Dealing with incompleteness: New advances for the use of fossils in phylogenetic analysis

Palaios

Volumn 26, Issue 3, 2011, Pages 121-124

  Escapa, Ignacio H ^a   Pol, Diego ^a  

^a MUSEO PALEONTOLÓGICO EGIDIO FERUGLIO   (Argentina)

Author keywords

[No Author keywords available]

Indexed keywords

FOSSIL RECORD; PALEOBIOLOGY; PHYLOGENETICS; PHYLOGENY;

EID: 81855191365     PISSN: 08831351     EISSN: None     Source Type: Journal    
DOI: 10.2110/palo.2011.S02     Document Type: Review

References (35)

1. AGOLIN, M., and D'HAESE, C., 2009, An application of dynamic homology to morphological characters: Direct optimization of setae sequences and phylogeny of the family Odontellidae (Poduromorpha, Collembola): Cladistics, v. 25, p. 353-385.
2. CATALANO, S., GOLOBOFF, P., and GIANNINI, N., 2010, Phylogenetic morphometrics (I): The use of landmark data in a phylogenetic framework: Cladistics, v. 26, p. 1-11.
3. COBBETT, A., WILKINSON, M., and WILLS, M. A., 2007, Fossils impact as hard as living taxa in parsimony analyses of morphology: Systematic Biology, v. 56, p. 753-766.
4. CREPET, W. L., NIXON, K. C., and GANDOLFO, M. A., 2004, Fossil evidence and phylogeny: The age of major angiosperm clades based on mesofossil and macrofossil evidence from Cretaceous deposits: American Journal of Botany, v. 91, p. 1666-1682. (Pubitemid 43193725)
5. DE PINNA, M. C. C., 1991, Concepts and tests of homology in the cladistic paradigm: Cladistics, v. 7, p. 367-394.
6. DONOGHUE, M. J., DOYLE, J. A., GAUTHIER, J., KLUGE, A. G., and ROWE, T., 1989, The importance of fossils in phylogeny reconstruction: Annual Review of Ecology and Systematics, v. 20, p. 431-460.
7. DOYLE, J. A., 2006, Seed ferns and the origin of angiosperms: Journal of the Torrey Botanical Society, v. 133, p. 169-209.
8. GAUTHIER, J. A., 1986, Saurischian monophyly and the origin of birds: Memoirs of the California Academy of Sciences, v. 8, p. 1-47.
9. GAUTHIER, J. A., KLUGE, A. G., and ROWE, T., 1988, Amniote phylogeny and the importance of fossils: Cladistics, v. 4, p. 105-209. (Pubitemid 19310711)
10. GIRIBET, G., 2002, Current advances in the phylogenetic reconstruction of metazoan evolution. A new paradigm for the Cambrian explosion?: Molecular Phylogenetics and Evolution, v. 24, p. 345-357.
11. GIRIBET, G., 2010, A new dimension in combining data? The use of morphology and phylogenetic data in metazoan systematics: Acta Zoologica, v. 91, p. 11-19.
12. GOLOBOFF, P. A., FARRIS, J. S., and NIXON, K. C., 2008, TNT, a free program for phylogenetic analysis: Cladistics, v. 24, p. 774-786.
13. GOLOBOFF, P. A., MATTONI, C. I., and QUINTEROS, S., 2006, Continuous characters analyzed as such: Cladistics, v. 22, p. 1-13.
14. GONZÁ LEZ-JOSÉ, R., ESCAPA, I., NEVES, W., CÚ NEO, R., and PUCCIARELLI, N., 2008, Cladistic analysis of continuous modularized traits provides phylogenetic signals in Homo evolution: Nature, v. 453, p. 775-778. (Pubitemid 351793776)
15. GRANDE, L., and BEMIS, W. E., 1998, A comprehensive phylogenetic study of amiid fishes (Amiidae) based on comparative skeletal anatomy. An empirical search for interconnected patterns of natural history: Journal of Vertebrate Paleontology, v. 18, p. 1-690.
16. HEATH, T. A., ZWICKL, D. J., KIM, J., and HILLIS, D. M., 2008, Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees: Systematic Biology, v. 57, p. 160-166.
17. HERMSEN, E. J., and HENDRICKS, J. R., 2006, The hierarchy of time: PALAIOS, v. 21, p. 403-405. (Pubitemid 44604655)
18. KEARNEY, M., 2002, Fragmentary taxa, missing data, and ambiguity: Mistaken assumptions and conclusions: Systematic Biology, v. 51, p. 369-381. (Pubitemid 35180714)
19. NIXON, K. C., 1996, Paleobotany in cladistics and cladistics in paleobotany: Enlightenment and uncertainty: Review of Palaeobotany and Palynology, v. 90, p. 361-373.
20. NOVACEK, M. J., 1992, Fossils, topologies, missing data, and the higher level phylogeny of eutherian mammals: Systematic Biology, v. 41, p. 58-73.
21. PATTERSON, C., 1981, Significance of fossils in determining evolutionary relationships: Annual Review of Ecology and Systematics, v. 12, p. 195-223.
22. PEREYRA, V., and MOUND, L., 2009, Phylogenetic relationships within the genus Cranothrips (Thysanoptera, Melanthripidae) with consideration of host associations and disjunct distributions within the family: Systematic Entomology, v. 34, p. 151-161.
23. POL, D., and ESCAPA, I. H., 2009, Unstable taxa in cladistic analysis: Identification and the assessment of relevant characters: Cladistics, v. 25, p. 515-527.
24. POL, D., and NORELL, M., 2006, Uncertainty in the age of fossils and the stratigraphic fit for phylogenies: Systematic Biology, v. 55, p. 512-521.
25. RAMIREZ, M. J., 2007, Homology as a parsimony problem: A dynamic homology approach for morphological data: Cladistics, v. 23, 588-612. (Pubitemid 350243498)
26. RAUP, D. M., 1986, Biological extinction in earth history: Science, v. 231, p. 1528-1533.
27. SANDERSON, M. J., 2003, R8s: Inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock: Bioinformatics, v. 19, p. 301-302. (Pubitemid 36181923)
28. VEGA, A., RUA, G. H., FABBRI, L. T., and RÚ GOLO DE AGRÁSAR, Z. E., 2009, A morphology-based cladistic analysis of Digitaria (Poaceae, Panicoideae, Paniceae): Systematic Botany, v. 34, p. 312-323.
29. WHEELER, W. C., AAGESEN, L., ARANGO, C. P., FAIVOVICH, J., GRANT, T., D'HAESE, C., JANIES, D., SMITH, W. L., VARON, V., and GIRIBET, G., 2006, Dynamic Homology and Phylogenetic Systematics: A Unified Approach Using POY: American Museum of Natural History Press, New York, 357 p.
30. WILKINSON, M., 1994, Common cladistic information and its consensus representation: Reduced Adams and reduced cladistic consensus trees and profiles: Systematic Biology, v. 43, p. 343-368. (Pubitemid 24976651)
31. WILKINSON, M., and BENTON, M. J., 1995, Missing data and rhynchosaur phylogeny: Historical Biology, v. 10, p. 137-150.
32. WILKINSON, M., COTTON, J., and THORLEY, J., 2004, The information content of trees and their matrix representations: Systematic Biology, v. 53, p. 989-1001. (Pubitemid 40141321)
33. WILKINSON, M., THORLEY, J. L., and UPCHURCH, P., 2000, A chain is no stronger than its weakest link: Double decay analysis of phylogenetic hypotheses: Systematic Biology, v. 49, p. 754-776. (Pubitemid 33213089)
34. XU, X., CLARK, J. M., MO, J., CHOINIERE, J., FORSTER, C. A., ERICKSON, G. M., HONE, D. W. E., SULLIVAN, C., EBERTH, D. A., NESBITT, S., ZHAO, Q., HERNÁNDEZ, R., JIA, C.-K., HAN, F.-L., and GUO, Y., 2009, A Jurassic ceratosaur from China helps clarify avian digital homologies: Nature, v. 459, p. 940-944.
35. ZWICKL, D. J., and HILLIS, D. M., 2002, Increased taxon sampling greatly reduces phylogenetic error: Systematic Biology, v. 51, p. 588-598. (Pubitemid 35180690)