(normalizing intensities to the category 1 results described above), hybridized at best only very weakly (again normalizing) and often not at all to many other lanes (i.e., lanes 3–4, 13–17, 19–21, 29–30, 32–34, 37, 44, 48). We conclude that most or all of the rps7 probe region is probably missing from these mt genomes. The third category of results was obtained with but a single probe, the cox1 intron shown in Fig. 1 Bottom. This probe gave a singularly patchy, sporadic hybridization pattern, whose molecular basis will be explained in a later section.

The survey blots were hybridized with probes for each of the 14 ribosomal protein genes known from angiosperm mt genomes, and with probes for 11 of the 21 known respiratory genes. The cases of inferred gene absences were plotted onto a multigene phylogeny of the surveyed angiosperms (Soltis et al., 1999) to estimate the number of phylogenetically separate gene losses. A total of only two losses were inferred among 10 of the respiratory genes; these include the previously described loss of mt cox2 in the legume Vigna (Nugent and Palmer, 1991, 1993; Covello and Gray, 1992; Adams et al., 1999) and the loss of nad3 in the Piperaceae. The small respiratory gene sdh4 was an exception, with about 10 separate losses inferred (K.A., Y.-L.Q., and J.D.P., unpublished data). In striking contrast to the respiratory genes as a group, probes for all 14 ribosomal protein gene probes failed to hybridize to mtDNAs of many, disparately related angiosperms (see, e.g., Fig. 1 Upper), suggesting numerous gene losses (at least 10 losses for most genes, over 200 losses in total). The losses vary in phylogenetic depth, with most being limited to one or two related families, whereas several encompass many related families or even orders (K.A., Y.-L.Q., and J.D.P., unpublished data). Probes for rps2 and rps11 did not hybridize to the lanes of most higher eudicots (a group comprising 182 of the 281 angiosperms in our survey), suggesting relatively ancient losses early in the evolution of eudicots. Both rps2 and rps11 have been isolated from the nucleus of Arabidopsis (Perrotta et al., 1998; rps11 expressed sequence tags from the GenBank database), suggesting that gene loss followed functional transfer to the nucleus. The relatively few losses of these two genes (4 and 6, respectively) reflect the reduced potential for many (“subsequent”) losses when such an ancient loss occurs.

Our blot surveys will not detect mt pseudogenes unless much or all of the probe region is missing, and thus our survey probably underestimates the number of gene losses. Several ribosomal protein pseudogenes have been reported in angiosperm mt genomes, for example, of rps14 and rps19