally, the parameter estimates for a second order autoregressive model using different data sets differ, and these differences are species‐specific. Despite the fact that annual harvest is a positive and linear function of annual grouse population density, the pattern of population dynamics derived from the bag data is different from that shown by the census data. This result urges caution in using wildlife bag data as reliable indices of population dynamics. deceased August 2008.