Topics in Biodiversity and Conservation Volume 17
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F.P.G. Princée Exploring Studbooks for Wildlife Management and Conservation 123
F.P.G. Princée Population Management and Wildlife Conservation East Rudham, Norfolk, UK ISSN 1875-1288 ISSN 1875-1296 (electronic) Topics in Biodiversity and Conservation ISBN 978-3-319-50031-7 ISBN 978-3-319-50032-4 (ebook) DOI 10.1007/978-3-319-50032-4 Library of Congress Control Number: 2016961290 Springer International Publishing AG 2016 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. Printed on acid-free paper This Springer imprint is published by Springer Nature The registered company is Springer International Publishing AG The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland
Preface Some 35 years ago, I became involved in conservation of endangered animal species. It all started while I was a biology student at the Biological Department of the Royal Rotterdam Zoological and Botanical Gardens ( Blijdorp Zoo ). It was around the time that the international zoo world introduced cooperative species management programmes, based on demographic and genetic science, in order to establish self-sustaining populations of endangered species. This created an environment in which applied and fundamental research were intertwined and which shaped my scientific background in population genetics. The introduction of personal computers opened a new creative platform that allowed me to develop the skills of computer programming. This resulted in developing simulation models to explore population genetic processes in real populations with their complex pedigrees. The first computer program that I developed was followed by the next, and the next, etc. resulting in studbook software that included a range of demographic and genetic analyses. The catalyst for writing this book dates back to the years that I worked for the Dutch National Foundation for Research in Zoological Gardens/European Association of Zoos and Aquaria. Teaching, training and advising coordinators of European Endangered Species Programmes (EEPs) in population biology and studbook software meant exposure to a diversity of practical problems in species management. Solutions to some of these problems may be embedded in the studbook itself, and that is where exploring starts. I participated in various workshops of the IUCN/SSC/Conservation Breeding Specialist Group in which the knowledge of zoo and wildlife professionals was exchanged and combined. These workshops, the Population and Habitat Viability Assessment of the Aruba island rattlesnake in particular, exposed me to the reality of field conservation. I became more directly involved in nature conservation projects in the 1990s through the conservation fund of the Dutch zoos. The induction was a population viability study on lions in the Queen Elizabeth National Park (Uganda) that was v
vi Preface carried out by Makerere University (Kampala). Individual identification of lions, a small population and urbanised areas acting as a barrier to movement do not make it difficult to foresee studbook-style management in the future. A few years later, I started to write the first chapters while living next to Ranomafana National Park, a rainforest in the south-east of Madagascar. No zoo environment, but wild nature. However, the state of some endangered species in this 42,000 ha protected area highlighted that nature is (gradually) becoming a big zoo. Take, for example, the closely monitored greater bamboo lemur population in this park at that time. One day there were six animals, the next day one animal was missing, and one month later a young was born, bringing the group total back to six. This doesn t sound like a wild population but more closely resembles a zoo group. Field conservation is exploring too, as researchers discovered four new groups, totalling more than 100 individuals, in fragmented bamboo forests within the peripheral zone of the park in 2009 and 2010. The idea of exploring studbook data for its relevance to conservation in the natural habitat was reinforced while I was living in Dzanga Sangha Protected Areas (Central African Republic). The secretive lifestyle of many of the inhabitants of this tropical rainforest not only makes it difficult to assess population sizes but also to obtain natural history data that are required for conservation measures. My background prompted me to ask zoo colleagues for studbook data in order to extract basic biological information on species in the protected area. I have included a PVA study on lowland bongo as an example in this book. Exploring studbook data forced me to explore statistics in more depth than I had done before. Studbooks are relatively small and the issue of reliability of estimated parameters cannot be ignored. Moreover, problem-solving involves comparative studies that simply require significance tests. However, this is not a book on studbook statistics. The main focus is exploring the wealth of (biological) data in studbooks, in which statistics can play a supporting role. I have selected topics in demographics and genetics of studbook populations that deserve more attention, but which can be studied in standard data sets. These topics are interconnected, which means that, for example, life tables are used in tests for inbreeding depression and litter size is considered as a trait in quantitative genetics. This book is intended for professionals in zoo and wildlife conservation who are involved in management of captive populations; reintroduction or management of small, isolated, fragmented populations in the wild; and for researchers and students who are planning studies that are based on studbook populations or who want to explore what studbook data can offer for topics in academic research. East Rudham, UK September, 2016 F.P.G. Princée
Acknowledgements A monograph is the work of a single author but not of a single mind. This book is the result of experiences and ideas that have been accumulated over years and have been shaped by discussions with colleagues, from zoo keeper to director and from ranger to game warden, as well as with colleagues in governments, NGOs and universities. First of all, I would like to thank Anna Feistner for reading this book through several times with an editorial eye and for her comments and ideas as a conservation biologist. I am indebted to Anna for her encouragement, support and trust in enabling me to realise a book which took considerably more time than I had once optimistically foreseen. I thank Bert de Boer for his valuable comments on an earlier draft and ideas that helped in streamlining this book. I could not have written this book without access to real-time computerised studbooks on endangered species. I thank the following species managers/studbook keepers and the institutions to whom they are or were affiliated: Richard Barnes (Port Lympne Reserve, UK), Rob Belterman (Rotterdam Zoo, The Netherlands), Leif Blomqvist (Nordic Ark, Sweden, and Helsinki Zoo, Finland), Lydia Frazier Bosley (Logsden, USA), Angela Glatston (Rotterdam Zoo, The Netherlands), Gerard Meijer (Ouwehands Zoo, The Netherlands), Hanny Verberkmoes and Wim Verberkmoes (GaiaZOO, The Netherlands) for providing their studbook data to be used as examples in this book. I acknowledge Andrea Turkalo (the Wildlife Conservation Society, USA) for field data on lowland bongo in Dzanga Baie. I would like to thank Jonathan Ballou, Laurie Bingaman-Lackey, Lisa Faust, Robert Lacy, Nathan Flesness and Andy Odum for discussions, some of which started years ago, on various topics in demography, genetics and studbook software. Erik Postma is acknowledged for explaining assumptions that are made regarding missing parents in the animal model. Ludwig Siefert is acknowledged for introducing me to the reality of field conservation when I was involved in supporting the Ugandan lion/carnivore project. I thank Jean-Claude Razafimahaimodison for all discussions when I exchanged the comfort of analysing zoo populations for interpreting transect data from Ranomafana National Park. Angelique Todd and Andrea Turkalo are acknowledged for introducing me to the world of gorillas, forest elephants and lowland bongo. vii
Contents Part I Introduction 1 Introduction... 3 1.1 A Brief History... 3 1.2 From Register to Management... 4 1.3 Population Management Triangle... 5 1.4 Exploring Studbooks... 7 1.4.1 Natural History... 7 1.4.2 Census... 8 1.4.3 Life Tables... 8 1.4.4 Genetic Analyses... 9 1.5 Conservation Data... 10 1.6 More Topics... 11 References... 11 2 Studbooks and Software... 15 2.1 Introduction... 15 2.2 Studbook Examples... 16 2.2.1 Red Crowned Crane Grus japonensis... 16 2.2.2 African Wild Dog Lycaon pictus... 17 2.2.3 Red Panda Ailurus fulgens... 17 2.2.4 European Wolverine Gulo gulo gulo... 18 2.2.5 Snow Leopard Uncia uncia... 18 2.2.6 Californian Sea Lion Zalophus californianus... 19 2.2.7 Bongo Tragelaphus eurycerus... 19 2.2.8 Blesbok Damalisicus pygargus phillipsi... 19 2.3 Software Tools... 20 2.3.1 Population Management Library... 21 References... 22 ix
x Contents Part II Demographic Analyses 3 Natural History... 27 3.1 Introduction... 27 3.2 Lifespan and Longevity... 28 3.2.1 Estimated Dates... 30 3.2.2 Longevity... 31 3.2.3 Pathologist s View... 34 3.2.4 History and Husbandry... 34 3.2.5 Early Life Stages... 36 3.2.6 Differences Between Sexes... 37 3.3 Reproductive Lifespan... 40 3.3.1 Age at First Reproduction... 41 3.3.2 Artefacts... 42 3.4 Litter Size... 42 3.4.1 Assessing Litter Size... 43 3.4.2 Date Range in Litter/Clutch Size... 44 3.5 Seasonality... 45 3.5.1 Mean Date... 45 3.5.2 Seasonality in Births... 46 3.5.3 Seasonality in Deaths... 51 3.6 Inter Birth Interval... 52 3.6.1 Management Effects... 53 3.6.2 Egg Laying Species... 55 References... 55 4 Census Analysis... 59 4.1 Counting Animals... 59 4.2 Census Date... 61 4.3 Census... 61 4.4 Population Growth... 63 4.5 Sex Ratio... 65 References... 66 5 Births, Deaths and Migration... 69 5.1 Census Events... 69 5.2 Births... 70 5.2.1 Sex Ratio at Birth... 73 5.3 Deaths... 76 5.4 Migration... 78 5.4.1 Migration Patterns... 79 5.5 Bringing it Together... 80 References... 81
Contents xi 6 Ecological Models... 83 6.1 Introduction... 83 6.2 Population Growth Models... 84 6.2.1 Exponential Growth... 85 6.2.2 Logistic Growth... 86 6.3 Remarks... 87 References... 88 7 Age, Mortality and Fecundity... 89 7.1 Introduction... 89 7.2 Cohort... 90 7.3 Age Class... 91 7.4 Age Distribution... 91 7.5 Mortality Table... 92 7.5.1 Death Records... 93 7.5.2 Mortality Measures... 94 7.5.3 Censored Data... 98 7.5.4 Logrank Statistic... 102 7.5.5 Comparative Survival Studies... 103 7.6 Fecundity Table... 104 7.7 Prorating... 105 7.8 Unknown Sex and Unknown Parents... 106 7.9 Remarks... 107 References... 108 8 Confidence in Life Tables... 111 8.1 Introduction... 111 8.2 Tossing a Coin... 112 8.2.1 Mortality... 113 8.2.2 Fecundity... 114 8.3 Resampling... 116 8.4 Sample Sizes... 119 8.4.1 Pooling... 119 8.4.2 Class Width... 120 8.5 Smoothing... 121 8.6 Parametric Models... 122 References... 125 9 Extended Life Table... 127 9.1 Introduction... 127 9.2 Growth Rates... 128 9.3 Reproductive Value... 129 9.4 Stable Age Distribution... 131 9.5 Breeding Season... 132 9.6 Life Tables and Census... 133 References... 134
xii Contents 10 Survival Analysis... 137 10.1 Introduction... 137 10.2 Kaplan Meier Product Limit Estimator... 139 10.2.1 Statistical Tests... 140 10.3 Cox Proportional Hazards Regression... 141 10.3.1 Frailty... 145 10.3.2 From Hazard Ratio to Survivorship... 146 10.4 Left Truncated and Recurrent Data... 147 10.5 Age at First Breeding... 148 References... 149 11 Population Projections... 151 11.1 Introduction... 151 11.2 Census Data... 152 11.3 Leslie Matrix... 154 11.3.1 Birth Pulse... 157 11.3.2 Birth Flow... 158 11.4 Some Matrix Algebra... 158 11.5 Sensitivity and Elasticity... 159 11.6 Simulations... 161 11.7 Projection or Prediction... 162 11.8 Back to the Future... 162 11.9 Stage Based Models... 164 References... 166 Part III Genetic Analyses 12 Genetic Variation and Generations... 171 12.1 Introduction... 171 12.2 Genetic Measures... 172 12.3 Generation... 173 12.3.1 Calculating Generations... 174 12.3.2 Effects of the Captive Environment: An Example... 175 References... 178 13 Inbreeding... 179 13.1 Introduction... 179 13.2 Inbreeding Coefficients... 180 13.3 Measuring Inbreeding Depression... 182 13.4 Neonatal and Juvenile Mortality... 183 13.4.1 Two Way Contingency Table... 184 13.4.2 Litter Effect... 185 13.4.3 Inbred and Non Inbred Parents... 185 13.4.4 Age Groups... 187 13.5 Lifespan... 187 13.6 Lethal Equivalents... 189
Contents xiii 13.7 Maternal Inbreeding... 192 13.8 Fecundity... 192 13.9 Reproductive Value... 193 13.10 Data Artefacts... 194 References... 195 14 Genetic Drift and Simulations... 199 14.1 Introduction... 199 14.2 Genetic Drift and Founder Effect... 200 14.3 Effective Population Size... 201 14.3.1 Unequal Sex Ratio... 201 14.3.2 Unequal Family Size... 202 14.3.3 Generation Overlap... 202 14.4 Estimating N e from Pedigrees... 203 14.5 Genetic Simulation Models... 204 14.5.1 Which Model?... 205 14.5.2 Effective Size... 207 References... 209 15 Avoidance of Selection... 211 15.1 Good or Bad Genes?... 211 15.2 Selection... 212 15.3 Founder Representation... 213 15.4 Mean Kinship... 214 References... 216 16 Quantitative Genetics... 219 16.1 Phenotypic Traits... 219 16.2 Phenotypic Variance... 221 16.3 Variance Components... 222 16.4 Heritability... 223 16.5 Repeatability... 223 16.6 Parent Offspring Regression... 225 16.6.1 Example: Parturition Date... 225 16.6.2 Example: Fitness... 227 16.6.3 Weighted Regression... 229 16.6.4 Assortative Mating and Artefacts... 229 16.7 Assumptions of Linear Regression... 230 16.7.1 Independent Data... 230 16.7.2 Normal Distribution... 231 16.7.3 Outliers... 231 16.8 Estimated Breeding Values... 232 16.9 Animal Model... 233 16.9.1 REML... 233 16.9.2 MCMC... 235
xiv Contents 16.10 Monitoring Phenotypic Variation... 236 16.10.1 Reliability of Breeding Values... 239 16.11 Remarks... 240 References... 241 Part IV Conservation 17 Conservation... 247 17.1 Wild Data... 247 17.2 Captive and Wild Environments... 249 17.3 Population Viability Analysis... 250 17.3.1 Studbook Data... 250 17.3.2 Sensitivity Analysis... 253 17.4 Justification... 255 References... 256 Part V More Topics 18 Incomplete and Missing Data... 261 18.1 Introduction... 261 18.2 Unknown Sex... 262 18.3 Incomplete Dates... 263 18.3.1 Unknown Parents... 265 References... 267 19 Statistical Topics... 269 19.1 Introduction... 269 19.2 Circular Statistics... 270 19.3 Pseudoreplication... 272 19.4 Estimated Age... 273 19.5 Constant Adult Mortality... 275 19.6 Remarks... 276 References... 276 Appendix A Software... 277 A.1 Population Management Library... 277 A.1.1 Commands... 277 A.2 studbookr... 280 A.2.1 Functions... 281 A.3 Availability... 283 Index... 285
Symbols Natural History T 1 Longevity, i.e. oldest age observed First age at reproduction Census N t B t D t E t I t b t d t e t i t Population size at census t Number of births in interval t Number of deaths in interval t Number of emigrants in interval t Number of immigrants in interval t Crude birth rate in interval t Crude death rate in interval t Crude emigration rate in interval t Crude immigration rate in interval t Life Tables n x Number of individuals in age class x d x Crude rate, number of individuals dying during the age interval x to x C 1 q x Mortality rate in age class x p x Survival rate in age class x l x Survivorship or survival rate to start of age class x L x Midpoint survivorship; individuals alive on average during the age interval x to x C 1. xv
xvi Symbols e x Mean expectation of life for individuals alive at start of age x m x Fecundity rate of individuals in age class x V x Reproductive value of individuals of age x; expected number of future offspring C x Proportion of individuals of age x in the stable age distribution NT Population generation time Finite rate of increase r Intrinsic rate of increase R 0 Net reproductive rate; growth rate per generation time! Oldest age class i Probability of surviving in stage i during a time step i Probability of moving to the next stage i C 1 during a time step G i Probability of surviving and moving to next stage i C 1 during a time step; G i D i i P i Probability of surviving and remaining in stage i during a time step; P i D i.1 i / Genetics ı B F f H e h e H o N e N f N m N ev nn a P r Measure of inbreeding depression Mutation rate Kinship coefficient Lethal equivalents Fixation index Inbreeding coefficient Expected heterozygosity or gene diversity in population Expected heterozygosity at a locus Observed heterozygosity in population Effective population size Number of breeding females in population Number of breeding males in population Variance effective population size Average number of alleles on r loci Proportion of polymorphic loci Number of loci Quantitative Genetics CV P EBV i H 2 Phenotypic coefficient of variation Estimated breeding value of individual i Broad-sense heritability
Symbols xvii h 2 h 2 adj r p r pp V A V D V E V Eg V Es V I V P V R Narrow-sense heritability Narrow-sense heritability adjusted for phenotypic correlation Repeatability Phenotypic correlation between parents (mates) Additive genetic variance Dominance variance Environmental variance General or permanent environmental variance Specialised environmental variance Epistatic variance Phenotypic variance Residual variance