Phylogeny and Stratigraphy Comparison


Phylogenetic relationships among taxa can be estimated in a number of ways. Given known fossil records, phylogenetic estimates implicitly hypothesise the latest possible origination times of taxa. One can use these inferences as models to evaluate the quality of the fossil record. Originally, it was hoped that these metrics would obviate the need for probabilistic models. However, subsequent research shows that all these metrics are affected by the same factors affecting probabilistic models while also being highly sensitive to the accuracy of the model phylogeny. Alternatively, one can treat these inferences as hypotheses to be tested by stratigraphic distribution data. Given the sensitivity of phylogenetic inference to ideas about character evolution and levels of convergence, this offers a promising avenue for reducing untested assumptions yielding initial phylogenetic estimates.

Key Concepts:

  • Particular ideas about phylogenetic relationships have implications about both macroevolutionary models and preservation models.

  • There are several ways to describe gaps implied by inferred phylogenies, but all reflect factors other than simple preservation rate, especially the accuracy of the phylogeny.

  • Using stratigraphic data to test phylogenetic inferences as hypotheses might help assess the assumptions underlying phylogenetic inference.

Keywords: palaeontology; phylogeny; stratigraphy

Figure 1.

How cladograms and inferred phylogenies imply range extensions and stratigraphic debt. A phylogeny (including temporal distributions and possible ancestor–descendant relationships) is inferred by combining stratigraphic ranges with a phylogenetic analysis. Horizontal black lines crossing through branches in the bottom part of the figure denote morphologic novelties; absence of such novelties indicates that a taxon is identical to a hypothesised ancestor. Dashed lines give range extensions (=ghost lineages when attached to species and ghost taxa when attached to clades). Stratigraphic debt is the sum of those range extensions, based on the stratigraphic scale presented on the far left. Exact phylogenetic hypotheses affect inferred extensions and debt. (a) and (b) are based on identical cladograms; however, in (b) the light grey species is identical to the reconstructed common ancestor of light grey and white whereas in (a) it is not. Thus, (a) infers that one or more unsampled morphologies spanned the duration between the first appearance of light grey and the first appearance of white. (c) Illustrates how small changes in estimated phylogeny can yield large differences in stratigraphic debt.

Figure 2.

Calculation of consistency metrics. (a) Stratigraphic ranges and estimated phylogeny for six species, with age ranks and clade ranks illustrated. All nodes but the most basal one are considered ‘consistent’ by the Stratigraphic Consistency Index (SCI) as only the basal node is ‘older’ than its sister taxon. (b) Age rank:clade rank comparisons for Spearman's Rank Correlation (SRC) tests. (c and d) The same analyses for an alternative topology that is more symmetrical than (a). Note that clades must be condensed for SRC comparisons. Note also that SCI comparisons necessarily consider one clade to be inconsistent when two clades are sister taxa but have different first appearances.



Benton MJ (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. Biological Sciences 268: 2123–2130.

Benton MJ and Storrs GW (1994) Testing the quality of the fossil record: paleontological knowledge is improving. Geology 22: 111–114.

Felsenstein J (1981) A likelihood approach to character weighting and what it tells us about parsimony and compatibility. Biological Journal of the Linnean Society 16: 183–196.

Fisher DC (1994) Stratocladistics: morphological and temporal patterns and their relation to phylogenetic process. In: Grande L and Rieppel O (eds) Interpreting the Hierarchy of Nature from Systematic Patterns to Evolutionary Process Theories, pp. 133–171. Orlando, FL: Academic Press.

Foote M (1997) Estimating taxonomic durations and preservation probability. Paleobiology 23: 278–300.

Foote M (2001) Inferring temporal patterns of preservation, origination, and extinction from taxonomic survivorship analysis. Paleobiology 27: 602–630.

Foote M (2003) Origination and extinction through the Phanerozoic: a new approach. The Journal of Geology 111: 125–148.

Fox DL, Fisher DC and Leighton LR (1999) Reconstructing phylogeny with and without temporal data. Science 284: 1816–1819.

Huelsenbeck JP (1994) Comparing the stratigraphic record to estimates of phylogeny. Paleobiology 20: 470–483.

Huelsenbeck JP and Rannala B (1997) Maximum likelihood estimation of topology and node times using stratigraphic data. Paleobiology 23: 174–180.

Huelsenbeck JP and Nielsen R (1999) Effects of nonindependent substitution on phylogenetic accuracy. Systematic Biology 48: 317–328.

Kuhner MK and Felsenstein J (1994) A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biology and Evolution 11: 459–468.

Lewis PO (2001) Maximum likelihood phylogenetic inference: modeling discrete morphological characters. Systematic Biology 50: 913–925.

Marshall CR (1990) Confidence intervals on stratigraphic ranges. Paleobiology 16: 1–10.

Marshall CR (1997) Confidence intervals on stratigraphic ranges with nonrandom distributions of fossil horizons. Paleobiology 23: 165–173.

Norell MA (1992) Taxic origin and temporal diversity: the effect of phylogeny. In: Novacek MJ and Wheeler QD (eds) Extinction and Phylogeny, pp. 89–118. New York: Columbia University Press.

Norell MA and Novacek MJ (1992) The fossil record and evolution: comparing cladistic and paleontologic evidence for vertebrate history. Science 255: 1690–1693.

Signor PW III and Lipps JH (1982) Sampling bias, gradual extinction patterns and catastrophes in the fossil record. Geological Society of America Special Paper 190: 291–296.

Smith AB (1988) Patterns of diversification and extinction in early Palaeozoic echinoderms. Palaeontology 31: 799–828.

Strauss D and Sadler PM (1989) Classical confidence intervals and Bayesian probability estimates for ends of local taxon ranges. Mathematical Geology 21: 411–427.

Wagner PJ (1998) A likelihood approach for estimating phylogenetic relationships among fossil taxa. Paleobiology 24: 430–449.

Wagner PJ (2000a) The quality of the fossil record and the accuracy of phylogenetic inferences about sampling and diversity. Systematic Biology 49: 65–86.

Wagner PJ (2000b) Likelihood tests of hypothesized durations: determining and accommodating biasing factors. Paleobiology 26: 431–449.

Wagner PJ (2000c) Phylogenetic analyses and the fossil record: tests and inferences, hypotheses and models. In: Erwin DH and Wing SL (eds) Deep time—Paleobiology's perspective. Paleobiology Memoir 26 (suppl. 4): 341–371.

Wagner PJ and Marcot JA (2010) Probabilistic phylogenetic inference in the fossil record: current and future applications. In: Alroy J and Hunt G (eds) Quantitative Paleobiology, pp. 195–217. New Haven, CT: Paleontological Society.

Wagner PJ and Sidor CA (2000) Age rank: clade rank metrics – sampling, taxonomy, and the meaning of “stratigraphic consistency.” Systematic Biology 49: 463–479.

Wills MA (1999) The congruence between phylogeny and stratigraphy: randomization tests and the Gap Excess Ratio. Systematic Biology 48: 559–580.

Yang Z (1994) Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. Journal of Molecular Evolution 39: 306–314.

Yang Z and Rannala B (1997) Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method. Molecular Biology and Evolution 14: 717–724.

Further Reading

Alroy J (2002) Stratigraphy in phylogeny reconstruction – reply to Smith (2000). Journal of Paleontology 76: 587–589.

Cobbett A, Wilkinson M and Wills MA (2007) Fossils impact as hard as living taxa in parsimony analyses of morphology. Systematic Biology 56: 753–766.

Fisher DC (2008) Stratocladistics: integrating temporal data and character data in phylogenetic inference. Annual Review of Ecology, Evolution, and Systematics 39: 365–385.

Fisher DC, Foote M, Fox DL and Leighton LR (2002) Stratigraphy in phylogeny reconstruction – comment on Smith (2000). Journal of Paleontology 76: 585–586.

Foote M (1996) On the probability of ancestors in the fossil record. Paleobiology 22: 141–151.

Pardo JD, Huttenlocker AK and Marcot JD (2008) Stratocladistics and evaluation of evolutionary modes in the fossil record: an example from the ammonite genus Semiformiceras. Palaeontology 51: 767–773.

Solow AR (2003) Estimation of stratigraphic ranges when fossil finds are not randomly distributed. Paleobiology 29: 181–185.

Wagner PJ (1995) Stratigraphic tests of cladistic hypotheses. Paleobiology 21: 153–178.

Wagner PJ (2002) Testing phylogenetic hypotheses with stratigraphy and morphology – a comment on Smith (2000). Journal of Paleontology 76: 590–593.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Wagner, Peter(Dec 2011) Phylogeny and Stratigraphy Comparison. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0001520.pub2]