Sensitivity of metrics of phylogenetic structure to scale, source of data and species pool of hummingbird assemblages along elevational gradients

PLoS ONE

Volumn 7, Issue 4, 2012, Pages

  González Caro, Sebastián ^a   Parra, Juan L ^b,c   Graham, Catherine H ^c   McGuire, Jimmy A ^d   Cadena, Carlos Daniel ^a  

^a UNIVERSIDAD DE LOS ANDES   (Colombia)

^b UNIVERSIDAD DE ANTIOQUIA   (Colombia)

^c STONY BROOK UNIVERSITY   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIRD; CONTROLLED STUDY; GENETIC ASSOCIATION; GENETIC DISTANCE; GENETIC PARAMETERS; HUMMINGBIRD; MOLECULAR PHYLOGENY; NEAREST TAXON INDEX; NET RELATEDNESS INDEX; NONHUMAN; PHYLOGENETIC SPECIES CLUSTERING; PHYLOGENETIC SPECIES VARIABILITY; PHYLOGENETIC TREE; POPULATION GENETIC STRUCTURE; SENSITIVITY ANALYSIS; SPECIES COEXISTENCE; SPECIES COMPOSITION; SPECIES DISTRIBUTION; SPECIES DIVERSITY; SPECIES RICHNESS; ALTITUDE; ANALYSIS OF VARIANCE; ANIMAL; BAYES THEOREM; BIOLOGICAL MODEL; BIOLOGY; COLOMBIA; DEMOGRAPHY; ECOSYSTEM; GENETICS; INFORMATION CENTER; PHYLOGENY; PHYLOGEOGRAPHY; SPECIES DIFFERENCE;

TROCHILIDAE;

ALTITUDE; ANALYSIS OF VARIANCE; ANIMALS; BAYES THEOREM; BIRDS; COLOMBIA; COMPUTATIONAL BIOLOGY; DEMOGRAPHY; ECOSYSTEM; MODELS, GENETIC; MUSEUMS; PHYLOGENY; PHYLOGEOGRAPHY; SPECIES SPECIFICITY;

EID: 84871089414     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0035472     Document Type: Article

References (51)

1. Colwell RK, Winkler DW, (1984) A null model for null models in biogeography. Ecological communities conceptual issues and the evidence (ed. by DR Strong) pp. 344-359. Princeton University Press, Princeton, NJ.
2. Webb CO, Ackerly DD, McPeek MA, Donoghue MJ, (2002) Phylogenies and community ecology. Annu Rev Ecol Evol S 33: 475-505.
3. Emerson BC, Gillespie RG, (2008) Phylogenetic analysis of community assembly and structure over space and time. Trends Ecol Evol 23: 619-630.
4. Cavender-Bares J, Kozak KH, Fine PVA, Kembel SW, (2009) The merging of community ecology and phylogenetic biology. Ecol Lett 12: 693-715.
5. Vamosi SM, Heard SB, Vamosi JC, Webb CO, (2009) Emerging patterns in the comparative analysis of phylogenetic community structure. Mol Ecol 18: 572-592.
6. Swenson NG, Enquist BJ, Pither J, Thompson J, Zimmerman JK, (2006) The problem and promise of scale dependency in community phylogenetics. Ecology 87: 2418-2424.
7. Swenson NG, Enquist BJ, Thompson J, Zimmerman JK, (2007) The influence of spatial and size scale on phylogenetic relatedness in tropical forest communities. Ecology 88: 1770-1780.
8. Lessard JP, Borregaard MK, Fordyce JA, Rahbek C, Weiser MD, et al. (2011) Strong influence of regional species pools on continent-wide structuring of local communities. Proceedings of the Royal Society B doi:10.1098/rspb.2011.0552.
9. Kraft NJB, Cornwell WK, Webb CO, Ackerly DD, (2007) Trait evolution, community assembly, and the phylogenetic structure of ecological communities. Am Nat 170: 271-283.
10. Kraft NJB, Ackerly DD, (2010) Functional trait and phylogenetic tests of community assembly across spatial scales in an Amazonian forest. Ecol Monogr 80: 401-422.
11. Weiher E, Keddy PA, (1995) Assembly rules, null models, and trait dispersion: new questions from old patterns. Oikos 74: 159-164.
12. MacArthur RH, (1958) Population ecology of some warblers of northeastern coniferous forests. Ecology 39: 599-619.
13. Sih A, Crowley P, McPeek M, Petranka J, Strohmeier K, (1985) Predation, competition, and prey communities: a review of field experiments. Annu Rev Ecol Evol S 16: 269-311.
14. Elias M, Gompert Z, Jiggins C, Willmott K, (2008) Mutualistic interactions drive ecological niche convergence in a diverse butterfly community. PLoS Biol 6: 2642-2649.
15. Hurlbert AH, White EP, (2005) Disparity between range map- and survey-based analyses of species richness: patterns, processes and implications. Ecol Lett 8: 319-327.
16. Graham CH, Hijmans RJ, (2006) A comparison of methods for mapping species ranges and species richness. Global Ecol Biogeogr 15: 578-587.
17. McPherson JM, Jetz W, (2007) Type and spatial structure of distribution data and the perceived determinants of geographical gradients in ecology: the species richness of African birds. Global Ecol Biogeogr 16: 657-667.
18. Kadmon R, Farber O, Danin A, (2004) Effect of roadside bias on the accuracy of predictive maps produced by bioclimatic models. Ecol Appl 14: 401-413.
19. Wiens JA, (1989) Spatial scaling in ecology. Funct Ecol 3: 385-397.
20. Wiens JA, Rotenberry JT, (1981) Habitat associations and community structure of birds in shrubsteppe environments. Ecol Monogr 51: 21-42.
21. Bleiweiss R, (1998) Origin of hummingbird faunas. Biol J Linn Soc 65: 77-97.
22. McGuire JA, Witt CC, Altshuler DL, Remsen JV, (2007) Phylogenetic systematics and biogeography of hummingbirds: bayesian and maximum likelihood analyses of partitioned data and selection of an appropriate partitioning strategy. Syst Biol 56: 837-856.
23. Altshuler DL, Dudley R, (2002) The ecological and evolutionary interface of hummingbird flight physiology. J Exp Biol 205: 2325-2336.
24. Graham CH, Parra JL, Rahbek C, McGuire JA, (2009) Phylogenetic structure in tropical hummingbird communities. P Natl Acad Sci USA 106: 19673-19678.
25. Parra JL, McGuire JA, Graham CH, (2010) Incorporating clade identity in analyses of phylogenetic community structure: an example with hummingbirds. Am Nat 176: 573-587.
26. Webb CO, (2000) Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. Am Nat 156: 145-155.
27. Helmus MR, Bland TJ, Williams CK, Ives AR, (2007) Phylogenetic measures of biodiversity. Am Nat 169: E68-E83.
28. Ronquist F, Huelsenbeck JP, (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
29. Posada D, Crandall KA, (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
30. Gotelli NJ, (2000) Null model analysis of species co-ocurrence patterns. Ecology 81: 2606-2621.
31. Webb CO, Ackerly DD, Kembel SW, (2008) Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 24: 2098-2100.
32. Kembel SW, (2009) Disentangling niche and neutral influences on community assembly: assessing the performance of community phylogenetic structure tests. Ecol Lett 12: 949-960.
33. Kembel SW, Cowan PD, Helmus MR, Cornwell WK, Morlon H, et al. (2010) Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26: 1463-1464.
34. R Development Core Team (2005) R: A language and environment for statistical computing. R foundation for Statistical computing, Vienna, Austria.
35. Stiles FG, (2004) Phylogenetic constraints upon morphological and ecological adaptation in hummingbirds (Trochilidae): Why are there no hermits in the paramo? Ornitologia Neotropical 15: 191-198.
36. Fosberg F, (1967) A classification of vegetation for general purposes. I.B.P. Handbook 4 (ed. by G.F., Peterken) pp. 73-120. Blackwell Scientific Publications, Oxford.
37. Terborgh J, Robinson SK, Parker TA, Munn CA, Pierpont N, (1990) Structure and organization of an amazonian forest bird community. Ecol Monogr 60: 213-238.
38. Lennon JJ, Koleff P, Greenwood JJD, Gaston KJ, (2001) The geographical structure of British bird distributions: diversity, spatial turnover and scale. J Anim Ecol 70: 966-979.
39. Tuomisto H, (2010) A diversity of beta diversities: straightening up a concept gone awary. Part 1. Defining beta diversity as a function of alpha and gamma diversity. Ecography 33: 2-22.
40. Heard SB, Cox GH, (2007) The shape of phylogenetic trees of clades, faunas and local assemblages: Exploring spatial pattern in differential diversidication. Am Nat 169: E108-E118.
41. Cavender-Bares J, Keen A, Miles B, (2006) Phylogenetic structure of floridian plant communities depends on taxonomic and spatial scale. Ecology 87: 109-122.
42. Rosenzweig M, (1995) Species Diversity in Space and Time. Cambridge University Press, Cambridge.
43. He F, Legendre P, (2002) Species diversity patterns derived from species-area models. Ecology 83: 1185-1198.
44. Swenson NG, Enquist BJ, (2009) Opposing assembly mechanisms in a Neotropical dry forest: implications for phylogenetic and functional community ecology. Ecology 90: 2161-2170.
45. Lovette IJ, Hochachka WM, (2006) Simultaneous effects of phylogenetic niche conservatism and competition on avian community structure. Ecology 87: 14-28.
46. Boakes EH, McGowan PJK, Fuller RA, Chang-qing D, Clark NE, et al. (2010) Distorted views of biodiversity: spatial and temporal bias in species occurrence data. PLoS Biol, 8, e1000385.
47. Jetz W, McPherson JM, Guralnick RP, (2012) Integrating biodiversity distribution knowledge: toward a global map of life. Trends Ecol Evol 27: 151-159.
48. Vamosi JC, Vamosi SM, (2007) Body size, rarity, and phylogenetic community structure: insights from diving beetle assemblages of Alberta. Divers Distrib 13: 1-10.
49. Cardillo M, Gittleman JL, Purvis A, (2008) Global patterns in the phylogenetic structure of island mammal assemblages. P Roy Soc B-Biol Sci 275: 1549-1556.
50. Stiles FG, (2008) Ecomorphological and phylogeny of hummingbird: divergence and convergence in adaptations to high elevations. Ornitol Neotrop 19: 511-519.
51. Gómez JP, Bravo GA, Brumfield RT, Tello JG, Cadena CD, (2010) A phylogenetic approach to disentangling the role of competition and habitat filtering in community assembly of Neotropical forest birds. J Anim Ecol 79: 1181-1192.