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3.3: Fossils and family relationships: introducing cladistics

As mentioned previously, we continue to discover new fossils and new organisms. In most cases, fossils appear to represent organisms that lived many millions to hundreds of millions of years ago but which are now extinct. We can expect there are dramatic differences between the ability of different types of organisms to become fossilized.61 Perhaps the easiest organisms to fossilize are those with internal or external skeletons, yet it is estimated that between 85 to 97% of such organisms are not represented in the fossil record. A number of studies indicate that many other types of organisms have left no fossils whatsoever62 and that the number of organisms (at the genus level) that have been preserved as fossils may be less (often much less) than 5%.63 For some categories of modern organisms, such as the wide range of microbes, essentially no informative fossils exist at all.

Once scientists recognized that fossils provide evidence for extinct organisms, the obvious question was, do extinct organisms fit into the same cladistic classification scheme as do living organisms or do they form their own groups or their own separate trees? This can be a difficult question to answer, since many fossils are only fragments of the intact organism. The fragmentary nature of the fossil record can lead to ambiguities. Nevertheless, the conclusion that has emerged upon careful characterization is that we can place almost all fossilized organisms within the cladistic classification scheme developed for modern organisms, with a few possible exceptions, such as the Ediacarian organisms that lived very long ago and appear (perhaps) to be structurally distinct from all known living organisms.64 The presumption, however, is that if we had samples of Ediacarian organisms for molecular analyses, we would find it that they would fall nicely into the same classification scheme as all other organisms do.65 A similar example are the dinosaurs, which while extinct, are clearly descended from a specific type of reptile that also gave rise to modern birds, while mammals are more closely related to a second, now extinct group, known as the “mammal-like reptiles.”

In rare cases, particularly relevant to human evolution, one trait that can be recovered from bones is DNA sequence data. For example, it has been possible to extract and analyze DNA from the bones of Neanderthals and Denisovian-type humanoids, that went extinct about 30,000 years ago. This is information that has been used to clarify their relationship to modern humans (Homo sapiens).66 In fact, such data has been interpreted as evidence for interbreeding between these groups and has led for calls to reclassify Neanderthals and Denisovians as subspecies of Homo sapiens.

The main unifying idea in biology is Darwin’s theory of evolution through natural selection.

– John Maynard Smith

Questions to answer and ponder:

• Explain why you might expect that extinct species fit into the modern cladistic classification scheme. How does extinction impact classification schemes or phylogenetic diagrams?

• Why are differences between organisms significantly less informative in determining relationships than similarities?

• What factors would influence your decision as to whether a trait found in two different organisms was present in their common ancestor?

• On what basis would you decide that a particular trait was important or unimportant (secondary) from a classification perspective?

• How could Neanderthals be a distinct species if there is evidence for in-breeding with H. sapiens?


61 Your inner fish: fish/home/

62 The incompleteness of the fossil record:

63 Absolute measures of the completeness of the fossil record:

64 Doser, 2015. The advent of animals: The view from the Ediacaran.

65 On the eve of animal radiation: phylogeny, ecology and evolution of the Ediacara biota:

66 Paleogenomics of archaic hominins:


  • Michael W. Klymkowsky (University of Colorado Boulder) and Melanie M. Cooper (Michigan State University) with significant contributions by Emina Begovic & some editorial assistance of Rebecca Klymkowsky.