Understanding tropical biodiversity to improve reforestation outcomes: examples from the Philippines and Northern Australia Jarrah Dominic Wills Bachelor of Applied Science (Ecology), Queensland University of Technology A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2016 School of Agriculture and Food Sciences Abstract Tropical regions such as the Philippines and the Wet Tropics (WTs) bioregion of Northern Australia have seen dramatic declines in forest cover, primarily since respective Spanish, American and English colonization events. This has led to declines in biodiversity and ecosystem services, both of which support the livelihoods of a vast number of people. For example, drastic declines in forest cover in the Philippines and Northern Australia have seen large reductions in timber resources. In view of this, different reforestation types, including the management of ‘secondary forest’ regeneration, are being applied across the tropics in order to mitigate biodiversity loss and contribute to ecosystem services including timber production and biodiversity enhancement. To date, the ecology of these novel forests within the study regions have not been thoroughly investigated, from either conservation or a socio-economic perspectives. This research applies functional and phylogenetic approaches to gain insights into complex ecological processes such as regeneration and growth dynamics within different forest types. The forest types studied were established as small-scale community-based plantations located on the Island of Leyte in the Philippines, and included monocultures of Swietenia macrophylla King (mahogany), one of the most valuable timber species in the tropics; and mixed-species plantations established as a reforestation system called ‘Rainforestation Farming’ (here after, Rainforestation). Naturally regenerating selectively logged native forest located within Leyte and the WTs Bioregion was also included in this study. Within the Philippines, species, functional and phylogenetic diversity of understorey recruitment beneath the different forest types were compared and contrasted, in order to identify species or groups that were favoured or limited, and to compare community assembly processes. Within the WTs bioregion, I utilized a unique historical dataset, to investigate if leaf functional traits, such as Specific Leaf Area (SLA) or leaf nutrient contents, obtained from regenerating selectively logged forest trees, can be used to predict tree growth over time and how this relationship may vary depending on the position in the canopy. An improved understanding of the influence of these leaf traits could help to inform practitioners’ design of reforestation projects. Understorey recruitment, including species, functional and phylogenetic diversity, was influenced by the reforestation type in the Philippines. Generally, monocultures had the lowest diversity and regenerating selectively logged forest the highest, with the Rainforestation showing intermediate understorey diversity. Species within the Moraceae family were common across all forest types and wind-dispersed emergent-tree species were absent within the monoculture forest types. These trees represent a limited group of species, and their absence has consequences for future ecosystem function. Using phylogenetic relatedness and leaf traits, seedling communities were assembled II more by environmental filtering within monoculture forest types. Both environmental filtering and competitive exclusion seemed to be operating within the seedling communities of regenerating selectively logged forests. Human-assisted dispersal increased the levels of understorey diversity within monoculture forest types, indicating simple monocultures can provide some biodiversity benefits, and that these benefits are valued by local communities. Within regenerating selectively logged forests of the WTs bioregion, leaf functional trait and growth rate analysis revealed that leaf traits are weakly correlated to growth for trees that have reached the top layer of the canopy. However, for sub-canopy trees, leaf traits and growth relationships become stronger, suggesting that soft leaf traits are a stronger determinant of growth and success in the sub-canopy, whereas in the canopy other traits become more important. In particular leaf phosphorus alone positively explained the variation in Periodic Annual Increment (PAI). This highlights that a more nuanced outlook on leaf traits is required if they are going to provide insights into growth rates across multiple life-stages, and in order for these traits to have practical reforestation applications. Collectively, my research highlights the value of analysing additional aspects of biodiversity, in order to gain insights into ecological questions relating to reforestation outcomes. Specific implications of my study include an increased understanding of the conservation and reforestation significance of wind-dispersed emergent tree species, and species that are phylogenetically and functionally distinct (in terms of the mean and variation in leaf traits), resulting in greater ecosystem functioning; the conservation and socio-economic value of small-scale community monoculture plantations within human-dominated tropical landscapes; and that a more detailed understanding of leaf trait and growth relationships is needed if this theoretical research discipline is to benefit practical reforestation efforts. Some important future research questions identified as a result of my research include: What are the environmental factors (e.g., cyclone frequency, rainfall, elevation etc.) that influence the relative biomass of wind- versus animal-dispersed tree species? How does this vary between tropical continents? Can functional trait ecology provide more detailed groupings beyond pioneer versus non-pioneer species? Can these groupings be replicated across tropical forest ecosystems? III 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, 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 research higher degree 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. IV Publications during candidature Peer-reviewed papers Wills, J., Herbohn, J., Moreno, M.O.M., Avela, M.S. & Firn, J. (2016) Next-generation tropical forests: reforestation type affects recruitment of species and functional diversity in a human- dominated landscape. Journal of Applied Ecology, doi:10.1111/1365-2664.12770. Conference abstracts Jarrah Wills, Jennifer Firn and John Herbohn, 2014. Understory species and functional diversity beneath different reforestation methods. Accepted by The Association for Tropical Biology and Conversation (ATBC) Conference, Cairns, Australia 20-24 July 2014. Jarrah Wills, Jennifer Firn and John Herbohn, 2015. Understory species, functional and phylogenetic diversity beneath different reforestation methods. Accepted by The IUFRO 3.08 Small-Scale and Community Forestry and the Changing Nature of Forest Landscapes, Sunshine Coast, Australia, 11-15 October 2015. Publications included in this thesis I have chosen to incorporate one publication into my thesis as per UQ policy (PPL 4.60.07 Alternative Thesis Format Options). Wills, J., Herbohn, J., Moreno, M.O.M., Avela, M.S. & Firn, J. (2016) Next-generation tropical forests: reforestation type affects recruitment of species and functional diversity in a human- dominated landscape. Journal of Applied Ecology, doi:10.1111/1365-2664.12770 Incorporated as Chapter 3. Contributor Statement of contribution Author Jarrah Wills (Candidate) Designed experiment (50%) Wrote the paper (90%) Conducted field and lab work (60%) Author Jennifer Firn Designed experiment (40%) Wrote and edited paper (15%) Author John Herbohn Designed experiments (10%) Wrote and edited paper (5%) V Author Ofelia Moreno Conducted field and lab work (20%) Author Mayet Avela Conducted field and lab work (20%) VI Contributions by others to the thesis In addition to my supervisors Associate Professor Jennifer Firn and Professor John Herbohn who contributed throughout my thesis; Dr Jessie Wells provided feedback and advice for chapter