Ecological Methods

Peter A. Henderson, Director of Pisces Conservation, Southampton, UK. T. R. E. Southwood, Lecturer, Department of Zoology, University of Oxford, UK.

• Prefaces xiiiAbout the Companion Website xix1 Introduction to the Study of Animal Populations 11.1 Population estimates 21.1.1 Absolute and related estimates 21.1.2 Relative estimates 31.1.3 Population indices 41.2 Errors and confidence 4References 52 The Sampling Programme and the Measurement and Description of Dispersion 72.1 Preliminary sampling 72.1.1 Planning and fieldwork 72.1.2 Statistical aspects 102.2 The sampling programme 162.2.1 The number of samples per habitat unit (e.g. plant, host or puddle) 162.2.2 The sampling unit, its selection, size and shape 202.2.3 The number of samples 212.2.4 The pattern of sampling 242.2.5 The timing of sampling 262.3 Dispersion 272.3.1 Mathematical distributions that serve as models 282.3.2 Biological interpretation of dispersion parameters 402.3.3 Nearest-neighbour and related techniques: measures of population size or of the departure from randomness of the distribution 482.4 Sequential sampling 512.4.1 Sampling numbers 512.5 Presence or absence sampling 552.6 Sampling a fauna 572.7 Biological and other qualitative aspects of sampling 592.8 Jack knife and Bootstrap techniques 60References 623 Absolute Population Estimates Using Capture–Recapture Experiments 773.1 Capture–recapture methods 783.1.1 Assumptions common to most methods 793.1.2 Estimating closed populations 863.1.3 Estimations for open populations 933.2 Methods of marking animals 1033.2.1 Handling techniques 1053.2.2 Release 1073.2.3 Surface marks using paints and solutions of dyes 1083.2.4 Dyes and fluorescent substances in powder form 1123.2.5 Pollen 1143.2.6 Marking formed by feeding on or absorption of dyes 1143.2.7 Marking by injection, panjet or tattooing 1163.2.8 External tags 1163.2.9 Branding 1173.2.10 Mutilation 1183.2.11 Natural marks, parasites and genes 1183.2.12 Rare elements 1193.2.13 Protein marking 1203.2.14 Radioactive isotopes 1203.2.15 Radio and sonic tags 120References 1214 Absolute Population Estimates by Sampling a Unit of Habitat – Air, Plants, Plant Products and Vertebrate Hosts 1394.1 Sampling from the air 1394.2 Sampling apparatus 1404.2.1 Exposed cone (Johnson–Taylor) suction trap 1404.2.2 Enclosed cone types of suction trap including the Rothamsted 12 m trap 1414.2.3 Rotary and other traps 1434.3 Comparison and efficiencies of the different types of suction traps 1444.3.1 Conversion of catch to aerial density 1454.3.2 Conversion of density to total aerial population 1464.4 Sampling from plants 1464.4.1 Assessing the plant 1474.4.2 Determining the numbers of invertebrates 1474.4.3 The extraction of animals from herbage and debris 1554.4.4 Methods for animals in plant tissues 1634.4.5 Special sampling problems with animals in plant material 1654.5 Sampling from vertebrate hosts 1664.5.1 Sampling from living hosts 1664.5.2 Sampling from dead hosts 1694.5.3 Sampling from vertebrate ‘homes’ 170References 1715 Absolute Population Estimates by Sampling a Unit of Aquatic Habitat 1835.1 Open water 1835.1.1 Nets 1835.1.2 Pumps 1875.1.3 Water-sampling bottles 1875.1.4 The Patalas–Schindler volume sampler 1875.1.5 Particular methods for insects 1885.2 Vegetation 1905.2.1 Floating vegetation 1915.2.2 Emergent vegetation 1925.2.3 Submerged vegetation 1945.3 Bottom fauna 1955.3.1 Hand net sampling of forest litter 1965.3.2 Sampling from under stones 1975.3.3 The planting of removable portions of the substrate 1995.3.4 Cylinders and boxes for delimiting an area 2005.3.5 Trawls, bottom sledges and dredges 2015.3.6 Grabs 2055.3.7 Dendy inverting sampler 2085.3.8 Box samplers and corers 2095.3.9 Air-lift and suction devices 2115.4 Poisons and anaesthetics used for sampling fish in rock pools and small ponds 211References 2136 Absolute Population Estimates by Sampling a Unit of Soil or Litter Habitat: Extraction Techniques 2216.1 Sampling 2216.2 Bulk staining 2246.3 Mechanical methods of extraction 2246.3.1 Dry sieving 2246.3.2 Wet sieving 2256.3.3 Soil washing and flotation 2266.3.4 Flotation separation of plankton, meiofauna and other small animals 2296.3.5 Separation of plant and insects by differential wetting 2316.3.6 Centrifugation 2336.3.7 Sedimentation 2336.3.8 Elutriation 2346.3.9 Sectioning 2356.3.10 Aeration 2366.4 Behavioural or dynamic methods 2366.4.1 Dry extractors 2376.4.2 Wet extractors 2436.5 Summary of the applicability of the methods 248References 2507 Relative Methods of Population Measurement and the Derivation of Absolute Estimates 2597.1 Factors affecting the size of relative estimates 2597.1.1 The ‘phase’ of the animal 2607.1.2 The activity of the animal 2617.1.3 Differences in the response between species, sexes and individuals 2637.1.4 The efficiency of the trap or searching method 2647.2 The uses of relative methods 2667.2.1 Measures of the availability 2667.2.2 Indices of absolute population 2667.2.3 Estimates of absolute population 2677.2.4 Removal trapping or collecting 2687.2.5 Collecting 2727.3 Relative methods: catch per unit effort 2727.3.1 Observation by radar 2727.3.2 Hydroacoustic methods 2737.3.3 Fish counters 2747.3.4 Electric fishing 2747.3.5 Aural detection 2757.3.6 Exposure by plough 2767.3.7 Collecting with a net or similar device 2767.3.8 Visual searching and pooting 2797.4 Relative methods: trapping 2807.4.1 Interception traps 2817.4.2 Flight traps combining interception and attraction 2907.4.3 Light and other visual traps 2947.5 Traps that attract animals by some natural stimulus or a substitute 3047.5.1 Shelter traps 3047.5.2 Trap host plants 3057.5.3 Baited traps 3057.5.4 The use of vertebrate hosts or substitutes as bait for insects 3087.6 Using Sound 314References 3148 Estimates of Species Richness and Population Size Based on Signs, Products and Effects 3378.1 Arthropod products 3378.1.1 Exuviae 3378.1.2 Frass 3388.2 Vertebrate products and effects 3418.3 Effects due to an individual insect 3428.4 General effects: plant damage 3438.4.1 Criteria 3448.5 Determining the relationship between damage and insect populations 347References 3489 Wildlife Population Estimates by Census and Distance Measuring Techniques 3559.1 Census methods 3569.2 Point and line survey methods 3579.2.1 Indices of abundance using transects 3579.2.2 Methods based on flushing 3579.2.3 Line transect methods: the Fourier series estimator 3609.2.4 Point transects 3659.3 Distance sampling software in R 3659.4 Spatial distribution and plotless density estimators 3679.4.1 Closest individual or distance method 3679.4.2 Nearest-neighbour methods 368References 36910 Observational and Experimental Methods for the Estimation of Natality, Mortality and Dispersal 37310.1 Natality 37310.1.1 Fertility 37310.1.2 Numbers entering a stage 37510.1.3 The birth-rate from mark and recapture data 38210.2 Mortality 38210.2.1 Total 38210.2.2 The death-rate from mark and recapture data 38310.2.3 Climatic factors 38310.2.4 Biotic factors 38310.2.5 Experimental assessment of natural enemies 39010.3 Dispersal 39610.3.1 Detecting and quantifying jump dispersal 39710.3.2 Quantifying neighbourhood dispersal 39710.4 The measurement and description of home range and territory 41010.4.1 The minimum convex polygon area method for estimating home range 41110.4.2 The kernel estimation method for home range 41210.5 The rate of colonisation of a new habitat and artificial substrates 41310.6 The direction of migration 413References 41311 The Construction, Description and Analysis of Age-specific Life-tables 42911.1 Types of life-table and the budget 42911.2 The construction of a budget 43011.3 Analysis of stage-frequency data 43111.3.1 Southwood’s graphical method 43211.3.2 Richards & Waloff’s first method 43211.3.3 Manly’s method 43411.3.4 Ruesink’s method 43511.3.5 Dempster’s method 43511.3.6 Richards & Waloff’s Second Method 43611.3.7 Kiritani, Nakasuji & Manly’s method 43711.3.8 Kempton’s method 43811.3.9 The Bellows and Birley Method 43911.4 The description of budgets and life-tables 44011.4.1 Survivorship curves 44011.4.2 Stock–recruitment (Moran–Ricker) curves 44011.4.3 The life-table and life expectancy 44311.4.4 Life and fertility tables and the net reproductive rate 44411.4.5 Population growth rates 44611.4.6 The calculation of r 44811.5 The analysis of life-table data 44911.5.1 The comparison of mortality factors within a generation 44911.5.2 Survival and life budget analysis 45111.5.3 Sibley’s λ contribution analysis 458References 45912 Age-grouping, Time-specific Life-tables and Predictive Population Models 46512.1 Age-grouping 46512.2 Aging young by developmental stage 46612.3 Aging by using structures 46712.3.1 Annelids 46712.3.2 Crustaceans 46712.3.3 Insects 46712.3.4 Molluscs 47212.3.5 Fish 47312.3.6 Lampreys 47412.3.7 Reptiles and amphibians 47412.3.8 Birds 47512.3.9 Mammals 47512.4 Time-specific life-tables and survival rates 47612.4.1 Physiological time 47812.4.2 Life-table parameters 47912.4.3 Recruitment in the field 47912.4.4 Empirical models 47912.4.5 Intrinsic rate models and variable life-tables 48012.4.6 Lewis–Leslie matrices and R packages 481References 48413 Species Richness, Diversity and Packing 49513.1 Diversity 49613.1.1 Description of α- and γ-diversity 49713.1.2 Species richness 49813.1.3 Models for the S:N relationship 50513.1.4 Non-parametric indices of diversity 50913.1.5 Which model or index? 51213.1.6 Comparing communities – diversity ordering 51313.1.7 Procedure to determine α-diversity 51513.1.8 Determining β-diversity 51713.2 Similarity and the comparison and classification of samples 52013.2.1 Measures of complementarity 52113.2.2 Similarity indices 52113.2.3 Multivariate analysis 52513.3 Species packing 53013.3.1 Measurement of interspecific association 53013.3.2 Measurement of resource utilisation 53413.3.3 Niche size and competition coefficients 540References 54214 The Estimation of Productivity and the Construction of Energy Budgets 55114.1 Estimation of standing crop 55314.1.1 Measurement of biomass 55314.2 Determination of energy density 55414.3 Estimation of energy flow 55514.4 The measurement of production 55714.5 The measurement of feeding and assimilation 56014.5.1 The quality of the food eaten 56014.6 Feeding and assimilation rates 56114.6.1 Radiotracer techniques 56114.6.2 Gravimetric techniques 56314.6.3 Indicator methods 56414.6.4 Measurement of faecal output 56514.7 The measurement of the energy loss due to respiration and metabolic process 56514.7.1 Calorimetric 56514.7.2 The exchange of respiratory gases 56514.7.3 The respiratory rate 56714.8 The energy budget, efficiencies and transfer coefficients 57314.8.1 The energy budget of a population (or trophic level) 57314.8.2 Energy transfer across trophic links 57414.9 Identification of ecological pathways using stable isotopes 57614.10 Assessment of energy and time costs of strategies 577References 57815 Studies at Large Spatial, Temporal and Numerical Scales and the Classification of Habitats 58715.1 Remote sensing data from satellites 58915.2 Remote sensing using piloted and unmanned aircraft 59115.3 Long-term studies 59215.3.1 Planning spatial and temporal sampling 59315.3.2 The classification of time series 59315.3.3 Detecting synchrony 60315.3.4 Measuring temporal variability 60315.3.5 Detecting break-points 60415.4 Geographical information systems 60715.5 Detection of density dependence in time series 60815.5.1 Bulmer’s (1975) test 60815.5.2 Pollard et al.’s (1987) randomisation test 60915.5.3 Dennis and Taper’s (1994) bootstrap approach 61115.5.4 Using a battery of approaches to detect density dependence 61115.6 Citizen science projects 61315.7 Ecosystem services 61315.8 Habitat classification 61415.8.1 Qualitative 61415.8.2 Quantitative 616References 617Index 623