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Ivan Nagelkerken - One of the best experts on this subject based on the ideXlab platform.
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importance of shallow water Biotopes of a caribbean bay for juvenile coral reef fishes patterns in biotope association community structure and spatial distribution
Marine Ecology Progress Series, 2000Co-Authors: Ivan Nagelkerken, Martijn Dorenbosch, Wilco C. E. P. Verberk, Cocheret E De La Moriniere, G. Van Der VeldeAbstract:Fish community structure of a non-estuarine inland bay on the Caribbean island of Curacao was determined in the mangroves, seagrass beds, algal beds, channel, fossil reef boulders, notches in fossil reef rock, and on the adjacent coral reef, using visual censuses in belt transects. Fish communities varied among Biotopes, but some overlap was present. Fish density and species richness were highest at the boulders and on the coral reef, and extremely low on the algal beds, whereas the total number of individuals calculated for the entire bay was highest on the seagrass beds. Differ- ences in fish densities between Biotopes were related to differences in structural complexity and amount of shelter. Fishes in the bay largely consisted of 17 (mainly commercially important) reef fish species, which used the bay Biotopes only as a nursery during the juvenile part of their life cycle. Small juveniles of these species were most often found in the mangroves, whereas at intermediate sizes some were found in the channel. Large individuals and adults were found on the reef, and den- sities of several of these species were higher on the reef near the bay than on reefs located farther down-current. Fishes which spent their entire life cycles in either the bay or on the coral reef were also found, and the latter group showed a strong decrease in abundance with increasing distance into the bay. The density distribution of individual fish species was not homogeneous within the bay. In the mangroves and seagrass beds, spatial distribution of fishes was correlated with distance to the mouth of the bay, water transparency, amount of shelter, and the structural complexity of the biotope. Juveniles of 3 reef species showed an increase in size on the seagrass beds with distance from the mouth into the bay, whereas 1 bay species showed a decrease in size with this distance.
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importance of mangroves seagrass beds and the shallow coral reef as a nursery for important coral reef fishes using a visual census technique
Estuarine Coastal and Shelf Science, 2000Co-Authors: Ivan Nagelkerken, M W Gorissen, Gabrielle Van Der Velde, G J Meijer, Den C HartogAbstract:Abstract The nursery function of various Biotopes for coral reef fishes was investigated on Bonaire, Netherlands Antilles. Length and abundance of 16 commercially important reef fish species were determined by means of visual censuses during the day in six different Biotopes: mangrove prop-roots ( Rhizophora mangle ) and seagrass beds ( Thalassia testudinum ) in Lac Bay, and four depth zones on the coral reef (0 to 3 m, 3 to 5 m, 10 to 15 m and 15 to 20 m). The mangroves, seagrass beds and shallow coral reef (0 to 3 m) appeared to be the main nursery Biotopes for the juveniles of the selected species. Mutual comparison between Biotopes showed that the seagrass beds were the most important nursery biotope for juvenile Haemulon flavolineatum , H. sciurus , Ocyurus chrysurus , Acanthurus chirurgus and Sparisoma viride , the mangroves for juvenile Lutjanus apodus , L. griseus , Sphyraena barracuda and Chaetodon capistratus , and the shallow coral reef for juvenile H. chrysargyreum , L. mahogoni , A. bahianus and Abudefduf saxatilis . Juvenile Acanthurus coeruleus utilized all six Biotopes, while juvenile H. carbonarium and Anisotremus surinamensis were not observed in any of the six Biotopes. Although fishes showed a clear preference for a specific nursery biotope, most fish species utilized multiple nursery Biotopes simultaneously. The almost complete absence of juveniles on the deeper reef zones indicates the high dependence of juveniles on the shallow water Biotopes as a nursery. For most fish species an (partial) ontogenetic shift was observed at a particular life stage from their (shallow) nursery Biotopes to the (deeper) coral reef. Cluster analyses showed that closely related species within the families Haemulidae, Lutjanidae and Acanthuridae, and the different size classes within species in most cases had a spatial separation in biotope utilization.
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Day-night shifts of fishes between shallow-water Biotopes of a Caribbean bay, with emphasis on the nocturnal feeding of Haemulidae and Lutjanidae
Marine Ecology Progress Series, 2000Co-Authors: Ivan Nagelkerken, Martijn Dorenbosch, Wilco C. E. P. Verberk, E. Cocheret De La Morinière, G. Van Der VeldeAbstract:Day-night changes in fish communities were quantified in 6 associated shallow-water Biotopes within a single bay: mangroves, seagrass beds, algal beds, channel, fossil reef boulders, and notches in fossil reef rock. All Biotopes, except the algal beds, showed a strong reduction in fish density and species richness at night, caused by absence of diurnally active fishes and migrations of Haemulidae and Lutjanidae to the seagrass beds. The fish fauna of the different Biotopes showed a relatively high dissimilarity between day and night. This dissimilarity is largely caused by absence of Acanthuridae, Chaetodontidae, Labridae, Pomacentridae, Scaridae and Sparidae at night. These fishes seek shelter at night in, amongst others, the channel, notches and boulders. The balloonfish Diodon holocanthus utilised almost all Biotopes as shelter as well as feeding sites. The wide distribution of its preferred food (molluscs) probably explains its distribution in most Biotopes at night. The nocturnally active Haemulidae and Lutjanidae, on the other hand, migrated from their daytime shelter sites to the seagrass beds at night to feed. Some of these fishes also migrated to the algal beds to feed. The preference of Haemulidae and Lutjanidae for the seagrass bed as a feeding biotope, instead of other bay Biotopes, appears to be related to the relatively high availability of their preferred food (Tanaidacea and Decapoda) as determined by digestive tract analysis. Other bay Biotopes showed much lower densities of such food items compared to the seagrass beds.
G. Van Der Velde - One of the best experts on this subject based on the ideXlab platform.
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importance of shallow water Biotopes of a caribbean bay for juvenile coral reef fishes patterns in biotope association community structure and spatial distribution
Marine Ecology Progress Series, 2000Co-Authors: Ivan Nagelkerken, Martijn Dorenbosch, Wilco C. E. P. Verberk, Cocheret E De La Moriniere, G. Van Der VeldeAbstract:Fish community structure of a non-estuarine inland bay on the Caribbean island of Curacao was determined in the mangroves, seagrass beds, algal beds, channel, fossil reef boulders, notches in fossil reef rock, and on the adjacent coral reef, using visual censuses in belt transects. Fish communities varied among Biotopes, but some overlap was present. Fish density and species richness were highest at the boulders and on the coral reef, and extremely low on the algal beds, whereas the total number of individuals calculated for the entire bay was highest on the seagrass beds. Differ- ences in fish densities between Biotopes were related to differences in structural complexity and amount of shelter. Fishes in the bay largely consisted of 17 (mainly commercially important) reef fish species, which used the bay Biotopes only as a nursery during the juvenile part of their life cycle. Small juveniles of these species were most often found in the mangroves, whereas at intermediate sizes some were found in the channel. Large individuals and adults were found on the reef, and den- sities of several of these species were higher on the reef near the bay than on reefs located farther down-current. Fishes which spent their entire life cycles in either the bay or on the coral reef were also found, and the latter group showed a strong decrease in abundance with increasing distance into the bay. The density distribution of individual fish species was not homogeneous within the bay. In the mangroves and seagrass beds, spatial distribution of fishes was correlated with distance to the mouth of the bay, water transparency, amount of shelter, and the structural complexity of the biotope. Juveniles of 3 reef species showed an increase in size on the seagrass beds with distance from the mouth into the bay, whereas 1 bay species showed a decrease in size with this distance.
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Day-night shifts of fishes between shallow-water Biotopes of a Caribbean bay, with emphasis on the nocturnal feeding of Haemulidae and Lutjanidae
Marine Ecology Progress Series, 2000Co-Authors: Ivan Nagelkerken, Martijn Dorenbosch, Wilco C. E. P. Verberk, E. Cocheret De La Morinière, G. Van Der VeldeAbstract:Day-night changes in fish communities were quantified in 6 associated shallow-water Biotopes within a single bay: mangroves, seagrass beds, algal beds, channel, fossil reef boulders, and notches in fossil reef rock. All Biotopes, except the algal beds, showed a strong reduction in fish density and species richness at night, caused by absence of diurnally active fishes and migrations of Haemulidae and Lutjanidae to the seagrass beds. The fish fauna of the different Biotopes showed a relatively high dissimilarity between day and night. This dissimilarity is largely caused by absence of Acanthuridae, Chaetodontidae, Labridae, Pomacentridae, Scaridae and Sparidae at night. These fishes seek shelter at night in, amongst others, the channel, notches and boulders. The balloonfish Diodon holocanthus utilised almost all Biotopes as shelter as well as feeding sites. The wide distribution of its preferred food (molluscs) probably explains its distribution in most Biotopes at night. The nocturnally active Haemulidae and Lutjanidae, on the other hand, migrated from their daytime shelter sites to the seagrass beds at night to feed. Some of these fishes also migrated to the algal beds to feed. The preference of Haemulidae and Lutjanidae for the seagrass bed as a feeding biotope, instead of other bay Biotopes, appears to be related to the relatively high availability of their preferred food (Tanaidacea and Decapoda) as determined by digestive tract analysis. Other bay Biotopes showed much lower densities of such food items compared to the seagrass beds.
Claire Nédellec - One of the best experts on this subject based on the ideXlab platform.
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overview of the bacteria biotope task at bionlp shared task 2016
Proceedings of the 4th BioNLP Shared Task Workshop, 2016Co-Authors: Louise Deleger, Robert Bossy, Philippe Bessieres, Estelle Chaix, Arnaud Ferré, Claire NédellecAbstract:This paper presents the Bacteria Biotope task of the BioNLP Shared Task 2016, which follows the previous 2013 and 2011 editions. The task focuses on the extraction of the locations (Biotopes and geographical places) of bacteria from PubMe abstracts and the characterization of bacteria and their associated habitats with respect to reference knowledge sources (NCBI taxonomy, OntoBiotope ontology). The task is motivated by the importance of the knowledge on bacteria habitats for fundamental research and applications in microbiology. The paper describes the different proposed subtasks, the corpus characteristics, the challenge organization, and the evaluation metrics. We also provide an analysis of the results obtained by participants.
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overview of the gene regulation network and the bacteria biotope tasks in bionlp 13 shared task
BMC Bioinformatics, 2015Co-Authors: Robert Bossy, Wiktoria Golik, Zorana Ratkovic, Dialekti Valsamou, Philippe Bessieres, Claire NédellecAbstract:Background We present the two Bacteria Track tasks of BioNLP 2013 Shared Task (ST): Gene Regulation Network (GRN) and Bacteria Biotope (BB). These tasks were previously introduced in the 2011 BioNLP-ST Bacteria Track as Bacteria Gene Interaction (BI) and Bacteria Biotope (BB). The Bacteria Track was motivated by a need to develop specific BioNLP tools for fine-grained event extraction in bacteria biology. The 2013 tasks expand on the 2011 version by better addressing the biological knowledge modeling needs. New evaluation metrics were designed for the new goals. Moving beyond a list of gene interactions, the goal of the GRN task is to build a gene regulation network from the extracted gene interactions. BB'13 is dedicated to the extraction of bacteria Biotopes, i.e. bacterial environmental information, as was BB'11. BB'13 extends the typology of BB'11 to a large diversity of Biotopes, as defined by the OntoBiotope ontology. The detection of entities and events is tackled by distinct subtasks in order to measure the progress achieved by the participant systems since 2011.
Regina Hofmannlehmann - One of the best experts on this subject based on the ideXlab platform.
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occurrence of ticks and prevalence of anaplasma phagocytophilum and borrelia burgdorferi s l in three types of urban Biotopes forests parks and cemeteries
Ticks and Tick-borne Diseases, 2014Co-Authors: Sandor Hornok, Marina L Meli, Enikő Gonczi, Robert Farkas, Edina Halasz, Nora Takacs, Regina HofmannlehmannAbstract:The aim of the present study was to compare different urban Biotopes for the occurrence of ixodid tick species, for the population density of Ixodes ricinus and for the prevalence rates of two emerging, zoonotic pathogens. Altogether 2455 ticks were collected from the vegetation on 30 places (forests, parks, cemeteries) of Budapest, Hungary. I. ricinus and Haemaphysalis concinna were collected in all three biotope types, but Dermacentor reticulatus only in parks and forests, and D. marginatus only in a forest. Highest population density of I. ricinus was observed in neglected parts of cemeteries. In females of this tick species the prevalence rates of Anaplasma phagocytophilum and Borrelia burgdorferi s.l. were significantly lower in cemeteries, than in parks or forests. In conclusion, risks associated with the presence of ticks and tick-borne pathogens may be high in a city, but this depends on biotope types, due to habitat-related differences in the vegetation, as well as in the availability of tick hosts and pathogen reservoirs.
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influence of the biotope on the tick infestation of cattle and on the tick borne pathogen repertoire of cattle ticks in ethiopia
PLOS ONE, 2014Co-Authors: Sandor Hornok, Getachew Abichu, Marina L Meli, Balazs Tanczos, Kinga M Sulyok, Miklos Gyuranecz, Enikő Gonczi, Robert Farkas, Regina HofmannlehmannAbstract:Background: The majority of vector-borne infections occur in the tropics, including Africa, but molecular eco- epidemiological studies are seldom reported from these regions. In particular, most previously published data on ticks in Ethiopia focus on species distribution, and only a few molecular studies on the occurrence of tick-borne pathogens or on ecological factors influencing these. The present study was undertaken to evaluate, if ticks collected from cattle in different Ethiopian Biotopes harbour (had access to) different pathogens. Methods: In South-Western Ethiopia 1032 hard ticks were removed from cattle grazing in three kinds of tick Biotopes. DNA was individually extracted from one specimen of both sexes of each tick species per cattle. These samples were molecularly analysed for the presence of tick-borne pathogens. Results: Amblyomma variegatum was significantly more abundant on mid highland, than on moist highland. Rhipicephalus decoloratus was absent from savannah lowland, where virtually only A. cohaerens was found. In the ticks Coxiella burnetii had the highest prevalence on savannah lowland. PCR positivity to Theileria spp. did not appear to depend on the biotope, but some genotypes were unique to certain tick species. Significantly more A. variegatum specimens were rickettsia-positive, than those of other tick species. The presence of rickettsiae ( R. africae ) appeared to be associated with mid highland in case of A. variegatum and A. cohaerens . The low level of haemoplasma positivity seemed to be equally distributed among the tick species, but was restricted to one biotope type. Conclusions: The tick biotope, in which cattle are grazed, will influence not only the tick burden of these hosts, but also the spectrum of pathogens in their ticks. Thus, the presence of pathogens with alternative (non-tick-borne) transmission routes, with transstadial or with transovarial transmission by ticks appeared to be associated with the biotope type, with the tick species, or both, respectively.
Wilco C. E. P. Verberk - One of the best experts on this subject based on the ideXlab platform.
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importance of shallow water Biotopes of a caribbean bay for juvenile coral reef fishes patterns in biotope association community structure and spatial distribution
Marine Ecology Progress Series, 2000Co-Authors: Ivan Nagelkerken, Martijn Dorenbosch, Wilco C. E. P. Verberk, Cocheret E De La Moriniere, G. Van Der VeldeAbstract:Fish community structure of a non-estuarine inland bay on the Caribbean island of Curacao was determined in the mangroves, seagrass beds, algal beds, channel, fossil reef boulders, notches in fossil reef rock, and on the adjacent coral reef, using visual censuses in belt transects. Fish communities varied among Biotopes, but some overlap was present. Fish density and species richness were highest at the boulders and on the coral reef, and extremely low on the algal beds, whereas the total number of individuals calculated for the entire bay was highest on the seagrass beds. Differ- ences in fish densities between Biotopes were related to differences in structural complexity and amount of shelter. Fishes in the bay largely consisted of 17 (mainly commercially important) reef fish species, which used the bay Biotopes only as a nursery during the juvenile part of their life cycle. Small juveniles of these species were most often found in the mangroves, whereas at intermediate sizes some were found in the channel. Large individuals and adults were found on the reef, and den- sities of several of these species were higher on the reef near the bay than on reefs located farther down-current. Fishes which spent their entire life cycles in either the bay or on the coral reef were also found, and the latter group showed a strong decrease in abundance with increasing distance into the bay. The density distribution of individual fish species was not homogeneous within the bay. In the mangroves and seagrass beds, spatial distribution of fishes was correlated with distance to the mouth of the bay, water transparency, amount of shelter, and the structural complexity of the biotope. Juveniles of 3 reef species showed an increase in size on the seagrass beds with distance from the mouth into the bay, whereas 1 bay species showed a decrease in size with this distance.
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Day-night shifts of fishes between shallow-water Biotopes of a Caribbean bay, with emphasis on the nocturnal feeding of Haemulidae and Lutjanidae
Marine Ecology Progress Series, 2000Co-Authors: Ivan Nagelkerken, Martijn Dorenbosch, Wilco C. E. P. Verberk, E. Cocheret De La Morinière, G. Van Der VeldeAbstract:Day-night changes in fish communities were quantified in 6 associated shallow-water Biotopes within a single bay: mangroves, seagrass beds, algal beds, channel, fossil reef boulders, and notches in fossil reef rock. All Biotopes, except the algal beds, showed a strong reduction in fish density and species richness at night, caused by absence of diurnally active fishes and migrations of Haemulidae and Lutjanidae to the seagrass beds. The fish fauna of the different Biotopes showed a relatively high dissimilarity between day and night. This dissimilarity is largely caused by absence of Acanthuridae, Chaetodontidae, Labridae, Pomacentridae, Scaridae and Sparidae at night. These fishes seek shelter at night in, amongst others, the channel, notches and boulders. The balloonfish Diodon holocanthus utilised almost all Biotopes as shelter as well as feeding sites. The wide distribution of its preferred food (molluscs) probably explains its distribution in most Biotopes at night. The nocturnally active Haemulidae and Lutjanidae, on the other hand, migrated from their daytime shelter sites to the seagrass beds at night to feed. Some of these fishes also migrated to the algal beds to feed. The preference of Haemulidae and Lutjanidae for the seagrass bed as a feeding biotope, instead of other bay Biotopes, appears to be related to the relatively high availability of their preferred food (Tanaidacea and Decapoda) as determined by digestive tract analysis. Other bay Biotopes showed much lower densities of such food items compared to the seagrass beds.