Evolution__3rd_Edition

438 PART 4 / Evolution and Diversity
. . . but the techniques differ
somewhat from morphology
The quantities of evidence are large
Different characters are
commensurable
species. The argument is relaxed for proteins, because there are 20 amino acid states,
but it still applies because 20 fixed states is still a small number compared with the variety
of morphological forms. Thus for molecules it is not so unlikely that similarity in
the states of two species could have evolved independently. Moreover, the morphologist’s
methods are absurd for molecules. The amino acid at site 12 of cytochrome c is
methionine in humans, chimps, and rattlesnakes, but glutamine in all other species a
including many mammals and birds a that have been studied. We cannot dissect the
rattlesnake’s methionine, or trace its embryonic development, to see whether it is only
“superficially” methionine and “more fundamentally” glutamine. It is a methionine
molecule, and that is that.
Nor can we usually assess the reliability of different pieces of molecular evidence by
thinking about how natural selection could have acted on them. When morphologists
examine a similarity between the organs of two species, they keep a look out for functional
convergences a such as the evolution of wings in species that fly. This kind of
analysis is impossible if we do not understand the relation between the structure (the
wing) and its function (flight). For molecules, we usually lack this understanding. If we
knew, for example, that a change from glutamine to methionine at site 12 of cytochrome
c made functional sense in certain kinds of animals, then the same kind of arguments as
appear in morphology could be used for the protein. Otherwise, we have to treat
molecules in the way a morphologist would treat an organ of unknown function.
Molecular sequences have other distinctive properties. The amount of evidence they
provide is large; cytochrome c alone, for example, has 104 amino acids, which can be
treated as 104 pieces of phylogenetic evidence. A typical morphological study might be
based on perhaps 20 or so characters, and it is exceptional for many more than about 50
characters to be used.
In addition, the recognition of independent units of evidence appears to be straightforward.
With morphological evidence, two apparently separate organs may really be a
single evolutionary unit. At one extreme, non-independence is obvious; no one would
think of treating the right leg and the left leg as two pieces of evidence. But less obvious
correlations can also arise as a consequence of developmental processes, which makes
the recognition of independence tricky. For nucleotides, the mutations down the DNA
molecule are effectively independent as each site can evolve independently of each
other site. 2
Evolution at different amino acid and nucleotide sites is easily comparable: one
change at one site is equivalent to one change at another. This is a huge advantage when
we are weighing up conflicting evidence. Suppose the nucleotides at 10 sites support
one phylogeny for a group of species, and the nucleotides at five other sites support a
different phylogeny. Each of the 10 sites in one set is approximately equivalent to each
of the five sites in the conflicting set. We can assume that the phylogeny supported
by the 10 nucleotides is the better estimate of the true phylogeny. However, if one
2 However, not all sites may in fact evolve independently. For instance, a change at one site may set up selection
for a compensatory change at another site. How much of a problem, if any, this creates for phylogenetic
inference is unsettled. Genomic analyses are starting to reveal the amount of non-independent change at different
sites. Averof et al. (2000) found non-independence in one sequence comparison; Silva & Kondrashov
(2002) did not in another. As genomic analyses proliferate, understanding should deepen.
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