The roots of diversity: Below ground species richness and rooting distributions in a tropical forest revealed by DNA barcodes and inverse modeling

PLoS ONE

Volumn 6, Issue 9, 2011, Pages

  Jones, F Andrew ^a,d   Erickson, David L ^b   Bernal, Moises A ^a,c   Bermingham, Eldredge ^a   Kress, W John ^b   Herre, Edward Allen ^a   Muller Landau, Helene C ^a   Turner, Benjamin L ^a  

^a SMITHSONIAN TROPICAL RESEARCH INSTITUTE   (Panama)

^b DEPARTMENT OF PALEOBIOLOGY   (United States)

^c UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^d IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DNA BARCODING; DNA SEQUENCE; GENE LOCUS; GEOGRAPHIC DISTRIBUTION; LAND SPREADING; MATHEMATICAL MODEL; NONHUMAN; ROOTING; SEED DISPERSAL; SEEDLING; SPECIES DIVERSITY; SPECIES IDENTIFICATION; SPECIES RICHNESS; TROPICAL RAIN FOREST; WOODY PLANT; BIODIVERSITY; CLASSIFICATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METHODOLOGY; PLANT ROOT; SOIL; THEORETICAL MODEL; TREE; TROPIC CLIMATE;

PLANT DNA;

BIODIVERSITY; DNA BARCODING, TAXONOMIC; DNA, PLANT; MODELS, THEORETICAL; PLANT ROOTS; SOIL; TREES; TROPICAL CLIMATE;

EID: 80052895372     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0024506     Document Type: Article

References (56)

1. Lal R, (2004) Soil carbon sequestration impacts on global climate change and food security. Science 304: 1623.
2. Wardle DA, Bardgett RD, Klironomos JN, Setala H, van der Putten WH, et al. (2004) Ecological Linkages Between Aboveground and Belowground Biota. Science 304: 1629-1633.
3. Tilman D, (1982) Resource competition and community structure Princeton, New Jersey Princeton University Press.
4. Tilman D, Pacala S, (1993) The maintenance of species richness in plant communities. In: Ricklefs RE, Schluter D, editors. Species Diversity in Ecological Communities Chicago University of Chicago Press pp. 13-25.
5. Freckleton RP, Lewis OT, (2006) Pathogens, density dependence and the coexistence of tropical trees. Proceedings of the Royal Society of London Series B-Biological Sciences 273: 2909.
6. Mangan SA, Schnitzer SA, Herre EA, Mack KML, Valencia MC, et al. (2010) Negative plant-soil feedback predicts tree-species relative abundance in a tropical forest. Nature 466: 752-755.
7. Comita LS, Muller-Landau HC, Aguilar S, Hubbell SP, (2010) Asymmetric Density Dependence Shapes Species Abundances in a Tropical Tree Community. Science 329: 330-332.
8. Herre EA, Kyllo DA, Mangan SA, Husband R, Mejia LC, et al. (2005) An overview of arbuscular mycorrhizal fungi composition, distribution, and host effects from a tropical moist forest. In: Burslem DFRP, Pinard MA, Hartley SE, editors. Biotic Interactions in the Tropics Cambridge Cambridge University Press pp. 204-225.
9. Casper BB, Schenk HJ, Jackson RB, (2003) Defining a plant's belowground zone of influence. Ecology 84: 2313-2321.
10. McNickle GG, St Clair CC, Cahill JF, (2009) Focusing the metaphor: plant root foraging behaviour. Trends in Ecology & Evolution 24: 419-426.
11. Bobowski BR, Hole D, Wolf PG, Bryant L, (1999) Identification of roots of woody species using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis. Molecular Ecology 8: 485-491.
12. Brunner I, Brodbeck S, Büchler U, Sperisen C, (2001) Molecular identification of fine roots of trees from the Alps: reliable and fast DNA extraction and PCR-RFLP analyses of plastid DNA. Molecular Ecology 10: 2079-2087.
13. Jackson RB, Moore LA, Hoffmann WA, Pockman WT, Linder CR, (1999) Ecosystem rooting depth determined with caves and DNA. Proceedings of the National Academy of Sciences of the United States of America 96: 11387-11392.
14. Mommer L, Ruijven Jv, Caluwe Hd, Smit-Tiekstra AE, Wagemaker CAM, et al. (2010) Unveiling below-ground species abundance in a biodiversity experiment: a test of vertical niche differentiation among grassland species. Journal of Ecology 98: 1117-1127.
15. Moore LA, Field CB, Wilson JB, (2005) A technique for identifying the roots of different species in mixed samples using nuclear ribosomal DNA. Journal of Vegetation Science 16: 131-134.
16. Ridgway K, Duck J, Young JP, (2003) Identification of roots from grass swards using PCR-RFLP and FFLP of the plastid trnL (UAA) intron. BMC Ecology 3: 8.
17. Taggart JM, Cahill JFC Jr, McNickle GG, Hall JC, (2010) Molecular identification of roots from a grassland community using size differences in fluorescently labelled PCR amplicons of three cpDNA regions. Molecular Ecology Resources 9999.
18. Kesanakurti PR, Fazekas AJ, Burgess KS, Percy DM, Newmaster SG, et al. (2011) Spatial patterns of plant diversity below-ground as revealed by DNA barcoding. Molecular Ecology 20: 1289-1302.
19. Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH, (2005) Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences of the United States of America 102: 8369-8374.
20. Kress WJ, Erickson DL, Swenson NG, Thompson J, Uriarte M, et al. (2010) Advances in the Use of DNA Barcodes to Build a Community Phylogeny for Tropical Trees in a Puerto Rican Forest Dynamics Plot. PLoS ONE 5: e15409.
21. Cowan RS, Chase MW, Kress WJ, Savolainen V, (2006) 300,000 species to identify: problems, progress, and prospects in DNA barcoding of land plants. Taxon 55: 611-616.
22. Hebert PDN, Cywinska A, Ball SL, DeWaard JR, (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society of London Series B-Biological Sciences 270: 313-321.
23. Kress WJ, Erickson DL, (2007) A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS ONE 2: e508.
24. Janzen DH, (2004) Now Is the Time. Philosophical Transactions: Biological Sciences 359: 731-732.
25. Valentini A, Pompanon F, Taberlet P, (2009) DNA barcoding for ecologists. Trends in Ecology & Evolution 24: 110-117.
26. Deagle BE, Kirkwood R, Jarman SN, (2009) Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces. Molecular Ecology 18: 2022-2038.
27. Jurado-Rivera JA, Vogler AP, Reid CAM, Petitpierre E, Gomez-Zurita J, (2009) DNA barcoding insect-host plant associations. Proceedings of the Royal Society B-Biological Sciences 276: 639-648.
28. Soininen EM, Valentini A, Coissac E, Miquel C, Gielly L, et al. (2009) Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures. Frontiers in Zoology 6.
29. Valentini A, Miquel C, Taberlet P, (2010) DNA Barcoding for Honey Biodiversity. Diversity 2: 610-617.
30. Kress WJ, Erickson DL, Jones FA, Swenson NG, Perez R, et al. (2009) Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama. Proceedings of the National Academy of Sciences of the United States of America 106: 18621-18626.
31. Hollingsworth PM, Forrest LL, Spouge JL, Hajibabaei M, Ratnasingham S, et al. (2009) A DNA barcode for land plants. Proceedings of the National Academy of Sciences 106: 12794-12797.
32. Hubbell SP, Foster RB, (1987) Large-scale spatial structure of a Neotropical forest. Revista De Biologia Tropical 35: 7-22.
33. Comita LS, Hubbell SP, (2009) Local neighborhood and species' shade tolerance influence survival in a diverse seedling bank. Ecology 90: 328-334.
34. Jones FA, Chen J, Weng GJ, Hubbell SP, (2005) A genetic evaluation of seed dispersal in the neotropical tree Jacaranda copaia (Bignoniaceae). American Naturalist 166: 543-555.
35. Dondoshansky I, (2002) Blastclust (NCBI Software Development Toolkit), 6.1 edition. NCBI, Bethesda, MD.
36. Ribbens E, Silander JA Jr, Pacala SW, (1994) Seedling recruitment in forests: calibrating models to predict patterns of tree seedling dispersion. Ecology 75: 1794-1806.
37. Clark JS, Macklin E, Wood L, (1998) Stages and spatial scales of recruitment limitation in Southern Appalachian forests. Ecological Monographs 68: 213-235.
38. Muller-Landau HC, Wright SJ, Calderon O, Condit R, Hubbell SP, (2008) Interspecific variation in primary seed dispersal in a tropical forest. Journal of Ecology 96: 653-667.
39. Robledo-Arnuncio JJ, (2008) Seed dispersal estimation without fecundities: a reply to Ralph. Molecular Ecology 17: 1883-1884.
40. Jones FA, Muller-Landau HC, (2008) Measuring long-distance seed dispersal in complex natural environments: an evaluation and integration of classical and genetic methods. Journal of Ecology 96: 642-652.
41. Yastrebov AB, (1996) Strength of tree phytogenic fields in lichen-green moss pine forests. Russian Journal of Ecology 27: 1-7.
42. Weiner J, Stoll P, Muller-Landau HC, Jasentuliyana A, (2001) Spatial pattern, competitive symmetry and size variability in a spatially-explicit, individual-based plant competition model. The American Naturalist 148.
43. Wright SJ, (2002) Plant diversity in tropical forests: a review of mechanisms of species coexistence. Oecologia 130: 1-14.
44. Paine CET, Harms KE, Schnitzer SA, Carson WP, (2008) Weak Competition Among Tropical Tree Seedlings: Implications for Species Coexistence. Biotropica 40: 432-440.
45. Svenning J, Fabbro T, Wright SJ, (2008) Seedling interactions in a tropical forest in Panama. Oecologia 155: 143-150.
46. Yavitt JB, Wright SJ, (2001) Drought and irrigation effects on fine root dynamics in a tropical moist forest, Panama. Biotropica 33: 421-434.
47. Wright SJ, Machado JL, Mulkey SS, Smith AP, (1992) Drought Acclimation among Tropical Forest Shrubs (Psychotria, Rubiaceae). Oecologia 89: 457-463.
48. Shinozaki K, Yoda K, Hozumi K, Kira T, (1964) A quantitative analysis of plant form - the pipe model theory II. Further evidence of the theory and its application in forest ecology. Japanese Journal of Ecology 14: 133-139.
49. Niiyama K, Kajimoto T, Matsuura Y, Yamashita T, Matsuo N, et al. (2010) Estimation of root biomass based on excavation of individual root systems in a primary dipterocarp forest in Pasoh Forest Reserve, Peninsular Malaysia. Journal of Tropical Ecology 26: 271-284.
50. Chave J, Andalo C, Brown S, Cairns MA, Chambers JQ, et al. (2005) Tree allometry and improved estimation of carbon stocks and balance in tropical forests. Oecologia 145: 87-99.
51. Silman MR, Krisel C, (2006) Getting to the root of tree neighbourhoods: hectare-scale root zones of a neotropical fig. Journal of Tropical Ecology 22: 727-730.
52. Weiner J, (1984) Neighbourhood interference amongst Pinus rigida individuals. Journal of Ecology 72: 183-195.
53. Brisson J, Reynolds JF, (1997) Effects of compensatory growth on population processes: a simulation study. Ecology 78: 2378-2384.
54. Hudson ME, (2008) Sequencing breakthroughs for genomic ecology and evolutionary biology. Molecular Ecology Resources 8: 3-17.
55. Pizano C, Mangan SA, Herre EA, Eom A-H, Dalling JW, (2011) Above- and belowground interactions drive habitat segregation between two cryptic species of tropical trees. Ecology 92: 47-56.
56. Stork N, Wright S, Mulkey S, (1997) Craning for a better view: The canopy crane network. Trends in Ecology & Evolution 12: 418-420.