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Reptile Ecology and Conservation
 Techniques in Ecology and Conservation Series
Series Editor: William J. Sutherland

Bird Ecology and Conservation: A Handbook of Techniques

William J. Sutherland, Ian Newton, and Rhys E. Green

Conservation Education and Outreach Techniques

Susan K. Jacobson, Mallory D. McDuff, and Martha C. Monroe

Forest Ecology and Conservation: A Handbook of Techniques

Adrian C. Newton

Habitat Management for Conservation: A Handbook of Techniques

Malcolm Ausden

Conservation and Sustainable Use: A Handbook of Techniques

E.J. Milner-Gulland and J. Marcus Rowcliffe

Invasive Species Management: A Handbook of Principles and Techniques

Mick N. Clout and Peter A. Williams

Amphibian Ecology and Conservation: A Handbook of Techniques

C. Kenneth Dodd, Jr.

Insect Conservation: A Handbook of Approaches and Methods

Michael J. Samways, Melodie A. McGeoch, and Tim R. New

Remote Sensing for Ecology and Conservation: A Handbook of Techniques

Ned Horning, Julie A. Robinson, Eleanor J. Sterling, Woody Turner, and Sacha Spector

Marine Mammal Ecology and Conservation: A Handbook of Techniques

Ian L. Boyd, W. Don Bowen, and Sara J. Iverson

Carnivore Ecology and Conservation: A Handbook of Techniques

Luigi Boitani and Roger A. Powell

Primate Ecology and Conservation: A Handbook of Techniques

Eleanor J. Sterling, Nora Bynum, and Mary E. Blair

Conservation Education and Outreach Techniques Second Edition

Susan K. Jacobson, Mallory D. McDuff, and Martha C. Monroe

Reptile Ecology and Conservation: A Handbook of Techniques

C. Kenneth Dodd, Jr.
 Reptile Ecology
and Conservation
A Handbook of Techniques

Edited by
C. Kenneth Dodd, Jr.

1
3
Great Clarendon Street, Oxford, OX2 6DP,
United Kingdom
Oxford University Press is a department of the University of Oxford.
It furthers the University’s objective of excellence in research, scholarship,
and education by publishing worldwide. Oxford is a registered trade mark of
Oxford University Press in the UK and in certain other countries
© Oxford University Press 2016
The moral rights of the author have been asserted
First Edition published in 2016
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a retrieval system, or transmitted, in any form or by any means, without the
prior permission in writing of Oxford University Press, or as expressly permitted
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Published in the United States of America by Oxford University Press
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CPI Group (UK) Ltd, Croydon, CR0 4YY
Links to third party websites are provided by Oxford in good faith and
for information only. Oxford disclaims any responsibility for the materials
contained in any third party website referenced in this work.
In memory of Jonathan Scott Loftis
Preface

As this volume is completed, more than 10,200 non-avian reptile species have been rec-
ognized (6175 lizards and amphisbaenians, 3496 snakes, 341 turtles, 25 crocodilians,
and 1 Tuatara), with new taxa being described nearly every day (Uetz, P. and Hošek,
J. (eds), The Reptile Database, http://www.reptile-database.org, accessed 17 August
2015). The life histories and conservation status of most of these species are imper-
fectly understood or completely unknown except for a few of the more charismatic or
popular larger species. Because of a host of threats such as habitat loss and fragmenta-
tion, trade, toxic and endocrine disrupting chemicals, emerging infectious diseases, and
global climate change, it seems likely that reptiles may be declining at rates approaching
those of amphibians (Gibbons et al., 2000; Böhm et al., 2013) and that many spe-
cies will disappear by the end of the twenty-first century (Alroy, 2015; Ceballos et al.,
2015; McCallum, 2015). At the same time, powerful economic interests have united to
adversely influence decisions affecting the environment, even rejecting well-established
scientific research such as the origin and extent of climate change. There is thus an
urgent need for field research on reptile species and their community interactions.
There are a great many techniques available for ecological and conservation-based
research on reptiles. Journals such as Herpetological Review, Herpetological Conservation
and Biology, and Chelonian Conservation and Biology frequently contain techniques
papers. Specialized books and papers, such Henle and Veith (1997), Gent and Gibson
(1998), Hachtel et al. (2009), Eekhout (2010), McDiarmid et al. (2012), Cacciali
(2013), and Graeter et al. (2013), offer additional summaries that are as applicable
today as when they were published. Although not strictly a techniques book, many
of the chapters in Lutterschmidt (2013) offer excellent guides as to the dynamic state
of research in reptile biology currently underway. The current volume is meant not to
supplant earlier works, but to supplement them and add new areas not previously sum-
marized, such as statistical modelling, landscape ecology, genetics, disease-biosecurity,
and human dimensions. Our objectives have been to delineate important new develop-
ments, to give an idea as to what the techniques tell or do not tell a researcher, to focus
attention on biases and data inference, and to get readers to appreciate sampling as an
integral part of their science, rather than just a means of capturing animals. The tech-
niques used will set the boundaries within which results can or should be interpreted.
No one volume can include all techniques, nor can the techniques included be dis-
cussed in more than passing detail. Because of space limitations, chapters on growth
(Andrews, 1982), behaviour, advanced spatial modelling, social science, relocation/
reintroduction (see Animal Conservation, Volume 17, Supplement 1, 2015), and the use
of stable isotopes (Fry, 2006) could not be included. Authors of individual chapters were
advised to incorporate some of these topics as best they could into existing chapters,
and to point readers to important references where more detailed information may be
obtained. In addition, many of the topics covered in the amphibian volume of this series
viii | Preface

also are pertinent to reptiles (Dodd, 2010). Lack of space also precludes the addition of
a comprehensive glossary. Readers should consult Lillywhite (2008) or online sources
when unfamiliar terms are encountered.
Publishing results is an integral component of research undertaken on reptile ecology
and conservation. It is simply not good enough to bury research findings in unpublished
reports or university theses. Although not all investigations result in ‘high impact’ pub-
lications, there are myriad outlets available for disseminating research results. At the
same time, researchers should avoid so-called ‘predatory’ or ‘pay to publish’ journals,
as publication in journals of dubious scholarly reputation will lead to a questioning of
research reliability and interpretation. A list of questionable publishers can be found at:
http://scholarlyoa.com/publishers/.
The editor thanks the following for taking their valuable time assisting with vari-
ous aspects of this project: Matthew Allender, George Balazs, Jaime Bertoluci, Bayard
Brattstrom, Steven J.B. Carter, Michael Cherkiss, William Cooper, Ben Croak, Wei-
Guo Du, Ruth Elsey, Kevin Enge, Neil Ford, Mercedes Foster, Frank Glaw, Gurutzeta
Guillera-Arroita, April Goodman Hall, John Iverson, Kate Jackson, Ambika Kamath,
Joshua Kapfer, Amy Lathrop, Harvey Lillywhite, Peter Lindeman, Scott Loarie, Victor
Loehr, Erin Marnocha, Jonathan Mawdsley, Shai Meiri, Damian Michael, Donald B.
Miles, Debra Miller, Joe Mitchell, Akira Mori, Paul Ouboter, Ted Papenfuss, Michael
Plummer, Thomas Rainwater, John H. Roe, Jose Rosado, Christopher Rowe, Andrew
Royle, Raul F.D. Sales, Benedikt Schmidt, Coleman Sheehy, Rick Shine, Cameron
Siler, Javier Manjarrez Silva, Lora Smith, Phillip Q. Spinks, James Spotila, Laurie
Vitt, Jayme Waldron, Dan Warner, James Watling, Kimberley M. Watson, Grahame
Webb, Scott Weir, Allan Woodward, and Amy Yackel. I greatly appreciate the support
from Ian Sherman and Lucy Nash at Oxford University Press, and thank series editor,
Bill Sutherland, for inviting me to edit the reptile volume. Alan Skull and Indumadhi
Srinivasan deserve special thanks for their efforts to improve the text and illustrations. A
special thanks to Marian Griffey, Morganna Fairchild (feline, not the actress), Allen K.
Fearless, and the rest of the cat pride. This volume is dedicated to all the biologists who
take up the challenge of reptile ecology and conservation.
C. Kenneth Dodd, Jr.

References
Alroy, J. (2015). Current extinction rates of reptiles and amphibians. Proceedings of the National
Academy of Science, USA, DOI: 10.1073/pnas.1508681112.
Andrews, R.M. (1982). Patterns of growth in reptiles. In C. Gans (ed) Biology of the Reptilia,
Volume 13. Physiology D: Physiological Ecology. London: Academic Press, pp. 273–320.
Böhm, M., Collen, B., Baillie, J.E.M., et al. (2013). The conservation status of the world’s rep-
tiles. Biological Conservation, 157, 372–85.
Cacciali, P. (2013). Colecta y Preparación de Anfibios y Reptiles. Saarbrücken, Germany: Editorial
Académica Española, AV Akademikerverlag GmbH & Co.
Ceballos, G., Ehrlich, P.R., Barnosky, A.D., et al. (2015). Accelerated modern human-induced
species losses: entering the sixth mass extinction. Science Advances, 1, e1400253.
Dodd, C.K., Jr. (ed). (2010). Amphibian Ecology and Conservation: A Handbook of Techniques.
Oxford: Oxford University Press.
 Preface | ix

Eekhout, X. (2010). Sampling amphibians and reptiles. ABC Taxa, 8, 530–57.

Fry, B. (2006). Stable Isotope Ecology. New York: Springer Science.
Gent, T., and Gibson, S. (eds). (1998). Herpetofauna Worker’s Manual. Peterborough, UK: Joint
Nature Conservation Committee.
Gibbons, J.W., Scott, D.E., Ryan, T.J., et al. (2000). The global decline of reptiles, déjà vu
amphibians. Bioscience, 50, 653–66.
Graeter, G.K., Buhlmann, K.A., Wilkinson, L.R., et al. (eds). (2013). Inventory and Monitoring:
Recommended Techniques for Amphibians and Reptiles. Technical Publication IM-1.
Birmingham, AL: Partners in Amphibian and Reptile Conservation.
Hachtel, M., Schlüpmann, M, Thiesmeier, B., et al. (eds). (2009). Methoden der Feldherpetologie.
Bielefeld, Germany: Laurenti Verlag.
Henle, K., and Veith, M. (eds). (1997). Naturschutzrelevante Methoden der Feldherpetologie.
Deutsche Gesellschaft für Herpetologie und Terrarienkunde.
Lillywhite, H.B. (2008). Dictionary of Herpetology. Malabar, FL: Krieger Publishing.
Lutterschmidt, W.I. (ed). (2013). Reptiles in Research. Investigations of Ecology, Physiology, and
Behavior from Desert to Sea. New York: Nova Biomedical.
McCallum, M.L. (2015). Vertebrate biodiversity losses point to a sixth mass extinction.
Biodiversity and Conservation, DOI: 10.1007/s10531-0940-6.
McDiarmid, R.W., Foster, M.S., Guyer, C., et al. (eds). (2012). Reptile Biodiversity. Standard
Methods for Inventory and Monitoring. Berkeley, CA: University of California Press.
Contents

List of Contributors  xxv

Part 1. Introduction 
1. Reptile diversity and life history  3
Laurie J. Vitt
1.1 Introduction  3
1.2 Reptile ‘diversity’  3
1.2.1 ‘Diversity’  3
1.2.2 Evolutionary history and numbers of reptile species  3
1.2.3 Morphological and ecological diversity  5
1.3 Diversity of life histories  8
1.3.1 Definitions  8
1.3.2 General observations  8
1.3.3 Turtle life histories  8
1.3.4 Crocodilian life histories  8
1.3.5 Squamate life histories  10
1.3.6 Tuatara life history  11
1.4 Summary  12
References  13

2. Planning and setting objectives in field studies  16

Robert N. Fisher
2.1 Introduction  16
2.2 Planning: goals versus objectives  16
2.3 Design  17
2.4 Conceptual models  19
2.5 Sampling considerations  20
2.6 Covariates  24
2.7 Timescales  24
2.8 Permits  25
2.9 Ethical considerations  28
2.10 Biosecurity  29
2.11 Conclusion  30
2.12 Example URLs for SMART objectives  30
References  30
xii | Contents

3. Data collection and storage  32

Richard A. Seigel
3.1 Introduction  32
3.2 Flexibility: the research proposal versus the real world  33
3.3 Field notes  34
3.3.1 Mechanics of field notes  34
3.3.2 The field notebook  35
3.3.3 What to record and how to record it  36
3.4 Data sheets  38
3.4.1 General considerations  38
3.4.2 Mechanics of data sheets  38
3.5 Documenting the field site: photographs, GIS, and
environmental data  39
3.6 Data: backing up and archiving  40
3.6.1 Data backups  41
3.6.2 Data archiving and metadata  41
3.7 Conclusions  42
Acknowledgements  42
References  42

Part 2. The Individual 

4. Marking and measuring reptiles  45
John W. Ferner and Michael V. Plummer
4.1 Introduction  45
4.2 Toe-clipping  46
4.3 Scale/scute-clipping  47
4.3.1 Snakes  47
4.3.2 Lizards  48
4.4 Branding and painting  49
4.4.1 Turtles  49
4.4.2 Lizards  50
4.4.3 Snakes  50
4.5 Shell notching  51
4.6 Tagging and banding  52
4.6.1 Lizards  52
4.6.2 Freshwater and terrestrial turtles  53
4.6.3 Snakes  54
4.7 Trailing devices  54
4.8 Passive integrated transponder (PIT) tags  54
4.8.1 Turtles  55
4.8.2 Lizards and snakes  55
4.9 Taking measurements  55
 Contents | xiii

4.10 Recommendations  56
References  56

5. Digital identification and analysis  59

Roberto Sacchi, Stefano Scali, Marco Mangiacotti, Marco Sannolo,
and Marco A.L. Zuffi
5.1 Introduction  59
5.2 Collecting images  61
5.2.1 Identification of distinctive features  62
5.2.2 Set-up of a photographic shoot  62
5.2.3 Photo shooting  63
5.2.4 Photo coding  63
5.2.5 Photo enhancement  63
5.3 Software and algorithms  63
5.3.1 I3S, Interactive Individual Identification System  63
5.3.2 Wild-ID  64
5.3.3 MYDAS  64
5.3.4 APHIS  65
5.4 How they work  65
5.5 Validation  66
5.6 Photo-identification in reptiles: present and future  69
5.6.1 The state of the art of photo-identification in reptiles  69
5.6.2 Where should we go from here?  71
References  71

6. Preserving reptiles for research  73

Steve W. Gotte, Jeremy F. Jacobs, and George R. Zug
6.1 Introduction  73
6.2 Planning and permits  74
6.3 Euthanasia  75
6.4 Specimen preservation and data collection  77
6.4.1 Record keeping  77
6.4.2 Preservation and positioning  79
6.5 Specimen transport and shipping  84
6.6 Useful resources  84
Acknowledgements and notice  85
References  85

7. Reproduction  87
Gunther Köhler
7.1 Introduction  87
7.2 A brief description of the genital tract in reptiles  87
xiv | Contents

7.3 Dissections  89
7.4 Endoscopy  91
7.5 External examination and palpation  92
7.6 Imaging methods  93
7.7 Blood chemistry  93
7.8 Hormonal induction of egg laying  94
7.9 Conclusions  94
References  94

8. Diet  97
Luca Luiselli and Giovanni Amori
8.1 Introduction  97
8.2 Sources of material  97
8.3 Methods for examining diet and trophic interactions  99
8.3.1 Direct observation  99
8.3.2 Dissection of stomachs  99
8.3.3 Stomach flushing  100
8.3.4 Faecal pellets  102
8.3.5 Forced regurgitation  103
8.3.6 Stable isotopes  104
8.3.7 Doubly labelled water  104
8.4 Diet by volume or mass vs. diet by prey number  105
8.5 Gut clearance times  105
8.6 Quantitative analyses of diet  106
References  107

9. Movement patterns and telemetry  110

Bruce A. Kingsbury and Nathan J. Robinson
9.1 Introduction  110
9.2 Common considerations for telemetry studies  110
9.3 Telemetry devices  111
9.3.1 VHF transmitters  111
9.3.2 Acoustic telemetry  113
9.3.3 Satellite telemetry  113
9.4 Statistical techniques for analysing telemetry data  114
9.5 Taxonomic considerations  116
9.5.1 Terrestrial and freshwater turtles  116
9.5.2 Lizards and snakes  117
9.5.3 Crocodilians  118
9.5.4 Sea turtles  118
9.6 Future directions  119
References  120
 Contents | xv

Part 3. Sampling Reptiles 

10. Surface-dwelling reptiles  125
John D. Willson
10.1 Introduction  125
10.2 Selecting a capture method  125
10.2.1 Study goals and preliminary considerations  126
10.2.2 Capture rates  127
10.2.3 Cost and effort  127
10.2.4 Repeatability  127
10.2.5 Bias  128
10.3 Active capture techniques  128
10.3.1 Visual encounter surveys  128
10.3.2 Cover boards  129
10.3.3 Road surveys  130
10.3.4 Lizard noosing  131
10.3.5 Considerations and limitations  131
10.4 Passive capture techniques  131
10.4.1 Pitfall traps  131
10.4.2 Funnel traps  132
10.4.3 Drift fences  134
10.4.4 Considerations and limitations  134
10.5 Conclusions and recommendations  136
References  136

11. Arboreal and fossorial reptiles  139

Robert W. Henderson, Robert Powell, Jose Martín, and Pilar Lopez
11.1 Arboreal reptiles  139
11.1.1 Introduction  139
11.1.2 General methods  140
11.1.3 Collecting methods  140
11.2 Fossorial reptiles  146
11.2.1 Introduction  146
11.2.2 Active searching  146
11.2.3 Below-ground trapping  149
References  150

12. Sea snakes  154

Xavier Bonnet, Arne R. Rasmussen, and François Brischoux
12.1 Introduction  154
12.2 Locating, catching, and identifying sea snakes  155
12.2.1 Locating and catching snakes  155
12.2.2 Amphibious sea snakes on land  155
12.2.3 Sea snakes at sea  156
xvi | Contents

12.3 Identifying sea snakes  157

12.4 Measuring and describing sea snakes  158
12.5 Photographing sea snakes  159
12.6 Recapture studies  160
12.6.1 Marking snakes  160
12.6.2 Organizing data  161
12.7 Blood and other tissue sampling  161
12.8 Bio-logging  162
12.9 Captivity  163
12.10 Conclusions  163
References  165

13. Freshwater turtles  168

Richard C. Vogt
13.1 Aquatic turtles on land  168
13.1.1 Miscellaneous techniques  168
13.1.2 Nest surveys  169
13.2 Aquatic turtles in water  169
13.2.1 Surprise, snorkelling, muddling, and polling  169
13.2.2 Basking traps  171
13.2.3 Basking surveys  171
13.2.4 Trapping  172
13.3 Capture biases  178
Acknowledgements  178
References  178

14. Terrestrial turtles and tortoises  181

Margaretha D. Hofmeyr and Brian T. Henen
14.1 Introduction  181
14.2 Concepts in survey design  181
14.3 Review of survey methods  184
14.3.1 Mark–recapture  184
14.3.2 Visual encounter surveys  185
14.3.3 Line distance sampling  187
14.3.4 Surrogates  188
14.3.5 Wildlife detector dog surveys  189
14.3.6 Other methods  190
14.4 Conclusions  191
References  191
 Contents | xvii

15. Sea turtles  194

Seth Stapleton and Karen L. Eckert
15.1 Introduction  194
15.2 Monitoring nesting beaches  196
15.2.1 Ground-based methods  196
15.2.2 Aerial survey methods  198
15.2.3 Nesting crawl identifications  199
15.2.4 Locating nests  200
15.2.5 Egg counts and nest excavations  202
15.3 Tagging  203
15.4 Local interviews  205
15.5 Summary  206
References  207

16. Crocodilians  211

Matthew Brien and Charlie Manolis
16.1 Introduction  211
16.2 Surveying  211
16.2.1 Spotlight surveys  211
16.2.2 Aerial count surveys  214
16.2.3 Day count surveys  214
16.2.4 Nest counts  214
16.2.5 Other survey methods  215
16.3 Capture  215
16.3.1 Hand capture or tongs  215
16.3.2 Noosing  215
16.3.3 Skin harpoon  216
16.3.4 Traps  216
16.3.5 Snatch hook  217
16.3.6 Fixed-position snares  217
16.3.7 Nets  217
16.3.8 Baited hooks  218
16.3.9 Baited digestible ‘hooks’  218
16.4 Handling  218
16.4.1 Controlling the head  218
16.4.2 Securing the jaws  219
16.4.3 Restraining the limbs  219
16.4.4 Temporary holding and transport  219
16.4.5 Immobilizing agents  219
16.5 Tagging  220
16.5.1 Scute-clipping  220
xviii | Contents

16.5.2 Webbing tags  221

16.5.3 PIT tags  221
16.5.4 Ear tags  221
16.5.5 Anchor fish tags  221
16.5.6 Electronic tags  221
References  222

Part 4. Reptiles in the Community 

17. Plot and transect censuses  227
Tiffany M. Doan
17.1 Introduction  227
17.2 Trade-off between intensity and area  228
17.3 Plots versus transects  229
17.4 Valid implementation of plot and transect techniques  230
17.5 Standard plot and transect techniques  232
17.5.1 Visual encounter surveys on trails  232
17.5.2 Line transects  233
17.5.3 Quadrats  233
17.5.4 Total removal plots  234
17.5.5 Other plot and transect techniques  235
17.6 Individual and habitat variables  236
17.7 Selecting the appropriate plot and transect techniques  236
Acknowledgements  238
References  238

18. Rapid assessments of reptile diversity  241

Indraneil Das
18.1 Introduction  241
18.2 What is an RA?  242
18.3 Planning components of RAs  242
18.3.1 Assembling literature and other resources  242
18.3.2 Permitting  243
18.3.3 Training of field personnel  243
18.3.4 Timing  244
18.4 Field sampling  244
18.4.1 Community questionnaire surveys  244
18.4.2 Visual encounter survey  245
18.4.3 Species list technique  246
18.4.4 Trapping  246
18.4.5 Taxon-specific techniques  246
18.4.6 Environmental DNA  248
18.5 Data analyses and limitations  248
 Contents | xix

18.6 Summary  249

Acknowledgements  250
References  250

19. Measuring microhabitats used by non-avian reptiles  254

Henry R. Mushinsky and Earl D. McCoy
19.1 Introduction  254
19.2 Types of habitats and variables  257
19.3 Marine habitats: sea and brackish water turtles, sea snakes, crocodiles,
marine iguanas  260
19.4 Freshwater habitats: freshwater turtles, water snakes, alligators, caimans  261
19.5 Terrestrial habitats: most lizards, most snakes, terrestrial turtles, Tuatara  263
19.6 Rocky habitats: lizards and snakes  264
19.7 Fossorial habitats: some lizards, amphisbaenids, some snakes  265
19.8 Arboreal habitats: some snakes, some lizards  266
19.9 Summary and recommendations  267
Acknowledgements  268
References  268

20. Water quality and toxicology  272

Christine Bishop
20.1 Introduction  272
20.2 Measurement of exposure and interpreting concentrations  273
20.3 Field collections to measure contamination in air, water,
sediment, biota  273
20.3.1 Water, sediment, and biota sample container preparation
for trace analyses  274
20.3.2 Sediments  274
20.3.3 Water  274
20.3.4 Water and sediment chemistry  275
20.3.5 Passive integrative samplers for air and water  275
20.4 Measurement of levels and effects of environmental contamination
in reptiles  275
20.4.1 Measurement of contaminants in reptiles  275
20.4.2 Eggs  276
20.4.3 Internal organs and bone  276
20.4.4 Blood and plasma  276
20.4.5 Scales, claws, tails, scutes  277
20.5 Measurement of effects of environmental contaminants on reptiles  277
20.6 Population level effects of environmental contaminants in reptiles  279
20.7 Summary  279
References  279
xx | Contents

21. Richness, diversity, and similarity  283

C. Kenneth Dodd, Jr.
21.1 Introduction  283
21.2 Data transformation  283
21.3 Species diversity  285
21.3.1 Sampling considerations  285
21.3.2 Species richness  286
21.3.3 Species accumulation curves  287
21.3.4 Heterogeneity  288
21.3.5 Evenness and dominance  290
21.4 Similarity  290
21.5 Software  293
21.6 Summary  294
References  294

22. Landscape ecology, biogeography, and GIS methods  298

Monika Böhm and Viorel D. Popescu
22.1 Introduction  298
22.1.1 Landscape ecology, biogeography, and macroecology  298
22.1.2 Geographic information systems (GIS)  299
22.2 Landscape ecology concepts applied to reptile ecology and conservation  303
22.2.1 Landscape composition and configuration  303
22.2.2 Structural and functional connectivity  303
22.2.3 Landscape thresholds and conservation management
decision-making  305
22.2.4 Edge effects  306
22.3 GIS for species conservation  306
22.3.1 Modelling and mapping species distributions  306
22.3.2 Landscape ecology for reptile conservation  307
22.3.3 Macroecology and biogeography for reptile conservation  308
22.4 Spatial statistics: the analysis of spatially correlated data  310
22.5 Shortcomings and future directions  311
References  313

Part 5. Experimental Applications, Physiological Ecology,

and Genetics 
23. Experimental applications  317
Stephen J. Mullin
23.1 Introduction  317
23.2 Selecting species  318
23.2.1 Terrestrial species  318
 Contents | xxi

23.2.2 Aquatic and semi-aquatic species  318

23.2.3 Additional considerations  319
23.3 Studies using cages  320
23.3.1 Lab-based mesocosms  320
23.3.2 In situ habitat enclosures  321
23.3.3 Cage construction and siting  326
23.3.4 The utility of zoological parks  328
23.4 Manipulative applications  328
23.4.1 Manipulating habitat  329
23.4.2 Manipulating individuals  329
23.5 Conclusions  331
Acknowledgements  332
References  332

24. Body temperatures and the thermal environment  337

Keith A. Christian, Christopher R. Tracy, and C. Richard Tracy
24.1 Introduction  337
24.1.1 The importance thermal biology  337
24.1.2 The importance of using appropriate techniques to study
thermal biology  337
24.1.3 Historical perspective  338
24.2 Techniques for quantifying thermal biology  342
24.2.1 Computational models  342
24.2.2 Physical models  343
24.3 Advantages and disadvantages of computational and physical models  344
24.4 Use of data loggers as surrogate physical Te models  345
24.5 Thermal transients  345
24.5.1 How to account for thermal transients in large animals  346
24.5.2 How big does an animal have to be before it is ‘large’?  347
24.6 Conclusions  347
References  349

25. Genetics in field ecology and conservation  352

Nancy N. FitzSimmons and Joanna Sumner
25.1 Introduction  352
25.2 Genetic markers  353
25.2.1 Allozymes and restriction fragment length polymorphisms  353
25.2.2 Mitochondrial DNA sequencing  354
25.2.3 Nuclear gene sequencing  355
25.2.4 Nuclear microsatellites  356
25.2.5 Single nucleotide polymorphisms  357
25.2.6 Whole genome research  358
xxii | Contents

25.3 Initiating a genetic study  358

25.4 Labwork  359
25.5 Sample design  359
25.6 Sample collection and storage  360
25.6.1 Sampling considerations  360
25.6.2 Sample preservation  361
25.6.3 Long-term storage  361
25.6.4 Sample curation  361
25.7 Data analysis and management  361
References  362

Part 6. Trends Analysis and Conservation Options 

26. Occupancy models  373
Darryl I. MacKenzie
26.1 Introduction  373
26.2 Method overview  374
26.3 Grand Skink example  377
26.4 Recent extensions  380
26.4.1 Multi-state occupancy  381
26.4.2 Multi-scale occupancy  381
26.4.3 Species misidentification  382
26.4.4 Correlated detections  382
26.5 Response to criticisms  383
26.6 Summary  384
References  386

27. Estimating abundance  388

Chris Sutherland and J. Andrew Royle
27.1 Introduction  388
27.2 Closed population capture–recapture  388
27.2.1 Sampling a population  388
27.2.2 Estimating abundance using model M0  390
27.2.3 Variation in p: beyond M0  391
27.2.4 Removal sampling  391
27.2.5 Hierarchical capture–recapture models  392
27.2.6 Individual covariate models and distance sampling  392
27.2.7 Spatial capture–recapture  394
27.3 Software  395
27.4 Example: population size and density estimation of Slow Worms  396
27.5 Summary  398
References  399
 Contents | xxiii

28. Collecting biological samples for disease monitoring  402

Elliott R. Jacobson
28.1 Introduction  402
28.2 Ethics and animal welfare  402
28.3 Institutional Animal Care and Use Committees  403
28.4 Pain  404
28.5 Analgesia and anaesthesia  404
28.5.1 Local analgesics and central acting injectable anaesthetics  404
28.5.2 Inhalant anaesthetics  405
28.5.3 Post-surgical analgesia  405
28.6 Major infectious and non-infectious diseases  405
28.6.1 Infectious diseases  405
28.6.2 Non-infectious diseases  408
28.7 Collecting samples for disease diagnostics  409
28.7.1 Equipment  409
28.7.2 Blood collection and handling  410
28.7.3 Serology  411
28.7.4 Biopsies  411
28.7.5 Pathological evaluations  412
28.7.6 Cytodiagnostics  412
28.7.7 Microbiology  412
28.7.8 Molecular diagnostics  413
28.7.9 Preserving ecto- and endoparasites for identification  414
28.8 Biosecurity: preventing pathogen transmission  414
28.9 Conclusions  415
References  415

29. Conservation management  419

David A. Pike
29.1 Introduction  419
29.1.1 Statutory protection  420
29.1.2 Habitat protection  421
29.1.3 Managing reptile populations  421
29.1.4 Monitoring populations  422
29.2 Habitats  422
29.2.1 Contiguous habitats, buffer zones, and edge effects  422
29.2.2 Habitat connectivity  426
29.2.3 Crossing transportation corridors  427
29.2.4 Microhabitats  428
29.3 Human-altered habitats  428
29.3.1 Agricultural landscapes  428
29.3.2 Silviculture  429
xxiv | Contents

29.3.3 Urban environments  430

29.3.4 Environmental contaminants  430
29.4 Intensive manipulation of individuals  430
29.4.1 Captive breeding  430
29.4.2 Relocation, repatriation, translocation (RRT)  431
29.4.3 Pest reduction  432
29.4.4 Biosecurity and disease  432
29.5 Conclusion  433
References  433

30. Education and outreach  436

Brian Gratwicke, Matthew Neff, Lindsay Renick Mayer, Sharon Ryan,
and Jennifer Sevin
30.1 Introduction  436
30.2 Setting goals  437
30.3 Campaigns and constituency-building  437
30.3.1 Audience  438
30.3.2 Story  438
30.3.3 Constituency-building  439
30.3.4 Community conservation  440
30.4 Nature centres, museums, and exhibits  440
30.5 Citizen science  442
30.6 Engaging teachers and schools  444
30.7 Tips for designing educational programmes for schoolchildren  444
30.8 Leadership development  445
30.9 Summary  446
References  446

Index  449
List of Contributors

Giovanni Amori CNR-Institute of Ecosystem Studies, viale dell’Università 32,

00185 Rome, Italy. E-mail: giovanni.amori@uniroma1.it
Christine Bishop Environment Canada, Science and Technology Branch, Wildlife
Research Division, 5421 Robertson Road, Delta, BC V4K 3N2, Canada.
E-mail: cab.bishop@canada.ca
Monika Böhm Institute of Zoology, Zoological Society of London, Regent’s Park,
London NW1 4RY, UK. E-mail: monika.bohm@ioz.ac.uk
Xavier Bonnet CEBC-CNRS, 79360 Villiers en Bois, France.
E-mail: bonnet@cebc.cnrs.fr
Matthew Brien IUCN-SSC Crocodile Specialist Group, 6 Fitzmaurice Drive,
Bentley Park, QLD 4869, Australia. E-mail: matthew_brien@hotmail.com
François Brischoux CEBC-CNRS, 79360 Villiers en Bois, France.
E-mail: francois.brischoux@gmail.com
Keith A. Christian Research Institute for the Environment and Livelihoods, Charles
Darwin University, Darwin, NT 0909, Australia. E-mail: keith.christian@cdu.edu.au
Indraneil Das Institute of Biodiversity and Environmental Conservation, Universiti
Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia.
E-mail: idas@ibec.unimas.my
Tiffany M. Doan Department of Biology, University of Central Florida, 4000 Central
Florida Boulevard, Orlando, FL 32816, USA. E-mail: tiffperu@yahoo.com
C. Kenneth Dodd, Jr. Department of Wildlife Ecology and Conservation, University
of Florida, Gainesville, FL 32611, USA. E-mail: Terrapene600@gmail.com
Karen L. Eckert Wider Caribbean Sea Turtle Conservation Network, 1348
Rusticview Drive, Ballwin, MO 63011, USA. E-mail: keckert@widecast.org
John W. Ferner Department of Biology, Thomas More College, Crestview Hills, KY
41017, USA. [Mailing address: Casa de los Lagartos, 2966 E. Placita Santa Lucia,
Tucson, AZ 85716, USA.] E-mail: fernerjw@gmail.com
Robert N. Fisher U.S. Geological Survey, Western Ecological Research Center, San
Diego Field Station, 4165 Spruance Road, Suite 200, San Diego, CA 92101, USA.
E-mail: rfisher@usgs.gov
Nancy N. FitzSimmons Australian Rivers Institute, Griffith School
of Environment, Griffith University, Nathan, QLD 4111, Australia.
E-mail: n.fitzsimmons@griffith.edu.au
xxvi | List of Contributors

Steve W. Gotte U.S. Geological Survey, Patuxent Wildlife Research Center, National
Museum of Natural History, Museum Support Center, 4210 Silver Hill Road,
Suitland, MD 27046, USA. E-mail: sgotte@usgs.gov
Brian Gratwicke Smithsonian’s National Zoological Park, Smithsonian Conservation
Biology Institute, 3001 Connecticut Avenue NW, Washington, DC 20009, USA.
E-mail: gratwickeb@si.edu
Robert W. Henderson Milwaukee Public Museum, 800 W. Wells St., Milwaukee,
WI 53233, USA. E-mail: rh@mpm.edu
Brian T. Henen Post Office Box 1676, Twentynine Palms, CA 92277, USA.
E-mail: bthenen@yahoo.com
Margaretha D. Hofmeyr Biodiversity and Conservation Biology Department,
University of the Western Cape, Private Bag X17, Bellville 7535, South Africa.
E-mail: mdhofmeyr@uwc.ac.za
Jeremy F. Jacobs Department of Vertebrate Zoology, National Museum of Natural
History, Museum Support Center, 4210 Silver Hill Road, Suitland, MD 27046,
USA. E-mail: jacobsj@si.edu
Elliott R. Jacobson College of Veterinary Medicine, University of Florida,
Gainesville, FL 32610, USA. E-mail: jacobsone@ufl.edu
Bruce A. Kingsbury Department of Biology, Indiana University-Purdue
University Fort Wayne, Fort Wayne, IN 46805, USA;
E-mail: Bruce.Kingsbury@ipfw.edu
Gunther Köhler Senckenberg Forschungsinstitut und Naturmuseum,
Senckenberganlage 25, 60325 Frankfurt a.M., Germany.
E-mail: gkoehler@senckenberg.de
Pilar Lopez Departamento de Ecologia Evolutiva, Museo Nacional de Ciencias
Naturales, CSIC, Jose Gutierrez Abascal 2, 28006 Madrid, Spain.
E-mail: pilar.lopez@mncn.csic.es
Luca Luiselli Environmental Studies Centre Demetra, via Olona 7, I-00198 Rome,
Italy. E-mail: lucamlu@tin.it
Darryl I. MacKenzie Proteus Wildlife Research Consultants, P.O. Box 7, Outram
9062, New Zealand. E-mail: darryl@proteus.co.nz
Marco Mangiacotti Museo Civico di Storia Naturale di Milano, Corso Venezia, 55,
20121 Milan, Italy. E-mail: marco.mangiacotti@gmail.com
Charlie Manolis Wildlife Management International, P.O. Box 530, Karama, NT
0813, Australia. E-mail: cmanolis@wmi.com.au
Jose Martín Departamento de Ecologia Evolutiva, Museo Nacional de Ciencias
Naturales, CSIC, Jose Gutierrez Abascal 2, 28006 Madrid, Spain.
E-mail: Jose.Martin@mncn.csic.es
Lindsay Renick Mayer Global Wildlife Conservation, P.O. Box 129, Austin, TX
78767, USA. E-mail: renickmayer@gmail.com
 List of Contributors | xxvii

Earl D. McCoy Department of Integrative Biology, University of South Florida,

Tampa, FL 33620, USA. E-mail: edm@mail.usf.edu
Stephen J. Mullin Department of Biology, Stephen F. Austin State University,
Nacogdoches, TX 75962, USA. E-mail: sjmullin@sfasu.edu
Henry R. Mushinsky Department of Integrative Biology, University of South Florida,
Tampa, FL 33620, USA. E-mail: mushinsk@usf.edu
Matthew Neff Smithsonian’s National Zoological Park, Reptile Discovery Center, 3001
Connecticut Avenue NW, Washington, DC 20009, USA. E-mail: NeffM@si.edu
David A. Pike College of Marine and Environmental Sciences, James Cook
University, Townsville, QLD 4811, Australia. [Mailing address: 5108 Holland
Avenue, Tampa, FL 33617, USA.] E-mail: david.pike22@gmail.com
Michael V. Plummer Department of Biology, Box 12251, Harding University, Searcy,
AR 72149, USA. E-mail: plummer@harding.edu
Viorel D. Popescu Ohio University, Biological Sciences, 107 Irvine Hall, Athens,
OH 45701, USA. E-mail: popescu@ohio.edu
Robert Powell Department of Biology, Avila University, 11901 Wornall Road,
Kansas City, MO 64145, USA. E-mail: Robert.Powell@avila.edu
Arne R. Rasmussen School of Conservation Esplanaden 34, 1263 København K,
Denmark. E-mail: arr@kadk.dk
Nathan J. Robinson The Leatherback Trust, Golding-Gund Marine Biology Station,
Playa Grande, Guanacaste, Costa Rica. E-mail: nathanjackrobinson@gmail.com
J. Andrew Royle USGS Patuxent Wildlife Research Center, 12100 Beech Forest
Road, Laurel, MD 20708, USA. E-mail: andy_royle@usgs.gov
Sharon Ryan Smithsonian Tropical Research Institute, Apartado Postal 0843–03092,
Panamá, República de Panamá. E-mail: RyanSM@si.edu
Roberto Sacchi Dipartimento di Scienze della Terra e dell’Ambiente, Università di
Pavia, 27100 Pavia, Italy. E-mail: roberto.sacchi@unipv.it
Marco Sannolo CIBIO, Research Centre in Biodiversity and Genetic
Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, Rua
Padre Armando Quintas N.7, 4485-661 Vairão, Vila do Conde, Portugal.
E-mail: marco.sannolo@gmail.com
Stefano Scali Museo Civico di Storia Naturale di Milano, Corso Venezia, 55, 20121
Milan, Italy. E-mail: stefano.scali@comune.milano.it
Richard A. Seigel Department of Biological Sciences, Towson University, 8000 York
Road, Towson, MD 21252, USA. E-mail: rseigel@towson.edu
Jennifer Sevin Center for Leadership in Global Sustainability, 900 North Glebe
Road, Arlington, VA 22203, USA. E-mail: jennifer.sevin@gmail.com
Seth Stapleton Jumby Bay Hawksbill Project, Jumby Bay, P.O. Box 243, St. John’s,
Antigua, West Indies. [Mailing address: 1317 Juno Ave., St. Paul, MN 55116,
USA.] E-mail: seth@jbhp.org
xxviii | List of Contributors

Joanna Sumner Museum Victoria, GPO Box 666, Melbourne, VIC 3001, Australia.
E-mail: jsumner@museum.vic.gov.au
Chris Sutherland Department of Environmental Conservation, University of
Massachusetts Amherst, Amherst, MA 01379, USA. E-mail: csutherland@umass.edu
Christopher R. Tracy Department of Biological Sciences, California State
University Fullerton, 800 N. State College Blvd., Fullerton, CA 92831, USA.
E-mail: ctracy@fullerton.edu
C. Richard Tracy Department of Biology, MS-315, University of Nevada, Reno,
Reno, NV 89557, USA. E-mail: dtracy@unr.edu
Laurie J. Vitt Sam Noble Museum, University of Oklahoma, 2401 Chautauqua
Avenue, Norman, OK 73072, USA. E-mail: vitt@ou.edu
Richard C. Vogt INPA/CBIO, Av. André Araújo, nº 2.936, Petrópolis, CEP 69.067–
375, Manaus, Amazonas, Brazil. E-mail: vogt@inpa.gov.br
John D. Willson Department of Biological Sciences, University of Arkansas,
Fayetteville, AR 72701, USA. E-mail: jdwillson@uark.edu
Marco A.L. Zuffi Museo Storia Naturale di Pisa, Università di Pisa, Via Roma 79,
56011 Calci (Pisa), Italy. E-mail: marco.zuffi@unipi.it
George R. Zug Department of Vertebrate Zoology-MRC162, National Museum of
Natural History, P.O. Box 37012, Washington, DC 20013, USA.
E-mail: zugg@si.edu
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