Evolution__3rd_Edition

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Protein and DNA sequences have
been transcribed in recent decades
Molecules are used in phylogenetic
inference ...
CHAPTER 15 / The Reconstruction of Phylogeny 437
phylogeny c, and 20 to other idiosyncratic arrangements. We then study the characters,
identify the homoplasies and ancestral homologies, and discard them. Maybe 30 of the
100 initial characters remain. If all 30 point to the same phylogeny, our job is done. But
in practice, 20 of the derived homologies may support phylogeny a, six support b, and
four support c. The reason is probably that some of the characters we think are derived
homologies are in fact homoplasies or ancestral homologies.
We have four options when faced with conflict in the evidence: we can scrutinize,
and rescrutinize, the contradictory results to test their reliability; we can suspend judgment;
we can collect more evidence; or we can infer that the phylogeny supported by
the most evidence is the correct one. If 20 of the 30 characters support phylogeny a,
then we could infer a is the correct answer. The viability of the four options will vary
from problem to problem.
15.8 Molecular sequences are becoming increasingly
important in phylogenetic inference, and they have
distinct properties
The sequences of proteins and DNA are both used in phylogenetic inference. Proteins
blazed the trail. The first protein to have its amino acid sequence worked out was
insulin, which was sequenced by Sanger in 1954. Protein sequencing became an automated
process through the 1960s, and the sequences of some proteins, such as
cytochrome c and hemoglobin, became available in enough species for large-scale phylogenies
to be inferred. DNA sequences followed on, about 20 years later. It was Sanger
again who sequenced the first decent-sized sequence of DNA, in this case the whole
genome (containing 5,375 bases) of the bacteriophage φX164, in 1977. DNA sequencing
since then has expanded, almost explosively, and most current molecular phylogenetic
work is concerned with DNA sequences. Many of the methods and concepts of
molecular phylogenetics were established for proteins, however, and here we consider
the two kinds of molecules together.
The deep logic of phylogenetic inference is identical for molecular and morphological
characters, but the two have distinct properties and the methods and concepts
used for each can appear very different. The homology/homoplasy distinction, in
particular, differs for the two. When confronted by apparently conflicting homologies
for morphological characters (like the wings of birds and bats), the first thing to do is to
re-examine the organs, and their embryology, in detail to see whether their similarity
really is fundamental, or superficial and homoplasious. Homology is a powerful concept
for morphological organs such as wings. Wings are complex in structure and can
take on an almost infinite variety of shapes; they have an embryonic development and
morphological relations with the rest of the body. If the information in the structure
and development of a wing in two species is the same, those wings are highly likely to
evolved from a common ancestor who had similar wings.
The homology/homoplasy distinction is much less powerful for molecular evidence.
Suppose a nucleotide is identical in two species. Evolutionary changes take place
among a very limited set of alternatives (the four bases A, C, G, and T) and it is fairly
probable that the same informational state could independently evolve in the two