Spatial processes underlie major species coexistence mechanisms. A range of spatial analysis techniques are increasingly applied to data of fully mapped communities to quantify spatial structures in species and phylogenetic and functional diversity at some given spatial scale with the goal of gaining insights into processes of community assembly and dynamics. We review these techniques, including spatial point pattern analysis, quadrat-based analyses, and individual-based neighborhood models, and provide a practical roadmap for ecologists in the analysis of local spatial structures in species and phylogenetic and functional diversity. We show how scale-dependent metrics of spatial diversity can be used in concert with ecological null models, statistical models, and dynamic community simulation models to detect spatial patterns, reveal the influence of the biotic neighborhood on plant performance, and quantify the relative contribution of species interactions, habitat heterogeneity, and stochastic processes to community assembly across scale. Future works should integrate these approaches into a dynamic spatiotemporal framework.


Article metrics loading...

Loading full text...

Full text loading...


Literature Cited

  1. Allesina S, Levine JM. 2011. A competitive network theory of species diversity. PNAS 108:145638–42 [Google Scholar]
  2. Anderson MJ, Crist TO, Chase JM, Vellend M, Inouye BD. et al. 2011. Navigating the multiple meanings of beta diversity: a roadmap for the practicing ecologist. Ecol. Lett. 14:119–28 [Google Scholar]
  3. Anderson-Teixeira KJ, Davies SJ, Bennett AC, Gonzalez-Akre EB, Muller-Landau HC. et al. 2015. CTFS-ForestGEO: a worldwide network monitoring forests in an era of global change. Glob. Change Biol. 21:2528–49 [Google Scholar]
  4. Baddeley A, Rubak E, Turner R. 2016. Spatial Point Patterns: Methodology and Applications with R Boca Raton, FL: Chapman and Hall/CRC Press [Google Scholar]
  5. Bolker BM, Pacala SW, Neuhauser C. 2003. Spatial dynamics in model plant communities: What do we really know. Am. Nat. 162:2135–48 [Google Scholar]
  6. Brown C, Illian JB, Burslem DFRP. 2016. Success of spatial statistics in determining underlying process in simulated plant communities. J. Ecol. 104:1160–72 [Google Scholar]
  7. Brown C, Law R, Illian JB, Burslem DFRP. 2011. Linking ecological processes with spatial and non-spatial patterns in plant communities. J. Ecol. 99:61402–1414 [Google Scholar]
  8. Canham CD, Lepage PT, Coates KD. 2004. A neighborhood analysis of canopy tree competition: effects of shading versus crowding. Can. J. For. Res. 34:4778–87 [Google Scholar]
  9. Canham CD, Uriarte M. 2006. Analysis of neighborhood dynamics of forest ecosystems using likelihood methods and modeling. Ecol. Appl. 16:162–73 [Google Scholar]
  10. Cavender-Bares J, Ackerly DD, Baum DA, Bazzaz FA. 2004. Phylogenetic overdispersion in Floridian oak communities. Am. Nat. 163:6823–43 [Google Scholar]
  11. Chacón-Labella J, de la Cruz M, Escudero A. 2016. Beyond the classical nurse species effect: diversity assembly in a Mediterranean semi-arid dwarf shrubland. J. Veg. Sci. 27:80–88 [Google Scholar]
  12. Chesson P. 2000. Mechanisms of maintenance of species diversity. Annu. Rev. Ecol. Syst. 31:343–66 [Google Scholar]
  13. Clarke KR, Warwick RM. 1998. A taxonomic distinctness index and its statistical properties. J. Appl. Ecol. 35:4523–31 [Google Scholar]
  14. Colwell RK, Winkler DW. 1984. A null model for null models in biogeography. Ecological Communities: Conceptual Issues and the Evidence DR Strong, DS Simberloff, LG Abele, AB Thistle 344–59 Princeton, NJ: Princeton Univ. Press [Google Scholar]
  15. Comita LS, Muller-Landau HC, Aguilar S, Hubbell SP. 2010. Asymmetric density dependence shapes species abundances in a tropical tree community. Science 329:330–32 [Google Scholar]
  16. Condit R. 1998. Tropical Forest Census Plots Berlin: Springer-Verlag [Google Scholar]
  17. Condit R, Pitman N, Leigh EG, Chave J, Terborgh J. et al. 2002. Beta diversity in tropical forest trees. Science 295:666–69 [Google Scholar]
  18. Connell JH. 1980. Diversity and the coevolution of competitors, or the ghost of competition past. Oikos 35:131–38 [Google Scholar]
  19. Connell JH, Tracey JG, Webb LJ. 1984. Compensatory recruitment, growth, and mortality as factors maintaining rain forest tree diversity. Ecol. Monogr. 54:141–64 [Google Scholar]
  20. Connor EF, Simberloff D. 1979. The assembly of species communities: chance or competition. Ecology 60:1132–40 [Google Scholar]
  21. Cornwell WK, Schwilk DW, Ackerly DD. 2006. A trait-based test for habitat filtering: convex hull volume. Ecology 87:1465–71 [Google Scholar]
  22. de Bello F, Carmona CP, Lepš J, Szava-Kovats R, Pärtel M. 2016. Functional diversity through the mean trait dissimilarity: resolving shortcomings with existing paradigms and algorithms. Oecologia 180:933–40 [Google Scholar]
  23. Dray S, Pélissier R, Couteron P, Fortin MJ, Legendre P. et al. 2012. Community ecology in the age of multivariate multiscale spatial analysis. Ecol. Monogr. 82:3257–75 [Google Scholar]
  24. Fortunel C, Valencia R, Wright SJ, Garwood NC, Kraft NJB. 2016. Functional trait differences influence neighbourhood interactions in a hyperdiverse Amazonian forest. Ecol. Lett. 19:1062–70 [Google Scholar]
  25. Gotelli NJ. 2000. Null model analysis of species co-occurrence patterns. Ecology 81:2606–21 [Google Scholar]
  26. Gotelli NJ, Graves GR. 1996. Null Models in Ecology Washington, DC: Smithsonian Inst. Press [Google Scholar]
  27. Grimm V, Revilla E, Berger U, Jeltsch F, Mooij W. et al. 2005. Pattern-oriented modeling of agent-based complex systems: lessons from ecology. Science 310:987–91 [Google Scholar]
  28. Hardy OJ. 2008. Testing the spatial phylogenetic structure of local communities: statistical performances of different null models and test statistics on a locally neutral community. J. Ecol. 96:914–26 [Google Scholar]
  29. Hardy OJ, Senterre B. 2007. Characterizing the phylogenetic structure of communities by an additive partitioning of phylogenetic diversity. J. Ecol. 95:493–506 [Google Scholar]
  30. Hartig FJ, Calabrese JM, Reineking B, Wiegand T, Huth A. 2011. Statistical inference for stochastic simulations models—theory and application. Ecol. Lett. 14:816–27 [Google Scholar]
  31. Helmus MR, Savage K, Diebel MW, Maxted JT, Ives AR. 2007. Separating the determinants of phylogenetic community structure. Ecol. Lett. 10:917–25 [Google Scholar]
  32. Hubbell SP. 2006. Neutral theory and the evolution of ecological equivalence. Ecology 87:1387–98 [Google Scholar]
  33. Hubbell SP, Ahumada JA, Condit R, Foster RB. 2001. Local neighborhood effects on long-term survival of individual trees in a neotropical forest. Ecol. Res. 16:5859–75 [Google Scholar]
  34. Hubbell SP, Foster RB. 1986. Biology, chance and history and the structure of tropical rain forest tree communities. Community Ecology JM Diamond, TJ Case 314–29 New York: Harper & Row [Google Scholar]
  35. Illian J, Penttinen A, Stoyan H, Stoyan D. 2008. Statistical Analysis and Modelling of Spatial Point Patterns Chichester, UK: John Wiley [Google Scholar]
  36. Kembel SW. 2009. Disentangling niche and neutral influences on community assembly: assessing the performance of community phylogenetic structure tests. Ecol. Lett. 12:949–60 [Google Scholar]
  37. Kembel SW, Cowan PD, Helmus MR, Cornwell WK, Morlon H. et al. 2010. Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26:1463–64 [Google Scholar]
  38. Kembel SW, Hubbell SP. 2006. The phylogenetic structure of a neotropical forest tree community. Ecology 87:S86–99 [Google Scholar]
  39. Kraft NJB, Ackerly DD. 2014. Assembly of plant communities. Ecology and the Environment RK Monson 67–88 New York: Springer [Google Scholar]
  40. Kraft NJB, Adler PB, Godoy O, James E, Fuller S. et al. 2015a. Community assembly, coexistence, and the environmental filtering metaphor. Funct. Ecol. 29:5592–99 [Google Scholar]
  41. Kraft NJB, Cornwell WK, Webb CO, Ackerly DD. 2007. Trait evolution, community assembly, and the phylogenetic structure of ecological communities. Am. Nat. 170:2271–83 [Google Scholar]
  42. Kraft NJB, Godoy O, Levine JM. 2015b. Plant functional traits and the multidimensional nature of species coexistence. PNAS 112:797–802 [Google Scholar]
  43. Kraft NJB, Valencia R, Ackerly DD. 2008. Functional traits and niche-based tree community assembly in an Amazonian forest. Science 322:5930580–82 [Google Scholar]
  44. Kunstler G, Lavergne S, Courbaud B, Thuiller W, Vieilledent G. et al. 2012. Competitive interactions between forest trees are driven by species’ trait hierarchy, not phylogenetic or functional similarity: implications for forest community assembly. Ecol. Lett. 15:8831–40 [Google Scholar]
  45. Lasky JR, Uriarte M, Boukili VK, Chazdon RL. 2014. Trait-mediated assembly processes predict successional changes in community diversity of tropical forests. PNAS 111:5616–21 [Google Scholar]
  46. Legendre P. 1993. Spatial autocorrelation: trouble or new paradigm?. Ecology 74:1659–73 [Google Scholar]
  47. Legendre P, Fortin MJ. 1989. Spatial pattern and ecological analysis. Vegetatio 80:107–38 [Google Scholar]
  48. Lehmann S, Huth A. 2015. Fast calibration of a dynamic vegetation model with minimum observation data. Ecol. Model. 301:98–105 [Google Scholar]
  49. Leibold MA, Holyoak M, Mouquet N, Amarasekare P, Chase JM. et al. 2004. The metacommunity concept: a framework for multi-scale community ecology. Ecol. Lett. 7:601–13 [Google Scholar]
  50. Levin SA. 1992. The problem of pattern and scale in ecology. Ecology 73:1943–67 [Google Scholar]
  51. Lieberman M, Lieberman D. 2007. Nearest-neighbor tree species combinations in tropical forest: the role of chance, and some consequences of high diversity. Oikos 116:377–86 [Google Scholar]
  52. Matesanz S, Gimeno TE, de la Cruz M, Escudero A, Valladares F. 2011. Competition may explain the fine-scale spatial patterns and genetic structure of two co-occurring plant congeners. J. Ecol. 99:838–48 [Google Scholar]
  53. May F, Huth A, Wiegand T. 2015. Moving beyond abundance distributions—neutral theory and spatial patterns in a tropical forest. Proc. R. Soc. B 282:180220141657 [Google Scholar]
  54. May F, Wiegand T, Lehmann S, Huth A. 2016. Do abundance distributions and species aggregation correctly predict macroecological biodiversity patterns in tropical forests. Glob. Ecol. Biogeogr. 25:575–85 [Google Scholar]
  55. Mayfield MM, Levine JM. 2010. Opposing effects of competitive exclusion on the phylogenetic structure of communities. Ecol. Lett. 13:1085–93 [Google Scholar]
  56. McGill BJ. 2010a. Matters of scale. Science 328:5978575 [Google Scholar]
  57. McGill BJ. 2010b. Towards a unification of unified theories of biodiversity. Ecol. Lett. 13:627–42 [Google Scholar]
  58. McIntire EJB, Fajardo A. 2009. Beyond description: the active and effective way to infer processes from spatial patterns. Ecology 90:46–56 [Google Scholar]
  59. Metz MR, Sousa WP, Valencia R. 2010. Widespread density-dependent seedling mortality promotes species coexistence in a highly diverse Amazonian rainforest. Ecology 92:1723–29 [Google Scholar]
  60. Miller ET, Farine DR, Trisos CH. 2017. Phylogenetic community structure metrics and null models: a review with new methods and software. Ecography 40:461–77 [Google Scholar]
  61. Morlon H, Chuyong G, Condit R, Hubbell S, Kenfack D. et al. 2008. A general framework for the distance-decay of similarity in ecological communities. Ecol. Lett. 11:904–17 [Google Scholar]
  62. Muller-Landau HC, Wright SJ, Calderón O, Hubbell SP, Foster RB. 2002. Assessing recruitment limitation: concepts, methods and examples for tropical forest trees. Seed Dispersal and Frugivory: Ecology, Evolution and Conservation J Levey, WR Silva, M Galetti 35–53 Oxfordshire, UK: CAB International [Google Scholar]
  63. Muscarella R, Uriarte M, Forero-Montaña J, Comita LS, Swenson NG. et al. 2013. Exploring the mechanisms behind life history tradeoffs during the seed-to-seedling transition for tropical trees and lianas. J. Ecol. 101:171–82 [Google Scholar]
  64. Pacala SW, Levin SA. 1997. Biologically generated spatial pattern and the coexistence of competing species. Spatial Ecology: The Role of Space in Population Dynamics and Interspecific Interactions D Tilman, P Kareiva 204–32 Princeton, NJ: Princeton Univ. Press [Google Scholar]
  65. Paine CET, Norden N, Chave J, Forget PM, Fortunel C. et al. 2012. Phylogenetic density dependence and environmental filtering predict seedling mortality in a tropical forest. Ecol. Lett. 15:34–41 [Google Scholar]
  66. Parmentier I, Réjou-Méchain M, Chave J, Vleminckx J, Thomas DW. et al. 2014. Prevalence of phylogenetic clustering at multiple scales in an African rain forest tree community. J. Ecol. 102:1008–16 [Google Scholar]
  67. Pélissier R, Goreaud F. 2015. Ads package for R: a fast unbiased implementation of the K-function family for studying spatial point patterns in irregular-shaped sampling windows. J. Stat. Softw. 63:1–18 [Google Scholar]
  68. Perry GLW, Miller BP, Enright NJ, Lamont BB. 2014. Stochastic geometry best explains spatial associations among species pairs and plant functional types in species-rich shrublands. Oikos 123:99–110 [Google Scholar]
  69. Perry GLW, Miller BP, Lamont BB, Enright NJ. 2017. Community‐level spatial structure supports a model of stochastic geometry in species-rich shrublands. Oikos 126:833–42 [Google Scholar]
  70. Peters HA. 2003. Neighbour-regulated mortality: the influence of positive and negative density dependence on tree populations in species-rich tropical forests. Ecol. Lett. 6:757–65 [Google Scholar]
  71. Phillips PD, Brash TE, Yasman I, Subagyo P, Gardingen PRV. 2003. An individual-based spatially explicit tree growth model for forests in East Kalimantan (Indonesian Borneo). Ecol. Model. 159:1–26 [Google Scholar]
  72. Plotkin JB, Potts MD, Leslie N, Manokaran N, LaFrankie JV. et al. 2000. Species-area curves, spatial aggregation, and habitat specialization in tropical forests. J. Theor. Biol. 207:81–99 [Google Scholar]
  73. Punchi-Manage R, Wiegand T, Wiegand K, Getzin S, Huth A. et al. 2015. Neighborhood diversity of large trees shows independent species patterns in a mixed dipterocarp forest in Sri Lanka. Ecology 96:71823–34 [Google Scholar]
  74. Rao CR. 1982. Diversity and dissimilarity coefficients—a unified approach. Theor. Popul. Biol. 21:24–43 [Google Scholar]
  75. Reed SC, Cleveland CC, Townsend AR. 2008. Tree species control rates of free-living nitrogen fixation in a tropical rain forest. Ecology 89:2924–34 [Google Scholar]
  76. Ripley BD. 1977. Modelling spatial patterns (with discussion). J. R. Stat. Soc. B 39:172–212 [Google Scholar]
  77. Shen G, Wiegand T, Mi X, He F. 2013. Quantifying spatial phylogenetic structures of fully stem-mapped plant communities. Methods Ecol. Evol. 4:1132–41 [Google Scholar]
  78. Shen G, Yu M, Hu XS, Mi X, Ren H. et al. 2009. Species-area relationships explained by the joint effects of dispersal limitation and habitat heterogeneity. Ecology 90:3033–41 [Google Scholar]
  79. Shimatani K. 2001. Multivariate point processes and spatial variation of species diversity. For. Ecol. Manag. 142:215–29 [Google Scholar]
  80. Simpson EH. 1949. Measurement of diversity. Nature 163:688 [Google Scholar]
  81. Soliveres S, Maestre FT, Ulrich W, Manning P, Boch S. et al. 2015. Intransitive competition is widespread in plant communities and maintains their species richness. Ecol. Lett. 18:790–98 [Google Scholar]
  82. Stoll P, Newbery DM. 2005. Evidence of species-specific neighborhood effects in the Dipterocarpaceae of a Bornean rain forest. Ecology 86:3048–62 [Google Scholar]
  83. Stoll P, Prati D. 2001. Intraspecific aggregation alters competitive interactions in experimental plant communities. Ecology 82:319–27 [Google Scholar]
  84. Swenson NG. 2011. Phylogenetic beta diversity metrics, trait evolution and inferring the functional beta diversity of communities. PLOS ONE 6:6e21264 [Google Scholar]
  85. Tilman D, Kareiva P. 1997. Spatial Ecology: The Role of Space in Population Dynamics and Interspecific Interactions Princeton, NJ: Princeton Univ. Press [Google Scholar]
  86. Tucker CM, Cadotte MW, Carvalho SB, Davies TJ, Ferrier S. et al. 2017. A guide to phylogenetic metrics for conservation, community ecology and macroecology. Biol. Rev. 92:698–715 [Google Scholar]
  87. Uriarte M, Bruna EM, Rubim P, Anciães M, Jonckheere I. 2010b. Effects of forest fragmentation on seedling recruitment of an understory herb: assessing seed vs. safe-site limitation. Ecology 91:1317–28 [Google Scholar]
  88. Uriarte M, Canham CD, Thompson J, Zimmerman JK. 2004a. A neighborhood analysis of tree growth and survival in a hurricane-driven tropical forest. Ecol. Monogr. 74:591–614 [Google Scholar]
  89. Uriarte M, Canham CD, Thompson J, Zimmerman JK. 2009. Understanding natural disturbance and human land use as determinants of tree community dynamics in a subtropical wet forest: results from a forest simulator. Ecol. Monogr. 79:423–43 [Google Scholar]
  90. Uriarte M, Condit R, Canham CD, Hubbell SP. 2004b. A spatially explicit model of sapling growth in a tropical forest: does the identity of neighbours matter. J. Ecol. 92:348–60 [Google Scholar]
  91. Uriarte M, Lasky JR, Boukili VK, Chazdon RL. 2016. A trait-mediated, neighborhood approach to quantify climate impacts on tropical rainforest succession. Funct. Ecol. 30:157–67 [Google Scholar]
  92. Uriarte M, Swenson NG, Chazdon RL, Comita LS, Kress WJ. et al. 2010a. Trait similarity, shared ancestry and the structure of neighbourhood interactions in a subtropical wet forest: implications for community assembly. Ecol. Lett. 13:1503–14 [Google Scholar]
  93. Uriarte M, Turner BL, Thompson J, Zimmerman JK. 2015. Linking spatial patterns of leaf litterfall and soil nutrients in a tropical forest: a neighborhood approach. Ecol. Appl. 25:2022–34 [Google Scholar]
  94. van der Valk AG. 1981. Succession in wetlands—a Gleasonian approach. Ecology 62:688–96 [Google Scholar]
  95. Velázquez E, Martínez I, Getzin S, Moloney KA, Wiegand T. 2016. An evaluation of the state of spatial point pattern analysis in ecology. Ecography 39:1042–55 [Google Scholar]
  96. Wang X, Swenson NG, Wiegand T, Wolf A, Howe R. et al. 2013. Phylogenetic and functional diversity area relationships in two temperate forests. Ecography 36:883–93 [Google Scholar]
  97. Wang X, Swenson NG, Wiegand T, Wolf A, Howe R. et al. 2015. Mechanisms underlying local functional and phylogenetic beta diversity in two temperate forests. Ecology 96:1062–73 [Google Scholar]
  98. Wang X, Wiegand T, Kraft NJB, Swenson NG, Davies SJ. et al. 2016. Stochastic dilution effects weaken deterministic effects of niche-based processes on the spatial distribution of large trees in species rich forests. Ecology 97:2347–60 [Google Scholar]
  99. Wang X, Wiegand T, Wolf A, Howe R, Davis S. et al. 2011. Spatial patterns of tree species richness in two temperate forests. J. Ecol. 99:1382–93 [Google Scholar]
  100. Webb CO. 2000. Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. Am. Nat. 156:145–55 [Google Scholar]
  101. Webb CO, Ackerly DD, McPeek MA, Donoghue MJ. 2002. Phylogenies and community ecology. Annu. Rev. Ecol. Syst. 33:475–505 [Google Scholar]
  102. Webb CO, Gilbert GS, Donoghue MJ. 2006. Phylodiversity-dependent seedling mortality, size structure, and disease in a Bornean rain forest. Ecology 87:S123–31 [Google Scholar]
  103. Wiegand T, Gunatilleke CVS, Gunatilleke IAUN, Huth A. et al. 2007. How individual species increase local diversity in tropical forests. PNAS 104:4819029–33 [Google Scholar]
  104. Wiegand T, He F, Hubbell SP. 2013. A systematic comparison of summary characteristics for quantifying point patterns in ecology. Ecography 36:92–103 [Google Scholar]
  105. Wiegand T, Huth A, Getzin S, Wang X, Hao Z. et al. 2012. Testing the independent species arrangement assertion made by theories of stochastic geometry of biodiversity. Proc. R. Soc. B 279:3312–20 [Google Scholar]
  106. Wiegand T, Moloney KA. 2014. Handbook of Spatial Point-Pattern Analysis in Ecology Boca Raton, FL: Chapman and Hall/CRC Press [Google Scholar]
  107. Wiens JA. 1989. Spatial scaling in ecology. Funct. Ecol. 3:385–97 [Google Scholar]
  108. Wills C, Condit R, Foster RB, Hubbell SP. 1997. Strong density- and diversity-related effects help to maintain tree species diversity in a neotropical forest. PNAS 94:1252–57 [Google Scholar]
  109. Yang J, Swenson NG, Cao M, Chuyong GB, Ewango CEN. et al. 2013. A phylogenetic perspective on the individual species-area relationship in temperate and tropical tree communities. PLOS ONE 8:5e63192 [Google Scholar]

Data & Media loading...

Supplementary Data

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error