A Model-Based Approach for Making Ecological Inference from Distance Sampling Data

We consider a fully model-based approach for the analysis of distance sampling data. Distance sampling has been widely used to estimate abundance (or density) of animals or plants in a spatially explicit study area. There is, however, no readily available method of making statistical inference on the relationships between abundance and environmental covariates. Spatial Poisson process likelihoods can be used to simultaneously estimate detection and intensity parameters by modeling distance sampling data as a thinned spatial point process. A model-based spatial approach to distance sampling data has three main benefits: it allows complex and opportunistic transect designs to be employed, it allows estimation of abundance in small subregions, and it provides a framework to assess the effects of habitat or experimental manipulation on density. We demonstrate the model-based methodology with a small simulation study and analysis of the Dubbo weed data set. In addition, a simple ad hoc method for handling overdispersion is also proposed. The simulation study showed that the model-based approach compared favorably to conventional distance sampling methods for abundance estimation. In addition, the overdispersion correction performed adequately when the number of transects was high. Analysis of the Dubbo data set indicated a transect effect on abundance via Akaike’s information criterion model selection. Further goodness-of-fit analysis, however, indicated some potential confounding of intensity with the detection function.

Ecological distribution of the shrimp Litopenaeus schmitti (Burkenroad, 1936) (Decapoda, Penaeoidea) in Ubatuba Bay, Sao Paulo, Brazil

The penaeidean Litopenaeus schmitti, popularly known as white shrimp, is a species of great economic importance, being a target of fishing fleets in the southeast region of Brazil. It is distributed through the western Atlantic, from Cuba to Brazil, until Rio Grande do Sul. Adults are found from shallow depths up to 30 m and have been found to depths of 47 m in the state of Rio de Janeiro, while juveniles are located in bays and estuaries. The studied species is seasonally distributed in the region of Ubatuba. The objectives of this study are to analyze the abundance and ecological distribution of L. schmitti and to assess if and when juveniles use the Indaia estuary during their life cycle. Furthermore, the hypothesis was tested that the main period of recruitment in the bay coincides with the period of closure of fisheries defined by the Instruction of IBAMA. To that end, samples were taken monthly from July 2005 through June 2007, both in Ubatuba Bay and in the estuary formed by the Rio Indaia. At each sampling station, salinity, temperature (bottom), depth, organic matter content (%), and grain size of sediments were measured. We found that the largest catches in the estuary were in late spring and early summer. In Ubatuba Bay, peak catches occurred during winter and early spring, whereas in the second year, already in May, there was a high peak capture. The variation in the number of individuals was correlated with some environmental factors both in the estuary and in the inlet (p < 0.05). In the estuary, abundance was positively correlated with temperature (p = 0.008) and organic matter (p = 0.025) and negatively with depth (p = 0.009). Regarding the Ubatuba Bay, only temperature (p = 0.034) and depth (p = 0.013) were significantly associated with the distribution of the shrimp, both being negative relations. The shrimp L. schmitti uses both the estuarine as well the shore environment, particularly the Ubatuba estuary and its adjacent bay, to complete its life cycle. The proposed period of fisheries closure (between March to May in the state of Sao Paulo) for this and other shrimps coincides with individuals capable of reproduction entering the inlet and thus are being protected.

Predation of Caiman yacare (Spix, 1825) (Crocodilia, Alligatoridae) by Busarellus nigricollis (Latham, 1790) (Accipitriformes, Accipitridae) in the Taiama Ecological Station, Alto Pantanal, State of Mato Grosso

Predation of Caiman yacare (Spix, 1825) (Crocodilia, Alligatoridae) by Busarellus nigricollis (Latham, 1790) (Accipitriformes, Accipitridae) in the Taiama Ecological Station, Alto Pantanal, State of Mato Grosso. The Black-collared Hawk Busarellus nigricollis is an Accipitridae commonly seen on river banks, lagoon shores, and marshy areas. It feeds mainly on fishes and aquatic insects. It hunts from dead tree branches at forest edges or emergent trunks in flooded areas. Detailed information about the Black-collared Hawk food habits is scarce. In this study, we describe the predation of Caiman yacare (Pantanal alligator) by an individual of B. nigricollis. The event was observed on 20 August 2010 at 10: 14 am, in the Taiama Ecological Station, municipality of Caceres, Alto Pantanal, state of Mato Grosso. The B. nigricollis individual was seen leaving the Paraguay River carrying a juvenile C. yacare around 40 cm long. The prey was torn apart and given to a Black-collared Hawk nestling sitting atop a nest in flooded forest, ca. 15 m way from the river bank. This is the first published record of Pantanal alligator predation by the Black-collared Hawk.

The Ecological Basis for Biogeographic Classification: an Example in Orchid Bees (Apidae: Euglossini)

Biogeography has been difficult to apply as a methodological approach because organismic biology is incomplete at levels where the process of formulating comparisons and analogies is complex. The study of insect biogeography became necessary because insects possess numerous evolutionary traits and play an important role as pollinators. Among insects, the euglossine bees, or orchid bees, attract interest because the study of their biology allows us to explain important steps in the evolution of social behavior and many other adaptive tradeoffs. We analyzed the distribution of morphological characteristics in Colombian orchid bees from an ecological perspective. The aim of this study was to observe the distribution of these attributes on a regional basis. Data corresponding to Colombian euglossine species were ordered with a correspondence analysis and with subsequent hierarchical clustering. Later, and based on community proprieties, we compared the resulting hierarchical model with the collection localities to seek to identify a biogeographic classification pattern. From this analysis, we derived a model that classifies the territory of Colombia into 11 biogeographic units or natural clusters. Ecological assumptions in concordance with the derived classification levels suggest that species characteristics associated with flight performance, nectar uptake, and social behavior are the factors that served to produce the current geographical structure.

Three in one: fixing marine nematodes for ecological, molecular, and morphological studies

Multidisciplinary benthic studies are still hindered by the lack of a unique fixative that satisfactorily preserves morphology and DNA, and that is simultaneously adequate for ecological surveys. The objective of this study is to test the performance of five fixatives: formalin, ethanol, dimethylsulfoxide with EDTA and NaCl salts (DESS), methanol with acetic acid (METHAC), and ethanol with acetic acid (ETHAC), for the preservation of estuarine and exclusively marine nematode assemblages for morphological, molecular, and ecological studies. The presence of the stain rose bengal in each fixative was also evaluated in the yield of PCR reactions. For molecular analyses, one species of each habitat was considered. Results revealed that fixative performance for morphological studies is habitat-and species-dependent. For studies of estuarine sediment nematodes, we recommend the use of pure ethanol, because it caused little morphological distortion (<10% of the assemblage), preserved all the species for ecological studies, and yielded high quality DNA sequences. For studies of exclusively marine environments, METHAC or DESS are the most adequate. The first performed better for morphological and ecological surveys, whereas the second was more appropriate for molecular research. For ecological studies, DESS should be used in comparison with formalin, in order to cross check the results. Finally, staining of samples with rose bengal is not recommended, because it hindered DNA amplification regardless of the fixative used.

Ecological aspects of the sandfly fauna (Diptera, Psychodidae) in an American cutaneous leishmaniasis endemic area under the influence of hydroelectric plants in Paranapanema river, State of Parana, Brazil

Introduction: An epidemiological study was undertaken to identify determinant factors in the occurrence of American cutaneous leishmaniasis in areas under the influence of hydroelectric plants in Paranapanema river, State of Parana, Brazil. The ecological aspects of the phlebotomine fauna were investigated. Methods: Sandflies were sampled with automatic light traps from February 2004 to June 2006 at 25 sites in the urban and rural areas of Itambaraca, and in Porto Almeida and Sao Joaquim do Pontal. Results: A total of 3,187 sandflies of 15 species were captured. Nyssomyia neivai predominated (34.4%), followed by Pintomyia pessoai (32.6%), Migonemyia migonei (11.6%), Nyssomyia whitmani (8.8%), and Pintomyia fischeri (2.7%), all implicated in the transmission of Leishmania. Males predominated for Ny. neivai, and females for the other vector species, with significant statistical differences (p < 0.001). Nyssomyia neivai, Pi. pessoai, Ny. whitmani, Brumptomyia brumpti, Mg. migonei, and Pi. fischeri presented the highest values for the Standardized Species Abundance Index (SSAI). The highest frequencies and diversities were found in the preserved forest in Porto Almeida, followed by forests with degradation in Sao Joaquim do Pontal and Vila Rural. Conclusions: Sandflies were captured in all localities, with the five vectors predominating. Ny. neivai had its highest frequencies in nearby peridomestic environments and Pi. pessoai in areas of preserved forests. The highest SSAI values of Ny. neivai and Pi. pessoai reflect their wider dispersion and higher frequencies compared with other species, which seems to indicate that these two species may be transmitting leishmaniasis in the area.

A trophic study of the sympatric Amazonian freshwater turtles Podocnemis unifilis and Podocnemis expansa (Testudines, Podocnemidae) using carbon and nitrogen stable isotope analyses

The Yellow-spotted River Turtle (Podocnemis unifilis Troschel, 1848) and the South American River Turtle (Podocnemis expansa (Schweigger, 1812)) are two turtles species that are widely distributed and have ecological, economic, and cultural importance in the Amazon basin. Although sympatric regarding most of their distribution, few studies have addressed the coexistence of these two species. To examine this, we analyzed the trophic level and the primary carbon source from the diets of both species in Baixo Araguaia, Tocantins, Brazil, using stable isotope analyses of carbon (delta C-13) and nitrogen (delta N-15). We also verified possible intraspecific variations (related to sex and body mass) in the trophic levels and primary carbon sources of their diets. Podocnemis unifilis had higher values of delta N-15 than P. expansa, averaging 7.59 parts per thousand and 5.06 parts per thousand, respectively, a difference which may indicate a possible trophic change owing to exploiting different food resources. No differences were found between the two species in relation to delta C-13 (mean values of -26.2 parts per thousand and -26.1 parts per thousand, respectively). The similarity between delta C-13 values suggests that the sources of their basal feeding are the same, consisting mainly of C-3 plants. There was no intraspecific variation in the values of delta C-13 and delta N-15.

Ecological aspects of the sandfly fauna (Diptera, Psychodidae) in an American cutaneous leishmaniasis endemic area under the influence of hydroelectric plants in Paranapanema river, State of Paraná, Brazil

INTRODUCTION: An epidemiological study was undertaken to identify determinant factors in the occurrence of American cutaneous leishmaniasis in areas under the influence of hydroelectric plants in Paranapanema river, State of Paraná, Brazil. The ecological aspects of the phlebotomine fauna were investigated. METHODS: Sandflies were sampled with automatic light traps from February 2004 to June 2006 at 25 sites in the urban and rural areas of Itambaracá, and in Porto Almeida and São Joaquim do Pontal. RESULTS: A total of 3,187 sandflies of 15 species were captured. Nyssomyia neivai predominated (34.4%), followed by Pintomyia pessoai (32.6%), Migonemyia migonei (11.6%), Nyssomyia whitmani (8.8%), and Pintomyia fischeri (2.7%), all implicated in the transmission of Leishmania. Males predominated for Ny. neivai, and females for the other vector species, with significant statistical differences (p < 0.001). Nyssomyia neivai, Pi. pessoai, Ny. whitmani, Brumptomyia brumpti, Mg. migonei, and Pi. fischeri presented the highest values for the Standardized Species Abundance Index (SSAI). The highest frequencies and diversities were found in the preserved forest in Porto Almeida, followed by forests with degradation in São Joaquim do Pontal and Vila Rural. CONCLUSIONS: Sandflies were captured in all localities, with the five vectors predominating. Ny. neivai had its highest frequencies in nearby peridomestic environments and Pi. pessoai in areas of preserved forests. The highest SSAI values of Ny. neivai and Pi. pessoai reflect their wider dispersion and higher frequencies compared with other species, which seems to indicate that these two species may be transmitting leishmaniasis in the area.

Landscape and soil regionalization in southern Brazilian Amazon and contiguous areas: methodology and relevance for ecological studies

Soils of a large tropical area with differentiated landscapes cannot be treated uniformly for ecological applications. We intend to develop a framework based on physiography that can be used in regional applications. The study region occupies more than 1.1 million km² and is located at the junction of the savanna region of Central Brazil and the Amazon forest. It includes a portion of the high sedimentary Central Brazil plateau and large areas of mostly peneplained crystalline shield on the border of the wide inner-Amazon low sedimentary plain. A first broad subdivision was made into landscape regions followed by a more detailed subdivision into soil regions. Mapping information was extracted from soil survey maps at scales of 1:250000-1:500000. Soil units were integrated within a homogenized legend using a set of selected attributes such as taxonomic term, the texture of the B horizon and the associated vegetation. For each region, a detailed inventory of the soil units with their area distribution was elaborated. Ten landscape regions and twenty-four soil regions were recognized and delineated. Soil cover of a region is normally characterized by a cluster composed of many soil units. Soil diversity is comparable in the landscape and the soil regions. Composition of the soil cover is quantitatively expressed in terms of area extension of the soil units. Such geographic divisions characterized by grouping soil units and their spatial estimates must be used for regional ecological applications.

Mediterranean brachiopods: morphological, ecological and phylogenetic aspects

The Brachiopoda of the Marine Protected Area “Secche di Tor Paterno”, Central Tyrrhenian Sea, have been investigated in order to give a first glance of the diversity of the brachiopods of this area and provide a new report on the Mediterranean Brachiopod fauna. Four species were reported: Novocrania anomala (Müller, 1776), Megathiris detruncata (Gmelin, 1790), Joania cordata (Risso,1826) and Argyrotheca cuneata (Risso,1826). For all the four species a morphological analysis was carried out. For the two most abundant species, J.cordata and A. cuneata, a morphometric study, based on thickness/width and length/width scattergrams, was carried out, in order to investigate their variability. Size-frequency distributions relative to the three dimensions of the shell were also computed, aimed at a evaluation of population dynamics of these two species. The results showed that, for both species, the parameters which most determine the rise of the shell during the growth of animal are width and length and that frequency distributions are mainly bi- or plurymodal and that they are difficult to interpret, as reported by other studies. Analysis of drill holes found on the shell of some specimens of the two same species revealed a predatory origin and that three different predators are responsible for them. Partial sequences of two different genetic markers, the Internal Transcribed Spacer 1 (ITS1) and the cytochrome oxidase subunit 1 (COI), were used to investigate the phylogenetic relationship between two populations of the eurybathic brachiopod species Gryphus vitreus (Born,1778) across the strait of Gibraltar. This represents the first genetic population study on brachiopods. Results from AMOVA and Bayesian analysis performed on 31 specimens highlighted no genetic differentiation indicating a likely panmixia, dispite the lecitotrophic development of the species.

Ecological modelling of the phytoplankton dynamics in the northern Gulf of Aqaba (Red Sea)

The Gulf of Aqaba represents a small scale, easy to access, regional analogue of larger oceanic oligotrophic systems. In this Gulf, the seasonal cycles of stratification and mixing drives the seasonal phytoplankton dynamics. In summer and fall, when nutrient concentrations are very low, Prochlorococcus and Synechococcus are more abundant in the surface water. This two populations are exposed to phosphate limitation. During winter mixing, when nutrient concentrations are high, Chlorophyceae and Cryptophyceae are dominant but scarce or absent during summer. In this study it was tried to develop a simulation model based on historical data to predict the phytoplankton dynamics in the northern Gulf of Aqaba. The purpose is to understand what forces operate, and how, to determine the phytoplankton dynamics in this Gulf. To make the models data sampled in two different sampling station (Fish Farm Station and Station A) were used. The data of chemical, biological and physical factors, are available from 14th January 2007 to 28th December 2009. The Fish Farm Station point was near a Fish Farm that was operational until 17th June 2008, complete closure date of the Fish Farm, about halfway through the total sampling time. The Station A sampling point is about 13 Km away from the Fish Farm Station. To build the model, the MATLAB software was used (version 7.6.0.324 R2008a), in particular a tool named Simulink. The Fish Farm Station models shows that the Fish Farm activity has altered the nutrient concentrations and as a consequence the normal phytoplankton dynamics. Despite the distance between the two sampling stations, there might be an influence from the Fish Farm activities also in the Station A ecosystem. The models about this sampling station shows that the Fish Farm impact appears to be much lower than the impact in the Fish Farm Station, because the phytoplankton dynamics appears to be driven mainly by the seasonal mixing cycle.

Spatial and temporal variability and ecological processes in the epibenthic assemblages of the northern Adriatic Sea

Several coralligenous reefs occur in the soft bottoms of the northern Adriatic continental shelf. Mediterranean coralligenous habitats are characterised by high species diversity and are intrinsically valuable for their biological diversity and for the ecological processes they support. The conservation and management of these habitats require quantifying spatial and temporal variability of their benthic assemblages. This PhD thesis aims to give a relevant contribution to the knowledge of the structure and dynamics of the epibenthic assemblages on the coralligenous subtidal reefs occurring in the northern Adriatic Sea. The epibenthic assemblages showed a spatial variation larger compared to temporal changes, with a temporal persistence of reef-forming organisms. Assemblages spatial heterogeneity has been related to morphological features and geographical location of the reefs, together with variation in the hydrological conditions. Manipulative experiments help to understand the ecological processes structuring the benthic assemblages and maintaining their diversity. In this regards a short and long term experiment on colonization patterns of artificial substrata over a 3-year period has been performed in three reefs, corresponding to the three main types of assemblages detected in the previous study. The first colonisers, largely depending by the different larval supply, played a key role in determining the heterogeneity of the assemblages in the early stage of colonisation. Lateral invasion, from the surrounding assemblages, was the driver in structuring the mature assemblages. These complex colonisation dynamics explained the high heterogeneity of the assemblages dwelling on the northern Adriatic biogenic reefs. The buildup of these coralligenous reefs mainly depends by the bioconstruction-erosion processes that has been analysed through a field experiment. Bioconstruction, largely due to serpulid polychaetes, prevailed on erosion processes and occurred at similar rates in all sites. Similarly, the total energy contents in the benthic communities do not differ among sites, despite being provided by different species. Therefore, we can hypothesise that both bioconstruction processes and energetic storage may be limited by the availability of resources. Finally the major contribution of the zoobenthos compared to the phytobenthos to the total energetic content of assemblages suggests that the energy flow in these benthic habitats is primarily supported by planktonic food web trough the filter feeding invertebrates.

Study of Italian isolates of Alternaria spp.: molecular and morphological characterization and pathogenesis on apple tree

It was decided to carry out a morphological and molecular characterization of the Italian Alternaria isolatescollected from apple , and evaluate their pathogenicity and subsequently combining the data collected. The strain collection (174 isolates) was constructed by collecting material (received from extension service personnel) between June and August of 2007, 2008, and 2009. A Preliminary bioassays were performed on detached plant materials (fruit and leaf wounded and unwounded), belonging to the Golden cultivar, with two different kind of inoculation (conidial suspension and conidial filtrate). Symptoms were monitored daily and a value of pathogenicity score (P.S.) was assigned on the basis of the diameter of the necrotic area that developed. On the basis of the bioassays, the number of isolates to undergo further molecular analysis was restricted to a representative set of single spore strains (44 strains). Morphological characteristics of the colony and sporulation pattern were determined according to previous systematic work on small-spored Alternaria spp. (Pryor and Michaelides, 2002 and Hong et al., 2006). Reference strains (Alternaria alternata, Alternaria tenuissima, Alternaria arborescens and four Japanese strains of Alternaria alternata mali pathotype), used in the study were kindly provided by Prof. Barry Pryor, who allows a open access to his own fungal collection. Molecular characterization was performed combining and comparing different data sets obtained from distinct molecular approach: 1) investigation of specific loci and 2) fingerprinting based on diverse randomly selected polymorphic sites of the genome. As concern the single locus analysis, it was chosen to sequence the EndoPG partial gene and three anonymous region (OPA1-3, OPA2- and OPa10-2). These markers has revealed a powerful tool in the latter systematic works on small-spored Alternaria spp. In fact, as reported in literature small-spored Alternaria taxonomy is complicated due to the inability to resolve evolutionary relationships among the taxa because of the lack of variability in the markers commonly used in fungi systematic. The three data set together provided the necessary variation to establish the phylogenetic relationships among the Italian isolates of Alternaria spp. On Italian strains these markers showed a variable number of informative sites (ranging from 7 for EndoPg to 85 for OPA1-3) and the parsimony analysis produced different tree topologies all concordant to define A. arborescens as a mophyletic clade. Fingerprinting analysis (nine ISSR primers and eight AFLP primers combination) led to the same result: a monophyleic A. arborescens clade and one clade containing both A. tenuissima and the A. alternata strains. This first attempt to characterize Italian Alternaria species recovered from apple produced concordant results with what was already described in a similar phylogenetic study on pistachio (Pryor and Michaelides, 2002), on walnut and hazelnut (Hong et al., 2006), apple (Kang et al., 2002) and citurus (Peever et al., 2004). Together with these studies, this research demonstrates that the three morphological groups are widely distributed and occupy similar ecological niches. Furthermore, this research suggest that these Alternaria species exhibit a similar infection pattern despite the taxonomic and pathogenic differences. The molecular characterization of the pathogens is a fundamental step to understanding the disease that is spreading in the apple orchards of the north Italy. At the beginning the causal agent was considered as Alteraria alternata (Marshall and Bertagnoll, 2006). Their preliminary studies purposed a pathogenic system related to the synthesis of toxins. Experimental data of our bioassays suggest an analogous hypothesis, considering that symptoms could be induced after inoculating plant material with solely the filtrate from pathogenic strains. Moreover, positive PCR reactions using AM-toxin gene specific primers, designed for identification of apple infecting Alternaria pathovar, led to a hypothesis that a host specific toxin (toxins) were involved. It remains an intriguing challenge to discover or not if the agent of the “Italian disease” is the same of the one previously typified as Alternaria mali, casual agent of the apple blotch disease.

The school environment as a teacher. The role of space and place in enhancing ecological literacy and social competence development in children and young people

Can space and place foster child development, and in particular social competence and ecological literacy? If yes, how can space and place do that? This study shows that the answer to the first question is positive and then tries to explain the way space and place can make a difference. The thesis begins with the review of literature from different disciplines – child development and child psychology, education, environmental psychology, architecture and landscape architecture. Some bridges among such disciplines are created and in some cases the ideas from the different areas of research merge: thus, this is an interdisciplinary study. The interdisciplinary knowledge from these disciplines is translated into a range of design suggestions that can foster the development of social competence and ecological literacy. Using scientific knowledge from different disciplines is a way of introducing forms of evidence into the development of design criteria. However, the definition of design criteria also has to pass through the study of a series of school buildings and un-built projects: case studies can give a positive contribution to the criteria because examples and good practices can help “translating” the theoretical knowledge into design ideas and illustrations. To do that, the different case studies have to be assessed in relation to the various themes that emerged in the literature review. Finally, research by design can be used to help define the illustrated design criteria: based on all the background knowledge that has been built, the role of the architect is to provide a series of different design solutions that can give answers to the different “questions” emerged in the literature review.

The ecological and socio-economic role of Prosopis juliflora in Eritrea

In Eritrea findet eine rasche Verbreitung von Prosopis (juliflora) statt, die sich negativ auf die Naturresourcen als auch die sozio-ökonomische Lage der ländlichen Bevölkerung auswirkt. Die Landbevölkerung Eritrea's ist davon überzeugt, dass die Pflanze vor allem die Ernährungssicherung beeinträchtigt und will deshalb, dass sie ausgerottet wird. Die vorliegende Dissertation beschreibt die Auswirkung von Posopis auf lokale Öko- und Wirtschaftssysteme und zieht Vergleiche mit der diesbezüglichen Situation in anderen Ländern. Im Weiteren stellt sie einen Prosopis Management-Plan vor, dessen Ziel es ist, die zunehmende Verbreitung zu verhindern. Auch liefert sie eine Gegenüberstellung der Ansichten von wissenschaftlichen Experten einerseits und Bauern und Nomaden andrerseits. Sie zeigt auf, dass die weit verbreitete Annahme der Experten das Problem Prosopis durch ökonomische Nutzung ("eradication by utilisation") in Schach halten zu können, fraglich ist.