Testing ecoregion limits with woody versus herbaceous taxa: Are ecoregions the same for different growth forms? Kelsey M. Dix Royal Botanic Garden Edinburgh, 20 Inverleith Row, Edinburgh EH3 5LR, UK Thesis submitted in partial fulfillment of the requirement for the degree of MSc in the Biodiversity and Taxonomy of Plants 2 “Quite obviously, the clarity of the boundaries between the floral kingdoms (and between the phytochoria at lower levels of Takhtajan’s system) is variable, depending on the nature of the barrier between them and on the history of their floras.” – Cox 2001, p. 521 “Following Wallace, we might stipulate that floral Kingdoms, like zoogeographic regions, must be areas of similar size, compact, and easily defined.” - Cox 2001, p. 520 3 Abstract Ecoregions are thought to be useful to understand patterns of species diversity across space and time. In principle, they are relatively uniform geographic areas in terms of biotic composition, often used as baseline units in biogeographical regionalization, and thus in ecological, evolutionary and global change research. This study tests the existence of ecoregions as floristic units, delineated by boundaries that reflect spatial discontinuities in species composition. It also examines the extent to which herbaceous and woody plants form similar ecoregions. Using the known flora of Nicaragua as a case study, both taxonomic and phylogenetic species turnover metrics are utilized to test for boundaries delineating ecoregions. Results from categorical wombling, a boundary detection method designed for depicting zones of rapid change across space, demonstrate that ecoregions do exist for both growth forms and that boundaries are greater and more efficent for woody taxa. Thus, ecoregions exhibit different patterns for herbs and trees, potentially due to niche conservatism and dispersal limitations. Keywords: Ecoregions, categorical wombling, Nicaragua, boundary detection, biogeography, beta-diversity 4 Acknowledgements Supervisors Dr. Tiina Särkinen and Dr. Iván Jiménez gave superb guidance in grasping the methods and results. Dr. Adam Smith contributed to the comprehension of species distribution modeling and offered feedback on initial results. Species distribution modeling was conducted by Smith, the flora phylogeny was completed by Särkinen and premliminary R scripts written by Jiménez. Olga Martha Montiel and Doug Stevens shared vital information on Nicaragua and its flora. Dr. Peter Stevens, who is quoted “the universe is inappropriate”, aided in evaluating and resolving phylogenetic topologies. Charlotte Taylor and Peter Moonlight supplied Rubiaceae and Begoniaceae phylogenetic affiliations, respectively. The Royal Society International Exchange Scheme provided funding for travel to Missouri Botanic Garden. Russ and Shelley Dix donated time and wordsmith knowledge for betterment of this thesis. 5 Contents Abstract....................................................... 3 Acknowledgements............................................... 4 Contents....................................................... 5 List of Figures .............................................. 7 List of Tables ............................................... 8 1 Introduction ............................................... 9 1.1 Ecoregions: Definition and debate ....................... 9 1.2 History, importance, and application of ecoregions ..... 11 1.1.1 History ............................................ 12 1.1.2 Importance and application ......................... 14 1.3 Evaluating ecoregions .................................. 16 1.4 Available methods for exploring ecoregions ............. 18 1.5 Effect of life history ................................. 22 1.6 Study aims and hypotheses .............................. 24 2 Methods ................................................... 25 2.1 Flora of Nicaragua ..................................... 25 2.2 Species occurrence data ................................ 28 2.3 Species Distribution Modeling .......................... 29 2.4 Flora phylogeny ........................................ 35 2.4.1 Phylogenetic tree estimation ....................... 35 2.4.2 Time calibration ................................... 36 2.5 Analysis of representativeness ......................... 39 2.5.1 Taxonomic .......................................... 39 2.5.2 Growth form ........................................ 41 2.6 Categorical wombling ................................... 46 6 2.6.1 Measuring β-diversity .............................. 46 2.6.2 Categorical wombling method ........................ 49 2.6.3 Null models ........................................ 51 2.6.4 Significance testing ............................... 53 3 Results ................................................... 56 3.1 Categorical wombling ................................... 56 3.1.1 Identifying ecoregions for growth forms ............ 59 3.1.2 Identifying differences in ecoregions .............. 59 4 Discussion ................................................ 69 4.1 General findings ....................................... 69 4.2 Why woody species show stronger ecoregions? ............ 71 4.3 Study limitations and strengths ........................ 73 4.4 Implications and further research ...................... 76 5 Conclusion ................................................ 79 6 References ................................................ 81 Appendix 1................................................... 104 7 List of Figures Figure 1. .................................................... 14 Figure 2...................................................... 26 Figure 3...................................................... 32 Figure 4...................................................... 33 Figure 5...................................................... 37 Figure 6...................................................... 42 Figure 7...................................................... 43 Figure 8...................................................... 44 Figure 9. .................................................... 45 Figure 10..................................................... 48 Figure 11..................................................... 51 Figure 12..................................................... 53 Figure 13..................................................... 57 Figure 14..................................................... 58 Figure 15..................................................... 61 Figure 16..................................................... 62 Figure 17..................................................... 63 Figure 18. ................................................... 65 Figure 19..................................................... 66 Figure 20..................................................... 67 Figure 21..................................................... 68 Figure 22..................................................... 78 8 List of Tables Table 1....................................................... 10 Table 2....................................................... 21 Table 3. ..................................................... 25 Table 4. ..................................................... 27 Table 5....................................................... 29 Table 6....................................................... 29 Table 7....................................................... 31 Table 8....................................................... 34 Table 9....................................................... 38 Table 10...................................................... 39 Table 11...................................................... 39 Table 12...................................................... 40 Table 13...................................................... 42 Table 14...................................................... 42 Table 15...................................................... 64 Table 16...................................................... 64 9 1 Introduction 1.1 Ecoregions: Definition and debate The widely accepted idea that the world consists of regions with differing biological structures has profoundly influenced how humanity comprehends and relates to natural landscapes (Whittaker et al., 2005). Ecoregions are categorical biogeographic divisions that have been used in science and conservation to characterize spatial variation in biotic composition at broad geographic scales (e.g., Olson et al., 2001). Ecoregions can be seen as baseline units of broad-scale biogeographic categorizations such as biogeographic realms (Holt et al., 2013) and floristic regions (Takhtajan, 1986). Definitions of ecoregions and biogeographic divisions vary between and within scientific fields, with inconsistencies in their categorization and partition (Table 1; Donoghue and Edwards, 2014; Hughes et al., 2013; Kent et al., 2006; Mackey et al., 2007). More recently, studies have aimed at developing biogeographic units that consider both ecological and biogeographic factors and conside the possibility that such units constitue evolutionary meta-communities through time (Hughes et al., 2013; Särkinen et al., 2011). The term ecoregion was initially introduced for land use management (Bailey, 1983, 1986, 1996; U.S. Forest Service, 1993), but has developed into a well-established concept across biology. Since the publication of one of the most influential biogeographic regionalizations by WWF in 2001, ecoregions have become a commonly used concept in biological sciences