Biology Reference
In-Depth Information
overall structure and function of genomes. Molecular evolution and phylogeny
are interrelated because phylogenetic knowledge is essential for determining
the order of changes in the molecular characters being studied, whereas knowl-
edge of the pattern and rate of change of a molecule is crucial in efforts to
reconstruct the evolutionary history of a group of organisms (
Li and Graur 1991,
Graur and Li 2000
). This chapter introduces several common molecular methods
and describes their applications, limitations, and relative costs for systematic and
evolutionary studies. First, key controversies are described.
12.3 Controversies in Molecular Systematics and Evolution
Significant controversies have been associated with using molecular tools,
including: debates over the relative importance of molecular versus morphologi-
cal data, the constancy of evolutionary rates (the molecular clock), the use of
the terms homology and similarity, and the neutrality of DNA sequence varia-
tion. Other controversies surround the choice of evolutionary models for analy-
sis of the data and the choice of which molecular data to use.
12.3.1 Molecular versus Morphological Traits
There was debate over whether morphological or molecular characters are
bet-
ter
for constructing phylogenies (
Adoutte et al. 2000
). When comparisons were
made, it appeared that morphological changes and molecular changes may
be independent, responding to different evolutionary pressures or differently
to evolutionary pressures.
Hillis and Moritz (1990)
noted that the real issue in
choosing a technique to answer a hypothesis should be whether the 1) spe-
cific characters chosen exhibit the variation that is appropriate to the question
posed, 2) characters have a genetic basis, and 3) data are collected and ana-
lyzed in such a way that it is possible to use both morphological and molecu-
lar information. Molecular and morphological data each have advantages and
disadvantages.
DNA-sequence data have the advantage of having a clear genetic basis and
the amount of data is limited only by the genome size and the time and funds
of the scientist! Morphological data have the advantage that they can be
obtained from fossils (if available) and preserved collections and can be inter-
preted in the context of ontogeny. Only limited amounts of DNA data can be
obtained from preserved fossils by the polymerase chain reaction (PCR) due to
degradation of DNA over time; see Chapter 8 for a discussion of PCR analyses
of ancient DNA.
Moritz and Hillis (1990)
concluded the debate should not be
either/or; studies that incorporate both molecular and morphological data pro-
vide better results than those using just one approach, and the recent trend is
