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11 - Fungi
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- By R. Watling, M. Fasham, Principal Consultant RPS Group plc, D. Dobson
- Edited by David Hill, RPS Group plc, UK, Matthew Fasham, RPS Group plc, UK, Graham Tucker, Ecological Solutions, UK, Michael Shewry, Scottish Natural Heritage, Philip Shaw, Scottish Natural Heritage
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Summary
The groups of fungi covered in this section are restricted to the macromycetes. This is not a precise taxonomic definition (it generally includes the basidiomycetes minus rusts, smuts and yeasts with some ascomycetes and myxomycetes), but it is convenient and commonly used (Watling, 1995). Although this grouping generally applies to the mushrooms and toadstools (correctly termed agarics), polypores and their relatives and jelly fungi, a few prominent ascomycetes such as the earth tongues, truffles and their allies are included. This grouping contains three different categories of fungi based on life strategy: biotrophs, which include basidiolichens and mycorrhizal species; saprotrophs, which include litter and wood rotters; and the necrotrophs or parasites. An informed biological approach should always be considered when dealing with members of each category. For example, a wood rotter may be restricted to a single tree trunk, whereas an ectomycorrhizal fungus may be associated with a widely spreading mycelial system that covers several square metres.
The survey and monitoring of fungi presents some difficulties that need to be taken into consideration when designing a monitoring strategy. Surveying for presence or absence of macromycetes depends upon the appearance of the fruiting body (sporome). The number of fruiting bodies is considered to reflect the health and spatial extent of a fungal colony, although there is little scientific evidence to support this. Sporome appearance is influenced by a number of environmental factors including temperature, amount and timing of rainfall, soil pH and nutrient status, and successional patterns of surrounding vegetation.
26 - Other mammals
- Edited by David Hill, RPS Group plc, UK, Matthew Fasham, RPS Group plc, UK, Graham Tucker, Ecological Solutions, UK, Michael Shewry, Scottish Natural Heritage, Philip Shaw, Scottish Natural Heritage
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Summary
There is a wide variety of methods for surveying and monitoring mammal species. Given that mammal species range in size from mice to whales, the techniques will vary considerably from one species to the next. Methods can be divided into indirect methods (Sections 26.3.1–26.3.5), which involve counting signs of presence rather than the animals themselves, and direct methods (Sections 26.4.1–26.4.4).
ATTRIBUTES FOR ASSESSING CONDITION
Population size
Many mammal species are secretive and make effective use of cover; this makes direct counts, even of small sample populations, impossible. However, larger mammals, such as Red Deer Cervus elaphus occupying open ranges, can be effectively counted by direct counts. Estimates of population size for the majority of small and medium-sized mammals depend on indirect methods, such as indices of evidence left by mammals or trapping. Population reconstructions can be made from knowledge of the age at death of animals dying naturally or being culled, if a large proportion of the dead animals are available.
Breeding success and condition
Breeding success is particularly time-consuming to evaluate in mammals as it requires location of a sample of breeding sites and direct observation of young at these sites. Observer bias is also an important issue here as disturbance around a breeding site may attract predators.
Alternatively, breeding status can be evaluated by examining trapped females. In most mammals, from large to small, lactation is easily diagnosed and breeding condition can be established from examining the vulva, or taking vaginal smears for signs of oestrus.
Contents
- Edited by David Hill, RPS Group plc, UK, Matthew Fasham, RPS Group plc, UK, Graham Tucker, Ecological Solutions, UK, Michael Shewry, Scottish Natural Heritage, Philip Shaw, Scottish Natural Heritage
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2 - Planning a programme
- Edited by David Hill, RPS Group plc, UK, Matthew Fasham, RPS Group plc, UK, Graham Tucker, Ecological Solutions, UK, Michael Shewry, Scottish Natural Heritage, Philip Shaw, Scottish Natural Heritage
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The major steps involved in planning and executing a monitoring programme are illustrated in Figure 2.1. Many of the aspects are relevant to planning and executing a survey. A list of key considerations that must be addressed when planning a monitoring programme is given in Box 2.1 with the relevant section numbers. All of these issues should be carefully considered in a step-by-step process before any fieldwork is started.
SETTING THE OBJECTIVES FOR THE MONITORING PROGRAMME
Clearly and explicitly defining your objectives is probably the most important single step of any monitoring programme. Failure to do somay render any results gained inappropriate to the question you wished to address, and therefore useless. Carefully defining your objectives will also allow you to select the most appropriate methodology. In particular it is essential that you ask yourself: What do I really need to know? The process of defining objectives underpins good sitemanagement principles and the development of management plans (see, for example, CCW, 1996) of which monitoring should be an integral part (Figure 1.1). Guidance on establishing clearly defined objectives is provided below.
What features of conservation interest are to be monitored?
The first step in defining the objectives of any ecological monitoring programme must be the identification of features of interest on the site. Biological features may be habitats, species or species assemblages.
Appendix 5 - The relocation of permanent plots
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- By David Hill, Director of Ecology RPS Group plc, Matthew Fasham, Principal Consultant RPS Group plc, Graham Tucker, Freelance Ecologist, Michael Shewry, Environmental Statistician, Philip Shaw, Environmental Audit Specialist
- Edited by David Hill, RPS Group plc, UK, Matthew Fasham, RPS Group plc, UK, Graham Tucker, Ecological Solutions, UK, Michael Shewry, Scottish Natural Heritage, Philip Shaw, Scottish Natural Heritage
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Various techniques (e.g. quadrats and transects) have been used to mark permanent plots; these are described briefly below. A general point to consider is that the more techniques used, the quicker it will normally be to find plots again.
MAPPING
Measurements to nearby features have been widely used to map locations of plots and are relatively foolproof, provided that mapping is accurate (use a backsighting compass for bearings and measure distances correctly) and that the features chosen are fixed and permanent. This is particularly important for long-term monitoring studies; features such as fence posts may be damaged or lost over time. However, the method is often difficult to apply in large homogeneous habitats, such as grasslands, where obvious permanent features are lacking. It is also time-consuming when a large number of plots need to be relocated.
MARKER POSTS
Wooden or metal posts are widely used and can be quick to re-find in relatively small sites. However, small markers can be hidden by vegetation. Large markers can cause significant damage to habitats, tend to be unsightly and attract the attention of people. Animals too may scratch against large markers, thereby causing disproportionate disturbance to vegetation, resulting in bias in the sampling. Unless markers are strong and well secured they may be broken by livestock or removed by vandals, etc. Posts may also be lost over time through rotting or corrosion and even frost heave.
PAINT
Paint has been used to mark plots, especially where rocks, walls or posts are available nearby.
Glossary
- Edited by David Hill, RPS Group plc, UK, Matthew Fasham, RPS Group plc, UK, Graham Tucker, Ecological Solutions, UK, Michael Shewry, Scottish Natural Heritage, Philip Shaw, Scottish Natural Heritage
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4 - Introduction to habitat evaluation
- Edited by David Hill, RPS Group plc, UK, Matthew Fasham, RPS Group plc, UK, Graham Tucker, Ecological Solutions, UK, Michael Shewry, Scottish Natural Heritage, Philip Shaw, Scottish Natural Heritage
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HOW TO USE THE HANDBOOK A RECAP
Part II of the Handbook is intended as a general-purpose source of detailed, practical information on study design, sampling and analysis as well as on the most commonly used methods for surveying and monitoring terrestrial and freshwater habitats.
The development and successful implementation of a survey and monitoring programme involves making a series of crucial decisions. Part II of the Handbook is therefore designed to provide a step-by-step guide through the process of planning and executing a survey and monitoring programme. However, the design and implementation of a programme is not a linear process, but often involves iterative steps that depend on the outcome of other decisions. Because monitoring is largely defined by a series of surveys, the term ‘survey’ is usually also implied where the term ‘monitoring’ is used throughout this Handbook. The main topics covered in Part II are listed below.
HABITAT SURVEY AND MONITORING
This chapter identifies the attributes of major habitat types that provide an indication of their condition. These should be the focus of habitat condition monitoring programmes. For each habitat a summary table lists these attributes and provides cross-references to descriptions of the recommended methods for monitoring them (provided in Chapter 5). Reference should also be made to generic guidelines on defining Condition Objectives for statutory sites that are being developed by the UK conservation agencies (visit their websites for latest information).
Appendix 4 - Determining appropriate quadrat size for vegetation sampling
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- By David Hill, Director of Ecology RPS Group plc, Matthew Fasham, Principal Consultant RPS Group plc, Graham Tucker, Freelance Ecologist, Michael Shewry, Environmental Statistician, Philip Shaw, Environmental Audit Specialist
- Edited by David Hill, RPS Group plc, UK, Matthew Fasham, RPS Group plc, UK, Graham Tucker, Ecological Solutions, UK, Michael Shewry, Scottish Natural Heritage, Philip Shaw, Scottish Natural Heritage
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The size of a quadrat affects the measured values of frequency, density, and cover, etc. (see Figure A4.1 below). It is therefore important to decide in advance which values are to be measured. Experience has shown that different vegetation types and different measurement types require different quadrat sizes. In Part II, quadrat methods for habitat monitoring are described in Sections 6.4.2 (frame quadrats for cover and density estimates); 6.4.3 (random mini-quadrats for frequency estimates); 6.4.4 (FIBS analysis); and 6.4.5 (point quadrats). Quadrat size is also considered in the section on NVC mapping (Section 6.1.6). In Part III, the chapters on species groups and Chapter 10 also contain discussions of quadrat methods, where appropriate to the species group concerned.
This appendix deals with the selection of the appropriate quadrat size. Methods for calculating the number of quadrats required are given in Part I, Section 2.3.4. Frequency estimates are given the most attention, because quadrat size affects frequency measures more than others (see Figure A4.1). However, the lists of optimum quadrat size for different vegetation types can generally be applied to all quadrat sampling methods (with the obvious exception of point quadrats).
Techniques for determining optimum quadrat size for frequency measures are subjective, and a quadrat of any size will sample some species more adequately than others. The quadrat size chosen will therefore depend upon the type of vegetation being sampled. The use of random mini-quadrats for estimating frequency is described in Part II, Section 6.4.3.
References
- Edited by David Hill, RPS Group plc, UK, Matthew Fasham, RPS Group plc, UK, Graham Tucker, Ecological Solutions, UK, Michael Shewry, Scottish Natural Heritage, Philip Shaw, Scottish Natural Heritage
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13 - Bryophytes
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- By G. Rothero, D. Dobson, M. Fasham, Principal Consultant RPS Group plc
- Edited by David Hill, RPS Group plc, UK, Matthew Fasham, RPS Group plc, UK, Graham Tucker, Ecological Solutions, UK, Michael Shewry, Scottish Natural Heritage, Philip Shaw, Scottish Natural Heritage
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Surveying and monitoring bryophytes poses considerable problems. Most are so small and difficult to identify that anything other than qualitative or at best semi-quantitative data is time-consuming and expensive to acquire. Some species are difficult to identify even for specialists, and some always require confirmation with a microscope. Working with bryophytes takes longer than working with most vascular plants. Many species grow in association with other species, and trying to quantify the amount of a target species can easily cause considerable damage to the habitat.
There are very few published studies on surveying and monitoring bryophytes in Britain. Most monitoring has consisted of merely checking that species are still present, with only limited attempts at recording population size.
A feature of some bryophytes is that they may be strongly associated with other plant species. This is obviously true with epiphytic species (e.g. Orthotrichum obtusifolium, which only occurs on trees with nutrient-rich bark) or Jamiesonella undulifolia, which is restricted to Sphagnum hummocks.
ATTRIBUTES FOR ASSESSING CONDITION
Presence–absence
Monitoring of bryophytes has in the past concentrated upon establishing that a species of interest is still in existence on sites where it has been previously recorded. Presence–absence in a series of samples (e.g. quadrats or transects or individual host plants for epiphytic species) can be used to establish frequency and to generate broad distribution maps for target species.
Population size
Semi-quantitative or quantitative methods will involve some measurement of extent.
Part I - Planning
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- By Graham Tucker, Freelance Ecologist, Matthew Fasham, Principal Consultant RPS Group plc, David Hill, Director of Ecology RPS Group plc, Michael Shewry, Environmental Statistician, Philip Shaw, Environmental Audit Specialist, Max Wade
- Edited by David Hill, RPS Group plc, UK, Matthew Fasham, RPS Group plc, UK, Graham Tucker, Ecological Solutions, UK, Michael Shewry, Scottish Natural Heritage, Philip Shaw, Scottish Natural Heritage
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Appendix 6 - Equipment required for undertaking different types of survey
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- By David Hill, Director of Ecology RPS Group plc, Matthew Fasham, Principal Consultant RPS Group plc, Graham Tucker, Freelance Ecologist, Michael Shewry, Environmental Statistician, Philip Shaw, Environmental Audit Specialist
- Edited by David Hill, RPS Group plc, UK, Matthew Fasham, RPS Group plc, UK, Graham Tucker, Ecological Solutions, UK, Michael Shewry, Scottish Natural Heritage, Philip Shaw, Scottish Natural Heritage
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Preface
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- By David Hill, Director of Ecology RPS Group plc, Matthew Fasham, Principal Consultant RPS Group plc, Graham Tucker, Freelance Ecologist, Michael Shewry, Environmental Statistician, Philip Shaw, Environmental Audit Specialist
- Edited by David Hill, RPS Group plc, UK, Matthew Fasham, RPS Group plc, UK, Graham Tucker, Ecological Solutions, UK, Michael Shewry, Scottish Natural Heritage, Philip Shaw, Scottish Natural Heritage
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This generation is living at a time when the world's biodiversity resources have never been so impoverished. If we take the UK as an example of what has happened across many parts of the planet, since 1945, largely as a result of agricultural intensification, we have lost over 50% of our ancient lowland woodlands, 150 000 miles of hedgerow, 95% of traditional hay meadows, 80% of chalk downland and 80% of wetland fens and mires. This has given rise to massive losses in some, once very common, farmland birds: in the past 30 years 40% of Song Thrushes, 54% of Yellowhammers, a staggering 87% of Starlings and 90% of Corn Buntings have disappeared.
In addition to agricultural intensification, development pressure as a result of industrialisation, human population expansion and resultant increases in the ‘ecological footprint’ of our own species through, for example, house building, airports, seaports, road infrastructure, water supply, energy generation, waste management, freight distribution and extraction of raw materials, has taken its toll on biodiversity. The UK government's sustainable development commission recently announced that the country has a very long way to go before existing developments, and the way we manage environmental resources, can be deemed to be ‘sustainable’. This is without any consideration of the impending threat from climate change.
But it would be wrong to focus entirely on the negatives.
16 - Dragonflies and damselflies
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Dragonflies and damselflies (Odonata) have an aquatic larval stage, which can last for a few years, followed by emergence, mating and dying all in the same season. As larvae can live for long periods before pupating, an absence (or decrease) of adults in one year does not necessarily imply that the population is in decline. Several years of negative results are required to confirm an absence.
Surveys of Odonata can provide a useful indicator of water and habitat quality where regional differences in diversity are taken into account. This is one reason why they are a useful group to survey as part of EIA studies.
Monitoring areas of suitable habitat may be appropriate, particularly if resources are not available for more detailed survey methods. Monitoring of micro-habitats is not specifically covered in this Handbook. However, some of the techniques in Part II may be adapted for this purpose.
ATTRIBUTES FOR ASSESSING CONDITION
Population range
Area of occupancy is an important attribute to monitor and can be best assessed by mapping presence – absence in suitable micro-habitats. Note that presence in the only pond in a 100 ha site gives 100% occupancy, even though most of the site lacks the species. At the same time, a presence in 50 ponds in the same area is only 50% occupancy if there are 100 ponds. Area of occupancy must therefore be defined in terms of the area of suitable micro-habitat occupied. Repeat surveys will illustrate expansions or contractions of range.
3 - Biodiversity evaluation methods
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- By David Hill, Director of Ecology RPS Group plc, Matthew Fasham, Principal Consultant RPS Group plc, G. Tucker, Freelance Ecologist, Michael Shewry, Environmental statistician Scottish Natural Heritage, Philip Shaw, Environmental Audit specialist with the Advisory Services of Scottish Natural Heritage
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BIODIVERSITY VALUES AND EVALUATION PURPOSES
In general terms, biodiversity evaluation is the process of measuring the value (ideally quantitatively) of biodiversity components, such as the number of species present, the population of a species, a habitat (usually meaning a vegetation community) or the sum of all such components within a given area or site. Such evaluations may be carried out for a variety of reasons, e.g. for conservation priority setting, as part of Biodiversity Action Plan (BAP) development, for the selection of Protected Areas, for the identification of a site's features of conservation interest, as part of conservation objective setting, management planning and monitoring processes, and as part of an EIA or other statement to comply with planning procedures for a proposed development.
Evaluations may be carried out on various components of biodiversity (i.e. from genetic variation within species, to individual species, species assemblages, biotopes and biomes) and at a variety of scales, from specific sites, to counties, regions, countries, biogeographical areas (although these may be smaller than countries) and global. A wide range of potential biodiversity values may be considered, including intrinsic and socio-cultural values (Daily, 1997; Posey, 2000), and more direct socio-economic benefits (Daily, 1997), such as food, building resources, medicines and waste decomposition, etc. (Spellerberg & Hardes, 1992).
As this Handbook concentrates on site surveys and monitoring, rather than on regional- or national-scale studies, this chapter focuses on site evaluations.
22 - Amphibians
- Edited by David Hill, RPS Group plc, UK, Matthew Fasham, RPS Group plc, UK, Graham Tucker, Ecological Solutions, UK, Michael Shewry, Scottish Natural Heritage, Philip Shaw, Scottish Natural Heritage
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Amphibians have a terrestrial and an aquatic phase to their life cycle, with the larvae being exclusively aquatic until they metamorphose. Adults return to water every year to breed but spend a proportion of each year on land. Amphibians also hibernate over winter. Most surveying and population monitoring of amphibians focuses on population studies of adults at breeding sites. It is important to remember that the numbers of amphibians counted by using most methods are influenced by air and soil temperature: a cold spell may reduce activity considerably. This must be taken into account when comparing studies between years or between sites or when assessing a site as part of an EIA study.
ATTRIBUTES FOR ASSESSING CONDITION
Population size
Estimates of population size for amphibians are generally best made during the mating season, when most adults will be gathered at their breeding sites. Breeding population size can therefore be estimated for each pond, with a total estimate for an area obtained by totalling numbers from each pond. This will probably be an overestimate of population size, because movement between ponds is likely.
Breeding success
Whether or not amphibians are breeding successfully can generally be examined in two ways. First, egg searches will establish if mating has taken place and eggs have been laid. With some species, population estimates can also be made from the number of egg clusters. Second, trapping larvae at various stages of development will establish whether eggs are hatching and larvae are surviving.
Appendix 1 - Monitoring and reporting obligations under international conservation agreements
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- By David Hill, Director of Ecology RPS Group plc, Matthew Fasham, Principal Consultant RPS Group plc, Graham Tucker, Freelance Ecologist, Michael Shewry, Environmental Statistician, Philip Shaw, Environmental Audit Specialist
- Edited by David Hill, RPS Group plc, UK, Matthew Fasham, RPS Group plc, UK, Graham Tucker, Ecological Solutions, UK, Michael Shewry, Scottish Natural Heritage, Philip Shaw, Scottish Natural Heritage
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9 - Introduction to species assessment
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- By David Hill, Director of Ecology RPS Group plc, Matthew Fasham, Principal Consultant RPS Group plc, Graham Tucker, Freelance Ecologist, Michael Shewry, Environmental Statistician, Philip Shaw, Environmental Audit Specialist
- Edited by David Hill, RPS Group plc, UK, Matthew Fasham, RPS Group plc, UK, Graham Tucker, Ecological Solutions, UK, Michael Shewry, Scottish Natural Heritage, Philip Shaw, Scottish Natural Heritage
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SPECIES SURVEYING AND MONITORING
Chapter 10 of this part gives an introduction to the theory and principles of population survey and monitoring and describes the general methods used to estimate population size. These methods will often need to be tailored to suit the requirements of the species being studied; this information is provided in the sections on species groups.
Chapters 11–26 contain details of the standard methods used to survey each group of species, from fungi to mammals. Attributes that provide an indication of the condition of species in each group are identified at the start of each chapter, and methodologies for monitoring these attributes are described; references for further information are listed at the end of the book. Specific recommendations and current survey and monitoring protocols for selected species that occur in the UK and appear on Annex II of the EU Habitats and Species Directive (apart from vagrant and introduced species) are described at the ends of these chapters.
Each section contains a table summarising the methods covered. A brief summary of the following points is given:
the recommended groups for which the method is appropriate;
the type of data that the method provides (i.e. presence/absence, population size, etc.);
the efficiency of the method, i.e. the combined quantity and quality of data produced in relation to cost and effort;
the precision obtainable;
the likely nature of any inherent bias; and
advantages and disadvantages.
Each method is then described in three sections: (1) principles; (2) field methods; and (3) data analysis and interpretation.
12 - Lichens
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The principles behind lichen survey and monitoring techniques are basically identical to those for other groups of lower plants. However, there are some considerations peculiar to lichen survey and monitoring, which must be considered when designing a suitable programme.
Many species of conservation importance are very scarce; some are known from only a single site. In the case of lichens, a single site can be something as small as a single tree, a rock or a tree stump. Many species are relict, and under prevailing conditions cannot colonise new habitats. The sites themselves may be small relics of larger areas of ancient habitat with long continuity and a history of minimal adverse disturbance. Thus the necessary conditions in which the species can persist may only occur in one location or in a series of distinct fragments. By definition, a relict species cannot colonise distant sites even if conditions are suitable. The destruction of ancient, unrecreatable habitat is an important cause of lichen rarity, but far from the only one.
Other lichens rely on extremely localised habitats. For example, Gyalideopsis scotica requires decaying bryophyte material on specific soils near the summits of a few Scottish mountains. Cladonia botrytes grows on dead pine (Pinus spp.) stumps at a particular stage of decay.
Lichens may therefore require ephemeral scarce habitats or ancient scarce habitats; in either case, their habitat requirements are often very specific and any alteration of the conditions under which lichen species will grow will frequently adversely affect the health of the colony.
24 - Birds
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Birds are highly mobile; although they are relatively conspicuous and easily identified, their populations are often difficult to estimate effectively. They are, none the less, the most intensively studied species group, and a large amount of data are available on the distribution, ecology and estimated population sizes of most species. A substantial network of experienced volunteers is involved in countrywide bird monitoring programmes such as the Breeding Bird Survey and the Wetland Birds Survey, organised by the British Trust for Ornithology (BTO) in the UK (the latter in association with the Wildfowl & Wetlands Trust, WWT). In some instances it may be possible to incorporate the information provided by these programmes into a site-based monitoring scheme.
The objectives of bird population assessment need to be clearly identified at the outset. Migratory birds may be winter or summer residents, or may only appear on passage between wintering and breeding grounds. Other species are resident all year round but may show seasonal variation in numbers owing to an influx of birds from other areas during the summer or winter. Autumn populations will also include birds that have fledged in that year (many of which will not survive over winter). It is important, therefore, to be able to separate natural population cycles from underlying trends in population size. Population estimates from similar times in each year should be compared, and it may be necessary to calculate 5 or 10 year means to remove ‘noise’ from the data.