Evolution__3rd_Edition

468 PART 4 / Evolution and Diversity
revolves a circular argument: see Hull (1967). Wagner (2000) is about the concept of a
“character.”
Homology has been much discussed recently, mainly because of the astonishing discoveries
in “evo-devo.” We look at that topic in Chapter 20 in this text; see the further
reading there. Meanwhile, see many of the chapters in Bock & Cardew (1999). Fitch
(2000) discusses molecular meanings of homology. Moore & Willmer (1997) discuss
homology as part of a review of convergence in invertebrates.
For methods of determining character polarity, see Meier (1997) on the ontogenetic
criterion (not discussed in this text), and its performance relative to outgroup comparison.
Fox et al. (1999) discuss a further way fossil evidence can be used in phylogenetic
inference.
Molecular phylogenetics. Page & Holmes (1998) and Graur & Li (2000) are introductory
texts. Hall (2001) is a practical text, aimed at molecular biologists. Li (1997) and
Nei & Kumar (2000) are more advanced. An authoritative general source is the book
edited by Hillis et al. (1996). The chapter by Swofford et al. (1996) is a fine introduction
to the theory. Whelan et al. (2001) is a modern overview of methods. Steel & Penny
(2000) also discuss models, and different methods. Huelsenbeck & Crandall (1997)
review maximum likelihood and discuss three main methods (distance, parsimony,
and maximum likelihood). A fourth, Bayesian inference, may be emerging: see
Huelsenbeck et al. (2001). Mooers & Holmes (2000) look at how to deal with codon
bias. Diamond (1991, chapter 1) is a popular essay that discusses DNA hybridization.
For phylogenetic studies of disease, for example on the west Nile virus, see Lanciotti
et al. (1999) and the newspiece in Science November 19, 1999, pp. 1450–1. There is
another newspiece in Science May 11, 2001, pp. 1090–3. Also, see some chapters in
Harvey et al. (1996) as well as Hahn et al. (2000) and Holmes (2000a) on HIV, and Page
& Holmes’s (1998) text.
For computer programs, MacClade (Maddison & Maddison 2000) is the most
friendly program, but is designed more for morphological than molecular characters.
The most widely used programs in molecular phylogenetic research are paup
(Swofford 2002) and phylip (Felsenstein 1993). Felsenstein’s web page also discusses
many computer packages for phylogenetic analysis.
The problems in molecular inference are covered by the general texts. See also
Doolittle (2000) and a newspiece in Science May 21, 1999, pp. 1305–7 on the case of the
deep root of life. Horizontal gene transfer has been discussed for the human genome,
see several issues of Nature and Science in mid 2001.
On long branch attraction, and the question of whether breaking up the branches by
more extensive taxon sampling solves the problem, see Hillis (1996), an exchange
among several authors in Trends in Ecology and Evolution (1997), vol. 12, pp. 357–8,
and Rosenberg & Kumar (2001).
Paralog rooting was first applied to find the deep root of all life, but see Philippe &
Forterre (1999) for problems (saturation, mainly) in this work, as well as references to
it. These problems probably do not apply to the angiosperm example in the text. Zanis
et al. (2002) provide further analysis of the angiosperm case. Chapter 18 contains further
references on angiosperms. The confusion caused by paralog rooting is sometimes
said to be compounded by rapid evolution following gene duplication, but this seems
not to be the case (Hughes 1999).
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