Mammalogy Techniques Lab Manual

Acknowledgments
Chapter 1. Introduction
Background
How to Use This Manual
R Statistical Environment
Chapter 2. Mammal Skulls
Background
Bones and Features of the Skull
Variation in Mammalian Skulls
Zygomatic Morphology in Rodents
Telescoping in Cetaceans
Skull Measurements
Exercise 1: The Nuts and Bolts
Exercise 2: Dichotomous Keys of Skulls
Exercise 3: Mystery Mammal Skull
Appendix
Chapter 3. Mammalian Teeth
Background
Internal Structure
Kinds of Teeth
Occlusal Patterns and Cusps
Types of Teeth and Diet
Tooth Replacement
Dental Formulas
Exercise 1: Dental Terminology
Exercise 2: Dental Key to North American Mammals
Chapter 4. Phylogeny Reconstruction
Background
How Do We Construct Phylogenetic Trees?
Exercise 1: Manual Sequence Alignment
Exercise 2: Sequence Alignment Using Computers
Exercise 3: Exploring the Open Tree of Life
Chapter 5. Keeping a Field Notebook
Background
Why Keep a Field Notebook?
Elements of a Field Journal
Two-Part Field Notes
Grinnell Method
Exercise 1: Locality Information Using Topo Maps
Exercise 2: Taking Field Notes
Chapter 6. Livetrapping Small Mammals
Background
Live Traps
Exercise 1: Setting up a Livetrapping Grid
Exercise 2: Checking Traps and Collecting Capture Data
Handling Captured Mammals
Marking Mammals
Sexing and Aging Small Mammals
Measuring Small Mammals
Exercise 3: Data Collection and Analysis
Appendix
Chapter 7. Specimen Preparation
Why Collect Specimens?
Documenting Specimens
Exercise 1: Taking Standard Measurements
Recording Reproductive Data
Preparing Museum Specimens
Exercise 2: Preparing a Museum Study Skin
Exercise 3: Preparing Skulls
Exercise 4: Preparing Skeletons
Chapter 8. Field Collecting and Preserving Mammalian Parasites
Background
Exercise 1: Making a Blood Smear
Exercise 2: Collecting Ectoparasites
Exercise 3: Collecting Endoparasites
Exercise 4: Preliminary Ectoparasite Identification
Exercise 5: Ectoparasite Population Ecology
Chapter 9. Mark-Recapture Studies
Background
Lincoln-Petersen Method
Schnabel Model
Jolly-Seber Model
Exercise 1: Single Mark-Recapture (Lincoln-Petersen Method)
Exercise 2: The Schnabel Method
Exercise 3: The Jolly-Seber Model Using Excel
Appendix
Chapter 10. Using Software for Mark-Recapture Data
Background
Capture Probability and Encounter Histories
Capture Models
Exercise 1: Using the Program CAPTURE
Exercise 2: Tigers in India
Exercise 3: Mark-Recapture Sampling Using Rcapture
Appendix A
Appendix B
Chapter 11. Transects: Using Distance Sampling
Background
Indirect Data
Field Procedures
Indirect Transect Surveys
Exercise 1: Conducting Deer Pellet Transect Surveys
Exercise 2: Dung Counts Using PELLET
Exercise 3: Data Analysis Using Rdistance in RStudio
Chapter 12. Camera Trapping
Background
Camera Selection
Survey Design
Exercise 1: A Camera-Trap Field Study
Data Analysis
Exercise 2: Data Analysis from Camera-Trap Studies
Exercise 3: Using camtrapR to Analyze Camera-Trap Data
Chapter 13. Radio Tracking
Background
Types of Radio-Telemetry Studies
Radio-Telemetry Equipment
Locating Animals
Exercise 1: Locating Animals by Homing
Exercise 2: Locating Animals via Triangulation
Exercise 3: Data Analysis: The Minimum Convex Polygon
Exercise 4: Data Analysis Using sigloc in RStudio
Exercise 5: Using adehabitatHR in RStudio
Chapter 14. GPS Tracking Using GPSVisualizer and MoveBank
Background
Exercise 1: Tracking Grizzly Bears with GPSVisualizer
Exercise 2: Exploring MoveBank Data
Chapter 15. Recording and Analyzing Mammal Sounds
Background
Equipment for Recording Sounds
Software for Analyzing Sounds
Interpreting a Sonogram
Exercise 1: Field Recording
Exercise 2: Sound Analysis Using Audacity
Exercise 3: Playback Experiments Using Alarm Calls
Chapter 16. Quantifying Mammalian Behavior
Background
Avoiding Common Problems
Exercise 1: Building an Ethogram
Exercise 2: Sampling Behaviors
Exercise 3: Creating a Time Budget
Exercise 4: Creating a Transition Diagram
Exercise 5: Creating a Dominance Hierarchy
Exercise 6: Dominance Hierarchy Analysis
Exercise 7: Social Network Analysis Using igraph
Chapter 17. Optimal Foraging Behavior
Background
Foraging in Patches
Exercise 1: Profitability and Prey Choice
Exercise 2: Foraging in Patches
Exercise 3: Foraging with Risk
Appendix
Chapter 18. Field Karyotyping
Background
What Is a Karyotype?
How Are Karyotypes Produced?
Exercise 1: Field Karyotyping
Exercise 2: G-banding Chromosomes with Trypsin
Exercise 3: Analyzing the Karyotype Manually
Exercise 4: Measuring Chromosomes with ImageJ Software
Appendix A
Appendix B
Chapter 19. Non-invasive Hair Sampling
Background
Hair Morphology
Exercise 1: Field Methods for Collecting Hairs
Exercise 2: Creating a Hair Reference Collection
Exercise 3: Quantifying Hair Structure Using ImageJ Software
Exercise 4: Extracting DNA from Hair Samples
Instructor Resources
General Field Equipment Sources
Mammalian Skulls and Skeletons
Biotelemetry Resources
Camera Traps
Sound Recording
Ultrasound Recording Equipment (Bat Detectors)
Glossary
Bibliography
Index