Search for other papers by C. Ricotta in
Current site
Google Scholar
PubMed
Search for other papers by E. Ari in
Current site
Google Scholar
PubMed
Search for other papers by G. Bonanomi in
Current site
Google Scholar
PubMed
Search for other papers by F. Giannino in
Current site
Google Scholar
PubMed
Search for other papers by D. Heathfield in
Current site
Google Scholar
PubMed
Search for other papers by S. Mazzoleni in
Current site
Google Scholar
PubMed
Ecology Research Group of the Hungarian Academy of Sciences, Budapest, Hungary
Search for other papers by J. Podani in
Current site
Google Scholar
PubMed
The increasing availability of phylogenetic information facilitates the use of evolutionary methods in community ecology to reveal the importance of evolution in the species assembly process. However, while several methods have been applied to a wide range of communities across different spatial scales with the purpose of detecting non-random phylogenetic patterns, the spatial aspects of phylogenetic community structure have received far less attention. Accordingly, the question for this study is: can point pattern analysis be used for revealing the phylogenetic structure of multi-species assemblages? We introduce a new individual-centered procedure for analyzing the scale-dependent phylogenetic structure of multi-species point patterns based on digitized field data. The method uses nested circular plots with increasing radii drawn around each individual plant and calculates the mean phylogenetic distance between the focal individual and all individuals located in the circular ring delimited by two successive radii. This scale-dependent value is then averaged over all individuals of the same species and the observed mean is compared to a null expectation with permutation procedures. The method detects particular radius values at which the point pattern of a single species exhibits maximum deviation from the expectation towards either phylogenetic aggregation or segregation. Its performance is illustrated using data from a grassland community in Hungary and simulated point patterns. The proposed method can be extended to virtually any distance function for species pairs, such as functional distances.
-
Anacker, B.L., Klironomos, J.N., Maherali, H., Reinhart, K.O. and Strauss S.Y. 2014. Phylogenetic conservatism in plant-soil feedback and its implications for plant abundance. Ecol. Lett. 17: 1613–1621.
-
Bagchi, R., Swinfield, S., Gallery, R.E., Lewis, O.T., Gripenberg, S., Narayan, L. and Freckleton R.P. 2010. Testing the Janzen—Connell mechanism: pathogens cause overcompensating density dependence in a tropical tree. Ecol. Lett. 13: 1262–1269.
-
Bever, J.D. 1994. Feedback between plants and their soil communities in an old field community. Ecology 75: 1965–1977.
-
Bever, J.D., Westover, M. and Antonovics, J. 1997. Incorporating the soil community into plant population dynamics: the utility of the feedback approach. J. Ecol. 85: 561–573.
-
Bonanomi, G., Antignani, V., Capodilupo, M. and Scala, F. 2010. Identifying the characteristics of organic soil amendments that suppress soilborne plant diseases. Soil Biol. Biochem. 42: 136–144.
-
Bonanomi, G., Giannino, F. and Mazzoleni, S. 2005. Negative plant—soil feedback and species coexistence. Oikos 111: 311–321.
-
Cadotte, M.W., Davies, T.J., Regetz, J., Kembel, S.W., Cleland, E. and Oakley, T.H. 2010. Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history. Ecol. Lett. 13: 96–105.
-
Cavender-Bares, J., Kozak, K.H., Fine, P.V.A. and Kembel, S.W. 2009. The merging of community ecology and phylogenetic biology. Ecol. Lett. 12: 693–715.
-
Chave, J., Muller-Landau, H.C. and Levin, S.A. 2002. Comparing classical community models: Theoretical consequences for patterns of diversity. Amer. Nat. 159: 1–23.
-
Chesson, P. 2000. Mechanisms of maintenance of species diversity. Annu. Rev. Ecol. Evol. Syst. 31: 343–366.
-
Coley, P.D. and Barone, J.A. 1996. Herbivory and plant defenses in tropical forests. Annu. Rev. Ecol. Evol. Syst. 27: 305–335.
-
Comita, L.S., Muller-Landau, H.C., Aguilar, S. and Hubbell S.P. 2010. Asymmetric density dependence shapes species abundances in a tropical tree community. Science 329: 330–332.
-
Connell, J.H. 1971. On the role of natural enemies in preventing competitive exclusion in some marine animals and in rain forest trees. In: den Boer, P.J. and Gradwell, G.R. (eds.), Dynamics of Populations. Center for Agricultural Publishing and Documentation, Wageningen, NL. pp. 298–312.
-
Devictor, V., Mouillot, D., Meynard, C., Jiguet, F., Thuiller, W. and Mouquet, N. 2010. Spatial mismatch and congruence between taxonomic, phylogenetic and functional diversity: the need for integrative conservation strategies in a changing world. Ecol. Lett. 13: 1030–1040.
-
Diggle, P.J. 2003. Statistical Analysis of Spatial Point Patterns. Arnold, London.
-
Felsenstein, J. 2005. PHYLIP (Phylogeny Inference Package) version 3.6. Department of Genetics, University of Washington, Seattle.
-
Ferrier, S., Manion, G., Elith, J. and Richardson K. 2007. Using generalized dissimilarity modelling to analyse and predict patterns of beta diversity in regional biodiversity assessment. Divers. Distrib. 13: 252–264.
-
Fuller, M.M. and Enquist, B.J. 2012. Accounting for spatial autocorrelation in null models of tree species association. Ecography 35: 510–518.
-
Gilbert, G.S. and Webb, C.O. 2007. Phylogenetic signal in plant pathogen—host range. PNAS USA 104: 4979–4983.
-
Gonzalez, M.A., Roger, A., Courtois, E.A., Jabot, F., Norden, N., Paine, C.E.T., Baraloto, C., Thébaud, C. and Chave, J. 2010. Shifts in species and phylogenetic diversity between sapling and tree communities indicate negative density dependence in a lowland rain forest. J. Ecol. 98: 137–146.
-
Gotelli, N.J. and Graves, G.R. 1996. Null Models in Ecology. Smithsonian Institution Press, Washington.
-
Grabarnik, P., Myllymaki, M. and Stoyan, D. 2011. Correct testing of mark independence for marked point patterns. Ecol. Model. 222: 3888–3894.
-
Hardy, O.J. 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: 914–926.
-
Heathfield, D., Kivistö, V., Mazzoleni, S. and Ricotta C. 2012. TreeCreeper a Computer Program for the Taxonomic Analysis of Species Assemblages. Department of Forestry and Environmental Sciences, University of Naples ‘Federico II’, Portici, Italy and World in a Box, Karkkila, Finland.
-
Illian, J., Penttinen, A., Stoyan, H. and Stoyan, D. 2008. Statistical Analysis and Modelling of Spatial Point Patterns. Wiley, Chichester.
-
Janzen, D.H. 1970. Herbivores and the numbers of tree species in tropical forests. Amer. Nat. 104: 501–528.
-
Johnson, D.J., Beaulieu, W.T., Bever, J.D. and Clay, K. 2012. Conspecific negative density dependence and forest diversity. Science 336: 904–907.
-
Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111–120.
-
Klimešová, J. and de Bello F. 2009. CLO—PLA: the database of clonal and bud bank traits of Central European flora. J. Veg. Sci. 20: 511–516.
-
Klironomos, J.N. 2002. Feedback with soil biota contributes to plant rarity and invasiveness in communities. Nature 417: 67–70.
-
Kraft, N.J.B. and Ackerly, D.D. 2010. Functional trait and phylogenetic tests of community assembly across spatial scales in an Amazonian forest. Ecol. Monog. 80: 401–422.
-
Law, R., Illian, J., Burslem, D.F.R.P., Gratzer, G., Gunatilleke, C.V.S. and Gunatilleke, I.A.U.N. 2009. Ecological information from spatial patterns of plants: insights from point process theory. J. Ecol. 97: 616–628.
-
Ling, Y. and Mahadevan, S. 2013. Quantitative model validation techniques: New insights. Reliability Engineering and System Safety 111: 217–231.
-
Losos, J.B. 2008. Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecol. Lett. 11: 995–1007.
-
Mangan, S.A., Schnitzer, S.A., Herre, E.A., Mack, K.M.L., Valencia, M.C., Sanchez, E.I. and Bever J.D. 2010. Negative plant—soil feedback predicts tree—species relative abundance in a tropical forest. Nature 466: 752–755.
-
Mazzoleni, S., Bonanomi, G., Giannino, F., Rietkerk, M., Dekker, S. and Zucconi, F. 2007. Is plant biodiversity driven by decomposition processes? An emerging new theory on plant diversity. Community Ecol. 8: 103–109.
-
Mazzoleni, S., Bonanomi, G., Incerti, G., Chiusano, M.L., Termolino, P., Mingo, A., Senatore, M., Giannino, F., Cartenì, F., Rietkerk, M. and Lanzotti, V. 2015a. Inhibitory and toxic effects of extracellular self-DNA in litter: a mechanism for negative plant-soil feedbacks? New Phytol. 205: 1195–1210.
-
Mazzoleni, S., Cartenì, F., Bonanomi, G., Senatore, M., Termolino, P., Giannino, F., Incerti, G., Rietkerk, M., Lanzotti, V. and Chiusano, M.L. 2015b. Inhibitory effects of extracellular self-DNA: a general biological process? New Phytol. 206: 127–132.
-
Metz, M.R., Sousa, W.P. and Valencia, R. 2010. Widespread density-dependent seedling mortality promotes species coexistence in a highly diverse Amazonian rain forest. Ecology 91: 3675–3685.
-
Milla, R., Escudero, A. and Iriondo, J.M. 2009. Inherited variability in multiple traits determines fitness in populations of an annual legume from contrasting latitudinal origins. Ann. Bot. 103: 1279–1289.
-
Morlon, H., Schwilk, D.W., Bryant, J.A., Marquet, P.A., Rebelo, A.G., Tauss, C., Bohannan, B.J.M. and Green, J.L. 2010. Spatial patterns of phylogenetic diversity. Ecol. Lett. 14: 141–149.
-
Ness, J.H., Rollinson, E.J. and Whitney, K.D. 2011. Phylogenetic distance can predict susceptibility to attack by natural enemies. Oikos 120: 1327–1334.
-
Novotny, V., Miller, S.E., Baje, L., Balagawi, S., Basset, Y., Cizek, L., Craft, K.J., Dem, F., Drew, R.A.I., Hulcr, J., Leps, J., Lewis, O.T., Pokon, R., Stewart, A.J.A., Samuelson, G.A. and Weiblen, G.D. 2010. Guild-specific patterns of species richness and host specialization in plant—herbivore food webs from a tropical forest. J. Anim. Ecol. 79: 1193–1203.
-
Packer A. , Clay K. (2000) Soil pathogens and spatial patterns of seedling mortality in a temperate tree. Nature 404: 278–281.
-
Paine, C.E.T., Norden, N., Chave, J., Forget, P.M., Fortunel, C., Dexter, K.G. and Baraloto, C. 2012. Phylogenetic density dependence and environmental filtering predict seedling mortality in a tropical forest. Ecol. Lett. 15: 34–41.
-
Petermann, J.S., Fergus, A.J.F., Turnbull, A. and Schmid, B. 2008. Janzen—Connell effects are widespread and strong enough to maintain diversity in grasslands. Ecology 89: 2399–2406.
-
Podani, J. and Czárán, T. 1997. Individual—centered analysis of mapped point patterns representing multi—species assemblages. J. Veg. Sci. 8: 259–270.
-
Podani, J., Czárán, T. and Scheuring, I. 1998. Individual—centered analysis of community pattern: some case studies. Abstr. Bot. 22: 101–112.
-
Rajala, T. and Illian, J. 2012. A family of spatial biodiversity measures based on graphs. Environ. Ecol. Stat. 19: 545–572.
-
Reynolds, H.L., Packer, A., Bever, J.D. and Clay, K. 2003. Grassroots ecology: plant-microbe-soil interactions as drivers of plant community structure and dynamics. Ecology 84: 2281–2291.
-
Ripley, BD. 1981. Spatial Statistics. Wiley, New York.
-
Rohlf, F.J. and Archie, J.W. 1978. Least—squares mapping using interpoint distances. Ecology 59: 126–132.
-
Rosenberg, M.S. and Anderson, C.D. 2011. PASSaGE: Pattern Analysis, Spatial Statistics and Geographic Exegesis. Version 2. Meth. Ecol. Evol. 2: 229–232.
-
Seidler, T.G. and Plotkin, J.B. 2006. Seed dispersal and spatial pattern in tropical trees. PLoS Biol. 4: e344. DOI: 10.1371/journal.pbio.0040344.
-
Simon, T. 1992. Guide to the Vascular Flora of Hungary. Tankönyvkiadó, Budapest (in Hungarian).
-
Singh, H.P., Batish, R.D. and Kohli, K.R. 1999. Autotoxicity: concept, organisms and ecological significance. Crit. Rev. Plant Sci. 18: 757–772.
-
Stanisci, A., Acosta, A.T.R., Di Iorio, A. and Vergalito, M. 2010. Leaf and root trait variability of alien and native species along Adriatic coastal dunes (Italy). Plant Biosyst. 144: 47–52.
-
Terborgh, J. 2012. Enemies maintain hyperdiverse tropical forests. Amer. Nat. 179: 303–314.
-
Thompson, K., Petchey, O.L., Askew, A.P., Dunnett, N.P., Beckerman, A.P. and Willis, A.J. 2010. Little evidence for limiting similarity in a long-term study of a roadside plant community. J. Ecol. 98: 480–487.
-
Thuiller, W., Gasso, N., Pino, J. and Vilà, M. 2012. Ecological niche and species traits: key drivers of regional plant invader assemblages. Biol. Invasions 14: 1963–1980.
-
Uriarte, M., Swenson, N.G., Chazdon, R.L., Comita, L.S., Kress, W.J., Erickson, D., Forero-Montana, J., Zimmerman, J.K. and Thompson, J. 2010. Trait similarity, shared ancestry and the structure of neighbourhood interactions in a subtropical wet forest: implications for community assembly. Ecol. Lett. 13: 1503–1514.
-
Vamosi, S.M., Heard, S.B., Vamosi, J.C. and Webb C.O. 2009. Emerging patterns in the comparative analysis of phylogenetic community structure. Mol. Ecol. 18: 572–592.
-
Van der Putten, W.H., Bardgett, R.D., Bever, J.D., Bezemer, T.M., Casper, B.B., Fukami, T., Kardol, P., Klironomos, J.N., Kulmatiski, A., Schweitzer, J.A., Suding, K.N., Van de Voorde, T.F.J. and Wardle, D.A. 2013. Plant—soil feedbacks: the past, the present and future challenges. J. Ecol. 101: 265–276.
-
Van der Putten, W.H., Van Dijk, C. and Peters, B.A.M. 1993. Plant-specific soil-borne diseases contribute to succession in foredune vegetation. Nature 362: 53–56.
-
Webb, C.O., Ackerly, D.D., McPeek, M.A. and Donoghue, M.J. 2002. Phylogenies and community ecology. Annu. Rev. Ecol. Evol. Syst. 33: 475–505.
-
Webb, C.O., Gilbert, G.S. and Donoghue, M.J. 2006. Phylodiversity-dependent seedling mortality, size structure, and disease in a Bornean rain forest. Ecology 87: S123–S131.
-
Wiegand, T., Gunatilleke, C.V.S., Gunatilleke, I.A.U.N. and Huth, A. 2007. How individual species structure diversity in tropical forests. PNAS USA 104: 19029–19033.
To see the editorial board, please visit the website of Springer Nature.
Manuscript Submission: HERE
For subscription options, please visit the website of Springer Nature.
| Community Ecology | |
|---|---|
| Language | English |
| Size | A4 |
| Year of Foundation |
2000 |
| Volumes per Year |
1 |
| Issues per Year |
3 |
| Founder | Akadémiai Kiadó |
| Founder's Address |
H-1117 Budapest, Hungary 1516 Budapest, PO Box 245 |
| Publisher | Akadémiai Kiadó Springer Nature Switzerland AG |
| Publisher's Address |
H-1117 Budapest, Hungary 1516 Budapest, PO Box 245. CH-6330 Cham, Switzerland Gewerbestrasse 11. |
| Responsible Publisher |
Chief Executive Officer, Akadémiai Kiadó |
| ISSN | 1585-8553 (Print) |
| ISSN | 1588-2756 (Online) |
Monthly Content Usage
| Abstract Views | Full Text Views | PDF Downloads | |
|---|---|---|---|
| Apr 2024 | 13 | 5 | 2 |
| May 2024 | 18 | 0 | 0 |
| Jun 2024 | 9 | 0 | 0 |
| Jul 2024 | 38 | 0 | 0 |
| Aug 2024 | 27 | 0 | 0 |
| Sep 2024 | 11 | 0 | 0 |
| Oct 2024 | 0 | 0 | 0 |
Copyright Akadémiai Kiadó AKJournals is the trademark of Akadémiai Kiadó's journal publishing business branch.