Ending a decade of deception: a valiant failure, a not-so-valiant failure, and a success story
dc.contributor.author | Brooks, Daniel R. | en_US |
dc.contributor.author | Dowling, Ashley P. G. | en_US |
dc.contributor.author | van Veller, Marco G. P. | en_US |
dc.contributor.author | Hoberg, Eric P. | en_US |
dc.date.accessioned | 2010-06-01T22:03:27Z | |
dc.date.available | 2010-06-01T22:03:27Z | |
dc.date.issued | 2004-02 | en_US |
dc.identifier.citation | Brooks, Daniel R.; Dowling, Ashley P. G.; van Veller, Marco G. P.; Hoberg, Eric P. (2004). "Ending a decade of deception: a valiant failure, a not-so-valiant failure, and a success story." Cladistics 20(1): 32-46. <http://hdl.handle.net/2027.42/75083> | en_US |
dc.identifier.issn | 0748-3007 | en_US |
dc.identifier.issn | 1096-0031 | en_US |
dc.identifier.uri | https://hdl.handle.net/2027.42/75083 | |
dc.description.abstract | Prior studies involving two methods, Brooks Parsimony Analysis (BPA) and TreeMap, have found BPA to be the more reliable method. Recent criticisms leveled at these studies argue that the tests were unfairly created and biased in favor of BPA. The authors of a recent critique offered new exemplars to demonstrate flaws in BPA, plus a simple fix to correct the flaws found in TreeMap. A re-evaluation of their exemplars clearly shows that the authors' calculations are incorrect, their understanding of the methods is lacking, and that their simple fix does not work. Additional analyses using TreeMap 2.02 are run to show that TreeMap 2.02, like TreeMap 1.0, cannot adequately deal with widespread parasites, contrary to the claims of its supporters. Furthermore, the exemplars corroborate previous findings that BPA, when calculated correctly, is more reliable than TreeMap1.0 and TreeMap 2.02 and therefore the method of choice in coevolutionary and biogeographic studies. | en_US |
dc.format.extent | 315666 bytes | |
dc.format.extent | 3109 bytes | |
dc.format.mimetype | application/pdf | |
dc.format.mimetype | text/plain | |
dc.publisher | Blackwell Science Ltd | en_US |
dc.rights | 2004 The Willi Hennig Society | en_US |
dc.title | Ending a decade of deception: a valiant failure, a not-so-valiant failure, and a success story | en_US |
dc.type | Article | en_US |
dc.subject.hlbsecondlevel | Ecology and Evolutionary Biology | en_US |
dc.subject.hlbtoplevel | Science | en_US |
dc.description.peerreviewed | Peer Reviewed | en_US |
dc.contributor.affiliationum | Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, MI 48109, USA | en_US |
dc.contributor.affiliationother | Department of Zoology, University of Toronto, M5S 3G5 Toronto, Ontario, Canada | en_US |
dc.contributor.affiliationother | Biosystematics Group, Wageningen University, Generaal Foulkesweg 37, 6703 BL Wageningen, the Netherlands | en_US |
dc.contributor.affiliationother | US National Parasite Collection and the Parasite Biology, Epidemiology and Systematics Laboratory, US Department of Agriculture, Agricultural Research Service, BARC East 1180, 10300 Baltimore Avenue, Beltsville, MD 20705, USA | en_US |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/75083/1/j.1096-0031.2003.00011.x.pdf | |
dc.identifier.doi | 10.1111/j.1096-0031.2003.00011.x | en_US |
dc.identifier.source | Cladistics | en_US |
dc.identifier.citedreference | Brooks, D. R., 1979. Testing the context and extent of host-parasite coevolution. Syst. Zool. 28, 299 – 307. | en_US |
dc.identifier.citedreference | Brooks, D. R., 1981. Hennig's Parasitological method: a proposed solution. Syst. Zool. 30, 229 – 249. | en_US |
dc.identifier.citedreference | Brooks, D. R., 1985. Historical ecology: a new approach to studying the evolution of ecological associates. Ann. Missouri Bot. Gard. 72, 660 – 680. | en_US |
dc.identifier.citedreference | Brooks, D. R., 1988. Macroevolutionary comparisons of host and parasite phylogenies. Annu. Rev. Ecol. Syst. 19, 235 – 259. | en_US |
dc.identifier.citedreference | Brooks, D. R., 1990. Parsimony analysis in historical biogeography and coevolution: methodological and theoretical update. Syst. Zool. 39, 14 – 30. | en_US |
dc.identifier.citedreference | Brooks, D. R., 2003. The new orthogenesis. Cladistics, 19, 443 – 448. | en_US |
dc.identifier.citedreference | Brooks, D. R., McLennan, D. A., 1991. Phylogeny, Ecology and Behavior: A Research Program in Comparative Biology. University of Chicago Press, Chicago, IL. | en_US |
dc.identifier.citedreference | Brooks, D. R., McLennan, D. A., 1993. Parascript: Parasites and the Language of Evolution. Smithsonian Institution Press, Washington, DC. | en_US |
dc.identifier.citedreference | Brooks, D. R., McLennan, D. A., 2002. The Nature of Diversity: An Evolutionary Voyage of Discovery. University of Chicago Press, Chicago, IL. | en_US |
dc.identifier.citedreference | Brooks, D. R., McLennan, D. A., 2003. Extending phylogenetic studies of coevolution: secondary Brooks parsimony analysis, parasites, and the Great Apes. Cladistics, 19, 104 – 119. | en_US |
dc.identifier.citedreference | Brooks, D. R., Van Veller, M. G. P., McLennnan, D. A., 2001. How to do BPA, really. J. Biogeogr. 28, 345 – 358. | en_US |
dc.identifier.citedreference | Charleston, M. A., 1998. Jungles: a new solution to the host/parasite phylogeny reconciliation problem. Math. Biocsci. 149, 191 – 223. | en_US |
dc.identifier.citedreference | Charleston, M. A., Perkins, S. L., 2003. Lizards, malaria, and jungles in the Caribbean. In: Page, R. D. M. (Ed.), Tangled Trees. University of Chicago Press, Chicago, IL, pp. 65 – 92. | en_US |
dc.identifier.citedreference | Clayton, D. H., Al-Tamimi, S., Johnson, K. P., 2003. The ecological basis of coevolutionary history. In: Page, R. D. M. (Ed.), Tangled Trees. University of Chicago Press, Chicago, IL, pp. 65 – 92. | en_US |
dc.identifier.citedreference | Cressey, R. F., Collette, B., Russo, J., 1983. Copepods and scombrid fishes: a study in host parasite relationships. Fish. Bull. 81, 227 – 265. | en_US |
dc.identifier.citedreference | Crisci., J., 2001. The voice of historical biogeography. J. Biogeogr. 28, 157 – 168. | en_US |
dc.identifier.citedreference | Dabert, J., 2003. The feather family Syringobiidae Trouessart. 1896 ( Acari, Astigmata, Pterlichoidea ). Acta Parasitologica Suppl. 48, S1 – S233. | en_US |
dc.identifier.citedreference | Dowling, A. P. G., 2002. Testing the accuracy of TreeMap and Brooks parsimony analyses of coevolutionary patterns using artificial associations. Cladistics, 18, 416 – 435. | en_US |
dc.identifier.citedreference | Dowling, A. P. G., van Veller, M. G. P., Hoberg, E. P., Brooks, D. R., 2003. A priori and a posteriori methods in comparative evolutionary studies of host–parasite associations. Cladistics, 19, 240 – 253. | en_US |
dc.identifier.citedreference | Ebach, M. C., 1999. Paralogy and the centre of origin concept. Cladistics, 13, 387 – 391. | en_US |
dc.identifier.citedreference | Ebach, M. C., 2001. Extrapolating cladistic biogeography: a brief comment on van Veller et al. (1999, 2000, 2001). Cladistics, 17, 383 – 388. | en_US |
dc.identifier.citedreference | Ebach, M. C., Humphries, C. J., 2002. Cladistic biogeography and the art of discovery. J. Biogeogr. 29, 427 – 444. | en_US |
dc.identifier.citedreference | Ebach, M. C., Humphries, C. J., Williams, D. M., 2003. Phylogenetic biogeography deconstructed. J. Biogeogr. 30, 1285 – 1296. | en_US |
dc.identifier.citedreference | Green, M., Van Veller, M. G. P., Brooks, D. R., 2002. Assessing modes of speciation: range asymmetry and biogeographical congruence. Cladistics, 18, 112 – 124. | en_US |
dc.identifier.citedreference | Hafner, M. S., Demastes, J. W., Spradling, T. A., Reed, D. L., 2003. Cophylogeny between pocket gophers and chewing lice. In: Page, R. D. M. (Ed.), Tangled Trees. University of Chicago Press, Chicago, IL, pp. 221 – 239. | en_US |
dc.identifier.citedreference | Hennig, W., 1966. Phylogenetic Systematics. University of Illinois Press, Urbana, IL. | en_US |
dc.identifier.citedreference | Hoberg, E. P., 1986. Evolution and historical biogeography of a parasite-host assemblage: Alcataenia spp. ( Cyclophyllidea: Dilepididae ) in Alcidae ( Charadriiformes ). Can. J. Zool. 64, 2576 – 2589. | en_US |
dc.identifier.citedreference | Hoberg, E. P., 1995. Historical biogeography and modes of speciation across high latitude seas of the Holarctic: concepts for host-parasite coevolution among the Phocini ( Phocidae ) and Tetrabothriidae ( Eucestoda ). Can. J. Zool. 73, 45 – 57. | en_US |
dc.identifier.citedreference | Hoberg, E. P., Adams, A. M., 1992. Phylogeny, historical biogeography and ecology of Anophryocephalus spp. ( Eucestoda: Tetrabothriidae ) among pinnipeds of the Holarctic during the late Tertiary and Pleistocene. Can. J. Zool. 70, 703 – 719. | en_US |
dc.identifier.citedreference | Hoberg, E. P., Adams, A., 2000. Phylogeny, history and biodiversity: understanding faunal structure and biogeography in the marine realm. Bull. Scand. Soc. Parasitol. 10, 19 – 37. | en_US |
dc.identifier.citedreference | Hoberg, E. P., Brooks, D. R., Siegel-Causey, D., 1997. Host-parasite phylogenies and cospeciation. In: Clayton, D., Moore, J. (Eds), Host-Parasite Evolution: General Principles and Avian Models. Oxford University Press, Oxford, UK, pp. 212 – 235. | en_US |
dc.identifier.citedreference | Hoberg, E. P., Klassen, G. J., 2002. Revealing the faunal tapestry: co-evolution and historical biogeography of hosts and parasites in marine systems. Parasitology, 124, S3 – S22. | en_US |
dc.identifier.citedreference | Johnson, K. P., Adams, R. J., Page, R. D. M., Clayton, D. H., 2003. When do parasites fail to speciate in response to host speciation? Syst Biol. 52, 37 – 47. | en_US |
dc.identifier.citedreference | Johnson, K. P., Clayton, D. H., 2003. Coevolutionary history of ecological replicates: comparing phylogenies of wing and body lice to columbiform hosts. In: Page, R. D. M. (Ed.), Tangled Trees. University of Chicago Press, Chicago, IL, pp. 262 – 286. | en_US |
dc.identifier.citedreference | McAllister, J. W., 1996. Beauty and Revolution in Science. Cornell University Press, Ithaca, NY. | en_US |
dc.identifier.citedreference | Mindell, D. P., Schultz, J. W., Ewald, P. W., 1995. The AIDS pandemic is new, but is HIV new? Syst. Biol. 44, 77 – 92. | en_US |
dc.identifier.citedreference | Mitter. C., Brooks, D. R., 1983. Phylogenetic aspects of coevolution. In: Futuyma, D. J., Slatkin, M. (Eds.), Coevolution. Sinauer Associates, Sunderland, MA. | en_US |
dc.identifier.citedreference | Morrone, J. J., Carpenter, J. M., 1994. In search of a method for cladistic biogeography: an empirical comparison of Component Analysis, Brooks Parsimony Analysis, and Three-area Statements. Cladistics, 10, 99 – 153. | en_US |
dc.identifier.citedreference | Nelson, G., Ladiges, P. Y., 1991. Three-area statements: standard assumptions for biogeographic analysis. Syst. Zool. 40, 470 – 485. | en_US |
dc.identifier.citedreference | Nelson, G., Ladiges, P. Y., 1996. Paralogy in cladistic biogeography and analysis of paralogy-free subtrees. Am. Mus. Novitates, 3167, 1 – 58. | en_US |
dc.identifier.citedreference | Nelson, G., Platnick, N. I., 1981. Systematics and Biogeography; Cladistics and Vicariance. Columbia University Press, New York/Guilford, UK. | en_US |
dc.identifier.citedreference | Page, R. D. M., 1993. Component 2. 0: Tree Comparison Software for Microsoft Windows. Program and User's Manual. Natural History Museum, London. | en_US |
dc.identifier.citedreference | Page, R. D. M., 1994a. Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Syst. Biol. 43, 58 – 77. | en_US |
dc.identifier.citedreference | Page, R. D. M., 1994b. Parallel phylogenies: reconstructing the history of host-parasite assemblages. Cladistics, 10, 155 – 173. | en_US |
dc.identifier.citedreference | Page, R. D. M., 1995. Treemap 1. 0. Program and User's Manual. Division of Environmental and Evolutionary Biology, Institute of Biomedical and Life Sciences. University of Glasgow, Glasgow, UK. | en_US |
dc.identifier.citedreference | Page, R. D. M., 2003a. Missing the boat. J. Evol. Biol. 16, 1064. | en_US |
dc.identifier.citedreference | Page, R. D. M., 2003b. Treemap 2. 02. Program and User's Manual. Division of Environmental and Evolutionary Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, UK. | en_US |
dc.identifier.citedreference | Page, R. D. M., ed., 2003c. Tangled Trees. University of Chicago Press, Chicago, Illinois. | en_US |
dc.identifier.citedreference | Paterson, A. M., Gray, R. D., 1997. Host-parasite co-speciation, host switching, and missing the boat. In: Clayton, D. H., Moore, J. (Eds.), Host-Parasite Evolution: General Principles and Avian Models. Oxford University Press, Oxford, UK, pp. 236 – 250. | en_US |
dc.identifier.citedreference | Paterson, A. M., Palma, R. L., Gray, R. D., 2003. Drowning on arrival, missing the boat, and X-events: How likely are sorting events? In: Page, R. D. M. (Ed.), Tangled Trees. University of Chicago Press, Chicago, IL, pp. 287 – 309. | en_US |
dc.identifier.citedreference | Perkins, S. L., Schall, J. J., 2002. A molecular phylogeny of malarial parasites recovered from cytochrome b gene sequences. J. Parasitol. 88, 972 – 978. | en_US |
dc.identifier.citedreference | Ronquist, F., 2003. Parsimony analysis of coevolving species associations. In: Page, R. D. M. (Ed.), Tangled Trees. University of Chicago Press, Chicago, IL, pp. 22 – 64. | en_US |
dc.identifier.citedreference | Siddall, M. E., Apakupakul, K., Burreson, E. M., Coates, K. A., Erseus, C., Gelder, S. R., Kallersjo, M., Trapido-Rosenthal, H., 2001. Validating Livanow: Molecular data agree that leeches, branchiobdellidans, and Acanthobdella peledina form a monophyletic group of oligochaetes. Mol. Phylo. Evol. 21, 346 – 351. | en_US |
dc.identifier.citedreference | Siddall, M. E., Perkins, S. L., 2003. Brooks Parsimony Analysis: a valiant failure. Cladistics, 19, 554 – 564. | en_US |
dc.identifier.citedreference | Siddall, M. E., Perkins, S. L., Desser, S. S., 2004. Leech mycetome endosymbionts are a new lineage of alphaproteobacteria related to the Rhizobiaceae. Mol. Phylo. Evol. 30, 178 – 186. | en_US |
dc.identifier.citedreference | Thompson, J., 1994. The Coevolutionary Process. University of Chicago Press, Chicago, IL. | en_US |
dc.identifier.citedreference | Van Soest, R. W. M., Hajdu, E., 1997. Marine area relationships from twenty sponge phylogenies. A comparison of methods and coding strategies. Cladistics, 13, 1 – 20. | en_US |
dc.identifier.citedreference | Van Veller, M. G. P., Brooks, D. R., 2001. When simplicity is not parsimonious: A priori and a posteriori methods in historical biogeography. J. Biogeogr. 28, 1 – 11. | en_US |
dc.identifier.citedreference | Van Veller, M. G. P., Brooks, D. R., Zandee, M., 2003. Cladistic and phylogenetic biogeography: the art and the science of discovery. J. Biogeogr. 30, 319 – 329. | en_US |
dc.identifier.citedreference | Van Veller, M. G. P., Kornet, D. J., Zandee, M., 2000. Methods in vicariance biogeography: assessment of the implementations of assumptions zero, 1 and 2. Cladistics, 16, 319 – 345. | en_US |
dc.identifier.citedreference | Van Veller, M. G. P., Kornet, D. J., Zandee, M., 2002. A posteriori and a priori methodologies for testing hypotheses of causal processes in vicariance biogeography. Cladistics, 18, 207 – 217. | en_US |
dc.identifier.citedreference | Van Veller, M. G. P., Zandee, M., Kornet, D. J., 1999. Two requirements for obtaining valid common patterns under different assumptions in vicariance biogeography. Cladisitcs, 15, 393 – 406. | en_US |
dc.identifier.citedreference | Van Veller, M. G. P., Zandee, M., Kornet, D. J., 2001. Measures for obtaining inclusive solution sets under assumptions zero, 1 and 2 with different methods for vicariance biogeography. Cladistics, 17, 248 – 259. | en_US |
dc.identifier.citedreference | Wiley, E. O., 1986. Methods in vicariance biogeography. In: Hovenkamp, P. (Ed.), Systematics and Evolution. University of Utrecht Press, Utrecht, Netherlands, pp. 283 – 306. | en_US |
dc.identifier.citedreference | Wiley, E. O., 1988a. Parsimony analysis and vicariance biogeography. Syst. Zool. 37, 271 – 290. | en_US |
dc.identifier.citedreference | Wiley, E. O., 1988b. Vicariance biogeography. Annu. Rev. Ecol. Syst, 19, 513 – 542. | en_US |
dc.identifier.citedreference | Zandee, M., Roos, M. C., 1987. Component-compatibility in historical biogeography. Cladistics, 3, 305 – 332. | en_US |
dc.owningcollname | Interdisciplinary and Peer-Reviewed |
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