Search

Metabarcoding of DNA extracted from community samples of whole organisms (whole organism community DNA, wocDNA) is increasingly being applied to terrestrial, marine and freshwater metazoan communities to provide rapid, accurate and high resolution data for novel molecular ecology research. The growth of this field has been accompanied by considerable development that builds on microbial metabarcoding methods to develop appropriate and efficient sampling and laboratory protocols for whole organism metazoan communities. However, considerably less attention has focused on ensuring bioinformatic methods are adapted and applied comprehensively in wocDNA metabarcoding. In this study we examined over 600 papers and identified 111 studies that performed COI metabarcoding of wocDNA. We then systematically reviewed the bioinformatic methods employed by these papers to identify the state-of-the-art. Our results show that the increasing use of wocDNA COI metabarcoding for metazoan diversity is characterised by a clear absence of bioinformatic harmonisation, and the temporal trends show little change in this situation. The reviewed literature showed (i) high heterogeneity across pipelines, tasks and tools used, (ii) limited or no adaptation of bioinformatic procedures to the nature of the COI fragment, and (iii) a worrying underreporting of tasks, software and parameters. Based upon these findings we propose a set of recommendations that we think the wocDNA metabarcoding community should consider to ensure that bioinformatic methods are appropriate, comprehensive and comparable. We believe that adhering to these recommendations will improve the long-term integrative potential of wocDNA COI metabarcoding for biodiversity science.

Plants interact with many organisms around them, and one of the most important groups that a plant has to deal with, are the herbivores. Insects represent the most diverse group of herbivores and have many different ways of using the plant as a food source. Plants can, however, defend themselves against those herbivores, either by constitutive defences, or by traits that are induced upon herbivory. These traits, such as the formation of more trichomes or the production of secondary metabolites, can deter an insect herbivore in its decision to eat from the plant, can be toxic, or otherwise hamper the insect to feed, grow or reproduce. The way a plant responds to herbivory is very specific, depending on the feeding mode or the species of the attacking insect. Furthermore, plant responses to dual herbivory differ from the sum of responses to each herbivore alone. Also the time and order at which multiple insects arrive on a plant, influence the plant’s response. Finally, plant species or populations can show different responses to herbivory. Altogether these factors result in a plant phenotype that the attacking herbivore has to deal with. In addition to the attacker, also subsequently arriving insects will be affected by a change in plant phenotype. Because plants and insects can respond to each other in a continuous chain of interactions, an herbivore early in the season can indirectly affect the later-season community composition through the induced plant response. However, we know only little about the consequences of a dual-herbivore induced plant phenotype for subsequent feeders, and ultimately, the effects on the assembly and dynamics of an insect community as a whole. The aim of this thesis project was to study the consequences of feeding by multiple insects from the same plant, not only to a subsequent herbivore, but also to the dynamics of a whole insect community over the course of a growing season, and beyond. Furthermore, I studied how the order of herbivo

Fish generally grow several orders of magnitude between the larval and adult stage. Many ecological properties of organisms are related to body size, and hence small fish often have very different ecological roles than large conspecifics. This also implies that omnivory, the feeding on more than one trophic level by individuals of the same species, is a common phenomenon in fish. Intraguild predation is omnivory in its simplest form, where two species compete for the same resource, but one of the species can also eat its competitor. In models, persistence of both species in such a configuration is difficult to obtain. In marine fish communities however, it is observed routinely. One way in which persistence of omnivorous species can be established is by incorporating it as an ontogenetic diet shift, where small individuals of both species compete, and large individuals of one can feed on the small individuals of the others species. We show in this study that this mechanism can not only lead to persistence of a single omnivorous species, but also to persistence of multiple omnivorous species. This is possible given that the adults have sufficiently different diets. It is shown that, while adults of both species can feed both on small competitors or on the basic resource, due to the population dynamical feedback, one species will in practice act as a predator, while the other acts as prey. This way, a system with two omnivores in practice persists as a tritrophic system. Which of the species assumes which role depends on the specific community characteristics. We show here that by incorporating complex size-dependent feeding relationships in food webs, many more species may be able to coexist than is possible based on either species-level considerations or size spectrum models which do incorporate within-population size differences, but relate diet only to individual body size irrespective of species identity. The mechanism underlying our result may be part of the exp

Ng, Ka Yan., "November 2009.", Thesis (M.Phil.)--Chinese University of Hong Kong, 2010., Includes bibliographical references (leaves 329-399)., s in English and Chinese., Acknowledgements --- p.i, (English) --- p.iv, (Chinese) --- p.ix, Contents --- p.xii, List of Tables --- p.xix, List of Figures --- p.xxi, Chapter Chapter 1 --- General Introduction, Chapter 1.1 --- Seaweeds as Beneficial Resources to Humans --- p.1, Chapter 1.2 --- Seaweed Communities as a Habitat --- p.5, Chapter 1.2.1 --- Reasons for being a Favourable Habitat in the Ocean ´Ø and the Coastal Region --- p.5, Chapter 1.2.2 --- Characteristics of Seagrass Habitat and its Associated Faunal Communities --- p.8, Chapter 1.2.3 --- Characteristics of Seaweed Habitat and its Associated Faunal Communities --- p.9, Chapter 1.2.3.1 --- Seasonality --- p.9, Chapter 1.2.3.2 --- Structural Complexity --- p.10, Chapter 1.2.3.3 --- Canopy Effect on Biota --- p.10, Chapter 1.3 --- Marine Environment and Sargassum Communities in Hong Kong --- p.11, Chapter 1.4 --- Study Organism: the Sargassum siliquastrum --- p.14, Chapter 1.5 --- Study Significance and Objectives --- p.16, Chapter 1.6 --- Study Sites --- p.18, Chapter 1.7 --- Thesis Organization --- p.21, Chapter Chapter 2 --- Zooplankton Assemblage in Seaweed Bed of Sargassum siliquastrum and Its Temporal Variation, Chapter 2.1 --- Introduction --- p.27, Chapter 2.2 --- Materials and Methods --- p.34, Chapter 2.2.1 --- Sample collection --- p.34, Chapter 2.2.2 --- Data acquisition --- p.36, Chapter 2.2.3 --- Data analysis --- p.37, Chapter 2.3 --- Results --- p.39, Chapter 2.3.1 --- Temporal Change in Zooplankton Assemblage Composition --- p.39, Chapter 2.3.1.1 --- Change in Zooplankton Abundance with Time --- p.43, Chapter 2.3.1.2 --- Temporal Change in Zooplankton Species Composition --- p.44, Chapter 2.3.2 --- Effects of Vegetation on Zooplankton Assemblage Structure --- p.47, Chapter 2.3.2.1 --- Comparison between Vegetated and Unvegetated Habitats in terms of Zooplankton Community Structure --- p.47, Chapter 2.3.2.2 --- Comparison between Vegetated and Unvegetated Habitats in terms of Zooplankton Abundance --- p.50, Chapter 2.3.2.3 --- Comparison between Vegetated and Unvegetated Habitats in terms of Zooplankton Species Composition --- p.51, Chapter 2.3.3 --- Temporal Trends of Environmental Factors and their Relationship with Zooplankton Assemblage --- p.58, Chapter 2.3.4 --- Relationship between Zooplankton Assemblage and Seaweed Phenology --- p.59, Chapter 2.4 --- Discussion --- p.61, Chapter 2.4.1 --- Macro-distribution Pattern and Temporal Change in Zooplankton Assemblage Structure in Sargassum siliquastrum Bed --- p.61, Chapter 2.4.2 --- Effects of Vegetation on the Micro-distribution of Zooplankton within and between Habitats ´ؤ Relationship between Sargassum Phenology and the associated Zooplankton Assemblage Structure --- p.66, Chapter 2.4.3 --- Species Composition of Zooplankton Assemblage in Seaweed Bed of Sargassum siliquastrum and its Potential Role as Nursery Ground for Fishery Resources --- p.70, Chapter 2.5 --- Summary and Conclusion --- p.74, Chapter Chapter 3 --- Effects of Seaweed Canopy on the Structure of Zooplankton Assemblage in the Sargassum siliquastrum Bed, Chapter 3.1 --- Introduction --- p.118, Chapter 3.2 --- Materials and Methods --- p.121, Chapter 3.2.1 --- Sample collection --- p.121, Chapter 3.2.2 --- Data acquisition --- p.122, Chapter 3.2.3 --- Data analysis --- p.123, Chapter 3.3 --- Results --- p.125, Chapter 3.3.1 --- Effects of Canopy on Zooplankton Community Structure --- p.125, Chapter 3.3.2 --- "Comparison between Control, Treatment and Unvegetated Habitats in terms of Zooplankton Abundance and Its Temporal Variation" --- p.127, Chapter 3.3.3 --- "Comparison between Control, Treatment and Unvegetated Habitats in terms of Zooplankton Species Composition and Its Temporal Variation" --- p.128, Chapter 3.4 --- Discussion --- p.134, Chapter 3.4.1 --- Effects of Canopy Removal on the Zooplankton Assemblage Structure --- p.134, Chapter 3.4.2 --- Role of Seaweed Canopy in Zooplankton Community and the Potential Impacts of Canopy Removal on the Coastal Ecosystem --- p.137, Chapter 3.5 --- Summary and Conclusion --- p.141, Chapter Chapter 4 --- Epiphytic Faunal Assemblages in Seaweed Bed of Sargassum siliquastrum and its Temporal Variation, Chapter 4.1 --- Introduction --- p.153, Chapter 4.2 --- Materials and Methods --- p.161, Chapter 4.2.1 --- Sample collection --- p.161, Chapter 4.2.2 --- Data acquisition --- p.162, Chapter 4.2.3 --- Data analysis --- p.163, Chapter 4.3 --- Results --- p.165, Chapter 4.3.1 --- Temporal Change in Epiphytic Faunal Assemblage Composition and Comparison among Sites --- p.165, Chapter 4.3.1.1 --- Temporal Change in Epiphytic Faunal Density and Comparison among Sites --- p.171, Chapter 4.3.1.2 --- Temporal Change in Epiphytic Faunal Species Richness and Comparison among Sites --- p.172, Chapter 4.3.1.3 --- Temporal Change in Epiphytic Faunal Species Composition --- p.175, Chapter 4.3.1.4 --- Occurrence of Caprellidean and Its Variation with Seaweed Growth Stages --- p.179, Chapter 4.3.2 --- Temporal Trends of Environmental Factors and their Relationship with Epiphytic Faunal Assemblage --- p.179, Chapter 4.4 --- Discussion --- p.181, Chapter 4.4.1 --- Temporal Change in Epiphytic Faunal Assemblage Structure --- p.181, Chapter 4.4.2 --- Species Composition of Epiphytic Faunal Assemblage in Seaweed Bed of Sargassum siliquastrum and Its Potential Role as Nursery Grounds --- p.191, Chapter 4.4.3 --- Distribution of Epiphytic Fauna in Seaweed Bed of Sargassum siliquastrum among Different Localities --- p.196, Chapter 4.4.4 --- Relationship of Epiphytic Faunal Assemblage with Environmental Factors --- p.197, Chapter 4.5 --- Summary and Conclusion --- p.198, Chapter Chapter 5 --- Relationship of Epiphytic Faunal Assemblage with the Structural Complexity of Seaweed Sargassum siliquastrum, Chapter 5.1 --- Introduction --- p.234, Chapter 5.2 --- Materials and Methods --- p.239, Chapter 5.2.1 --- Sample collection --- p.239, Chapter 5.2.2 --- Data acquisition --- p.241, Chapter 5.2.3 --- Data analysis --- p.243, Chapter 5.3 --- Results --- p.245, Chapter 5.3.1 --- Effects of Macroalgal Structural Complexity on the Associated Epiphytic Faunal Assemblage Structure --- p.245, Chapter 5.3.1.1 --- Effects on Epiphytic Faunal Abundance --- p.245, Chapter 5.3.1.2 --- Effects on Epiphytic Faunal Species Richness --- p.247, Chapter 5.3.1.3 --- Relationship among Parameters of Sargassum siliquastrum --- p.248, Chapter 5.3.2 --- Within-plant Zonation of Epiphytic Faunal Assemblage Structure --- p.249, Chapter 5.3.2.1 --- Within-plant Distribution of Epiphytic Faunal Density --- p.250, Chapter 5.3.2.2 --- Within-plant Distribution of Epiphytic Species Richness --- p.252, Chapter 5.3.2.3 --- Within-plant Distribution of Epiphytic Faunal Species Composition --- p.253, Chapter 5.3.2.4 --- Physical Parameters Associated with Each Zone of Sargassum siliquastrum --- p.257, Chapter 5.4 --- Discussion --- p.260, Chapter 5.4.1 --- Effects of Macroalgal Structural Complexity and Biomass on the Associated Epiphytic Faunal Assemblage Structure --- p.260, Chapter 5.4.2 --- Within-plant Zonation of Epiphytic Faunal Assemblage Structure --- p.264, Chapter 5.5 --- Summary and Conclusion --- p.273, Chapter Chapter 6 --- Synthesis and Perspectives --- p.320, References --- p.329, http://library.cuhk.edu.hk/record=b5896613, Use of this resource is governed by the terms and conditions of the Creative Commons “Attribution-NonCommercial-NoDerivatives 4.0 International” License (http://creativecommons.org/licenses/by-nc-nd/4.0/)

Terrestrial Species Assessments, Region 6 Forest Plan Revisions

Om meer informatie te verkrijgen over de habitat van larven van de Beekrombout in de Roer is de rivier op vier locaties in de periode 2006-2009 jaarlijks op larven geïnventariseerd. Hieruit blijkt dat een kleinschalige afwisseling van fijnkorrelige substraten en detritus belangrijk is voor het larvenhabitat. Verder blijkt ook dat in de Roer het grootste deel van de larven in het voorjaar na de derde overwintering uitsluipen, hetgeen ook in de rest van Noordwest- Europa het meest gebruikelijk is.

In het park Paradiso, bij de abdij van Cambron in het Belgische dorp Cambron-Casteau, leven duizenden vogelachtigen, afkomstig uit alle windstreken en werelddelen

Het belang van ruigten voor de soort, een aantal van deze soorten is aan een opmerkelijke areaalsuitbreiding bezig

The objectives of this workpackage are to synthesise the available data on the effects of gamebird management and hunting on biodiversity. In particular, the objectives of WP2 are to review available information on the effect of habitat management and species management (reinforcement of gamebird populations, predator control) on gamebird populations and on species other than gamebirds., Additionally, in order to evaluate whether quantitative estimates of the impact of hunting practices on biodiversity are currently possible at any scale, we review the available information on the extent of the implementation of the main management practices in each country/area. In particular, we review and discuss levels of implementation of different measures of habitat management, predator control, and restocking.

Spoorwegen als leefgebied voor bedreigde diersoorten zoals reptielen en amphibieën

Het project Zandmaas / Maasroute is een megaproject waarbij de Maas van Maastricht tot s'Hertogenbosch wordt aangepast om de kans op overstromingen in de toekomst te verkleinen. De methodiek en de effecten van de ingreep zijn uiteengezet

De huidige stand van het onderzoek waarbij de soorten uit het Kunrader en Maastrichts Krijt zijn behandeld

Geconcludeerd wordt dat het natuurgebied De Meinweg mogelijk de grootste diversiteit binnen de oppervlakte- en waterwantsen in Nederland heeft. De methode van onderzoek en de resultaten zijn behandeld

Stand van zaken, knelpunten en bedreigingen m.b.t. het voorkomen van ringslangpopulaties, potentiele leefgebieden en de belangrijkste verbindingszones in Flevoland en de Noordoostpolder. Flevoland heeft de potentie om de drie geisoleerde metapopulaties (Friesland-Overijssel, Gooi-Amsterdam en Veluwe) met elkaar te verbinden. Landschapsbeheer Flevoland is daarom twee jaar geleden gestart met het project 'Ringslang in het Kruiswater'

De ontdekking van een vierde soort van het zee-egel geslacht

Umbra pygmaea werd omstreeks 1900 in Nederland geintroduceerd. Het vermoeden bestaat dat deze vissoort in Noord-Brabant is uitgezet, gezien de Valkenswaardse visvijvers van de voormalige Heidemaatschappij

De in de jaren zeventig uit Nederland verdwenen dagvlinders Pimpernelblauwtje (Maculinea teleius) en Donker pimpernelblauwtje (Maculinea nausithous) zijn succesvol geherintroduceerd in het natuurreservaat "De Moerputten" bij Den Bosch. Om verdere verspreiding mogelijk te maken is een aangepast natuur- en bermbeheer in de wijdere omgeving noodzakelijk, waardoor ruigtezones ontstaan waarin waardmieren zich kunnen vestigen, gevolgd door kolonisatie van de vlinders

Lange tijd was de noordse woelmuis de enige woelmuissoort op Texel, maar na de komst van de aardmuis in de jaren 80, blijkt er recent ook een populatie van de rosse woelmuis geintroduceerd te zijn. Deze snelle ontwikkelingen kunnen een bedreiging vormen voor de Texelse noordse woelmuis

Er wordt geconcludeerd dat in het Gulpens Krijt en omgeving drie soorten Echinogalerus voorkomen, met name E. belgicus, E. pusillus en E. galerus sp.

Enige gegevens over levenswijze, voortplanting en onderzoek van deze vleermuis-soort

Interview met veldbiologe over de dispersie (wegtrekken uit het geboortegebied) en populatiedynamiek van de eekhoorn (Sciurus vulgaris) in sterk versnipperde bosgebieden

by Tam Tze Wai., Thesis (M.Phil.)--Chinese University of Hong Kong, 1998., Includes bibliographical references (leaves 107-114)., also in Chinese., p.i, ACKNOWLEDGEMENTS --- p.v, TABLE OF CONTENTS --- p.vi, LIST OF TABLES --- p.viii, LIST OF FIGURES --- p.ix, Chapter CHAPTER1 --- INTRODUCTION, Chapter 1.1 --- Modelling the Dynamics of a Coral Community --- p.1, Chapter 1.2 --- New Paradigm in Understanding Complex System --- p.2, Chapter 1.3 --- Ecological Models under the New Paradigm --- p.3, Chapter 1.4 --- Hong Kong Marine Environment and Its Degradation --- p.6, Chapter 1.5 --- Objectives of the Present Study --- p.8, Chapter CHAPTER2 --- FIELD STUDIES OF A CORAL COMMUNITY IN HONG KONG, Chapter 2.1 --- Introduction --- p.9, Chapter 2.2 --- Study Area --- p.10, Chapter 2.3 --- Materials and Methods --- p.12, Chapter 2.3.1 --- Preliminary Study of the Coral Cover and Diversity, Chapter 2.3.2 --- Extensive Study of the Coral Cover and Diversity, Chapter 2.3.3 --- Relative Abundance and Species Diversity, Chapter 2.4 --- Results and Discussion --- p.14, Chapter 2.4.1 --- Preliminary Study, Chapter 2.4.2 --- Extensive Study, Chapter CHAPTER3 --- COMPUTER SIMULATION OF A CORAL COMMUNITY, Chapter 3.1 --- Introduction --- p.40, Chapter 3.2 --- Object-oriented Programming (OOP) --- p.42, Chapter 3.2.1 --- Objects, Chapter 3.2.2 --- "Classes, Hierarchies and Inheritance", Chapter 3.2.3 --- Object-oriented Simulation, Chapter 3.3 --- Object-oriented Simulation of a Five-Coral Community --- p.46, Chapter 3.3.1 --- Class BenthicEnvir, Chapter 3.3.2 --- Class Coral, Chapter 3.3.3 --- The Objects Behaviour, Chapter 3.3.4 --- The Simulation, Chapter 3.3.5 --- Diversity Index and Statistical Analysis, Chapter 3.4 --- Results and Discussion --- p.66, Chapter 3.4.1 --- Growing Behaviour of the Corals, Chapter 3.4.2 --- Dynamical Behaviour of the Coral Community in Simulation without Disturbance, Chapter 3.4.3 --- Dynamical Behaviour of the Simulated Coral Community with Disturbance, Chapter 3.4.4 --- Utility of the Object-oriented Model, Chapter CHAPTER4 --- GENERAL DISCUSSION, Chapter 4.1 --- Mechanisms Structuring a Coral Community --- p.94, Chapter 4.2 --- Comparison between Field Studies and the Computer Model, Chapter 4.3 --- Utilities and Limitations of the Present Model, REFERENCES --- p.107, APPENDIX --- p.115, http://library.cuhk.edu.hk/record=b5889742, Use of this resource is governed by the terms and conditions of the Creative Commons “Attribution-NonCommercial-NoDerivatives 4.0 International” License (http://creativecommons.org/licenses/by-nc-nd/4.0/)

Travelling routes and foraging areas of many bat species are mainly along edge habitats, such as treelines, hedgerows, forest edges, and canal banks. This thesis deals with the effects of density, configuration, and structural features of edge habitats on the occurrence of bats. Four hypothetical functions of edge habitats for bats were studied: foraging areas, shelter from wind, shelter from avian predators, and acoustical landmarks.Both wind and food abundance were found to affect the occurrence of foraging pipistrelle bats, Pipistrellus pipistrellus, near treelines. Feeding activity of pipistrelle bats was positively related to height, width and foliage density of treelines. The preference by pipistrelle bats of commuting routes leading from the roost to foraging areas was explained by the distribution of potentially good feeding sites at close distance from the roost.The results stress the importance of wind protected areas where bats can feed during windy conditions. Predator avoidance is argued to be a constraint on the movements of commuting bats at relatively high light levels, i.e. at dusk and dawn. Indications that vertical landscape elements play a role in the navigation by bats as acoustical landmarks come from a study where pond bats, Myotis dasycneme, commuting over canals gradually adapted their pulse emissions to the distance to the banks. Practical guidelines are provided to implement the results into the planning, conservation, and management of edge habitats for bats.

Ingegaan wordt op de levenswijze, verspreiding en recente waarnemingen van de Neushoornkever