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amount of change between individual species, represented by the proportion of shared sites, to be
used not only to construct dendrograms, but to provide an indication as to when particular radiations
took place.
For example. restriction mapping of mitochondrial DNA from both black and white
rhinoceros has helped provide an estimate of their time of divergence from a common ancestor to
compare with fo ss il evidence (O'Ryan and Harley, 1993). An illustration of the use of restriction
mapping in sys tematics is shown in Figure 8.2. Dendrograms were constructed from mitochondrial
DNA restriction maps for a number of individual bovid species taken from four tribes, Tragelaphini,
Antilopini, Connochaetini and Alcelaphini, analyzed by a distance method and by maximum
parsimony. In the absence of a suitable outgroup the maximum parsimony tree was rooted using
information from the distance analysis. The only difference between the topologies produced by
these two very different tree-building methods is in the positions of the Tragelaphine antelopes
relative to each other, and the exchange of Red Hartebeest Alcelaphus caama and Tsessebe
Damaliscus luna/us. It is noteworthy that in general the topologies are consistent with current
classifications.
Cladograms are generally more concerned with the branching order than with branch lengths,
although the number of shared derived characters supponing each node are frequently indicated, as
here, and can provide an indication of relative branch length. Other statistical approaches, such as
the consistency index, which here = 0.55, and the bootstrap (Felsenstein, 1985), can be used to assess
the robustness or otherwise of the overall topology or of pa!1icular monophyletic groupings. The
distance tree is particularly concerned with relative branch lengths, from which its estimate of the
topology is derived, and if a calibration is available, can give an estimate of when lineages divided.
A detailed critique of the relative merits of the two methods is beyond the scope of thi s article, but is
the subject of much controversy (sometimes acrimonious). The major weakness of the cladistic
approach for molecular data is the amount of unrecognized homoplasy in the data, and the major
weakness of the distance approach is the degree of stochastic error when measuring small numbers of
random events.
A similar study using the restriction mapping method was performed on mitochondrial DNA
prepared from twelve members of the Odontoceti (toothed whales). Distance analyses showed
surprisingly little variation between members of the Delphinidae (dolphins). This indicated an
unexpectedly recent radiation in the Delphinidae, and therefore directs further study to a reevaluation
of the fos sil record, or to the need for studies on the calibration of the molecular clock in
marine mammals.
DNA Sequencing
This method is able to provide information at any level of phylogenetic analysis. and is the method of
choice for definitive systematic studies. The ability to obtain sequence data from long dead tissues
provides totally novel uses for museum material and the opportunity to demonstrate the phylogenetic
affinities of extinct species. For example, DNA extracted and amplified from 14,000 year-old bones
of the sabre-toothed cat Smilodon jaJalis have affirmed the placement of Smilodon within the modem
radiation of Felidae. The advent of the polymerase chain reaction (PCR) technique as a means of
amplifying specific regions of DNA suitable for sequencing has greatly enhanced and simplified the
use of DNA sequencing, making it the method of choice for many applications. Aligned DNA
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