Development, armed conflict and conservation: improving the effectiveness of conservation decisions in conflict hotspots using Colombia as a case study Pablo Jose Negret Master in Biological Science, Los Andes University A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2019 School of Earth and Environmental Sciences Abstract Pressure on Earth’s biodiversity is increasing worldwide, with at least one million species threatened with extinction and a 67% decline in vertebrate species populations over the last half century. Practical conservation actions that are able to generate the greatest conservation benefit in the most efficient way are needed. Colombia, a mega-diverse country, has the potential to preserve a considerable portion of the world’s biodiversity, making conservation in the country both regionally and globally relevant. However, human activities are transforming the country’s natural landscapes at an extremely high rate, making urgent the generation of effective conservation actions. Colombia, after decades of civil unrest, is now entering a post-conflict era. But the peace agreement signed in 2016 between the Colombian government and the strongest illegal armed group, FARC-EP is impacting the country’s biodiversity. New pressures are being imposed on areas of high biodiversity that previously were off-limits for development because of the conflict. This makes the generation of conservation plans particularly urgent. Post-conflict planning initiatives have the potential to limit environmental damage and increase formal protection of the most irreplaceable natural areas of Colombia. These plans need to be informed by an understanding of changes in risks to areas of high biodiversity importance, and the effectiveness of conservation efforts such as protected areas. i The aim of this thesis was to contribute knowledge to improve the effectiveness of conservation decisions in Colombia through a better understanding of the threats to forest ecosystems and the species that inhabit them, and an evaluation of the effectiveness of land protection for biodiversity conservation in the country. I first reviewed the effect of armed conflict on biodiversity in other countries in order to explore what may change with the peace agreement in Colombia. Post-conflict periods in other regions have often had negative impacts on biodiversity. Based on this, I recommended that the Colombian conservation science community engage actively in the development of environmental zoning plans on territories that were under the control of illegal armed groups to ensure positive and durable outcomes for the nation’s globally significant biodiversity. Second, in order to understand the effect of armed conflict on deforestation in Colombia I analysed the spatial association between deforestation drivers and forest cover change in the country, with a particular focus on the effect of armed conflict and coca plantations (Erythroxylum coca). I generated spatial predictions of deforestation pressure based on the period 2000-2015 and then explored how armed conflict and coca cultivation were associated with spatial patterns of deforestation. My results showed that proximity to coca plantation and armed conflict intensity both increased deforestation pressure, as did proximity to roads, mining concessions and oil exploitation wells. In some regions of Colombia, lack of stable governance after the peace accords is actually increasing armed conflict at a local level, and my results suggest that those increases in conflict may increase deforestation in those areas. Third, I aimed to understand the impact of deforestation on biodiversity in Colombia, by assessing the loss of habitat for forest dependent birds in the country up to 2015, and explored the projected loss to 2040. A total of 550 forest-dependent species were individually analysed, including 69 regional endemics. I assessed the extent of deforestation impacts on entire forest bird assemblages at different scales and for different bird groups. I found that the vast majority of forest dependent birds (536; 96.5%) had been affected by loss of potential habitat and that 35% of the forest dependent bird species in Colombia had lost at least 35% of their potential habitat by 2015. If deforestation trajectories remain the same, 43% of forest dependent species will lose 43% or more of their suitable habitat by 2040. The Amazon foothills was highlighted as an area where habitat for particularly diverse assemblages of forest-dependent species was projected to be lost, while the north-east of the Antioquia ii department was highlighted as an area where projected deforestation will affect bird assemblages that have a particularly high concentration of endemic species. My analysis shows the far-reaching impact of deforestation not only on endangered species, but also on common and widely distributed ones as well as on entire assemblages. The main tool the Colombian government has used to avoid biodiversity loss and prevent land conversion has been the creation of nationally designated protected areas. However, the effectiveness of these areas in preventing deforestation is not known. I evaluated the effectiveness of protected areas in Colombia at reducing forest loss between 2000 and 2015. I used statistical matching to account for confounding factors in park location and accounted for spatial autocorrelation to determine statistical significance. The performance of different matching procedures - ways of generating matching pairs at different scales - were compared, as there is no standard procedure for applying this technique at multiple scales (such as nationally versus within departments). Differences in matching procedures affected substantially the performance of matching, resulting in different estimates of the effectiveness of protected areas. Independent matching performed best, and these estimates suggested that average forest loss inside protected areas in Colombia was 40% lower than average forest loss in matched unprotected sites. Protection significantly reduced deforestation but its effect differed among regions; protected areas in Caribe were the most effective, but this region had the smallest percentage of protected area coverage. Protected areas in the Amazon were moderately effective but had the highest net forest loss, and protected areas in Orinoco and Pacific regions were least effective. Overall, this thesis improves understanding of how armed conflict increases deforestation, including how its effect can be indirect, such as through the expansion of illegal crops such as coca; and of the extent to which deforestation continues to threaten forest-dependent birds in the country that is home to more bird species than any other. Losses of habitat for common and widespread forest-dependent species are as great as for endangered ones, and due to their crucial roles in ecosystem functioning common species need safeguarding as well. While protected areas do reduce deforestation in Colombia, statistical comparison with similar areas is needed to understand the magnitude of the effect, and some protected areas particularly in the Pacific and Orinoco regions are less effective when this comparison is done. As Colombia continues to move towards a post-conflict scenario the increased understanding of forest iii dynamics, their causes and consequences, are fundamental to helping improve conservation decisions to safeguard Colombia’s biodiversity. iv Declaration by author This thesis is composed of my original work, and contains no material previously published or written by another person except where due reference has been made in the text. I have clearly stated the contribution by others to jointly-authored works that I have included in my thesis. I have clearly stated the contribution of others to my thesis as a whole, including statistical assistance, survey design, data analysis, significant technical procedures, professional editorial advice, financial support and any other original research work used or reported in my thesis. The content of my thesis is the result of work I have carried out since the commencement of my higher degree by research candidature and does not include a substantial part of work that has been submitted to qualify for the award of any other degree or diploma in any university or other tertiary institution. I have clearly stated which parts of my thesis, if any, have been submitted to qualify for another award. I acknowledge that an electronic copy of my thesis must be lodged with the University Library and, subject to the policy and procedures of The University of Queensland, the thesis be made available for research and study in accordance with the Copyright Act 1968 unless a period of embargo has been approved by the Dean of the Graduate School. I acknowledge that copyright of all material contained in my thesis resides with the copyright holder(s) of that material. Where appropriate I have obtained copyright permission from the copyright holder to reproduce material in this thesis and have sought permission from co- authors for any jointly authored works included in the thesis. v Publications during candidature Peer reviewed papers – lead author Negret PJ, Allan J, Braczkowski A, Maron M, Watson JEM (2017). Need for conservation planning in postconflict Colombia. Conservation Biology 31, 1–6. Negret PJ, Sonter LJ, Watson JEM, Possingham HP, Jones KR, Suarez C, Ochoa-Quintero JM, Maron M (2019). Emerging evidence