Topics in Biodiversity and Conservation. Volume 17

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1 Topics in Biodiversity and Conservation Volume 17

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3 F.P.G. Princée Exploring Studbooks for Wildlife Management and Conservation 123

4 F.P.G. Princée Population Management and Wildlife Conservation East Rudham, Norfolk, UK ISSN ISSN (electronic) Topics in Biodiversity and Conservation ISBN ISBN (ebook) DOI / Library of Congress Control Number: 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

5 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

6 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 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

7 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

8 Contents Part I Introduction 1 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 Introduction 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 References ix

9 x Contents Part II Demographic Analyses 3 Natural History Introduction 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 References Census Analysis Counting Animals Census Date Census Population Growth Sex Ratio References Births, Deaths and Migration Census Events Births Sex Ratio at Birth Deaths Migration Migration Patterns Bringing it Together References... 81

10 Contents xi 6 Ecological Models Introduction Population Growth Models Exponential Growth Logistic Growth Remarks References Age, Mortality and Fecundity Introduction 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 Remarks References Confidence in Life Tables Introduction Tossing a Coin Mortality Fecundity Resampling Sample Sizes Pooling Class Width Smoothing Parametric Models References Extended Life Table Introduction Growth Rates Reproductive Value Stable Age Distribution Breeding Season Life Tables and Census References

11 xii Contents 10 Survival Analysis Introduction 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 References Population Projections Introduction 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 References Part III Genetic Analyses 12 Genetic Variation and Generations Introduction Genetic Measures Generation Calculating Generations Effects of the Captive Environment: An Example References Inbreeding Introduction Inbreeding Coefficients Measuring Inbreeding Depression Neonatal and Juvenile Mortality Two Way Contingency Table Litter Effect Inbred and Non Inbred Parents Age Groups Lifespan Lethal Equivalents

12 Contents xiii 13.7 Maternal Inbreeding Fecundity Reproductive Value Data Artefacts References Genetic Drift and Simulations Introduction Genetic Drift and Founder Effect Effective Population Size Unequal Sex Ratio Unequal Family Size Generation Overlap Estimating N e from Pedigrees Genetic Simulation Models Which Model? Effective Size References Avoidance of Selection Good or Bad Genes? Selection Founder Representation Mean Kinship References 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

13 xiv Contents Monitoring Phenotypic Variation Reliability of Breeding Values Remarks References Part IV Conservation 17 Conservation Wild Data Captive and Wild Environments Population Viability Analysis Studbook Data Sensitivity Analysis Justification References Part V More Topics 18 Incomplete and Missing Data Introduction Unknown Sex Incomplete Dates Unknown Parents References Statistical Topics Introduction Circular Statistics Pseudoreplication Estimated Age Constant Adult Mortality Remarks References Appendix A Software A.1 Population Management Library A.1.1 Commands A.2 studbookr A.2.1 Functions A.3 Availability Index

14 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

15 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

16 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

Randy Fulk and Jodi Wiley North Carolina Zoo

Randy Fulk and Jodi Wiley North Carolina Zoo Population Management Overview Jodi Neely Wiley North Carolina Zoo Hamadryas Baboon Studbook Keeper and SSP Coordinator Studbooks include the pedigree and location