High-Throughput Sequencing: A Roadmap Toward Community Ecology

Ecology and Evolution

Volumn 3, Issue 4, 2013, Pages 1125-1139

  Poisot, Timothée ^a,b   Péquin, Bérangère ^c,d,e   Gravel, Dominique ^a,b  

^a UNIVERSITÉ DU QUÉBEC À RIMOUSKI   (Canada)

^b QC Centre for Biodiversity Science   (Canada)

^c UNIVERSITÉ LAVAL   (Canada)

^d Québec Océan   (Canada)

^e Centre d Étude de la Forêt CEF and Institut de Biologie Intégrative et des Systèmes IBIS   (Canada)

Author keywords

Biogeography; Community ecology; High throughput sequencing; Microbial ecology

Indexed keywords

EID: 84886281130     PISSN: None     EISSN: 20457758     Source Type: Journal    
DOI: 10.1002/ece3.508     Document Type: Article

References (123)

1. Acinas, S. G., V. Klepac-Ceraj, D. E. Hunt, C. Pharino, I. Ceraj, D. L. Distel, et al. 2004. Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430:551-4.
2. Albert, C. H., F. de Bello, I. Boulangeat, G. Pellet, S. Lavorel, and W. Thuiller 2012. On the importance of intraspecific variability for the quantification of functional diversity. Oikos 121:116-126.
3. Amend, A. S., K. A. Seifert, and T. D. Bruns 2010. Quantifying microbial communities with 454 pyrosequencing: does read abundance count? Mol. Ecol. 19:5555-65.
4. Andersen, J. R., and T. Lübberstedt 2003. Functional markers in plants. Trends Plant Sci. 8:554-560.
5. Araújo, M. S., D. I. Bolnick, and C. A. Layman 2011a. The ecological causes of individual specialisation. Ecol. Lett. 14:948-958.
6. Araújo, M. B., A. Rozenfeld, C. Rahbek, and P. A. Marquet 2011b. Using species co-occurrence networks to assess the impacts of climate change. Ecography 34:897-908.
7. Barberán, A., S. T. Bates, E. O. Casamayor, and N. Fierer 2011. Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME J. 6:343-351.
8. Beman, J. M., J. A. Steele, and J. A. Fuhrman 2011. Co-occurrence patterns for abundant marine archaeal and bacterial lineages in the deep chlorophyll maximum of coastal California. ISME J. 5:1077-1085.
9. Benson, D. A., I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, and E. W. Sayers 2010. GenBank. Nucleic Acids Res. 39:D32-7.
10. Bik, H. M., D. L. Porazinska, S. Creer, J. G. Caporaso, R. Knight, and W. K. Thomas 2012. Sequencing our way towards understanding global eukaryotic biodiversity. Trends Ecol. Evol. 27:233-243.
11. Bolnick, D. I., and B. M. Fitzpatrick 2007. Sympatric speciation: models and empirical evidence. Annu. Rev. Ecol. Evol. Syst. 38:459-487.
12. Bolnick, D. I., R. Svanbäck, J. A. Fordyce, L. H. Yang, J. M. Davis, C. D. Hulsey, et al. 2003. The ecology of individuals: incidence and implications of individual specialization. Am. Nat. 161:1-28.
13. Bolnick, D. I., P. Amarasekare, M. S. Araújo, R. Bürger, J. M. Levine, M. Novak, et al. 2011. Why intraspecific trait variation matters in community ecology. Trends Ecol. Evol. 26:183-192.
14. Boulangeat, I., D. Gravel, and W. Thuiller 2012. Accounting for dispersal and biotic interactions to disentangle the drivers of species distributions and their abundances. Ecol. Lett. 15:584-593.
15. Brown, M. V., G. K. Philip, J. A. Bunge, M. C. Smith, A. Bissett, F. M. Lauro, et al. 2009. Microbial community structure in the North Pacific ocean. ISME J. 3:1374-1386.
16. Bryant, J. A., F. J. Stewart, J. M. Eppley, and E. F. DeLong 2012. Microbial community phylogenetic and trait diversity declines with depth in a marine oxygen minimum zone. Ecology 93:1659-1673.
17. Buckling, A., R. C. MacLean, M. A. Brockhurst, and N. Colegrave 2009. The Beagle in a bottle. Nature 457:824-829.
18. Burke, C., P. D. Steinberg, D. Rusch, S. Kjelleberg, and T. Thomas 2011. Bacterial community assembly based on functional genes rather than species. Proc. Nat. Acad. Sci. U.S.A. 108:14288-14293.
19. Cadotte, M. W., T. Jonathan Davies, J. Regetz, S. W. Kembel, E. Cleland, and T. H. Oakley 2010. Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history. Ecol. Lett. 13:96-105.
20. Campagna, C., F. T. Short, B. A. Polidoro, R. McManus, B. B. Collette, N. J. Pilcher, et al. 2011. Gulf of Mexico Oil Blowout Increases Risks to Globally Threatened Species. Bioscience 61:393-397.
21. Cardenas, E., and J. M. Tiedje 2008. New tools for discovering and characterizing microbial diversity. Curr. Opin. Biotechnol. 19:544-9.
22. Cavender-Bares, J., K. H. Kozak, P. V. A. Fine, and S. W. Kembel 2009. The merging of community ecology and phylogenetic biology. Ecol. Lett. 12:693-715.
23. Chaffron, S., H. Rehrauer, J. Pernthaler, and C. von Mering 2010. A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Res. 20:947-959.
24. Chamberlain, S. A., S. M. Hovick, C. J. Dibble, N. L. Rasmussen, B. G. Van Allen, B. S. Maitner, et al. 2012. Does phylogeny matter? Assessing the impact of phylogenetic information in ecological meta-analysis. Ecol. Lett. 15:627-636.
25. Cody, M., and J. M. Diamond 1975. Ecology and Evolution of communities. Harvard University Press, Cambrige, Mass.
26. Comeau, A. M., W. K. W. Li, J. -E. Tremblay, E. C. Carmack, and C. Lovejoy 2011. Arctic Ocean Microbial Community Structure before and after the 2007 Record Sea Ice Minimum. PLoS ONE 6:e27492.
27. Cottenie, K. 2005. Integrating environmental and spatial processes in ecological community dynamics. Ecol. Lett. 8:1175-82.
28. De Wit, R., and T. Bouvier 2006. 'Everything is everywhere, but, the environment selects'; what did Baas Becking and Beijerinck really say? Environ. Microbiol. 8:755.
29. Deans, A. R., M. J. Yoder, and J. P. Balhoff 2012. Time to change how we describe biodiversity. Trends Ecol. Evol. 27:78-84.
30. Degnan, P. H., and H. Ochman 2012. Illumina-based analysis of microbial community diversity. ISME J. 6:183-94.
31. Devictor, V., J. Clavel, R. Julliard, S. Lavergne, D. Mouillot, W. Thuiller, et al. 2010a. Defining and measuring ecological specialization. J. Appl. Ecol. 47:15-25.
32. Devictor, V., D. Mouillot, C. N. Meynard, F. Jiguet, W. Thuiller, and N. Mouquet 2010b. 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.
33. Díaz, S., S. Lavorel, F. de Bello, F. Quétier, K. Grigulis, and T. M. Robson 2007. Incorporating plant functional diversity effects in ecosystem service assessments. Proc. Nat. Acad. Sci. U.S.A. 104:20684-9.
34. Diniz-Filho, J. A. F., and L. M. Bini 2008. Macroecology, global change and the shadow of forgotten ancestors. Glob. Ecol. Biogeogr. 17:11-17.
35. Dowd, S. E., Y. Sun, P. R. Secor, D. D. Rhoads, B. M. Wolcott, G. A. James, et al. 2008. Survey of bacterial diversity in chronic wounds using pyrosequencing, DGGE, and full ribosome shotgun sequencing. BMC Microbiol. 8:43.
36. Faith, D. 1992. Conservation evaluation and phylogenetic diversity. Biol. Conserv. 61:1-10.
37. Feddermann, N., R. Finlay, T. Boller, and M. Elfstrand 2010. Functional diversity in arbuscular mycorrhiza - the role ofgene expression, phosphorous nutrition and symbiotic efficiency. Fungal Ecol. 3:1-8.
38. Flores, G. E., S. T. Bates, D. Knights, C. L. Lauber, J. Stombaugh, R. Knight, et al. 2011. Microbial biogeography of public restroom surfaces. PLoS ONE 6:e28132.
39. Fontana, G., K. I. Ugland, J. S. Gray, T. J. Willis, and M. Abbiati 2008. Influence of rare species on beta diversity estimates in marine benthic assemblages. J. Exp. Mar. Biol. Ecol. 366:104-108.
40. Galand, P. E., E. O. Casamayor, D. L. Kirchman, and C. Lovejoy 2009. Ecology of the rare microbial biosphere of the Arctic Ocean. Proc. Nat. Acad. Sci. U.S.A. 106:22427-32.
41. Gihring, T. M., S. J. Green, and C. W. Schadt 2012. Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes. Environ. Microbiol. 14:285-90.
42. Gilbert, B. 2012. Joint consequences of dispersal and niche overlap on local diversity and resource use. J. Ecol. 100:287-296.
43. Gilbert, B., and M. J. Lechowicz 2004. Neutrality, niches, and dispersal in a temperate forest understory. Proc. Nat. Acad. Sci. U.S.A. 101:7651-6.
44. Gilbert, J. A., D. Field, P. Swift, S. Thomas, D. Cummings, B. Temperton, et al. 2010. The taxonomic and functional diversity of microbes at a temperate coastal site: a 'multiomic' study of seasonal and diel temporal variation. PLoS ONE 5:e15545.
45. Gomulkiewicz, R., D. M. Drown, M. F. Dybdahl, W. Godsoe, S. L. Nuismer, K. M. Pepin, et al. 2007. Dos and don'ts of testing the geographic mosaic theory of coevolution. Heredity 98:249-258.
46. Gormley, A. M., D. M. Forsyth, P. Griffioen, M. Lindeman, D. S. L. Ramsey, M. P. Scroggie, et al. 2011. Using presence-only and presence-absence data to estimate the current and potential distributions of established invasive species. J. Appl. Ecol. 48:25-34.
47. Gotelli, N. J. 2000. Null model analysis of species co-occurrence patterns. Ecology 81:2606-2621.
48. Gotelli, N. J., and G. R. Graves 1996. Null models in ecology. Smithsonian Institution Press, Washington.
49. Gravel, D., C. D. Canham, M. Beaudet, and C. Messier 2006. Reconcilingniche and neutrality: the continuum hypothesis. Ecol. Lett. 9:399-409.
50. Gravel, D., M. Beaudet, and C. Messier 2008. Partitioning the factors of spatial variation in regeneration density of shade-tolerant tree species. Ecology 89:2879-88.
51. Gravel, D., E. Canard, F. Guichard, and N. Mouquet 2011. Persistence increases with diversity and connectance in trophic metacommunities. PLoS ONE 6:e19374.
52. Green, J., and B. J. M. Bohannan 2006. Spatial scaling of microbial biodiversity. Trends Ecol. Evol. 21:501-7.
53. Green, J. L., B. J. M. Bohannan, and R. J. Whitaker 2008. Microbial biogeography: from taxonomy to traits. Science 320:1039-43.
54. Guisan, A., and W. Thuiller 2005. Predicting species distribution: offering more than simple habitat models. Ecol. Lett. 8:993-1009.
55. Harding, T., A. D. Jungblut, C. Lovejoy, and W. F. Vincent 2011. Microbesin higharctic snow and implications for the cold biosphere. Appl. Environ. Microbiol. 77:3234-3243.
56. Huse, S. M., J. A. Huber, H. G. Morrison, M. L. Sogin, and D. M. Welch 2007. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol. 8:R143.
57. Ihaksi, T., T. Kokkonen, I. Helle, A. Jolma, T. Lecklin, and S. Kuikka 2011. Combining conservation value, vulnerability, and effectiveness of mitigation actions in spatial conservation decisions: an application to coastal oil spill combating. Environ. Manag. 47:802-13.
58. Ives, A. R., and M. R. Helmus 2010. Phylogenetic Metrics of Community Similarity. Am. Nat. 176:E128-E142.
59. Johnson, Z., E. Zinser, and A. Coe 2006. Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science 311:1737-1740.
60. Johnson, K. P., J. R. Malenke, and D. H. Clayton 2009. Competition promotes the evolution of host generalists in obligate parasites. Proc. Roy. Soc. B Biol. Sci. 276:3921-3926.
61. Kawecki, T. J., and D. Ebert 2004. Conceptual issues in local adaptation. Ecol. Lett. 7:1225-1241.
62. Kembel, S. W. 2009. Disentangling niche and neutral influences on community assembly: assessing the performance of community phylogenetic structure tests. Ecol. Lett. 12:949-60.
63. Kembel, S. W., P. D. Cowan, M. R. Helmus, W. K. Cornwell, H. Morlon, D. D. Ackerly, et al. 2010. Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26:1463-1464.
64. Kissling, W. D., C. F. Dormann, J. Groeneveld, T. Hickler, I. Kühn, G. J. McInerny, et al. 2012. Towards novel approaches to modelling biotic interactions in multispecies assemblages at large spatial extents. J. Biogeogr. 39:2163-2178.
65. Klappenbach, J. A., J. M. Dunbar, and T. M. Schmidt 2000. rRNA operon copy number reflects ecological strategies of bacteria. Appl. Environ. Microbiol. 66:1328-33.
66. Koopman, M. M., and B. C. Carstens 2011. The microbial phyllogeography of the carnivorous plant sarracenia alata. Microb. Ecol. 61:750-758.
67. Kremp, A., A. Godhe, J. Egardt, S. Dupont, S. Suikkanen, S. Casabianca, et al. 2012. Intraspecific variability in the response of bloom-forming marine microalgae to changed climate conditions. Ecol. Evol. 2:1195-1207.
68. Langille, M. G. I., M. R. Laird, W. W. L. Hsiao, T. A. Chiu, J. A. Eisen, and F. S. L. Brinkman 2012. MicrobeDB: a locally maintainable database of microbial genomic sequences. Bioinformatics 28:1947-1948.
69. Legendre, P., and L. Legendre 1998. Numerical ecology. Vol. 20. Developments in environmental modelling. Elsevier, Oxford, U.K.
70. Leibold, M. A., M. Holyoak, N. Mouquet, P. Amarasekare, J. M. Chase, M. F. Hoopes, et al. 2004. The metacommunity concept: a framework for multi-scale community ecology. Ecol. Lett. 7:601-613.
71. Leibold, M. A., E. P. Economo, and P. Peres-Neto 2010. Metacommunity phylogenetics: separating the roles of environmental filters and historical biogeography. Ecol. Lett. 13:1290-9.
72. Leininger, S., T. Urich, M. Schloter, L. Schwark, J. Qi, G. W. Nicol, et al. 2006. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:806-9.
73. Liu, Z., C. Lozupone, M. Hamady, F. D. Bushman, and R. Knight 2007. Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acid Res. 35:e120.
74. Loreau, M. 2004. Does functional redundancy exist? Oikos 104:606-611.
75. Loreau, M., N. Mouquet, and A. Gonzalez 2003. Biodiversity as spatial insurance in heterogeneous landscapes. Proc. Nat. Acad. Sci. U.S.A. 100:12765-70.
76. Lovejoy, C., and M. Potvin 2010. Microbial eukaryotic distribution in a dynamic Beaufort Sea and the Arctic Ocean. J. Plankton Res. 33:431-444.
77. Lurgi, M., B. C. Lopez, and J. M. Montoya 2012. Novel communities from climate change. Philos. Trans. R. Soc. B Biol. Sci. 367:2913-2922.
78. Manavski, S. A., and G. Valle 2008. CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment. BMC Bioinformatics 9:S10.
79. Meynard, C. N., V. Devictor, D. Mouillot, W. Thuiller, F. Jiguet, and N. Mouquet 2011. Beyond taxonomic diversity patterns: how do α, β and γ components of bird functional and phylogenetic diversity respond to environmental gradients across France? Glob. Ecol. Biogeogr. 20:893-903.
80. Miner, B. E., L. De Meester, M. E. Pfrender, W. Lampert, and N. G. Hairston 2012. Linking genes to communities and ecosystems: Daphnia as an ecogenomic model. Proc. Roy. Soc. B Biol. Sci. 279:1873-1882.
81. Morlon, H., G. Chuyong, R. Condit, S. Hubbell, D. Kenfack, D. Thomas, et al. 2008. A general framework for the distance-decay of similarity in ecological communities. Ecol. Lett. 11:904-17.
82. Morlon, H., D. W. Schwilk, J. A. Bryant, P. A. Marquet, A. G. Rebelo, C. Tauss, et al. 2011. Spatial patterns of phylogenetic diversity. Ecol. Lett. 14:141-149.
83. Mouquet, N., V. Devictor, C. N. Meynard, F. Munoz, L. -F. Bersier, J. Chave, et al. 2012. Ecophylogenetics: advances and perspectives. Biol. Rev. Camb. Philos. Soc. 87:769-785.
84. Münkemüller, T., F. de Bello, C. N. Meynard, D. Gravel, S. Lavergne, D. Mouillot, et al. 2012. From diversity indices to community assembly processes: a test with simulated data. Ecography 35:468-480.
85. Myllykangas, S., J. Buenrostro, and H. P. Ji 2012. Overview of Sequencing Technology Platforms. Pp. 11-26 in N. Rodríguez-Ezpeleta, M. Hackenberg and A. M. Aransay, eds. Bioinformatics for High Throughput Sequencing. Springer, New York, NY.
86. Nekola, J. C., and P. S. White 1999. The distance decay of similarity in biogeography and ecology. J. Biogeogr. 26:867-878.
87. Novotny, V., and Y. Basset 2005. Host specificity of insect herbivores in tropical forests. Proc. Roy. Soc. B Biol. Sci. 272:1083-1090.
88. O'Dwyer, J. P., and J. L. Green 2010. Field theory for biogeography: a spatially explicit model for predicting patterns of biodiversity. Ecol. Lett. 13:87-95.
89. Oksanen, J., R. Kindt, P. Legendre, B. O'Hara, G. L. Simpson, P. Solymos, et al. 2009. vegan: Community Ecology Package.
90. Opik, M., M. Metsis, T. J. Daniell, M. Zobel, and M. Moora 2009. Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest. New Phytol. 184:424-37.
91. Parnell, J. J., T. A. Crowl, B. C. Weimer, and M. E. Pfrender 2009. Biodiversity in microbial communities: system scale patterns and mechanisms. Mol. Ecol. 18:1455-1462.
92. Parr, C. S., R. Guralnick, N. Cellinese, and R. D. M. Page 2012. Evolutionary informatics: unifying knowledge about the diversity of life. Trends Ecol. Evol. 27:94-103.
93. Paterson, S., T. Vogwill, A. Buckling, R. Benmayor, A. J. Spiers, N. R. Thomson, et al. 2010. Antagonistic coevolution accelerates molecular evolution. Nature 464:275-278.
94. Pedrós-Alió, C. 2006. Marine microbial diversity: can it be determined? Trends Microbiol. 14:257-63.
95. Pereira, H. M., P. W. Leadley, V. Proença, R. Alkemade, J. P. W. Scharlemann, J. F. Fernandez-Manjarrés, et al. 2010. Scenarios for global biodiversity in the 21st century. Science 330:1496-501.
96. Poisot, T., E. Canard, D. Mouillot, N. Mouquet, and D. Gravel 2012. The dissimilarity of species interaction networks. Ecol. Lett. 15:1353-1361.
97. Poole, A. M., D. B. Stouffer, and J. M. Tylianakis 2012. 'Ecosystomics': ecology by sequencer. Trends Ecol. Evol. 27:309-310.
98. Purdy, K. J., P. J. Hurd, J. Moya-Laraño, M. Trimmer, B. B. Oakley, and G. Woodward 2010. Systems biology for ecology. Pp. 87-149 in Advances in Ecological Research. Elsevier, Oxford, U.K.
99. Reiss, J., J. R. Bridle, J. M. Montoya, and G. Woodward 2009. Emerging horizons in biodiversity and ecosystem functioning research. Trends Ecol. Evol. 24:505-514.
100. Richardson, D. M. 2012. Conservation biogeography: what's hot and what's not? Divers. Distrib. 18:319-322.
101. Rodrigue, S., A. C. Materna, S. C. Timberlake, M. C. Blackburn, R. R. Malmstrom, E. J. Alm, et al. 2010. Unlocking short read sequencing for metagenomics. PLoS ONE 5:e11840.
102. Routledge, R. D. 1983. Evenness indices: are any admissible? En. Oikos 40:149.
103. Scheiner, S. M., and M. R. Willig 2011. The Theory of Ecology. University of Chicago Press, Chicago.
104. Schloss, P. D., S. L. Westcott, T. Ryabin, J. R. Hall, M. Hartmann, E. B. Hollister, et al. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75:7537-41.
105. Schreiber, S. J., R. Bürger, and D. I. Bolnick 2011. The community effects of phenotypic and genetic variation within a predator population. Ecology 92:1582-1593.
106. Sogin, M. L., H. G. Morrison, J. A. Huber, D. M. Welch, S. M. Huse, and P. R. Neal, et al. 2006. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc. Nat. Acad. Sci. 103:12115-12120.
107. Stevenson, B. S., and T. M. Schmidt 2004. Life history implications of rRNA gene copy number in Escherichia coli life history implications of rRNA gene copy number in Escherichia coli. Appl. Environ. Microbiol. 70:6670.
108. Sun, Y., R. D. Wolcott, and S. E. Dowd 2011. Tag-Encoded FLX Amplicon Pyrosequencing for the Elucidation of Microbial and Functional Gene Diversity in Any Environment. Pp. 129-141 in Y. M. Kwon and S. C. Ricke, eds. High-Throughput Next Generation Sequencing. Methods in Molecular Biology. Humana Press, Totowa, NJ.
109. Tedersoo, L., R. H. Nilsson, K. Abarenkov, T. Jairus, A. Sadam, I. Saar, et al. 2010. 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. New Phytol. 188:291-301.
110. Thompson, A. R. 2005. Dynamics of demographically open mutualists: immigration, intraspecific competition, and predation impact goby populations. Oecologia 143:61-9.
111. Tuomisto, H. 2011. Commentary: do we have a consistent terminology for species diversity? Yes, if we choose to use it. Oecologia 167:903-911.
112. Urban, M. C., M. A. Leibold, P. Amarasekare, L. De Meester, R. Gomulkiewicz, M. E. Hochberg, et al. 2008. The evolutionary ecology of metacommunities. Trends Ecol. Evol. 23:311-317.
113. Vacharaksa, A., and B. B. Finlay 2010. Gut microbiota: metagenomics to study complex ecology. Curr. Biol.: CB 20:R569-71.
114. Violle, C., M. -L. Navas, D. Vile, E. Kazakou, C. Fortunel, I. Hummel, et al. 2007. Let the concept of trait be functional!. Oikos 116:882-892.
115. Webb, C. O., D. D. Ackerly, M. A. McPeek, and M. J. Donoghue 2002. Phylogenies and community ecology. Annu. Rev. Ecol. Evol. Syst. 33:475-505.
116. Webb, C. O., J. B. Losos, and A. A. Agrawal 2006. Integrating phylogenies into community ecology. Ecology 87:1-2.
117. Weitz, J. S., T. Poisot, J. R. Meyer, C. O. Flores, S. Valverde, M. B. Sullivan, et al. 2013. Phage-bacteria infection networks. Trends Microbiol. 21:82-91.
118. Wetzel, C. E., D. de C. Bicudo, L. Ector, E. A. Lobo, J. Soininen, V. L. Landeiro, et al. 2012. Distance decay of similarity in neotropical diatom communities. PLoS ONE 7:e45071.
119. Whitham, T. G., J. K. Bailey, J. A. Schweitzer, S. M. Shuster, R. K. Bangert, C. J. LeRoy, et al. 2006. A framework for community and ecosystem genetics: from genes to ecosystems. Nature rev. Genet. 7:510-23.
120. Xie, W., Q. -S. Meng, Q. -J. Wu, S.-L. Wang, X. Yang, N.-N. Yang, et al. 2012. Pyrosequencing the Bemisia tabaci Transcriptome Reveals a Highly Diverse Bacterial Community and a Robust System for Insecticide Resistance. PLoS ONE 7:e35181.
121. Yang, Z., and B. Rannala 2012. Molecular phylogenetics: principles and practice. Nat. Rev. Genet. 13:303-314.
122. Yu, D. W., Y. Ji, B. C. Emerson, X. Wang, C. Ye, C. Yang, et al. 2012. Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods Ecol. Evol. 3:613-623.
123. Zhang, L., U. H. Thygesen, K. Knudsen, and K. H. Andersen 2012. Trait diversity promotes stability of community dynamics. Theoretical Ecology 6:57-69.