The University of San Francisco USF Scholarship: a digital repository @ Gleeson Library | Geschke Center Master's Theses Theses, Dissertations, Capstones and Projects Spring 5-18-2018 Seeing Red: Analyzing IUCN Red List Data of South and Southeast Asian Amphibians Alexandra Gonzalez [email protected] Follow this and additional works at: https://repository.usfca.edu/thes Part of the Biology Commons Recommended Citation Gonzalez, Alexandra, "Seeing Red: Analyzing IUCN Red List Data of South and Southeast Asian Amphibians" (2018). Master's Theses. 1090. https://repository.usfca.edu/thes/1090 This Thesis is brought to you for free and open access by the Theses, Dissertations, Capstones and Projects at USF Scholarship: a digital repository @ Gleeson Library | Geschke Center. It has been accepted for inclusion in Master's Theses by an authorized administrator of USF Scholarship: a digital repository @ Gleeson Library | Geschke Center. For more information, please contact [email protected]. González 1 THESIS SEEING RED: ANALYZING IUCN RED LIST DATA OF SOUTH AND SOUTHEAST ASIAN AMPHIBIANS Submitted by Alexandra González Department of Biology, University of San Francisco In partial fulfillment of the requirements For the Degree of Master of Science University of San Francisco San Francisco, California 2018 Committee: Advisor: Dr. Jennifer Dever Dr. Patricia Francis-Lyon Dr. Naupaka Zimmerman González 2 ACKNOWLEDGMENTS To my committee members, Dr. Patricia Francis-Lyon and Dr. Naupaka Zimmerman, thank you for guiding me and for inspiring me to increase my technical abilities. I could not have done this without your support. To my advisor, Dr. Jennifer Dever, thank you for always believing in me and for bringing out the best in me. Your dedication to your work and commitment to your students have made a difference in my life. González 3 TABLE OF CONTENTS I. Introduction ………………………………………………………………………..……….6 Amphibian life history traits………………………………..………………………………………..7 Southeast Asia…………………………………………………...………………………………………….8 Threatening Processes: Southeast Asian Amphibian Threats……………………….……………………...9 Threatening Processes: Global Amphibian Threats…………………………...…………………….…… 10 IUCN Red List of Threatened Species…………………………………….…………………................... 13 Purpose…………………………………………………………………………..……………………..… 15 II. Materials and Methods………………………………………………..………………. 16 Threat Data Acquisition…………….…………………..………………………………………...16 Threat Data Analyses….………………………………..………………………………………...17 Threat Data Spatial Mapping……..………………………………………………………………19 III. Results……………………………………………………………………………………..21 Threat Data Analyses ……………………………………………………………………………………...21 Threat Data Spatial Mapping …………………….………………………………………………35 IV. Discussion …………………………………………………………………………..……41 Future Directions ……………………………………….……………………………………......44 V. Concluding Remarks ………………………………………………………..………….44 References………………………………………………………………………………….………….46 Appendix I: Increasing the Accessibility to Red List Threat Data …………..….50 Appendix II: Reclassifying Red List Categories ….…………….…….……..……….60 Appendix III: Hierarchical Clustering of Red List Threats ….…………….…….60 Appendix IV: Threat Data…………….………………….………………………………..61 Appendix V: Scripted Code ………….…….…………….………………………………..62 González 4 TABLE OF FIGURES Figure 1: Global amphibians, number of threats by Red List Category…………………………………….………..22 Figure 2: Global amphibians, Density Distribution of the number of threats by Red List Category………….…….23 Figure 3: Global amphibians, Total number of threat codes of Threatened (Critically Endangered, ………….……24 Endangered, Vulnerable) and Not Threatened (Least Concern, Near Threatened) amphibians Figure 4: Threats affecting Least Concern, Global Amphibians ……………………………………………………25 Figure 5: Threats affecting Near Threatened, Global amphibians ……………………………………..……………25 Figure 6: Threats affecting Vulnerable, Global amphibians ……………………………………...…………………25 Figure 7: Threats affecting Endangered, Global amphibians ………………………………………….……………25 Figure 8: Threats affecting Critically Endangered, Global amphibians …………………………….………………25 Figure 9: South and Southeast Asian amphibians, Red List Category by Threat Count …………..………………..26 Figure 10: Density Distribution of South and Southeast Asian amphibians, Red List Category by Threat Count …27 Figure 11: South and Southeast Asian amphibians, Total number of threat codes of Threatened (Critically ………28 Endangered, Endangered, Vulnerable) and Not Threatened (Least Concern, Near Threatened) amphibians. Figure 12: SE Asian amphibian threat totals, Least Concern ……………………………………………….………29 Figure 13: SE Asian amphibian threat totals, Near Threatened ……………………………………….…………….29 Figure 14: SE Asian amphibian threat totals, Vulnerable …………………………………...………………………29 Figure 15: SE Asian amphibian threat totals, Endangered ……………………………….…………………………29 Figure 16: SE Asian amphibian threat totals, Critically Endangered ………………………………………….……29 Figure 17: Species assessment year by Red List status. (Blue = Least Concern, Purple = Near Threatened, ...….…30 Pink = Vulnerable, Orange = Critically Endangered, Yellow = Data Deficient, Green = Endangered. Figure 18: Threat Score count by Threatened vs. Not Threatened category. ………….……………………………30 Figure 19: Figure 19: Correlation Heatmap of Threat Processes ……………………………………………………31 Map 1: Vulnerable amphibian distribution in Southeast Asia. ………………………………………………….......36 Map 2: Endangered amphibian distribution in Southeast Asia………………………………………………………36 Map 3: Threatened amphibians (Critically Endangered, Endangered, Vulnerable) distribution. ……….…………..36 Map 4: Species with a listed threat of Agriculture 2.1, in the Philippines ……………………………........………..37 Map 5: Species with a listed threat of Agriculture 2.2 in Borneo…………………………………………....………37 Map 6: Distribution of species that are being hunted and collected…………………………………………………37 Map 7: Species threatened by mining………………………………………………………………………………. 39 Map 8: Species threatened by human disturbances. …………………………………………………………………39 Map 9: Species threatened by Invasive non-native species/diseases……………………………………………….. 39 Map 10: Species threatened by Fire and fire suppression (includes threats of all timing)…………………………. 40 Map 11: Close up of species threatened by Fire and Figure suppression (includes threats of all timing)………...... 40 Map 12: Species threatened by residential and commercial development in Mindanao Islands, Philippines……… 41 Map 13: Species threatened by residential and commercial development in Borneo………………………………. 41 TABLE OF TABLES Table 1: Logistic Regression results #1……………………………………………………………………………...32 Table 2: Logistic Regression results #2……………………………………………………………………………...34 González 5 Abstract In the midst of the sixth mass extinction event which is currently underway, it appears that amphibians are one of the most impacted vertebrates. Over 6,500 amphibian species are listed on the IUCN Red List (an assessment tool which provides species’ conservation status, perceived threats, and distribution range). While it is well-known that populations under multiple stressors are more likely to undergo significant declines, there are little to no resources available for visualizing how these threats may work synergistically and interact within a species’ range. This is especially the case for Southeast Asian amphibians, which much less attention has been paid as compared to other parts of the globe. While the IUCN Red List provides a description of threats affecting species and categorizes species into Red List Categories (Least Concern, Near Threatened, Vulnerable, Endangered, Critically Endangered), this data is not easily accessible for wide-scale analyses. The aims of this project were as follows: (1) utilize bioinformatics to increase accessibility to IUCN Red List data, (2) analyze the IUCN data repository to identify trends in South and South East Asian amphibian threat data, and (3) plot IUCN threat data. I. INTRODUCTION Plagued by anthropogenic-induced activity, disease, and other threats, amphibian populations have been declining for decades, signaling a modern biodiversity crisis. These biodiversity losses are more than just declines, however. They are indicative of the 6th mass extinction that is currently underway (McCallum 2015). The current extinction rate for endangered amphibians ranges between 25,039-45,474 times the background extinction rate González 6 (McCallum 2007). Other models estimate the extinction rate at four orders-of-magnitude higher than the background extinction rate (Alroy 2015). Extinction rates may be greater than these models suggest, however, because single-threat drivers of extinction are often considered instead of synergetic threats (Brook et al. 2008). When the effects of multiple threat processes are considered, the overall risk of extinction is greater than previously speculated (Brook et al. 2008). Approximately 32.4% of amphibian species are threatened with extinction (Stuart 2004), representing 2,030 species (IUCN 2017). While 1/3 of amphibians are threatened with extinction, as many as 22.5% do not have sufficient data for their Red List Category to be characterized. On the IUCN Red List, these species are listed as Data Deficient (DD) and as of the 2017 IUCN update, 191 species (52.5%) of the 366 species added to the database in 2008 were DD. Current mathematical models strongly suggest that DD species are more likely to face extinction than documented amphibians (Howard et al. 2014). While the 6th mass extinction threatens all life, it seems as though amphibian