1 Foundational Skills and Values for Research in Conservation Biology

Exercise 1 Developing Critical Writing Skills

Background and Rationale

Analyzing and Evaluating a Scientific Paper

Assignment 1.A Writing a Summary of a Scientific Paper

The Scientific Abstract—A Useful Tool for Scientists

Assignment 1.B Preparing to Write a Scientific Abstract

Assignment 1.C Writing an Original Abstract

Questions and Assessment

Further Help in Scientific Writing

Synthesis

Literature Cited

Exercise 2 Developing Critical Reading Skills

Background and Rationale

Methods for Writing a Literature Review

Assignment 2.A Using Electronic Search Techniques

Questions and Assessment

Synthesis

Exercise 3 Analyzing Economic Values in Conservation Biology

Background and Rationale

Evaluating Economic Benefits and Costs in an Australian Forest

Assignment 3.A Calculating Total Costs and Benefits

Assignment 3.B Calculating the Value of Public Goods and Services

Questions and Assessment

Synthesis

Literature Cited

Exercise 4 Quantitative Measurement and Analysis of Biodiversity

Background and Rationale

Selecting Sampling Methods for Collecting Biodiversity Data

Assignment 4.A Line-Intercept Sampling

Assignment 4.B Point-Centered ("Point Quarter") Sampling

Assignment 4.C Using Spot Mapping

Computation of Biodiversity Data

Assignment 4.D Applying the Shannon Index

Assignment 4.E Comparing and Analyzing Biodiversity Data

Questions and Assessment

Synthesis

Literature Cited

2 Techniques for Genetic Conservation and Management

Exercise 5 Evaluating Phylogenetic Relationships through Genetic Criteria in Conservation

Background and Rationale

Using Mitochondrial DNA in Taxonomic Classification

Using Web-Based Resources for Genetic Analysis

Assignment 5.A Using Taxonomy Browser to Assess Genetic Data in Black Bear Subspecies

Assignment 5.B Using Genebee to Assess Genetic Diversity in Black Bear Subspecies

Questions and Assessment

Further Investigations

Synthesis

Literature Cited

Exercise 6 Conducting Simple Pedigree Analysis for a Captive Population

Background and Rationale

Pedigree Analysis

Assignment 6.A Drawing a Family Pedigree

Kinship

Assignment 6.B Determining Individual Kinship

Mean Kinship

Assignment 6.C Determining Mean Kinship

Population Mean Kinship

Assignment 6.D Calculating Population Mean Kinship

Inbreeding

Assignment 6.E Calculating the Inbreeding Coefficient

Questions and Assessment

Synthesis

Literature Cited

Exercise 7 Managing Gene Diversity in Captive Populations

Background and Rationale

Measuring Gene Diversity

Assignment 7.A Determining Gene Diversity in a Closed, Captive Population

Genetic Drift

Assignment 7.B Measuring the Effects of Genetic Drift

Retention of Gene Diversity

Assignment 7.C Effect of Number of Founders

Modeling and Managing Captive Populations

Assignment 7.D Calculating Effective Population Size

Assignment 7.E Modeling Future Gene Diversity in a Captive Population

Questions and Assessment

Synthesis

Literature Cited

Exercise 8 Implementing Alternative Captive-Breeding Strategies

Background and Rationale

Random Mating Strategy

Assignment 8.A Measuring Gene Diversity in a Strategy of Random Mating

Maximum-Avoidance-of-Inbreeding Strategy

Assignment 8.B Managing Captive Mating to Avoid Inbreeding

Mean Kinship Strategy

Assignment 8.C Devising and Evaluating a Mean Kinship Breeding Strategy

Combining Managed Mating Strategies and Natural Breeding Biology

Assignment 8.D Designing Mating Strategies for Breeding Groups

Combining Avoidance of Inbreeding with Minimizing Mean Kinship

Assignment 8.E Combining Avoidance of Inbreeding with Minimizing Mean Kinship

Questions and Assessment

Synthesis

Further Reading

Literature Cited

Exercise 9 Designing a Captive-Breeding Plan with Real-World Constraints

Background and Rationale

Realities of Managed Breeding Strategies in Captive Populations

Assignment 9.A Developing a Feasible Breeding Management Plan for Okapi

Questions and Assessment

Synthesis

3 Studies of Communities and Habitats

Exercise 10 Describing Communities and Populations Quantitatively for Conservation

Background and Rationale

Calculating Density, Dominance, Frequency, and Importance in Populations - An Example Using Forest Trees

Assignment 10.A Determining Density

Assignment 10.B Determining Dominance, Frequency, and Importance Values

Questions and Assessment

Synthesis

Literature Cited

Exercise 11 Estimation of Animal Home Ranges for Conservation

Background and Rationale

Methods of Estimating Home Range

Assignment 11.A Calculating and Interpreting Home Ranges Using the Program CALHOME

Assignment 11.B Making Calculations and Comparisons of Different Home Range Methods

Assignment 11.C Spatially Integrating Home Range Analysis and Environmental Disturbance

Assignment 11.D Creating a New Data Set

Questions and Assessment

Synthesis

Literature Cited

4 Experiences in Population Modeling and Population Viability Analysis

Exercise 12 Creating a Stage-Based Deterministic PVA Model - The Western Prairie Fringed Orchid

Background and Rationale

Natural History and Conservation Status of the Western Prairie Fringed Orchid

Stage-Based Deterministic Models

Assignment 12.A Determining Transition Probabilities between Stages

Assignment 12.B Constructing Transition Matrices for the Western Prairie Fringed Orchid

Assignment 12.C Calculating Population Data

Assignment 12.D Predicting Outcomes for Average Conditions

Assignment 12.E Predicting Outcomes for Wet Conditions

Assignment 12.F Predicting Outcomes for Dry Conditions

Questions and Assessment

Synthesis

Literature Cited

Exercise 13 The Concept and Use of Elasticity in Population Viability Analysis

Background and Rationale

Making Projections

Assignment 13.A Elasticity Analysis of Model Transitions

Assignment 13.B Analyzing the Effect of Zero Seed Viability

Assignment 13.C Analyzing the Effect of Zero Seed Viability with Increased Seed Production

Assignment 13.D Analyzing the Effect of Zero Seed Viability Using the Wet Conditions Model

Questions and Assessments

Synthesis

Literature Cited

Exercise 14 Using Stochastic Models to Incorporate Spatial and Temporal Variability

Background and Rationale

Demographic and Environmental Stochasticity in the Western Prairie Fringed Orchid

Assignment 14.A Running a Staged-Based, Stochastic Population Viability Analysis Model

Adding Environmental Stochasticity

Assignment 14.B Running the Model with Three Climate Scenarios

Questions and Assessment

Synthesis

Literature Cited

Exercise 15 Conservation and Management Applications in Population Viability Analysis

Background and Rationale

Simulating the Effects of Lowering the Water Table

Assignment 15.A Simulating the Effects of Drier Conditions and Lowering of the Water Table

Using Core Protected Areas in Orchid Conservation

Assignment 15.B Simulating Orchid Management Using Core Protected Areas

Global Climate Trends and Orchid Conservation

Assignment 15.C Assessing the Effects of Global Climate Trends

Water Table Drawdown, Global Climate Trends, and Grazing Management

Assignment 15.D Simulating the Effects of Multiple Factors at Once

Questions and Assessment

Synthesis

Literature Cited

5 Applications on Habitat Assessment and Conservation Planning

Exercise 16 Land-Use Classification and Species Conservation

Background and Rationale

Using Geographic Information Systems

Assignment 16.A Steps in Spatial Analysis

Assignment 16.B Selecting Themes of Interest

Assignment 16.C Identifying Specific Information for Analysis

Assignment 16.D Making Computations from and Intersections of Selected Data Sets

Assignment 16.E Calculating the Area of Sage Grouse Nesting Habitat on BLM Lands

Assignment 16.F Calculating Total Area of Sage Grouse Nesting Habitat

Questions and Assessment

Synthesis

Literature Cited

Exercise 17 Using GIS to Classify Habitat Types and Identify Habitat Conservation Areas

Background and Rationale

GIS and Remotely Sensed Data

Assignment 17.A Arranging and Activating GIS Themes for Habitat Classification

Assignment 17.B Constructing a Classification Function for Sagebrush Habitat

Assignment 17.C Incorporating Physical Attributes to Refine and Apply a Habitat Classification Algorithm

Uncertainty in Habitat Classification Using GIS

Assignment 17.D Identifying Sagebrush Habitat on Bureau of Land Management Lands

Assignment 17.E Identifying Potential Habitat Conservation Areas - Refuge Design

Questions and Assessment

Synthesis

Appendix: Notes for Instructors