Phylogeny, phylogeography, phylobetadiversity and the molecular analysis of biological communities

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 366, Issue 1576, 2011, Pages 2391-2402

  Emerson, Brent C ^a,b   Cicconardi, Francesco ^c   Fanciulli, Pietro P ^c   Shaw, Peter J A ^d  

^a UNIVERSITY OF EAST ANGLIA   (United Kingdom)

^b INSTITUTO DE PRODUCTOS NATURALES Y AGROBIOLOGÍA   (Spain)

^c UNIVERSITY OF SIENA   (Italy)

^d UNIVERSITY OF ROEHAMPTON   (United Kingdom)

Author keywords

Collembola; Cryptic species; DNA barcoding; High throughput sequencing; Mesofauna; Next generation sequencing

Indexed keywords

CYTOCHROME C OXIDASE; MITOCHONDRIAL DNA;

ASSEMBLY RULE; COMMUNITY COMPOSITION; GENETIC ANALYSIS; INSECT; MITOCHONDRIAL DNA; MOLECULAR ECOLOGY; PHYLOGENY; PHYLOGEOGRAPHY; SPECIATION (BIOLOGY); SPECIES DIVERSITY; TAXONOMY;

ANIMAL; ARTHROPOD; ARTICLE; CHEMISTRY; GENETICS; METHODOLOGY; MICROBIOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; PHYLOGEOGRAPHY;

ANIMALS; ARTHROPODS; DNA, MITOCHONDRIAL; ELECTRON TRANSPORT COMPLEX IV; EVOLUTION, MOLECULAR; PHYLOGENY; PHYLOGEOGRAPHY; SOIL MICROBIOLOGY;

COLLEMBOLA;

EID: 79960535651     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2011.0057     Document Type: Article

References (77)

1. Webb, C. O. 2000 Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. Am. Nat. 156, 145-155. (doi:10. 1086/303378)
2. Cavender-Bares, J., Kozak, K. H., Fine, P. V. A. & Kembel, S. W. 2009 The merging of community ecology and phylogenetic biology. Ecol. Lett. 12, 693-715. (doi:10.1111/j.1461-0248.2009.01314.x)
3. Emerson, B. C. & Gillespie, R. G. 2008 Phylogenetic analysis of community assembly and structure over space and time. Trends Ecol. Evol. 23, 619-630. (doi:10.1016/j.tree.2008.07.005)
4. Johnson, M. T. J. & Stinchcombe, J. R. 2007 An emerging synthensis between community ecology and evolutionary biology. Trends Ecol. Evol. 22, 250-257. (doi:10.1016/j.tree.2007.01.014)
5. Vamosi, S. M., Heard, S. B., Vamosi, J. C. & Webb, C. O. 2009 Emerging patterns in the comparative analysis of phylogenetic community structure. Mol. Ecol. 18, 572-592. (doi:10.1111/j.1365-294X.2008.04001.x)
6. Hubbell, S. P. 2001 The unified neutral theory of biodiversity and biogeography. Princeton, NJ: Princeton University Press.
7. MacArthur, R. H. & Wilson, E. O. 1967 The theory of island biogeography. Princeton, NJ: Princeton University Press.
8. Weiher, E., Freund, D., Bunton, T., Stefanski, A., Lee, T. & Bentivenga, S. 2011 Advances, challenges, and a developing synthesis of ecological community assembly theory. Phil. Trans. R. Soc. B. 366, 2403-2413. (doi:10. 1098/rstb.2011.0056)
9. Ricklefs, R. E. 1987 Community diversity: relative roles of local and regional processes. Science 235, 167-171. (doi:10.1126/science.235.4785.167)
10. Emerson, B. C. & Kolm, N. 2005 Species diversity can drive speciation. Nature 434, 1015-1017. (doi:10.1038/ nature03450)
11. Ricklefs, R. E. 2006 Evolutionary diversification and the origin of the diversity-environment relationship. Ecology 87, S3-S13. (doi:10.1890/0012-9658(2006)87[3:EDA TOO]2.0.CO;2)
12. Hickerson, M. J., Carstens, B. C., Cavender-Bares, J., Crandall, K. A., Graham, C. H., Johnson, J. B., Rissler, L., Victoriano, P. F. & Yoder, A. D. 2010 Phylogeog-raphy's past, present, and future: 10 years after Avise, 2000. Mol. Phylogenet. Evol. 54, 291-301. (doi:10. 1016/j.ympev.2009.09.016)
13. Avise, J. C. 2000 Phylogeography: the history and formation of species. Cambridge, MA: Harvard University Press.
14. Carstens, B. C. & Knowles, L. L. 2007 Shifting distributions and speciation: species divergence during rapid climate change. Mol. Ecol. 16, 619-627. (doi:10.1111/ j.1365-294X.2006.03167.x)
15. Knowles, L. L. & Carstens, B. C. 2006 Estimating a geographically explicit model of population divergence. Evolution 61, 477-493. (doi:10.1111/j.1558-5646.2007. 00043.x)
16. Knowles, L. L. & Maddison, W. P. 2002 Statistical phylogeography. Mol. Phylogeogr. 11, 2623-2635.
17. Knowles, L. L. 2009 Statistical phylogeography. Annu. Rev. Ecol. Evol. Syst. 40, 593-612. (doi:10.1146/ annurev.ecolsys.38.091206.095702)
18. Galbreath, K. E., Hafner, D. J., Zamudio, K. R. & Agnew, K. 2010 Isolation and introgression in the inter-mountain west: contrasting gene genalogies reveal the complex biogeographic history of the American pike (Ochotona princeps). J. Biogeogr. 37, 344-362. (doi:10. 1111/j.1365-2699.2009.02201.x)
19. Peters, J. L., Zhuravlev, Y. N., Fefelov, I., Humphries, E. M. & Omland, K. E. 2008 Multilocus phylogeography of a holarctic duck: colonization of North America from Eurasia by Gadwall (Anas strepera). Evolution 62, 1469-1483. (doi:10.1111/j.1558-5646.2008.00372.x)
20. Carnaval, A. C., Hickerson, M. J., Haddad, C. F. B., Rodrigues, M. T. & Moritz, C. 2009 Stability predicts genetic diversity in a Brazilian Atlantic forest hotspot. Science 323, 785-789. (doi:10.1126/science. 1166955)
21. Garrick, R. C., Rowell, D. M., Simmons, C. S., Hillis, D. M. & Sunnucks, P. 2008 Fine-scale phylogeographic congruence despite demographic incongruence in two low-mobility saproxylic springtails. Evolution 62, 1103-1118. (doi:10.1111/j.1558-5646.2008.00349.x)
22. Ilves, K. L., Huang, W., Wares, J. P. & Hickerson, M. J. 2010 Colonization and/or mitochondrial selective sweeps across the North Atlantic intertidal assemblage revealed by multi-taxa Bayesian computation. Mol. Ecol. 19, 4505-4519. (doi:10.1111/j.1365-294X.2010. 04790.x)
23. McCulloch, G. A., Wallis, G. P. & Waters, J. M. 2010 Onset of glaciation drove simultaneous vicariant isolation of alpine insects in New Zealand. Evolution 64, 2033-2043. (doi:10.1111/j.1558-5646.2010.00980.x)
24. Emerson, B. C. & Hewitt, G. M. 2005 Phylogeography. Curr. Biol. 15, R367-R371. (doi:10.1016/j.cub.2005.05. 016)
25. Pons, J., Barraclough, T. G., Gomez-Zurita, J., Cardoso, A., Duran, D. P., Hazell, S., Kamoun, S., Sumlin, W. & Vogler, A. 2006 Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst. Biol. 55, 595-609. (doi:10.1080/10635150600852011)
26. Beaumont, M. A., Zhang, W. & Balding, D. J. 2002 Approximate Bayesian computation in population genetics. Genetics 162, 2025-2035.
27. Hickerson, M. J. & Meyer, C. P. 2008 Testing comparative phylogeographic models of marine vicariance and dispersal using a hirearchical Bayesian approach. BMC Evol. Biol. 8, 322. (doi:10.1186/1471-2148-8-322)
28. Lemey, P., Rambaut, A., Drummond, A. & Suchard, M. A. 2009 Bayesian phylogeography finds its roots. PLoS Comput. Biol. 5, e1000520. (doi:10.1371/journal. pcbi.1000520)
29. Navascués, M., Depaulis, F. & Emerson, B. C. 2010 Combining contemporary and ancient DNA in population genetic and phylogeographical studies. Mol. Ecol. Resour. 10, 760-772. (doi:10.1111/j.1755-0998.2010. 02895.x)
30. Navascue ́s, M. & Emerson, B. C. 2009 Elevated substitution rate estimates from ancient DNA: model violation and bias of Bayesian methods. Mol. Ecol. 18, 4390-4397. (doi:10.1111/j.1365-294X.2009.04333.x)
31. Crandall, K. A. & Templeton, A. R. 1993 Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny construction. Genetics 134, 959-969.
32. Posada, D. & Crandall, K. A. 2001 Intraspecific gene genealogies: trees grafting into networks. Trends Ecol. Evol. 16, 37-45. (doi:10.1016/S0169-5347(00)02026-7)
33. Emerson, B. C., Forgie, S., Goodacre, S. L. & Oromi, P. 2006 Testing phylogeographic predictions on an active volcanic island: Brachyderes rugatus (Coleoptera: Curculionidae) on La Palma (Canary Islands). Mol. Ecol. 15, 449-458. (doi:10.1111/j.1365-294X.2005. 02786.x)
34. Miraldo, A., Hewitt, G. M., Paulo, O. S. & Emerson, B. C. Submitted. Phylogeography and demographic history of Lacerta lepida in the Iberian Peninsula: multiple refugia, range expansions and secondary contact zones. BMC Evol. Biol.
35. Zarza, E., Reynoso, V. H. & Emerson, B. C. 2008 Diversification in the northern neotropics: mitochondrial and nuclear DNA phylogeography of the iguana Ctenosaura pectinata and related species. Mol. Ecol. 17, 3259-3275. (doi:10.1111/j.1365-294X.2008.03826.x)
36. Graham, C. H. & Fine, P. V. A. 2008 Phylogenetic beta diversity: linking ecological and evolutionary processes over space and time. Ecol. Lett. 11, 1265-1277. (doi:10.1111/j.1461-0248.2008.01256.x)
37. Chu, H. Y., Fierer, N., Lauber, C. L., Caporaso, J. G., Knight, R. & Grogan, P. 2010 Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes. Environ. Microbiol. 12, 2998-3006. (doi:10.1111/j.1462-2920.2010.02277.x)
38. Fulthorpe, R. R., Roesch, L. F. W., Riva, A. & Triplett, E. W. 2008 Distantly sampled soils carry few species in common. ISME J. 2, 901-910. (doi:10.1038/ismej. 2008.55)
39. Kaspari, M., Stevenson, B. S., Shik, J. & Kerekes, J. F. 2010 Scaling community structure: how bacteria, fungi, and ant taxocenes differentiate along a tropical forest floor. Ecology 91, 2221-2226. (doi:10.1890/09-2089.1)
40. Lauber, C. L., Hamady, M., Knight, R. & Fierer, N. 2009 Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl. Environ. Microbiol. 75, 5111-5120. (doi:10.1128/AEM.00335-09)
41. Rousk, J., Baath, E., Brookes, P. C., Lauber, C. L., Lozupone, C., Caporaso, J. G., Knight, R. & Fierer, N. 2010 Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 4, 1340-1351. (doi:10.1038/ismej.2010.58)
42. Creer, S. et al. 2010 Ultra-deep sequencing of the meiofaunal biosphere: practice, pitfalls and promises. Mol. Ecol. 19, 4-20. (doi:10.1111/j.1365-294X.2009. 04473.x)
43. Fonseca, V. G. et al. 2010 Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nat. Commun. 1, 98. (doi:10.1038/ncomms1095)
44. Decaëns, T. 2010 Macroecological patterns in soil communities. Global Ecol. Biogeogr. 19, 287-302. (doi:10. 1111/j.1466-8238.2009.00517.x)
45. Usher, M. B., Davis, P., Harris, J. & Longstaff, B. 1979 A profusion of species? Approaches towards understanding the dynamics of the populations of microarthropods in decomposer communities. In Population dynamics (eds A. M. Anderson, B. D. Turner & L. R. Taylor), pp. 359-384. Oxford, UK: Blackwell Scientific.
46. Giller, P. S. 1996 The diversity of soil communities, the 'poor man's tropical rainforest'. Biodivers. Conserv. 5, 135-168. (doi:10.1007/BF00055827)
47. Hopkin, S. P. 1997 Biology of the springtails (Insecta: Collembola). Oxford, UK: Oxford University Press.
48. Regier, J. C., Schultz, J. W., Zwick, A., Hussey, A., Ball, B., Wetzer, R., Martin, J. W. & Cunningham, C. W. 2010 Athropod relationships revealed by phylogenomic analysis of nuclear protein coding sequences. Nature 463, 1079-1083. (doi:10.1038/nature08742)
49. Rapoport, E. H. 1971 The geographical distribution of Neotropical and Antarctic Collembola. Pacific Insects Monogr. 25, 99-118.
50. Christiansen, K. 1971 Notes on Miocene amber Collem-bola from Chiapas. Univ. California Publ. Entomol. 63, 45-48.
51. Mari Mutt, J. A. 1983 Collembola in amber from the Dominican Republic. Proc. Entomol. Soc. Wash. 85, 575-587.
52. Cicconardi, F., Nardi, F., Emerson, B. C., Frati, F. & Fanciulli, P. P. 2010 Deep phylogeographic divisions and long-term persistence of forest invertebrates in the North-Western Mediterranean basin. Mol. Ecol. 19, 386-400. (doi:10.1111/j.1365-294X.2009.04457.x)
53. Mayr, E. 1942 Systematics and the origin of species from the viewpoint of a zoologist. Cambridge, MA: Harvard University Press.
54. Timmermans, M. J. T. N., Ellers, J., Marien, J., Verhoeff, S. C. & Ferwerda, E. B. & Van Straalen, N. M. 2005 Genetic structure in Orchesella cincta (Collembola): strong subdivision of European populations inferred from mtDNA and AFLP markers. Mol. Ecol. 14, 2017-2024. (doi:10.1111/j.1365-294X.2005.02548.x)
55. Stevens, M. I., Greenslade, P., Hogg, I. D. & Sunnucks, P. 2006 Southern hemisphere springtails: could any have survived glaciation of Antarctica? Mol. Biol. Evol. 23, 874-882. (doi:10.1093/molbev/msj073)
56. Torricelli, G., Carapelli, A., Convey, P., Nardi, F., Boore, J. L. & Frati, F. 2009 High divergence across the whole mitochondrial genome in the 'pan-Antarctic' springtail Friesea grisea: evidence for cryptic species? Gene 449, 30-40. (doi:10.1016/j.gene.2009.09.006)
57. Garrick, R. C., Sands, C. J., Rowell, D. M., Hillis, D. M. & Sunnucks, P. 2007 Catchments catch all: long-term population history of a giant springtail from the southeast Australian highlands-a multigene approach. Mol. Ecol. 16, 1865-1882. (doi:10.1111/j.1365-294X.2006. 03165.x)
58. Folmer, O., Black, M., Hoeh, W., Lutz, R. & Vrijenhoek, R. 1994 DNA primers for amplification of mitochon-drial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3, 294-299.
59. Ratnasingham, S. & Hebert, P. D. N. 2007 BOLD: the barcode of life data system. Mol. Ecol. Notes 7, 355-364. (doi:10.1111/j.1471-8286.2007.01678.x)
60. Blaxter, M. L. 2004 The promise of a DNA taxonomy. Phil. Trans. R. Soc. B 359, 669-679. (doi:10.1098/rstb. 2003.1447)
61. Blaxter, M. L., Elsworth, B. & Daub, J. 2004 DNA taxonomy of a neglected anumal phylum: an unexpected diversity of tardigrades. Biol. Lett. 271, S189-S192. (doi:10.1098/rsbl.2003.0130)
62. Heethoff, M., Domes, K., Laumann, M., Maraun, M., Norton, R. A. & Scheu, S. 2007 High genetic divergences indicate ancient separation of parthenogenetic lineages of the oribatid mite Platynothrus peltifer (Acari, Oribatida). J. Evol. Biol. 20, 392-402. (doi:10.1111/j. 1420-9101.2006.01183.x)
63. Mortimer, E., van Vuuren, B. J., Lee, J. E., Marshall, D. J., Convey, P. & Chwon, S. L. 2010 Mite dispersal among the Southern Ocean Islands and Antarctica before the last glacial maximum. Proc. R. Soc. Lond. B 278, 1247-1255. (doi:10.1098/rspb.2010.1779)
64. Schäffer, S., Pfingstl, T., Koblmüller, S., Winkler, K. A., Sturmbauer, C. & Krisper, G. 2010 Phylogenetic analysis of European Scutovertex mites (Acari, Oribatida, Scutoverticidae) reveals paraphyly and cryptic diversity: a molecular genetic and morphological approach. Mol. Phylogenet. Evol. 55, 677-688. (doi:10.1016/j.ympev. 2009.11.025)
65. Stevens, M. I. & Hogg, I. D. 2006 Contrasting levels of mitochondrial DNA variability between mites (Penthalodidae) and springtails (Hypogastruridae) from Trans-Antarctic Mountains suggest long-term effects of glaciation and life history on substitution rates, and speciation process. Soil Biol. Biochem. 38, 3171-3180. (doi:10.1016/j.soilbio.2006.01.009)
66. Powers, T. O., Neher, D. A., Mullin, P., Esquivel, A., Giblin-Davis, R. M., Kanzaki, N., Stock, S. P., Mora, M. M. & Uribe-Lorio, L. 2009 Tropical nematode diversity: vertical stratification of nematode communities in a Costa Rican humid lowland rainforest. Mol. Ecol. 18, 985-996. (doi:10.1111/j.1365-294X.2008.04075.x)
67. Huber, J. A., Mark Welch, D., Morrison, H. G., Huse, S. M., Neal, P. R., Butterfield, D. A. & Sogin, M. L. 2007 Microbial population structures in the deep marine biosphere. Science 318, 97-100. (doi:10.1126/science. 1146689)
68. Roesch, L. F., Fulthorpe, R. R., Riva, A., Casella, G., Hadwin, A. K. M., Kent, A. D. et al. 2007 Pyrosequen-cing enumerates and contrasts soil microbial diversity. ISME J. 1, 283-290. (doi:10.1038/ismej.2007.53)
69. Sogin, M. L., Morrison, H. G., Huber, J. A., Mark Welch, D., Huse, S. M., Neal, P. R., Arrieta, J. M. & Herndl, G. J. 2006 Microbial diversity in the deep sea and the underexplored 'rare biosphere'. Proc. Natl Acad. Sci. USA 103, 12115-12120. (doi:10.1073/ pnas.0605127103)
70. Medinger, R., Nolte, V., Pandey, R. V., Jost, S., Ottenwalder, B., Schlotterer, C. & Boenigk, J. 2010 Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms. Mol. Ecol. 19, 32-40. (doi:10.1111/j.1365-294X.2009.04478.x)
71. Nolte, V., Pandey, R. V., Jost, S., Medinger, R., Ottenwalder, B., Boenigk, J. & Schlötterer, C. 2010 Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity. Mol. Ecol. 19, 2908-2915. (doi:10.1111/j.1365-294X. 2010.04669.x)
72. Hamilton, H. C., Strickland, M. S., Wickings, K., Bradford, M. A. & Fierer, N. 2009 Surveying soil faunal communities using a direct molecular approach. Soil Biol. Biochem. 41, 1311-1314. (doi:10.1016/j.soilbio. 2009.03.021)
73. Quince, C., Lanzén, A., Curtis, T. P., Davenport, R. J., Hall, N., Head, I. M., Read, L. F. & Sloan, W. T. 2009 Accurate determination of microbial diversity from 454 pyrosequencing data. Nat. Meth. 6, 639-641. (doi:10. 1038/nmeth.1361)
74. Reeder, J. & Knight, R. 2009 The 'rare biosphere': a reality check. Nat. Meth. 6, 636-637. (doi:10.1038/ nmeth0909-636)
75. Boyce, R., Chilana, P. & Rose, T. P. 2009 iCODEHOP: a new interactive program for designing COnsensus-DEgenerate Hybrid Oligonucleotide Primers from multiply aligned protein sequences. Nucleic Acids Res. 37, w222-w228. (doi:10.1093/nar/gkp379)
76. Rose, T. M., Henikoff, J. G. & Henikoff, S. 2003 CODEHOP (COnsensus-DEgenerate Hybrid Oligo-nucleotide Primer) PCR primer design. Nucleic Acids Res. 31, 3763-3766. (doi:10.1093/nar/ gkg524)
77. Bensasson, D., Zhang, D.-X., Hartl, D. L. & Hewitt, G. M. 2001 Mitochondrial pseudogenes: evolution's misplaced witnesses. Trends Ecol. Evol. 16, 314-321. (doi:10.1016/S0169-5347(01)02151-6)