Hostname: page-component-78c5997874-g7gxr Total loading time: 0 Render date: 2024-11-18T01:24:37.216Z Has data issue: false hasContentIssue false
  • English
  • Français

Exploring new uses for measures of fit of phylogenetic hypotheses to the fossil record

Published online by Cambridge University Press:  08 April 2016

Kenneth D. Angielczyk  and
David L. Fox
Kenneth D. Angielczyk
Affiliation:
Department of Invertebrate Zoology and Geology, California Academy of Sciences, 875 Howard Street, San Francisco, California 94103
David L. Fox
Affiliation:
Department of Geology and Geophysics, University of Minnesota, 310 Pillsbury Drive SE, Minneapolis, Minnesota 55455. E-mail: [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

Intrinsic features of organisms, such as morphology or DNA sequences, and the stratigraphic occurrence of fossils provide distinct evidence of the phylogenetic history of life. Because there is only one true history, we expect the historical signals preserved by these data sets to be similar, and several metrics have been developed to measure the fit of phylogenetic hypotheses to the fossil record. However, a variety of biases affect these metrics, and it is unclear whether they can provide more than an estimate of whether one tree fits the fossil record better than another when used on their own. Here we explore two novel applications of stratigraphic fit metrics when they are used with a combination of phylogeny reconstruction methods that do and do not directly include stratigraphic occurrence data (e.g., cladistics and stratocladistics). In particular, we are interested in whether differences in the stratigraphic fit of cladistic and stratocladistic trees can be used to identify cases in which the stratocladistic results are likely to be more accurate, as well as whether such differences can be used to identify potential problems in the underlying data sets.

Using 550 simulated data sets that were analyzed with cladistics and stratocladistics, we found that the absolute difference in fit to stratigraphy between the results of the two methods was strongly correlated with the probability of character state transition and the accuracy of the stratocladistic results relative to the cladistic results. Completeness of the fossil record and number of taxa included in the analysis were more weakly correlated with stratigraphic fit, and the statistical significance of the differences in fit between the two sets of results did not show a meaningful relationship with improvements in accuracy or potential data problems. These results suggest that measuring the difference in stratigraphic fit between cladistic and stratocladistic trees might be useful for qualitatively estimating whether the addition of stratigraphic data benefited a phylogenetic analysis, and for identifying data sets with high average rates of character state change.

Type
Articles
Information
Paleobiology , Volume 32 , Issue 1 , Winter 2006 , pp. 147 - 165
Copyright
Copyright © The Paleontological Society 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Literature Cited

Angielczyk, K. D. 2002a. A character-based method for measuring the fit of a cladogram to the fossil record. Systematic Biology 51:176–191.CrossRefGoogle ScholarPubMed
Angielczyk, K. D. 2002b. Character state transformations and the fit of phylogenies to the fossil record. Palaeontologia Africana 38:27–32.Google Scholar
Behrensmeyer, A. K., Kidwell, S. M., and Gastaldo, R. A. 2000. Taphonomy and paleobiology. In Erwin, D. H. and Wing, S. L., eds. Deep time: Paleobiology‘s perspective. Paleobiology 26(Suppl. to No. 4):103–147.Google Scholar
Benton, M. J. 1998a. The quality of the fossil record of the vertebrates. Pp. 269–303 in Donovan, S. K. and Paul, C. R. C., eds. The adequacy of the fossil record. Wiley, Chichester, U.K. Google Scholar
Benton, M. J. 1998b. Molecular and morphological phylogenies of mammals: congruence with stratigraphy. Molecular Phylogenetics and Evolution 9:398–407.CrossRefGoogle Scholar
Benton, M. J. 2001. Finding the tree of life: matching phylogenetic trees to the fossil record through the 20th century. Proceedings of the Royal Society of London B 268: 2213–2130.CrossRefGoogle Scholar
Benton, M. J., and Storrs, G. W. 1994. Testing the quality of the fossil record: paleontological knowledge is improving. Geology 22:111–114.Google Scholar
Benton, M. J., and Storrs, G. W. 1996. Diversity in the past: comparing cladistic phylogenies and stratigraphy. Pp. 19–40 in Hochberg, M. E., Colbert, J., and Barbault, R., eds. Aspects of the genesis and maintenance of biological diversity. Oxford University Press, Oxford.Google Scholar
Benton, M. J., Hitchin, R., and Wills, M. A. 1999. Assessing congruence between cladistic and stratigraphic data. Systematic Biology 48:581–596.CrossRefGoogle ScholarPubMed
Benton, M. J., Wills, M. A., and Hitchin, R. 2000. Quality of the fossil record through time. Nature 403:534–537.Google Scholar
Bloch, J. I., Fisher, D. C., Rose, K. D., and Gingerich, P. D. 2001. Stratocladistic analysis of Paleocene Carpolestidae (Mammalia, Plesiadapiformes) with a description of a new Late Tiffanian genus. Journal of Vertebrate Paleontology 21:119–131.CrossRefGoogle Scholar
Bodenbender, B. E., and Fisher, D. C. 2001. Stratocladistic analysis of blastoid phylogeny. Journal of Paleontology 75:351–369.2.0.CO;2>CrossRefGoogle Scholar
Brochu, C. A., and Norell, M. A. 2000. Temporal congruence and the origin of birds. Journal of Vertebrate Paleontology 20:197–200.CrossRefGoogle Scholar
Brochu, C. A., and Norell, M. A. 2001. Time and trees: a quantitative assessment of temporal congruence in the bird origins debate. Pp. 511–535 in Gauthier, J. and Gall, L. F., eds. New perspectives on the origin and early evolution of birds. Peabody Museum of Natural History, New Haven, Conn. Google Scholar
Clyde, W. C., and Fisher, D. C. 1997. Comparing the fit of stratigraphic and morphologic data in phylogenetic analysis. Paleobiology 23:1–19.Google Scholar
Colless, D. H. 1980. Congruence between morphometric and allozyme data for Menidia species: a reappraisal. Systematic Zoology 29:288–299.CrossRefGoogle Scholar
Finarelli, J. A., and Clyde, W. C. 2002. Comparing the gap excess ratio and the retention index of the stratigraphic character. Systematic Biology 51:166–176.Google Scholar
Fisher, D. C. 1982. Phylogenetic and macroevolutionary patterns within the Xiphosurida. Pp. 175–180 in Mamet, B. and Copeland, M. J., eds. Proceedings of the Third North American Paleontological Convention. Geological Survey of Canada, Montreal.Google Scholar
Fisher, D. C. 1988. Stratocladistics: integrating stratigraphic and morphologic data in phylogenetic inference. Geological Society of America Abstracts with Programs 20:A186.Google Scholar
Fisher, D. C. 1991. Phylogenetic analysis and its application in evolutionary paleobiology. Pp. 103–122 in Gilinsky, N. L. and Signor, P. W., eds. Analytical paleobiology. Paleontological Society Short Course 4: 103–122.Google Scholar
Fisher, D. C. 1992. Stratigraphic parsimony. Pp. 124–129 in Maddison, W. P. and Maddison, D. R., eds. MacClade, Version 3.0. Sinauer, Sunderland, Mass. Google Scholar
Fisher, D. C. 1994a. Stratocladistics: morphological and temporal patterns and their relation to phylogenetic process. Pp. 133–171 in Grande, L. and Rieppel, O., eds. Interpreting the hierarchy of nature. Academic Press, San Diego.Google Scholar
Fisher, D. C. 1994b. Measures of congruence between stratigraphic data and phylogenetic hypotheses. Geological Society of America Abstracts with Programs 26:A123.Google Scholar
Fisher, D. C., Foote, M., Fox, D. L., and Leighton, L. R. 2002. Stratigraphy in phylogeny reconstruction—comment on Smith (2000). Journal of Paleontology. 76:585–586.2.0.CO;2>CrossRefGoogle Scholar
Foote, M., and Raup, D. M. 1996. Fossil preservation and the stratigraphic ranges of taxa. Paleobiology 22:121–140.Google Scholar
Foote, M., and Sepkoski, J. J. 1999. Absolute measures of the completeness of the fossil record. Nature 398:415–417.CrossRefGoogle ScholarPubMed
Foote, M., Hunter, J. P., Janis, C. M., and Sepkoski, J. J. Jr. 1999. Evolutionary and preservational constraints on origins of biologic groups: divergence times of eutherian mammals. Science 283:310–314.CrossRefGoogle ScholarPubMed
Fox, D. L., Fisher, D. C., and Leighton, L. R. 1999. Reconstructing phylogeny with and without temporal data. Science 284:1816–1819.Google Scholar
Gauthier, J., Kluge, A. G., and Rowe, T. 1988. Amniote phylogeny and the importance of fossils. Cladistics 4:105–210.CrossRefGoogle ScholarPubMed
Harvey, E. W., and Ausich, W. I. 1997. Phylogeny of calceocrinid crinoids (Paleozoic: Echinodermata): biogeography and mosaic evolution. Journal of Paleontology 71:299–305.CrossRefGoogle Scholar
Hitchin, R., and Benton, M. J. 1997a. Congruence between parsimony and stratigraphy: comparisons of three indices. Paleobiology 23:20–32.Google Scholar
Hitchin, R., and Benton, M. J. 1997b. Stratigraphic indices and tree balance. Systematic Biology 46:563–569.CrossRefGoogle Scholar
Holland, S. M. 2000. The quality of the fossil record: a sequence stratigraphic perspective. In Erwin, D. H. and Wing, S. L., eds. Deep time: Paleobiology‘s perspective. Paleobiology 26(Suppl. to No. 4):148–168.Google Scholar
Holland, S. M., and Patzkowsky, M. E. 1999. Models for simulating the fossil record. Geology 27:491–494.2.3.CO;2>CrossRefGoogle Scholar
Huelsenbeck, J. P. 1994. Comparing the stratigraphic record to estimates of phylogeny. Paleobiology 20:470–483.Google Scholar
Huelsenbeck, J. P., and Hillis, D. M. 1993. Success of phylogenetic methods in the four-taxon case. Systematic Biology 42:247–264.Google Scholar
Kuhner, M. K., and Felsenstein, J. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biology and Evolution 11:459–468.Google ScholarPubMed
Leighton, L. R., and Maples, C. G. 2002. Evaluating internal versus external characters: phylogenetic analyses of the Echinoconchidae, Buxtoniinae, and Juresaniinae (Phylum Brachiopoda). Journal of Paleontology 76:659–671.2.0.CO;2>CrossRefGoogle Scholar
Lewis, P. O. 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology 50:913–925.Google Scholar
Maddison, W. P., and Maddison, D. R. 1992. MacClade: analysis of phylogeny and character evolution, Version 3. 0. Sinauer, Sunderland, Mass. Google Scholar
Maddison, W. P., and Maddison, D. R. 2000. MacClade: analysis of phylogeny and character evolution, Version 4. 0. Sinauer, Sunderland, Mass. Google Scholar
Norell, M. A., and Novacek, M. J. 1992a. The fossil record and evolution: comparing cladistic and paleontologic evidence for vertebrate history. Science 255:1690–1693.Google Scholar
Norell, M. A., and Novacek, M. J. 1992b. Congruence between superpositional and phylogenetic patterns: comparing cladistic patterns with fossil records. Cladistics 8:319–337.CrossRefGoogle ScholarPubMed
Paul, C. R. C. 1982. The adequacy of the fossil record. Pp. 75–117 in Joysey, K. A. and Friday, A. E., eds. Problems of phylogenetic reconstruction. Academic Press, London.Google Scholar
Pol, D., and Norell, M. A. 2001. Comments on the Manhattan stratigraphic measure. Cladistics 17:285–289.Google Scholar
Polly, P. D. 1997. Ancestry and species definition in paleontology: a stratocladistic analysis of Paleocene-Eocene Viverravidae (Mammalia, Carnivora) from Wyoming. Contributions from the Museum of Paleontology, University of Michigan 30:1–53.Google Scholar
Siddall, M. E. 1996. Stratigraphic consistency and the shape of things. Systematic Biology 45:111–115.Google Scholar
Siddall, M. E. 1997. Stratigraphic indices and tree balance: a reply to Hitchin and Benton. Systematic Biology 46:569–573.Google Scholar
Siddall, M. E. 1998. Stratigraphic fit to phylogenies: a proposed solution. Cladistics 14:201–208.Google Scholar
Swofford, D. L. 1993. PAUP: phylogenetic analysis using parsimony, Version 3.1.1. Illinois Natural History Survey, Champaign.Google Scholar
Swofford, D. L. 2001. PAUP*: phylogenetic analysis using parsimony (*and other methods), Version 4.0b10. Sinauer, Sunderland, Mass. Google Scholar
Uhen, M. D. 1998. Middle to Late Eocene basilosaurines and dorudontines. Pp. 29–61 in Thewissen, J. G. M., ed. The emergence of whales: evolutionary patterns in the origin of Cetacea. Plenum, New York.Google Scholar
Uhen, M. D. 1999. New species of protocetid archaeocete whale, Eocetus wardii (Mammalia: Cetacea from the middle Eocene of North Carolina. Journal of Paleontology 73:512–528.Google Scholar
Uhen, M. D., and Gingerich, P. D. 2001. New genus of dorudontine archaeocete from the Middle-to-Late Eocene of South Carolina. Marine Mammal Science 17:1–34.CrossRefGoogle Scholar
Vermeij, G. J., and Carlson, S. J. 2000. The muricid gastropod subfamily Rapaninae: phylogeny and ecological history. Paleobiology 26:19–46.Google Scholar
Wagner, P. J. 1997. Patterns of morphologic diversification among the Rostroconchia. Paleobiology 23:115–150.CrossRefGoogle Scholar
Wagner, P. J. 1998a. A likelihood approach for evaluating estimates of phylogenetic relationships among fossil taxa. Paleobiology 24:430–449.CrossRefGoogle Scholar
Wagner, P. J. 1998b. Phylogenetic analyses and the quality of the fossil record. Pp. 165–287 in Donovan, S. K. and Paul, C. R. C., eds. The adequacy of the fossil record. Wiley, Chichester, U.K. Google Scholar
Wagner, P. J. 1999. The utility of fossil data in phylogenetic analyses: a likelihood example using Ordovician-Silurian species of the Lophospiridae (Gastropoda: Murchisoniina). American Malacological Bulletin 15:1–31.Google Scholar
Wagner, P. J. 2000a. Phylogenetic analyses and the fossil record: tests and inferences, hypotheses and models. In Erwin, D. H. and Wing, S. L., eds. Deep time: Paleobiology‘s perspective. Paleobiology 26(Suppl. to No. 4):341–371.Google Scholar
Wagner, P. J. 2000b. The quality of the fossil record and the accuracy of phylogenetic inferences about sampling and diversity. Systematic Biology 49:65–86.CrossRefGoogle ScholarPubMed
Wagner, P. J. 2001. Rate heterogeneity in shell character evolution among lophospiroid gastropods. Paleobiology 27:290–310.Google Scholar
Wagner, P. J., and Sidor, C. A. 2000. Age rank/clade rank metrics—sampling, taxonomy, and the meaning of “stratigraphic consistency.” Systematic Biology 49:463–480.CrossRefGoogle ScholarPubMed
Wills, M. A. 1999. Congruence between phylogeny and stratigraphy: randomization tests and the gap excess ratio. Systematic Biology 48:559–580.CrossRefGoogle Scholar
Supplementary material: File

Angielczyk and Fox supplementary material

Supplementary Material

Download Angielczyk and Fox supplementary material(File)
File 47.1 KB