Determining Relationships The Evidence ofEvolution

Two fundamental kinds of evidence are used to determine relationships and phylogeny of mammals and other organisms: anatomical and molecular (genetic). Anatomical evidence usually includes features of the skeleton, dentition, or soft anatomy. Molecular evidence typically consists of sequences of proteins or segments of mitochondrial or nuclear genes. Until the last 25 years or so, mammalian relationships were usually based largely or entirely on anatomical features. The extent of similarity was often the chief criterion, and the distinction between specialized or derived (apomorphic) and primitive (plesiomorphic) features was often blurred. However, it is now virtually universally accepted that only shared derived features or synapomorphies —specialized traits inherited from a common ancestor—are significant for establishing close relationship, whereas shared primitive features (symplesiomorphies) do not reflect special relationship.

In practice it is not always self-evident whether a trait is primitive or derived. This distinction, the polarity of the trait, is always relative to previous or later conditions, hence its correct determination depends to some extent on the phylogeny we are trying to decipher. It follows that the same character can be derived relative to more primitive taxa and primitive with respect to more advanced taxa. Circularity is avoided by using many independent characters to determine phylogeny; nevertheless, polarity is usually an a priori judgment, based on predetermined ingroup and out-group taxa. The choice of such taxa (and their character states) ultimately determines the polarity of characters in the ingroup. Thus a change in perceived relationships can result in a change in character polarity. The polarity of some characters is relatively obvious. For example, modification of the forelimbs into wings in bats is an apomorphic condition among mammals, a synapomorphy of all bats, and at the same time a symplesiomorphy of the genera within any family of bats. Less obvious is the polarity of transverse crests or cross-lophs on the upper molars of some basal peris-sodactyls. This feature has been considered either primitive or derived, depending on the presumed sister-group of peris-sodactyls. The terms "primitive" or "plesiomorphic" versus "derived" or "apomorphic" are sometimes extended to taxa, to reflect their general morphological condition, but they are more properly restricted to characters.

Of course, not all derived features shared by two animals necessarily reflect close relationship. It is well known that similar anatomical features have independently evolved repeatedly in evolution. Such iterative evolution is often associated with similar function, and it occurs both in groups with no close relationship (convergence) and in closely allied lineages with a common ancestor that lacked the derived trait (parallelism). Independent evolution of similar traits is called homoplasy. The challenge for systematists is distinguishing synapomorphic from homoplastic traits. This problem has long been realized by morphologists, and examples of morphological homoplasy abound. In some cases it is easily recognized by the lack of homology of the similar trait or by significant differences in other characters. For instance, there is ample evidence to demonstrate that the Pleistocene saber-toothed cat Smilodon was convergent to the Miocene saber-toothed marsupial Thylacosmilus, that creodonts and borhyaenid marsupials were dentally convergent to Carnivora, and that remarkably similar running and gliding adaptations evolved multiple times independently But whether the specialized three-ossicle middle ear evolved only once in mammals or multiple times convergently is more ambiguous and may require additional evidence (see Chapter 4 for new evidence suggesting multiple origins). Despite widespread assumption to the contrary, molecular sequences are also susceptible to homoplasy, as recent examples demonstrate (e.g., Bull et al., 1997; Pecon Slattery et al., 2000).

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