Plant Molecular Biology 42: 1–23, 2000.
© 2000 Kluwer Academic Publishers. Printed in the Netherlands.
Evolution of genes and taxa: a primer
Jeff J. Doyle
and Brandon S. Gaut
L. H. Bailey Hortorium, 466 Mann Library Building, Cornell University, Ithaca, NY 14853, USA (e-mail:
Dept. of Ecology and Evolutionary Biology, 321 Steinhaus Hall, U.C. Irvine, Irvine, CA
92697-2525,USA (e-mail: firstname.lastname@example.org)
Key words: homology, molecular population genetics, multigene families, phylogenetic methods, rates of
The rapidly growing ﬁelds of molecular evolution and systematics have much to offer to molecular biology, but
like any ﬁeld have their own repertoire of terms and concepts. Homology, for example, is a central theme in
evolutionary biology whose deﬁnition is complexand often controversial. Homology extends to multigenefamilies,
where the distinction between orthology and paralogy is key. Nucleotide sequence alignment is also a homology
issue, and is a key stage in any evolutionary analysis of sequence data. Models based on our understanding of
the processes of nucleotide substitution are used both in the estimation of the number of evolutionary changes
between aligned sequences and in phylogeny reconstruction from sequence data. The three common methods of
phylogenyreconstruction – parsimony, distance and maximum likelihood – differ in their use of these models. All
three face similar problems in ﬁnding optimal – and reliable – solutions among the vast number of possible trees.
Moreover, even optimal trees for a given gene may not reﬂect the relationships of the organisms from which the
gene was sampled. Knowledge of how genes evolve and at what rate is critical for understanding gene function
across species or within gene families. The Neutral Theory of Molecular Evolution serves as the null model of
molecular evolution and plays a central role in data analysis. Three areas in which the Neutral Theory plays a vital
role are: interpreting ratios of nonsynonymous to synonymous nucleotide substitutions, assessing the reliability of
molecular clocks, and providing a foundation for molecular population genetics.
Molecular systematics and evolutionary biology are
dynamic disciplines, with their own research goals,
journals, and jargon. The complexity of these ﬁelds
can be daunting to those who do not routinely employ
their methods, and it is apparent that molecular biolo-
gists occasionally misapplythe tools of thedisciplines.
One simple example is the term ‘homology’, which is
persistently misused in molecular biological literature.
Another example are phylogenies based on molecular
data; papers in even the best molecular biology jour-
nals present gene trees whose methods of construction
are not speciﬁed and that may not be robust. Such
trees may constitute a poor basis for interpretation and
This chapter provides a short primer on what we
consider to be some of the key concepts in molecular
evolution and systematics. Our goal is to help dis-
pel some of the confusion over the basic principles
of molecular evolution for a target audience of plant
molecular biologists. We make no effort to be compre-
hensive in our citations, seeking instead to highlight
important (and often controversial)issues and to point
readers in the direction of some key references. More
exhaustive treatment of these topics is available from
a variety of texts and reviews (e.g. [81, 132]). Ad-
ditional resources in this issue include the paper by
Soltis and Soltis, which provides information about
phylogenetic analyses with large data sets, and the
paper by Muse, which discusses statistical aspects of
molecular evolutionary analysis.