THE EXPLOITATION OF NATURAL ANIMAL POPULATIONS

By SARAH THOMAS

CONTENTS PART I INTRODUCTION INTRODUCTION A BRIEF HISTORY FROM REGISTER TO MANAGEMENT POPULATION MANAGEMENT TRIANGLE EXPLORING STUDBOOKS NATURAL HISTORY CENSUS LIFE TABLES GENETIC ANALYSES CONSERVATION DATA MORE TOPICS REFERENCES STUDBOOKS AND SOFTWARE STUDBOOK EXAMPLES RED CROWNED CRANE GRUS JAPONENSIS AFRICAN WILD DOG LYCAON PICTUS RED PANDA AILURUS FULGENS EUROPEAN WOLVERINE GULO GULO GULO SNOW LEOPARD UNCIA UNCIA CALIFORNIAN SEA LION ZALOPHUS CALIFORNIANUS BONGO TRAGELAPHUS EURYCERUS BLESBOK DAMALISICUS PYGARGUS PHILLIPSI SOFTWARE TOOLS POPULATION MANAGEMENT LIBRARY PART II DEMOGRAPHIC ANALYSES LIFESPAN AND LONGEVITY ESTIMATED DATES LONGEVITY PATHOLOGIST’S VIEW HISTORY AND HUSBANDRY EARLY LIFE STAGES DIFFERENCES BETWEEN SEXES REPRODUCTIVE LIFESPAN AGE AT FIRST REPRODUCTION ARTEFACTS LITTER SIZE ASSESSING LITTER SIZE DATE RANGE IN LITTER/CLUTCH SIZE SEASONALITY MEAN DATE SEASONALITY IN BIRTHS SEASONALITY IN DEATHS INTER–BIRTH INTERVAL MANAGEMENT EFFECTS EGG–LAYING SPECIES CENSUS ANALYSIS COUNTING ANIMALS CENSUS DATE POPULATION GROWTH SEX–RATIO BIRTHS, DEATHS AND MIGRATION CENSUS EVENTS BIRTHS SEX–RATIO AT BIRTH DEATHS MIGRATION MIGRATION PATTERNS BRINGING IT TOGETHER ECOLOGICAL MODELS POPULATION GROWTH MODELS EXPONENTIAL GROWTH LOGISTIC GROWTH REMARKS AGE, MORTALITY AND FECUNDITY COHORT AGE CLASS AGE DISTRIBUTION MORTALITY TABLE DEATH RECORDS MORTALITY MEASURES CENSORED DATA LOGRANK STATISTIC COMPARATIVE SURVIVAL STUDIES FECUNDITY TABLE PRORATING UNKNOWN SEX AND UNKNOWN PARENTS CON?DENCE IN LIFE TABLES TOSSING A COIN MORTALITY FECUNDITY RESAMPLING SAMPLE SIZES POOLING CLASS–WIDTH SMOOTHING PARAMETRIC MODELS EXTENDED LIFE TABLE GROWTH RATES REPRODUCTIVE VALUE STABLE AGE DISTRIBUTION BREEDING SEASON LIFE TABLES AND CENSUS SURVIVAL ANALYSIS KAPLAN–MEIER PRODUCT LIMIT ESTIMATOR STATISTICAL TESTS COX PROPORTIONAL HAZARDS REGRESSION FRAILTY FROM HAZARD RATIO TO SURVIVORSHIP LEFT TRUNCATED AND RECURRENT DATA AGE AT FIRST BREEDING POPULATION PROJECTIONS CENSUS DATA LESLIE MATRIX BIRTH–PULSE BIRTH–FLOW SOME MATRIX ALGEBRA SENSITIVITY AND ELASTICITY SIMULATIONS PROJECTION OR PREDICTION BACK TO THE FUTURE STAGE–BASED MODELS PART III GENETIC ANALYSES GENETIC VARIATION AND GENERATIONS GENETIC MEASURES GENERATION CALCULATING GENERATIONS EFFECTS OF THE CAPTIVE ENVIRONMENT: AN EXAMPLE INBREEDING INBREEDING COEF?CIENTS MEASURING INBREEDING DEPRESSION NEONATAL AND JUVENILE MORTALITY TWO–WAY CONTINGENCY TABLE LITTER EFFECT INBRED AND NON–INBRED PARENTS AGE GROUPS LIFESPAN LETHAL EQUIVALENTS MATERNAL INBREEDING DATA ARTEFACTS GENETIC DRIFT AND SIMULATIONS GENETIC DRIFT AND FOUNDER EFFECT EFFECTIVE POPULATION SIZE UNEQUAL SEX–RATIO UNEQUAL FAMILY SIZE GENERATION OVERLAP ESTIMATING NE FROM PEDIGREES GENETIC SIMULATION MODELS WHICH MODEL? EFFECTIVE SIZE AVOIDANCE OF SELECTION GOOD OR BAD GENES? SELECTION FOUNDER REPRESENTATION MEAN KINSHIP QUANTITATIVE GENETICS PHENOTYPIC TRAITS PHENOTYPIC VARIANCE VARIANCE COMPONENTS HERITABILITY REPEATABILITY PARENT–OFFSPRING REGRESSION EXAMPLE: PARTURITION DATE EXAMPLE: FITNESS WEIGHTED REGRESSION ASSORTATIVE MATING AND ARTEFACTS ASSUMPTIONS OF LINEAR REGRESSION INDEPENDENT DATA NORMAL DISTRIBUTION OUTLIERS ESTIMATED BREEDING VALUES ANIMAL MODEL REML MCMC MONITORING PHENOTYPIC VARIATION RELIABILITY OF BREEDING VALUES PART IV CONSERVATION CONSERVATION WILD DATA CAPTIVE AND WILD ENVIRONMENTS POPULATION VIABILITY ANALYSIS STUDBOOK DATA SENSITIVITY ANALYSIS JUSTI?CATION PART V MORE TOPICS INCOMPLETE AND MISSING DATA UNKNOWN SEX INCOMPLETE DATES UNKNOWN PARENTS STATISTICAL TOPICS CIRCULAR STATISTICS PSEUDOREPLICATION ESTIMATED AGE CONSTANT ADULT MORTALITY