Reptile Ecology and Conservation

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.

1

Reptile Ecology

and Conservation

A Handbook of Techniques

Edited by

C. Kenneth Dodd, Jr.

3

Great Clarendon Street, Oxford, OX2 6DP,

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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 I

3S, 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