Cladograms and stratigraphy
Until recently, the only answer to the question 'How complete is the fossil record?'
was a qualitative assertion that it was either wonderful, terrible, or all right. In
the absence of a time machine, the only way to assess completeness was in a relative
way. However, now that new semi-objective tree-making techniques are available to deal
with both morphological and molecular data, the shapes of these trees can be compared
with stratigraphic data.
- Comparisons of tree shape vs. stratigraphy offer a variety of methods of assessing
the quality of the fossil record and the congruence of competing trees with the known
fossil record, on the basis of statistical analyses of large samples of trees.
- Comparative metrics include methods to assess the match of node order and order
of first appearance in the fossil record (Spearman Rank Correlation, SRC), the
relative amount of cladistically implied gap to known record (Relative Completeness
Index, RCI), the stratigraphic consistency of dating of nodes with nodes lower in
the cladogram (Stratigraphic Consistency Index, SCI), and a measure of the relative
amount of gap to the minimum possible (Gap Excess Ratio, GER).
- The SRC technique was introduced for this purpose by Norell and Novacek (1992a),
the RCI by Benton (1994), the SCI by Huelsenbeck (1994), and the GER by Wills (1999).
- Further information can be found in these papers, and in Benton (1994, 1995),
Benton and Hitchin (1996), Benton and Simms (1995), Benton and Storrs (1996), Benton
et al. (1999, 2000) Hitchin and Benton (1997a, b), Norell and Novacek (1992b),
Siddall (1996, 1997), and Smith (1994). Several more recent papers (Wagner 2000; Wagner
and Sidor 2000; Angielczyk 2002; Finarelli and Clyde 2002; Fara and Langer 2004; Pol et
al. 2004; Angielczyk and Fox 2006)
present valuable critiques of the different metrics, highlighting how some are affected by
tree size (number of terminals), tree balance, relative time span involved, and other factors.
To some extent, the resampling error bars offered in the Ghosts package take account of
- The data base presented here
has been published in part in Benton and Hitchin (1996), but a further 700 trees
have been added since then.
Testing cladograms with stratigraphy
Phylogenetic trees, whether based on molecular techniques or from cladistic analysis of
morphological characters are essentially independent of stratigraphy. Therefore, it is
reasonable to compare the results of stratigraphy and phylogeny: do they agree or not?
If they do not agree (lack congruence), then either the fossil record, or the phylogeny, or both
are wrong. If the results are broadly congruent, then they are both probably
telling the same story, and it can be assumed that that story is the true story of
the history of life.
In assessing congruence, a claim is not made for the primacy of tree over stratigraphy, or
vice versa. Indeed, there are many uncertainties involved in the construction
of any tree, and in the recording of any stratigraphic sequence. It is the question of congruence
that is important. So, stratigraphy can be assessed for congruence with trees, and trees
can be assessed for congruence with stratigraphy.
One application of these approaches has been to use stratigraphy to test
cladograms. In particular, stratocladistics (Fisher, 1992) is a method whereby
stratigraphic information is actually incorporated into the tree-finding methods.
Stratigraphic data are converted into 'character' data, and then combined with
apomorphy coding. We do not pursue this technique since we feel
that it obscures the real information content of the characters on the one hand,
and the stratigraphy on the other. It is impossible to say what the resulting trees
mean: they have lost character-based parsimony, and they have also diluted the
stratigraphic signal. The technique has been criticised for these reasons, and others:
Techniques for comparison of cladograms with stratigraphic implications can, however, be
informative in examining specific cases. For example, where several most parsimonious
trees (MPTs) result from a cladistic analysis, it may be of interest to know which of
these best fits current stratigraphic knowledge. The various metrics noted above can
readily be calculated for each MPT.
- Dilution of both the character-based and the stratigraphic signal.
- Mixing of inclusive hierarchical data (from characters) with linear data (from
stratigraphy) (Smith, 1994).
- In particular, combining the two kinds of data obscures several specific issues in
cladistics: the meaning of ancestors, initial grouping criteria, and asymmetry in rates
of morphological evolution (Norell and Novacek, 1997).
- A stratigraphic overlay on a most-parsimonious tree obscures the falsifiability of the
phylogenetic hypothesis, and confuses two philosophical stances (Rieppel, 1997).
Metrics and software
(1) The Spearman Rank Correlation (SRC) test is a well-established non-parametric test that
simply compares the rank order of two series of numbers, in this case the order of
first fossil appearances and the order of nodes. The technique has associated measures
of confidence, but it is a rather poor estimator of the quality of matching of
trees and stratigraphy, since it looks only at rank order, taking no account of the
amount of time between specific fossils, and the relative ordering of nodes can be
(2) The Relative completeness index (RCI), Stratigraphic consistency index (SCI), and
Gap excess ratio (GER) are more informative, each assessing a different aspect of tree
fit to stratigraphy. All three should be used in parallel. Hitherto, each has been a
simple metric, but it is possible to assess a proxy for confidence intervals by means
of randomization of the data sets. Methods are outlined more fully in Wills (1999)
and Benton et al. (1999, 2000).
(3) Software is now available to assess the significance of RCI, SCI, and GER values,
by random permutation of the raw data, and tests of the values against means of the
generated random distributions. The software, 'Ghosts',
written by Matthew Wills, is now available.
- Angielczyk, K. D. (2002) A character-based method for measuring the fit of a cladogram to the fossil record. Systematic Biology 51, 176-191.
- Angielczyk, K. D. and Fox, D. L. (2006) Exploring new uses for measures of fit of phylogenetic hypotheses to the fossil record. Paleobiology 32, 147-165.
- Benton, M. J. (1994). Palaeontological data, and identifying mass extinctions. Trends in Ecology and Evolution, 9, 181-185. Download pdf version.
- Benton, M. J. (1995) Testing the time axis of phylogenies. Philosophical Transactions of the Royal Society, Series B, 349, 5-10. Download pdf version.
- 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, Series B 268, 2123-2130. Download pdf version.
- Benton, M. J. and Hitchin, R. (1996) Testing the quality of the fossil record by groups and by major habitats. Historical Biology, 12, 111-157.
- Benton, M. J. and Hitchin, R. (1997) Congruence between phylogenetic and stratigraphic data on the history of life. Proceedings of the Royal Society, Series B 264, 885-890. Download pdf version.
- Benton, M. J., Hitchin, R., and Wills, M. A. (1999) Assessing congruence between cladistic and stratigraphic data. Systematic Biology, 48, 581-596. Download pdf version.
- Benton, M. J., Wills, M. A., and Hitchin, R. (2000) Quality of the fossil record through time. Nature, 403, 534-537. Download pdf version.
- Benton, M. J. and Simms, M. J. (1995) Testing the marine and continental fossil records. Geology, 23, 601-604. Download pdf version.
- Benton, M. J. and Storrs, G. W. (1994) Testing the quality of the fossil record: paleontological knowledge is improving. Geology, 22, 111-114. Download pdf version.
- Benton, M. J. and Storrs, G. W. (1996) Diversity in the past: comparing cladistic phylogenies and stratigraphy. In Aspects of the genesis and maintenance of biological diversity, edited by M. E. Hochberg, J. Clobert, and R. Barbault, pp. 19-40. Oxford: Oxford University Press.
- Fara, E. and Langer, M. C. (2004) Estimates of phylogeny and biochronology. Revista Brasiliera de Paleontologia 7, 301-310.
- 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.
- Fisher, D. C. (1992) Stratigraphic parsimony. In MacClade: Analysis of phylogeny and character evolution, edited by W. P. Maddison and D. R. Maddison, pp. 124-129. Sunderland, Mass.: Sinauer Associates.
- Hitchin, R. and Benton, M. J. (1997a) Congruence between parsimony and stratigraphy: comparisons of three indices. Paleobiology, 23, 20-32. Download pdf version.
- Hitchin, R. and Benton, M. J. (1997b) Stratigraphic indices and tree balance. Systematic Biology, 46, 563-569. Download pdf version.
- Huelsenbeck, J. P. (1994) Comparing the stratigraphic record to estimates of phylogeny. Paleobiology, 20, 470-483.
- 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.
- Norell, M. A. and Novacek, M. J.(1997) The ghost dance: a cladistic critique of stratigraphic approaches to paleobiology and phylogeny. Journal of Vertebrate Paleontology, Supplement, 17, 67A.
- Norell, M. A. and Novacek, M. J. (1992b) Congruence between superpositional and phylogenetic patterns: Comparing cladistic patterns with fossil records: Cladistics, 8, 319-337.
- Pol, D., Norell, M. A. and Siddall, M. E. (2004) Measures of stratigraphic fit to phylogeny and their sensitivity to tree size, tree shape, and scale. Cladistics 20, 64-75.
- Rieppel, O. (1997) Falsificationist versus verificationist approaches to history. Journal of Vertebrate Paleontology, Supplement, 17, 71A.
- Siddall, M. E. (1996) Stratigraphic consistency and the shape of things. Systematic Biology, 45, 111-115.
- Siddall, M. E. (1997) Stratigraphic indices in the balance: A reply to Hitchin and Benton. Systematic Biology, 46, 569-573.
- Smith, A. B. (1994) Systematics and the Fossil Record. Oxford: Blackwell Scientific.
- Wagner, P. J. 2000a. The quality of the fossil record and the accuracy of estimated phylogenies. Systematic Biology 49, 65Ð86.
- Wagner, P. J. and Sidor, C. A. (2000) Age Rank/Clade Rank Metrics-Sampling, Taxonomy, and the Meaning of "Stratigraphic Consistency". Systematic Biology 49, 463-479.
- Wills, M. A. (1999) Congruence between phylogeny and stratigraphy: randomization tests. Systematic Biology, 48, 559-580.