Incorporating clade identity in analyses of phylogenetic community structure: An example with hummingbirds

American Naturalist

Volumn 176, Issue 5, 2010, Pages 573-587

  Parra, Juan L ^a   McGuire, Jimmy A ^b   Graham, Catherine H ^a  

^a STONY BROOK UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Algorithm; Biogeography; Ecuador; Environment; Nodesig; Phylogeny; Trochilidae

Indexed keywords

ALGORITHM; BIOGEOGRAPHY; BIRD; CLADISTICS; COEXISTENCE; ENVIRONMENTAL GRADIENT; GEOGRAPHICAL REGION; IDENTIFICATION METHOD; PHYLOGENY; PRECIPITATION INTENSITY; SEASONALITY; SPATIOTEMPORAL ANALYSIS; TEMPERATURE EFFECT;

ALGORITHM; ANIMAL; ARTICLE; BIOLOGICAL MODEL; BIRD; CLASSIFICATION; ECUADOR; ENVIRONMENT; GEOGRAPHY; PHYLOGENY; PHYSIOLOGY; POPULATION DYNAMICS;

ALGORITHMS; ANIMALS; BIRDS; ECUADOR; ENVIRONMENT; GEOGRAPHY; MODELS, BIOLOGICAL; PHYLOGENY; POPULATION DYNAMICS;

AMAZONIA; ECUADOR;

TROCHILIDAE;

EID: 78349301198     PISSN: 00030147     EISSN: None     Source Type: Journal    
DOI: 10.1086/656619     Document Type: Article

References (68)

1. Altshuler, D. L., and R. Dudley. 2002. The ecological and evolutionary interface of hummingbird flight physiology. Journal of Experimental Biology 205:2325-2336.
2. -. 2006. The physiology and biomechanics of avian flight at high altitude. Integrative and Comparative Biology 46:62-71.
3. Altshuler, D. L., R. Dudley, and J. A. McGuire. 2004. Resolution of a paradox: hummingbird flight at high elevation does not come without a cost. Proceedings of the National Academy of Sciences of the USA 101:17731-17736.
4. Bleiweiss, R. 1998a. Origin of hummingbird faunas. Biological Journal of the Linnean Society 65:77-97.
5. -. 1998b. Tempo and mode of hummingbird evolution. Biological Journal of the Linnean Society 65:63-76.
6. Brown, J. H., and M. A. Bowers. 1985. Community organization in hummingbirds: relationships between morphology and ecology. Auk 102:251-269.
7. Brown, J. H., and A. Kodric-Brown. 1979. Convergence, competition and mimicry in a temperate community of hummingbird-pollinated flowers. Ecology 60:1022-1035.
8. Bryant, J. A., C. Lamanna, H. Morlon, A. J. Kerkhoff, B. J. Enquist, and J. L. Green. 2008. Microbes on mountainsides: contrasting elevational patterns of bacterial and plant diversity. Proceedings of the National Academy of Sciences of the USA 105:11505-11511.
9. Calenge, C. 2006. The package adehabitat for the R software: a tool for the analysis of space and habitat use by animals. Ecological Modelling 197:516-519.
10. Cardillo, M., J. L. Gittleman, and A. Purvis. 2008. Global patterns in the phylogenetic structure of island mammal assemblages. Proceedings of the Royal Society B: Biological Sciences 275:1549-1556.
11. Cavender-Bares, J., D. D. Ackerly, D. A. Baum, and F. A. Bazzaz. 2004. Phylogenetic overdispersion in Floridian oak communities. American Naturalist 163:823-843.
12. Cavender-Bares, J., A. Keen, and B. Miles. 2006. Phylogenetic structure of Floridian plant communities depends on taxonomic and spatial scale. Ecology 87:S109-S122.
13. Cavender-Bares, J., K. H. Kozak, P. V. A. Fine, and S. W. Kembel. 2009. The merging of community ecology and phylogenetic biology. Ecology Letters 12:693-715.
14. Chave, J., H. C. Muller-Landau, and S. A. Levin. 2002. Comparing classical community models: theoretical consequences for patterns of diversity. American Naturalist 159:1-23.
15. Emerson, B. C., and R. G. Gillespie. 2008. Phylogenetic analysis of community assembly and structure over space and time. Trends in Ecology & Evolution 23:619-630.
16. Feinsinger, P. 1976. Organization of a tropical guild of nectarivorous birds. Ecological Monographs 46:257-291.
17. Freckleton, R. P., P. H. Harvey, and M. Pagel. 2002. Phylogenetic analysis and comparative data: a test and review of evidence. American Naturalist 160:712-726.
18. Gillespie, R. 2004. Community assembly through adaptive radiation in Hawaiian spiders. Science 303:356-359.
19. Gotelli, N., and G. L. Entsminger. 2003. Swap algorithms in null model analysis. Ecology 84:532-535.
20. Graham, C. H., and P. V. A. Fine. 2008. Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time. Ecology Letters 11:1265-1277.
21. Graham, C. H., J. L. Parra, C. Rahbek, and J. A. McGuire. 2009. Phylogenetic structure in tropical hummingbird communities. Proceedings of the National Academy of Sciences of the USA 106: 19673-19678.
22. Hardy, O. J., and B. Senterre. 2007. Characterizing the phylogenetic structure of communities by an additive partitioning of phylogenetic diversity. Journal of Ecology 95:493-506.
23. Heard, S. B., and H. C. Graham. 2007. The shapes of phylogenetic trees of clades, faunas, and local assemblages: exploring spatial pattern in differential diversification. American Naturalist 169: E107-E118.
24. Helmus, M. R., T. J. Bland, C. K. Williams, and A. R. Ives. 2007. Phylogenetic measures of biodiversity. American Naturalist 169: E68-E83.
25. Hijmans, R. J., S. E. Cameron, J. L. Parra, P. G. Jones, and A. Jarvis. 2005. Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology 25:1965-1978.
26. Ihaka, R., and R. Gentleman. 1996. R: a language for data analysis and graphics. Journal of Computational and Graphical Statistics 5:299-314.
27. Kembel, S. W. 2009. Disentangling niche and neutral influences on community assembly: assessing the performance of community phylogenetic structure tests. Ecology Letters 12:949-960.
28. Kraft, N. J. B., W. K. Cornwell, C. O. Webb, and D. D. Ackerly. 2007. Trait evolution, community assembly, and the phylogenetic structure of ecological communities. American Naturalist 170:271-283.
29. Lack, D. 1973. The numbers of species of hummingbirds in theWest Indies. Evolution 27:326-337.
30. Leibold, M. A., M. Holyoak, N. Mouquet, P. Amarasekare, J. M. Chase, M. F. Hoopes, R. D. Holt, et al. 2004. The metacommunity concept: a framework for multi-scale community ecology. Ecology Letters 7:601-613.
31. Levin, S. A. 1992. The problem of pattern and scale in ecology. Ecology 73:1943-1967.
32. Losos, J. B., and R. E. Glor. 2003. Phylogenetic comparative methods and the geography of speciation. Trends in Ecology & Evolution 18:220-227.
33. Losos, J. B., T. R. Jackman, A. Larson, K. de Queiroz, and L. Rodriguez-Schettino. 1998. Contingency and determinism in replicated adaptive radiations of island lizards. Science 279:2115-2118.
34. Lovette, I., and W. M. Hochachka. 2006. Simultaneous effects of phylogenetic niche conservatism and competition on avian community structure. Ecology 87:S14-S28.
35. McGuire, J. A., C. C. Witt, D. L. Altshuler, and J. V. Remsen. 2007. Phylogenetic systematics and biogeography of hummingbirds: Bayesian and maximum likelihood analyses of partitioned data and selection of an appropriate partitioning strategy. Systematic Biology 56:837-856.
36. McPeek, M. A. 2007. The macroevolutionary consequences of ecological differences among species. Palaeontology 50:111-129.
37. Moen, D. S., S. A. Smith, and J. J.Wiens. 2009. Community assembly through evolutionary diversification and dispersal in Middle American treefrogs. Evolution 63:3228-3247.
38. Pagel, M. 1999. Inferring the historical patterns of biological evolution. Nature 401:877-884.
39. Parent, C. E., and B. J. Crespi. 2009. Ecological opportunity in adaptive radiation of Galápagos endemic land snails. American Naturalist 174:898-905.
40. Pavoine, S., M. S. Love, and M. B. Bonsall. 2009. Hierarchical partitioning of evolutionary and ecological patterns in the organization of phylogenetically-structured species assemblages: application to rockfish (genus: Sebastes) in the Southern California Bight. Ecology Letters 12:898-908.
41. Perret, M., A. Chautems, R. Spichiger, T. G. Barraclough, and V. Savolainen. 2007. The geographical pattern of speciation and floral diversification in the Neotropics: the tribe Sinningieae (Gesneriaceae) as a case study. Evolution 61:1641-1660.
42. Posada, D., and K. A. Crandall. 1998. ModelTest: testing the model of DNA substitution. Bioinformatics 14:817-818.
43. Rabosky, D. L. 2009. Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions. Ecology Letters 12:735-743.
44. Rabosky, D. L., and I. J. Lovette. 2008. Density-dependent diversification in North American wood warblers. Proceedings of the Royal Society B: Biological Sciences 275:2363-2371.
45. Rahbek, C., and G. R. Graves. 2000. Detection of macro-ecological patterns in South American hummingbirds is affected by spatial scale. Proceedings of the Royal Society B: Biological Sciences 267: 2259-2265.
46. Rahbek, C., N. J. Gotelli, R. K. Colwell, G. L. Entsminger, T. Rangel, and G. R. Graves. 2007. Predicting continental-scale patterns of bird species richness with spatially explicit models. Proceedings of the Royal Society B: Biological Sciences 274:165-174.
47. Ree, R. H., and S. A. Smith. 2008. Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Systematic Biology 57:4-14.
48. Remsen, J. V., C. D. Cadena, A. Jaramillo, M. Nores, J. F. Pacheco, M. B. Robbins, T. S. Schulenberg, F. G. Stiles, D. F. Stotz, and K. J. Zimmer. 2008. A classification of the bird species of South America. American Ornithologists' Union, Washington, DC.
49. Ricklefs, R. E. 1987. Community diversity: relative roles of local and regional processes. Science 235:167-171.
50. -. 2007. History and diversity: explorations at the intersection of ecology and evolution. American Naturalist 170(suppl.):S56-S70.
51. -. 2008. Disintegration of the ecological community. American Naturalist 172:741-750.
52. Ricklefs, R. E., and E. Bermingham. 2007. The causes of evolutionary radiations in archipelagoes: passerine birds in the Lesser Antilles. American Naturalist 169:285-297.
53. Ridgely, R. S., T. F. Allnutt, T. Brooks, D. K. McNicol, D.W. Mehlman, B. E. Young, and J. R. Zook. 2007. Digital distribution maps of the birds of the Western Hemisphere. Version 3.0. NatureServe, Arlington, VA.
54. Ronquist, F., and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
55. Sanderson, M. J. 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy.Molecular Biology and Evolution 14:1218-1231.
56. Sierra, R. 1999. Propuesta preliminar de un sistema de clasificación de vegetación para el Ecuador continental. Proyecto INEFAN/GEFBIRF y Ecociencia. Indugraf del Ecuador, Quito.
57. Sokal, R. R., and F. J. Rohlf. 1995. Biometry. New York,W. H. Freeman.
58. Stiles, F. G. 2008. Ecomorphology and phylogeny of hummingbirds: divergence and convergence in adaptations to high elevations. Ornitología Neotropical 19:511-519.
59. Swenson, N. G., B. J. Enquist, J. Pither, J. Thompson, and J. K. Zimmerman. 2006. The problem and promise of scale dependency in community phylogenetics. Ecology 87:2418-2424.
60. Swenson, N. G., B. J. Enquist, J. Thompson, and J. K. Zimmerman. 2007. The influence of spatial and size scale on phylogenetic relatedness in tropical forest communities. Ecology 88:1770-1780.
61. Temeles, E. J., Y. B. Linhart, M. Masonjones, and H. D. Masonjones. 2002. The role of flower width in hummingbird bill length-flower length relationships. Biotropica 34:68-80.
62. Temeles, E. J., C. R. Koulouris, S. E. Sander, and W. J. Kress. 2009. Effect of flower shape and size on foraging performance and tradeoffs in a tropical hummingbird. Ecology 90:1147-1161.
63. Terborgh, J. 1985. The role of ecotones in the distribution of Andean birds. Ecology 66:1237-1246.
64. Vamosi, S. M., S. B. Heard, J. C. Vamosi, and C. O. Webb. 2009. Emerging patterns in the comparative analysis of phylogenetic community structure. Molecular Ecology 18:572-592.
65. Webb, C. O., D. D. Ackerly, M. A. McPeek, and M. J. Donoghue. 2002. Phylogenies and community ecology. Annual Review of Ecology and Systematics 33:475-505.
66. Webb, C. O., D. D. Ackerly, and S. W. Kembel. 2008. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 24:2098-2100.
67. Weiher, E., and P. A. Keddy. 1995. Assembly rules, null models, and trait dispersion: new questions from old patterns. Oikos 74:159-164.
68. Wolf, L. L., F. G. Stiles, and F. R. Hainsworth. 1976. Ecological organization of a tropical, highland hummingbird community. Journal of Animal Ecology 45:349-379.