TPI is a glycolytic enzyme essential for efficient energy production. It catalyses the
interconversion of dihydroxyacetone phosphate and D-glyceraldehyde 3-
phosphate, coupling the branches between triglyceride metabolism and glycolysis. TPI is
metabolically adjacent to GPDH.
XDH is a complex metalloflavoprotein that plays an important role in nucleic acid
degradation in all organisms: it catalyses the oxidation of hypoxanthine to xanthine and
xanthine to uric acid with concomitant reduction of NAD to NADH. XDH protects the
cell against damage induced by free oxygen radicals through the antioxidant action of uric
acid (Xu et al. 1994). The chief physiological function of the enzyme changes, none the
less, from one organism to another: its primary role is purine metabolism in mammals and
chicken, but pteridine metabolism in Drosophila (review et al. 1994); in Drosophila
melanogaster (rosy locus) and Bombyx mori it is transcribed in the fat body, midgut, and
Malpighian tubules, and in D. melanogaster some Chovnic et al. 1977). The Xdh locus is
widely expressed in human tissues (Xu part of the protein is transported to the eyes. In
higher plants, XDH takes part in ureide biosynthesis through de novo synthesis of purines
from glutamine (Sagi et al. 1998). In mammals, but not in chicken and Drosophila, the
enzyme can be converted to the oxidase form xanthine oxidase (XO; Hille and Nishino
1995). Defective xanthine dehydrogenase causes xanthinuria in humans; the enzyme is a
target of drugs against gout and hyperuricaemia, and has been associated with blood
pressure regulation (Enroth et al. 2000). We have previously investigated the rate of
molecular evolution of Xdh in Drosophila as well as other species, including mammals,
fungi, and plants (Rodríguez-Trelles et al. 2001b; see also Rodríguez-Trelles et al. 2001a).
Sources and modelsThe 95 species studied and GenBank accession numbers are given in Figure 1.1 (#8 and #
in Figure 1.1 refer each to two species; respectively, Nicotiana tabacum and N. plumbaginifolia,
and Scaptomyza adusta and S. albovittata). For GPDH and SOD we use the protein
alignments from Ayala et al. (1996), and Fitch and Ayala (1994), slightly modified to fit
additional sequences newly deposited in GenBank. For XDH we use the alignment from
Rodríguez-Trelles et al. (2001b). ADH, AMD, DDC, G6PD, PGD, and TPI alignments
were generated using ClustalX with default options. After removal of the gaps, the actual
ADH, AMD, DDC, GPDH, G6PD, PGD, SOD, TPI, and XDH alignments consisted of
236, 344, 298, 241, 367, 208, 107, 78, and 599 amino acid residues, respectively. We
treat Dorsilopha, Hirtodrosophila, and Zaprionus as Drosophila subgenera, following
Tatarenkov et al. (1999), and Tarrío et al. (2001), but Scaptodrosophila as a genus, according
to Grimaldi (1990), Tatarenkov et al. (1999), and Tarrío et al. (2001).
We follow a model-based maximum likelihood framework of statistical inference. We
first model the substitution processes of the genes using a tree topology that is
approximately correct; with the models so identified we proceed to generate maximum
likelihood distances between pairs of amino acid sequences. As a tree topology for model
fitting, we use the hypothesis shown in Figure 1.1. Relationships which are not well
established (e.g. the branching order of animal phyla) are set as polytomies. Use of other
reasonable topologies does not change parameter estimates (see also Yang 1994).
MOLECULAR CLOCKS: WHENCE AND WHITHER? 11